Locus 982

Sequence ID	3R_DroMel_CAF1
Location	3,163,243 – 3,163,523
Length	280
Max. P	0.999918

overview

Window 3

Location	3,163,243 – 3,163,363
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.83
Mean single sequence MFE	-46.00
Consensus MFE	-45.00
Energy contribution	-44.64
Covariance contribution	-0.36
Combinations/Pair	1.11
Mean z-score	-1.88
Structure conservation index	0.98
SVM decision value	2.97
SVM RNA-class probability	0.997939
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3163243 120 + 27905053
UUUGUGCCCCGGUGGGCGUUGCCCAGAGCGAAAAUUUCGAUGACGAGUGUCCUUGCAGCGUCUGCAAAUCUGCAUAGACGUCACCUCCCUGAUGGAGGAGAAAUUUUCGGCUGCGCAAGU
.....((((....)))).((((.(((..((((((((((..(((((.((((..((((((...))))))....))))...)))))(((((.....))))).)))))))))).))).)))).. ( -47.20)
>DroSec_CAF1 11134 120 + 1
UUUGUGCCCCGGUGGGCGUUGCCCAGAGCGAAAAUUUCGAUGACGAGUGUCCUUGCAGCGUCUGCAAAUCUGCAUAGACGUCACCUCCCUGAUGGAGGAGAAAUUUUCGGCUGCGCAAGU
.....((((....)))).((((.(((..((((((((((..(((((.((((..((((((...))))))....))))...)))))(((((.....))))).)))))))))).))).)))).. ( -47.20)
>DroSim_CAF1 13303 120 + 1
UUUGCGCCCCGGUGGGCGUUGCCCAGAGCGAAAAUUUCGAUGACGAGUGUCCUUGCAGCGUCUGCAAAUCUGCAUAGACGUCACCUCCCUGAUGGAGGAGAAAUUUUCGGCUGCGCAAGU
...((((((....))))))(((.(((..((((((((((..(((((.((((..((((((...))))))....))))...)))))(((((.....))))).)))))))))).))).)))... ( -49.30)
>DroEre_CAF1 2812 119 + 1
UUUGUGGCC-GGUGGGCGUUGCCCAGAGCGAAAGUUUCGAUGACGAGUGUCCUUGCAGCGUCUGCAAAUCUGCAUAGACGUCACCUCCCUGAUGGAGGAGAAGUUUUCGGCUGCGCAAGU
...(..(((-((..((((((((.(..(((....)))..)..(((....)))...))))))))..)..........((((.((.(((((.....))))).)).)))).))))..)...... ( -45.80)
>DroYak_CAF1 12532 120 + 1
UUUGUGUCCUGGUGGGCGUUGCCCAGAGUGAACAUUUCGAUGACGAGUGUCCUUGCAGCGUCUGCAAAUCUGCAUAGACGUCACCUCCCUGACGGAGGAGAAAUUUUCGGCUGCGCAAGU
.....((((....)))).((((.(((..((((.(((((..(((((.((((..((((((...))))))....))))...)))))(((((.....))))).))))).)))).))).)))).. ( -40.50)
>consensus
UUUGUGCCCCGGUGGGCGUUGCCCAGAGCGAAAAUUUCGAUGACGAGUGUCCUUGCAGCGUCUGCAAAUCUGCAUAGACGUCACCUCCCUGAUGGAGGAGAAAUUUUCGGCUGCGCAAGU
(((((((.....(((((...))))).((((((((((((..(((((.((((..((((((...))))))....))))...)))))(((((.....))))).))))))))).)))))))))). (-45.00 = -44.64 +  -0.36)

