Locus 6536

Sequence ID	3L_DroMel_CAF1
Location	17,282,536 – 17,282,856
Length	320
Max. P	0.998784

overview

Window 8

Location	17,282,536 – 17,282,656
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.90
Mean single sequence MFE	-40.38
Consensus MFE	-27.86
Energy contribution	-29.28
Covariance contribution	1.42
Combinations/Pair	1.09
Mean z-score	-2.04
Structure conservation index	0.69
SVM decision value	-0.02
SVM RNA-class probability	0.524862
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17282536 120 + 23771897
GAUCUCUAUGGAAACGUGAAGCUGAGGCCGUAGCUGGAGCUGAAGCUGAAGCGCAGCUAAUAAGGUCUGCGGGCCUGCAGGGCGUAUGCUUAAUAUUUUGAGCCAGUUGGCGCAUAUAUA
...((.((((....)))).))((((((((...(((..(((....)))..)))((((((.....)).)))).))))).)))...((((((((((....))))(((....)))))))))... ( -42.70)
>DroSec_CAF1 166263 118 + 1
G--CUCUAUGGAAACUUGAAGCUGAGGCCGUAGCUGGAGCUGACGCUGAGGGUCAGCUAAUAAGGUCUGCGGGCCUGCAGGGCGUAUUCUUAAUAUUUUGAGCCAGUUGGCGCUUAUAUA
(--((.((.(....).)).)))((((((((..((((((((((((.(...).)))))))((((.(.((((((....)))))).).))))(((((....)))))))))))))).)))).... ( -40.60)
>DroSim_CAF1 162449 118 + 1
G--CUCUAUGGAAACUUGAAGCUGAGGCCGUAGCUGGAGCUGAAGCUGAAGCGCAGCUAAUAAGGUCUGCGGGCCUGCAGGGCGUAUGCUUAAUAUUUUGAGCCAGUUGGCGCUUAUAUA
(--((.((.(....).)).)))(((((((...(((..(((....)))..)))((((((.....)).)))).))))).))((((((..((((((....))))))......))))))..... ( -40.80)
>DroEre_CAF1 169305 118 + 1
G--CUCUAUGGAAACUUGAAGCUGAGGCCAUAGCUGGAGCCGAAGCUGAAGCGCAGCUAAUAAGGUCUGCGGACCUGCGGGGCGUAUGCUUAAUAUUUUGAGCCAGUUGGCGCUUAUAUA
(--((.((.(....).)).)))((((((((..(((((..(.(((....(((((..(((....(((((....)))))....)))...)))))....))).)..))))))))).)))).... ( -40.80)
>DroYak_CAF1 174370 106 + 1
G--CUCUAUGGAAACUUGAAGCUAAGGCUGUAG------------CUAAAACGCAGCUAAUAAGGUCUGCGGAGCUGCAGGGCGUAUGCUUAAUAUUUUGAGCCAGUUGGCGCUUAUAUA
(--((.((.(....).)).))).....((((((------------((....(((((((.....)).))))).))))))))(((((..((((((....))))))......)))))...... ( -37.00)
>consensus
G__CUCUAUGGAAACUUGAAGCUGAGGCCGUAGCUGGAGCUGAAGCUGAAGCGCAGCUAAUAAGGUCUGCGGGCCUGCAGGGCGUAUGCUUAAUAUUUUGAGCCAGUUGGCGCUUAUAUA
....((...(....)..))..((((((((.(((((........)))))...(((((((.....)).)))))))))).)))(((((..((((((....))))))......)))))...... (-27.86 = -29.28 +   1.42)

alignment

secondary structure

dotplot

Window 9

Location	17,282,616 – 17,282,736
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.50
Mean single sequence MFE	-26.46
Consensus MFE	-25.04
Energy contribution	-24.92
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-1.13
Structure conservation index	0.95
SVM decision value	-0.03
SVM RNA-class probability	0.519578
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17282616 120 - 23771897
AAAAAAGUUUUCAUUUGCAUGUUUUUAGUUAAUUGAAUUUAUGCAGAACUUUCCGCUUUGGUGCUCUGGGCAACGGCAUUUAUAUAUGCGCCAACUGGCUCAAAAUAUUAAGCAUACGCC
...(((((((.....((((((..(((((....)))))..)))))))))))))..((....(((((...(....).((((......))))(((....)))...........)))))..)). ( -25.70)
>DroSec_CAF1 166341 120 - 1
AAAAAAGUUUUCAUUUGCAUGUUUUUAGUUAAUUGAAUUUAUGCAGAACUUUCCGCUUUGGUGCUCUGGGCAACGGCAUUUAUAUAAGCGCCAACUGGCUCAAAAUAUUAAGAAUACGCC
......((.(((.((((((((..(((((....)))))..)))))))).......((((((((((((((.....)))..........))))))))..)))............))).))... ( -27.10)
>DroSim_CAF1 162527 120 - 1
AAAAAAGUUUUCAUUUGCAUGUUUUUAGUUAAUUGAAUUUAUGCAGAACUUUACGCUUUGGUGCUCUGGGCAACGGCAUUUAUAUAAGCGCCAACUGGCUCAAAAUAUUAAGCAUACGCC
...(((((((.....((((((..(((((....)))))..)))))))))))))..((((.((((((...(....))))))).....))))(((....)))............((....)). ( -25.60)
>DroEre_CAF1 169383 120 - 1
AAAAAAGUUUUCAUUUGCAUGUUUUUAGUUAAUUGAAUUUAUGCAGAACUUUCCGCUUUGGUGCUCUGGCCAACGGCAUUUAUAUAAGCGCCAACUGGCUCAAAAUAUUAAGCAUACGCC
......((((...((((((((..(((((....)))))..)))))))).......(((((((((((...(((...))).........))))))))..)))..........))))....... ( -25.80)
>DroYak_CAF1 174436 120 - 1
AAAAAAGUUUUCAUUUGCAUGUUUUUAGUUAAUUGAAUUUAUGCAGAACUUUCCGCUUUGGCGCUCCGGCCAGCGGCAUUUAUAUAAGCGCCAACUGGCUCAAAAUAUUAAGCAUACGCC
......((((...((((((((..(((((....)))))..)))))))).......((((((((((((((.....)))..........))))))))..)))..........))))....... ( -28.10)
>consensus
AAAAAAGUUUUCAUUUGCAUGUUUUUAGUUAAUUGAAUUUAUGCAGAACUUUCCGCUUUGGUGCUCUGGGCAACGGCAUUUAUAUAAGCGCCAACUGGCUCAAAAUAUUAAGCAUACGCC
...(((((((.....((((((..(((((....)))))..)))))))))))))..((((((((((((((.....)))..........))))))))..)))..................... (-25.04 = -24.92 +  -0.12)