alignment

secondary structure

dotplot

Window 4

Location	3,163,243 – 3,163,363
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.83
Mean single sequence MFE	-44.56
Consensus MFE	-42.10
Energy contribution	-43.30
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-2.88
Structure conservation index	0.94
SVM decision value	4.55
SVM RNA-class probability	0.999918
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3163243 120 - 27905053
ACUUGCGCAGCCGAAAAUUUCUCCUCCAUCAGGGAGGUGACGUCUAUGCAGAUUUGCAGACGCUGCAAGGACACUCGUCAUCGAAAUUUUCGCUCUGGGCAACGCCCACCGGGGCACAAA
..((((.(((.((((((((((.(((((.....)))))((((((((.(((((...........))))).))))....))))..))))))))))..))).)))).((((....))))..... ( -48.10)
>DroSec_CAF1 11134 120 - 1
ACUUGCGCAGCCGAAAAUUUCUCCUCCAUCAGGGAGGUGACGUCUAUGCAGAUUUGCAGACGCUGCAAGGACACUCGUCAUCGAAAUUUUCGCUCUGGGCAACGCCCACCGGGGCACAAA
..((((.(((.((((((((((.(((((.....)))))((((((((.(((((...........))))).))))....))))..))))))))))..))).)))).((((....))))..... ( -48.10)
>DroSim_CAF1 13303 120 - 1
ACUUGCGCAGCCGAAAAUUUCUCCUCCAUCAGGGAGGUGACGUCUAUGCAGAUUUGCAGACGCUGCAAGGACACUCGUCAUCGAAAUUUUCGCUCUGGGCAACGCCCACCGGGGCGCAAA
..((((.(((.((((((((((.(((((.....)))))((((((((.(((((...........))))).))))....))))..))))))))))..))).))))(((((....))))).... ( -49.40)
>DroEre_CAF1 2812 119 - 1
ACUUGCGCAGCCGAAAACUUCUCCUCCAUCAGGGAGGUGACGUCUAUGCAGAUUUGCAGACGCUGCAAGGACACUCGUCAUCGAAACUUUCGCUCUGGGCAACGCCCACC-GGCCACAAA
..((((.(((.(((((..(((.(((((.....)))))((((((((.(((((...........))))).))))....))))..)))..)))))..))).)))).(((....-)))...... ( -38.00)
>DroYak_CAF1 12532 120 - 1
ACUUGCGCAGCCGAAAAUUUCUCCUCCGUCAGGGAGGUGACGUCUAUGCAGAUUUGCAGACGCUGCAAGGACACUCGUCAUCGAAAUGUUCACUCUGGGCAACGCCCACCAGGACACAAA
.((((.(((((........((.(((((.....))))).)).((((..((......)))))))))))..(((((.(((....)))..)))))....(((((...))))).))))....... ( -39.20)
>consensus
ACUUGCGCAGCCGAAAAUUUCUCCUCCAUCAGGGAGGUGACGUCUAUGCAGAUUUGCAGACGCUGCAAGGACACUCGUCAUCGAAAUUUUCGCUCUGGGCAACGCCCACCGGGGCACAAA
..((((.(((.((((((((((.(((((.....)))))((((((((.(((((...........))))).))))....))))..))))))))))..))).)))).((((....))))..... (-42.10 = -43.30 +   1.20)