alignment

secondary structure

dotplot

Window 0

Location	17,282,656 – 17,282,776
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.83
Mean single sequence MFE	-29.44
Consensus MFE	-25.78
Energy contribution	-25.82
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.35
Structure conservation index	0.88
SVM decision value	-0.02
SVM RNA-class probability	0.521233
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17282656 120 + 23771897
AAUGCCGUUGCCCAGAGCACCAAAGCGGAAAGUUCUGCAUAAAUUCAAUUAACUAAAAACAUGCAAAUGAAAACUUUUUUCGAGGGCGACAAAGCCGCGGGGCGAAAGCAGGGAAAUGCU
..(((..((((((...((......(((((....))))).............................(((((.....)))))..(((......))))).))))))..))).......... ( -30.00)
>DroSec_CAF1 166381 120 + 1
AAUGCCGUUGCCCAGAGCACCAAAGCGGAAAGUUCUGCAUAAAUUCAAUUAACUAAAAACAUGCAAAUGAAAACUUUUUUCGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCU
..(((..((((((...((......(((((....))))).............................(((((.....)))))..(((......))))).))))))..))).......... ( -30.00)
>DroSim_CAF1 162567 120 + 1
AAUGCCGUUGCCCAGAGCACCAAAGCGUAAAGUUCUGCAUAAAUUCAAUUAACUAAAAACAUGCAAAUGAAAACUUUUUUCGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCU
..(((..((((((...((.......((.((((((((((((....................)))))...))..)))))...))..(((......))))).))))))..))).......... ( -28.05)
>DroEre_CAF1 169423 120 + 1
AAUGCCGUUGGCCAGAGCACCAAAGCGGAAAGUUCUGCAUAAAUUCAAUUAACUAAAAACAUGCAAAUGAAAACUUUUUUCGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCU
...(((...)))...((((((...(((((....)))))........................((...(((((.....)))))..(((......))))))).((....)).......)))) ( -26.70)
>DroYak_CAF1 174476 120 + 1
AAUGCCGCUGGCCGGAGCGCCAAAGCGGAAAGUUCUGCAUAAAUUCAAUUAACUAAAAACAUGCAAAUGAAAACUUUUUUCGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCU
....((((.(((.....((((...(..(((((((((((((....................)))))...))..))))))..)...)))).....))))))).((....))........... ( -32.45)
>consensus
AAUGCCGUUGCCCAGAGCACCAAAGCGGAAAGUUCUGCAUAAAUUCAAUUAACUAAAAACAUGCAAAUGAAAACUUUUUUCGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCU
..(((((((......))).((...(((((....)))))........................((...(((((.....)))))..(((......)))))))))))..((((......)))) (-25.78 = -25.82 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	17,282,696 – 17,282,816
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.33
Mean single sequence MFE	-28.70
Consensus MFE	-28.48
Energy contribution	-28.52
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.33
Structure conservation index	0.99
SVM decision value	3.22
SVM RNA-class probability	0.998784
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17282696 120 + 23771897
AAAUUCAAUUAACUAAAAACAUGCAAAUGAAAACUUUUUUCGAGGGCGACAAAGCCGCGGGGCGAAAGCAGGGAAAUGCUAAAAUGCAACUCAUUCAGAUGCACAGAAGUGGCAAUUGGA
...(((((((..(((......((((..((((.......((((..(((......))).))))((....)).(((...(((......))).))).))))..))))......))).))))))) ( -28.20)
>DroSec_CAF1 166421 120 + 1
AAAUUCAAUUAACUAAAAACAUGCAAAUGAAAACUUUUUUCGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCUAAAAUGCAACUCAUUCAGAUGCACAGAAGUGGCAAUUGGA
...(((((((..(((......((((..((((.......((((..(((......))).))))((....)).(((...(((......))).))).))))..))))......))).))))))) ( -29.10)
>DroSim_CAF1 162607 120 + 1
AAAUUCAAUUAACUAAAAACAUGCAAAUGAAAACUUUUUUCGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCUAAAAUGCAACUCAUUCAGAUGCACAGAAGUGGCAAUUGGA
...(((((((..(((......((((..((((.......((((..(((......))).))))((....)).(((...(((......))).))).))))..))))......))).))))))) ( -29.10)
>DroEre_CAF1 169463 120 + 1
AAAUUCAAUUAACUAAAAACAUGCAAAUGAAAACUUUUUUCGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCUAAAAUGCAACUCAUUCAGAUGCACAGAAGUGGCAAUUGGA
...(((((((..(((......((((..((((.......((((..(((......))).))))((....)).(((...(((......))).))).))))..))))......))).))))))) ( -29.10)
>DroYak_CAF1 174516 120 + 1
AAAUUCAAUUAACUAAAAACAUGCAAAUGAAAACUUUUUUCGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCUAAAAUGCAACUCACUCAGAUGCACAGAAGUGGCAAUUGGA
...(((((((..(((......((((..(((........((((..(((......))).))))((....)).(((...(((......))).)))..)))..))))......))).))))))) ( -28.00)
>consensus
AAAUUCAAUUAACUAAAAACAUGCAAAUGAAAACUUUUUUCGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCUAAAAUGCAACUCAUUCAGAUGCACAGAAGUGGCAAUUGGA
...(((((((..(((......((((..((((.......((((..(((......))).))))((....)).(((...(((......))).))).))))..))))......))).))))))) (-28.48 = -28.52 +   0.04)

alignment

secondary structure

dotplot

Window 2

Location	17,282,696 – 17,282,816
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.33
Mean single sequence MFE	-25.52
Consensus MFE	-25.36
Energy contribution	-25.20
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.44
Structure conservation index	0.99
SVM decision value	0.87
SVM RNA-class probability	0.871383
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17282696 120 - 23771897
UCCAAUUGCCACUUCUGUGCAUCUGAAUGAGUUGCAUUUUAGCAUUUCCCUGCUUUCGCCCCGCGGCUUUGUCGCCCUCGAAAAAAGUUUUCAUUUGCAUGUUUUUAGUUAAUUGAAUUU
..((((((..(((...(((((..((((.(((.(((......))).))).((..(((((....(((((...)))))...)))))..))..))))..)))))......)))))))))..... ( -25.10)
>DroSec_CAF1 166421 120 - 1
UCCAAUUGCCACUUCUGUGCAUCUGAAUGAGUUGCAUUUUAGCAUUUCUCUGCUUUCGCCCCGCGGCUUUGUCGCCCUCGAAAAAAGUUUUCAUUUGCAUGUUUUUAGUUAAUUGAAUUU
..((((((..(((...(((((..((((.(((.(((......)))...)))...(((((....(((((...)))))...)))))......))))..)))))......)))))))))..... ( -25.70)
>DroSim_CAF1 162607 120 - 1
UCCAAUUGCCACUUCUGUGCAUCUGAAUGAGUUGCAUUUUAGCAUUUCUCUGCUUUCGCCCCGCGGCUUUGUCGCCCUCGAAAAAAGUUUUCAUUUGCAUGUUUUUAGUUAAUUGAAUUU
..((((((..(((...(((((..((((.(((.(((......)))...)))...(((((....(((((...)))))...)))))......))))..)))))......)))))))))..... ( -25.70)
>DroEre_CAF1 169463 120 - 1
UCCAAUUGCCACUUCUGUGCAUCUGAAUGAGUUGCAUUUUAGCAUUUCUCUGCUUUCGCCCCGCGGCUUUGUCGCCCUCGAAAAAAGUUUUCAUUUGCAUGUUUUUAGUUAAUUGAAUUU
..((((((..(((...(((((..((((.(((.(((......)))...)))...(((((....(((((...)))))...)))))......))))..)))))......)))))))))..... ( -25.70)
>DroYak_CAF1 174516 120 - 1
UCCAAUUGCCACUUCUGUGCAUCUGAGUGAGUUGCAUUUUAGCAUUUCUCUGCUUUCGCCCCGCGGCUUUGUCGCCCUCGAAAAAAGUUUUCAUUUGCAUGUUUUUAGUUAAUUGAAUUU
..((((((..(((...(((((..((((.(((.(((......)))...)))...(((((....(((((...)))))...)))))......))))..)))))......)))))))))..... ( -25.40)
>consensus
UCCAAUUGCCACUUCUGUGCAUCUGAAUGAGUUGCAUUUUAGCAUUUCUCUGCUUUCGCCCCGCGGCUUUGUCGCCCUCGAAAAAAGUUUUCAUUUGCAUGUUUUUAGUUAAUUGAAUUU
..((((((..(((...(((((..((((.(((.(((......))).))).((..(((((....(((((...)))))...)))))..))..))))..)))))......)))))))))..... (-25.36 = -25.20 +  -0.16)

alignment

secondary structure

dotplot

Window 3

Location	17,282,736 – 17,282,856
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.96
Mean single sequence MFE	-35.84
Consensus MFE	-32.08
Energy contribution	-31.64
Covariance contribution	-0.44
Combinations/Pair	1.11
Mean z-score	-1.28
Structure conservation index	0.90
SVM decision value	0.52
SVM RNA-class probability	0.767269
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17282736 120 + 23771897
CGAGGGCGACAAAGCCGCGGGGCGAAAGCAGGGAAAUGCUAAAAUGCAACUCAUUCAGAUGCACAGAAGUGGCAAUUGGAAGUGGCCACCAGGCGCAUCCUCUAUCCUCUAUCCUCCAGU
.(((((((.......)))(((((....))((((...(((......))).........(((((.(....(((((.((.....)).)))))...).))))))))).))).....)))).... ( -36.60)
>DroSec_CAF1 166461 113 + 1
CGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCUAAAAUGCAACUCAUUCAGAUGCACAGAAGUGGCAAUUGGAAGUGGCCACCAGGCGCAUCCUCU-------AUCCUCCAGU
.(((((((.......)))(((((....)).(((...(((......))).))).....(((((.(....(((((.((.....)).)))))...).)))))))).-------..)))).... ( -35.40)
>DroSim_CAF1 162647 113 + 1
CGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCUAAAAUGCAACUCAUUCAGAUGCACAGAAGUGGCAAUUGGAAGUGGCCACCAGGCGCAUCCUCU-------AUCCUCCAGU
.(((((((.......)))(((((....)).(((...(((......))).))).....(((((.(....(((((.((.....)).)))))...).)))))))).-------..)))).... ( -35.40)
>DroEre_CAF1 169503 111 + 1
CGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCUAAAAUGCAACUCAUUCAGAUGCACAGAAGUGGCAAUUGGAAGUGGCCACCAGGCGCCUCC--U-------AUUCCGCAUU
....(((......)))(((((((....)).......(((((...((((.((.....)).))))......)))))...(((.(((.((....))))).)))--.-------..)))))... ( -34.60)
>DroYak_CAF1 174556 113 + 1
CGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCUAAAAUGCAACUCACUCAGAUGCACAGAAGUGGCAAUUGGAAGUGGCCACCAGGCGCAUCCUCU-------AUUCCCCAUU
....(((......)))..(((((....))((((...(((......))).........(((((.(....(((((.((.....)).)))))...).)))))))))-------....)))... ( -37.20)
>consensus
CGAGGGCGACAAAGCCGCGGGGCGAAAGCAGAGAAAUGCUAAAAUGCAACUCAUUCAGAUGCACAGAAGUGGCAAUUGGAAGUGGCCACCAGGCGCAUCCUCU_______AUCCUCCAGU
....(((......)))(.(((((....)).(((...(((......))).))).....(((((.(....(((((.((.....)).)))))...).))))).............))).)... (-32.08 = -31.64 +  -0.44)