alignment

secondary structure

dotplot

Window 5

Location	3,163,323 – 3,163,443
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.83
Mean single sequence MFE	-37.86
Consensus MFE	-35.94
Energy contribution	-35.94
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.16
Structure conservation index	0.95
SVM decision value	3.64
SVM RNA-class probability	0.999476
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3163323 120 + 27905053
UCACCUCCCUGAUGGAGGAGAAAUUUUCGGCUGCGCAAGUCUCUAAAAAGGGGAGCCACGCCCCUAGCACUAGUGCAACAAAAACAGCAAGUUCAAGUUGAACGGGGUGAUUUAAUAAGC
((.(((((.....))))).)).......((((((....))((((....)))).)))).((((((..(((....)))..............((((.....))))))))))........... ( -38.50)
>DroSec_CAF1 11214 120 + 1
UCACCUCCCUGAUGGAGGAGAAAUUUUCGGCUGCGCAAGUCUCUAAAAAGGGCAGCCACGCCCCUAACACCGGUGCAACAAAAACAGCAAGUUCAAGUUGAACGGGGUGAUUUAAUAAAC
((.(((((.....))))).)).......((((((.(.............).)))))).((((((.........(((..........))).((((.....))))))))))........... ( -38.22)
>DroSim_CAF1 13383 120 + 1
UCACCUCCCUGAUGGAGGAGAAAUUUUCGGCUGCGCAAGUCUCUAAAAAGGGGAGCCACGCCCCUAGCUCUGGUGCAACAAAAACAGCAAGUUCAAGUUGAACGGGGUGAUUUAAUAAAC
((.(((((.....))))).)).......((((((....))((((....)))).)))).((((((..((......))..............((((.....))))))))))........... ( -37.10)
>DroEre_CAF1 2891 120 + 1
UCACCUCCCUGAUGGAGGAGAAGUUUUCGGCUGCGCAAGUCUCUAAAAAGGGGAGCCACGCCCCUCGCAGCGGUGCAACAAAAACAGCAAGUUCAAGUUGAACGGGGUGAUUUAAUAAAC
((.(((((.....))))).)).......((((((....))((((....)))).)))).((((((..(((....)))..............((((.....))))))))))........... ( -37.30)
>DroYak_CAF1 12612 120 + 1
UCACCUCCCUGACGGAGGAGAAAUUUUCGGCUGCGCAAGUCUCUAUAAAGGGGAGCCACGCCCCCAGCACUGGUGCAACAAAAACAGCAAGUUCAAGUUGAACGGGGUGAUUUAAUAAAC
((.(((((.....))))).)).......((((((....))((((....)))).)))).((((((..(((....)))..............((((.....))))))))))........... ( -38.20)
>consensus
UCACCUCCCUGAUGGAGGAGAAAUUUUCGGCUGCGCAAGUCUCUAAAAAGGGGAGCCACGCCCCUAGCACUGGUGCAACAAAAACAGCAAGUUCAAGUUGAACGGGGUGAUUUAAUAAAC
((.(((((.....))))).)).......((((((....))((((....)))).)))).((((((.........(((..........))).((((.....))))))))))........... (-35.94 = -35.94 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	3,163,403 – 3,163,523
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.25
Mean single sequence MFE	-26.75
Consensus MFE	-21.80
Energy contribution	-22.84
Covariance contribution	1.04
Combinations/Pair	1.03
Mean z-score	-1.50
Structure conservation index	0.82
SVM decision value	0.14
SVM RNA-class probability	0.600732
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3163403 120 + 27905053
AAAACAGCAAGUUCAAGUUGAACGGGGUGAUUUAAUAAGCGGACUUGCAAAAAAGCACGGACUCGGAAAAUGUGCAAUGUAAAUAGCAAACAACAAUGUUGACAUUGAUAUUGCCGUGUG
......((((((((..((((((........))))))....))))))))......((((((........(((((.((((((...(((((........)))))))))))))))).)))))). ( -28.90)
>DroSec_CAF1 11294 120 + 1
AAAACAGCAAGUUCAAGUUGAACGGGGUGAUUUAAUAAACGGACUUGCAAAAAAGCACGGACUCGGAAAAUGUGCAAUGUAAAUAGCAAACAACAAAGUUGACAUUGAUAUCGCCGUGUG
......((((((((..((((((........))))))....))))))))......((((((........(((((((.((....)).))...((((...))))))))).......)))))). ( -27.06)
>DroSim_CAF1 13463 120 + 1
AAAACAGCAAGUUCAAGUUGAACGGGGUGAUUUAAUAAACGGACUUGCAAAAAAGCACGGACUCGGAAAAUGUGCAAUGUAAAUAGCAAACAACAAAGUUGACAUUGAUAUCGCCGUGUG
......((((((((..((((((........))))))....))))))))......((((((........(((((((.((....)).))...((((...))))))))).......)))))). ( -27.06)
>DroEre_CAF1 2971 117 + 1
AAAACAGCAAGUUCAAGUUGAACGGGGUGAUUUAAUAAACGGACUGGCGAAAAAGCACGGACUCGGAAAAUGUGCAAUGUAAAUAGCAAGCAACAAAGUUGACAUUGAUAUCG---UGCG
......((.(((((..((((((........))))))....))))).))......((((((..((((......(((.((....)).))).(((((...)))).).))))..)))---))). ( -21.10)
>DroYak_CAF1 12692 120 + 1
AAAACAGCAAGUUCAAGUUGAACGGGGUGAUUUAAUAAACGGACUUGCGAAACAGCACGGACUCGGAAAAUGUGCAAUGUAAAUAGGCAACAACAAAGUUGACAUUGAUAUCGCCCUGUG
....((((........)))).((((((((((.........(..(.(((......))).)..)......(((((.((((.......(....)......)))))))))...)))))))))). ( -29.62)
>consensus
AAAACAGCAAGUUCAAGUUGAACGGGGUGAUUUAAUAAACGGACUUGCAAAAAAGCACGGACUCGGAAAAUGUGCAAUGUAAAUAGCAAACAACAAAGUUGACAUUGAUAUCGCCGUGUG
......((((((((..((((((........))))))....))))))))......((((((........(((((((.((....)).))...((((...))))))))).......)))))). (-21.80 = -22.84 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:28 2006