alignment

secondary structure

dotplot

Window 4

Location	17,282,736 – 17,282,856
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.96
Mean single sequence MFE	-38.40
Consensus MFE	-33.44
Energy contribution	-34.00
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.41
Structure conservation index	0.87
SVM decision value	0.69
SVM RNA-class probability	0.822805
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17282736 120 - 23771897
ACUGGAGGAUAGAGGAUAGAGGAUGCGCCUGGUGGCCACUUCCAAUUGCCACUUCUGUGCAUCUGAAUGAGUUGCAUUUUAGCAUUUCCCUGCUUUCGCCCCGCGGCUUUGUCGCCCUCG
....((((...(((..(((.((((((((..((((((...........))))))...))))))))....(((.(((......))).))).)))..))).....(((((...))))))))). ( -39.40)
>DroSec_CAF1 166461 113 - 1
ACUGGAGGAU-------AGAGGAUGCGCCUGGUGGCCACUUCCAAUUGCCACUUCUGUGCAUCUGAAUGAGUUGCAUUUUAGCAUUUCUCUGCUUUCGCCCCGCGGCUUUGUCGCCCUCG
....((((..-------...((((((((..((((((...........))))))...))))))))(((.(((.(((......)))...)))....))).....(((((...))))))))). ( -38.10)
>DroSim_CAF1 162647 113 - 1
ACUGGAGGAU-------AGAGGAUGCGCCUGGUGGCCACUUCCAAUUGCCACUUCUGUGCAUCUGAAUGAGUUGCAUUUUAGCAUUUCUCUGCUUUCGCCCCGCGGCUUUGUCGCCCUCG
....((((..-------...((((((((..((((((...........))))))...))))))))(((.(((.(((......)))...)))....))).....(((((...))))))))). ( -38.10)
>DroEre_CAF1 169503 111 - 1
AAUGCGGAAU-------A--GGAGGCGCCUGGUGGCCACUUCCAAUUGCCACUUCUGUGCAUCUGAAUGAGUUGCAUUUUAGCAUUUCUCUGCUUUCGCCCCGCGGCUUUGUCGCCCUCG
...((((...-------.--(((((((((.((((((...........))))))...).))........(((.(((......)))...))).))))))...))))(((......))).... ( -34.50)
>DroYak_CAF1 174556 113 - 1
AAUGGGGAAU-------AGAGGAUGCGCCUGGUGGCCACUUCCAAUUGCCACUUCUGUGCAUCUGAGUGAGUUGCAUUUUAGCAUUUCUCUGCUUUCGCCCCGCGGCUUUGUCGCCCUCG
...((((...-------.((((((((((..((((((...........))))))...))))))))(((((((.(((......)))...))).)))))).))))(((((...)))))..... ( -41.90)
>consensus
ACUGGAGGAU_______AGAGGAUGCGCCUGGUGGCCACUUCCAAUUGCCACUUCUGUGCAUCUGAAUGAGUUGCAUUUUAGCAUUUCUCUGCUUUCGCCCCGCGGCUUUGUCGCCCUCG
....((((............((((((((..((((((...........))))))...))))))))((..(((((((.....((((......))))........)))))))..))..)))). (-33.44 = -34.00 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:28 2006