Locus 4644

Sequence ID	3L_DroMel_CAF1
Location	13,183,178 – 13,183,487
Length	309
Max. P	0.999934

overview

Window 2

Location	13,183,178 – 13,183,288
Length	110
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	93.87
Mean single sequence MFE	-37.84
Consensus MFE	-33.74
Energy contribution	-34.18
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.42
Structure conservation index	0.89
SVM decision value	0.94
SVM RNA-class probability	0.886329
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13183178 110 + 23771897
AUAUAGAAAAUUGUUGAGGGCAGGC----GUGCGGAGGUCUAGCCACGUUUUCUGGCAGAUCCGAGCAUGAUUUAAAGGGC-GA---CGGCCCAGUCCUGUCUAUUGGCUUUGUUGUU
............((..(((((((((----((((...(((((.((((.......)))))))))...))))).......((((-..---..))))...))))))).)..))......... ( -38.30)
>DroSec_CAF1 34739 111 + 1
AUAUAGAAAAUUGUUGAGGGCAGGC----GUGCGGAGAUCUAGCCACGUUUUCUGGCAGAUCCGAGCAUGAUUUAAAGGGCAGA---CGGCCCAGUCCUGUCUGUUGGCUUUGUUGUU
............((..(((((((((----((((...(((((.((((.......)))))))))...))))).......((((...---..))))...))))))).)..))......... ( -38.70)
>DroSim_CAF1 32981 111 + 1
GUAUAGAAAAUUGUUGAGGGCAGGC----GUGCGGAGAUCUAGCCACGUUUUCUGGCAGAUCCGAGCAUGAUUUAAAGGGCAGA---CGGCCCAGUCCUGUCUGUUGGCUUUGUUGUU
............((..(((((((((----((((...(((((.((((.......)))))))))...))))).......((((...---..))))...))))))).)..))......... ( -38.70)
>DroEre_CAF1 38245 109 + 1
AUCUAGAAAAUUGUUGAGGGCAGGCG-----GCGGAGAUCUAGCCACGUU-UCUGGCAGAUCCGAGCAUGAUUUAAAGGGCAGA---CGGCCCAGUCCAGUCUGUUGGCUUUGUUGUU
.................((((..((.-----.((((..(((.((((....-..))))))))))).))..........((((...---..)))).))))((((....))))........ ( -32.00)
>DroYak_CAF1 33946 117 + 1
-UAUAGAAAAUUGUUGAGGGCAGGCAGGCGUGCGGAGAUCUAGCCACGUUUUCUGGCAGAUCCGAGCAUGAUUUAAAGGGCAGACGACGGCCCAGUCCUGUCUGUUGGCUUUGUUGUU
-..............(..(((((((((((((((...(((((.((((.......)))))))))...))))).......((((........))))...))))))))))..)......... ( -41.50)
>consensus
AUAUAGAAAAUUGUUGAGGGCAGGC____GUGCGGAGAUCUAGCCACGUUUUCUGGCAGAUCCGAGCAUGAUUUAAAGGGCAGA___CGGCCCAGUCCUGUCUGUUGGCUUUGUUGUU
............((..((((((((.....((((...(((((.((((.......)))))))))...))))........((((........))))...))))))).)..))......... (-33.74 = -34.18 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	13,183,252 – 13,183,367
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.22
Mean single sequence MFE	-26.97
Consensus MFE	-20.86
Energy contribution	-21.26
Covariance contribution	0.40
Combinations/Pair	1.15
Mean z-score	-1.83
Structure conservation index	0.77
SVM decision value	0.31
SVM RNA-class probability	0.683314
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13183252 115 - 23771897
CAAAUGCAGAGACUACA-ACUACAGUGCUGCAGAAUGCGAAUCAACAAAGGCUUACAAUCUAUAAAGUACAAUCACUUUCAACAACAAAGCCAAUAGACAGGACUGGGCCG---UC-GCC
....(((((..(((...-.....))).)))))....((((.........(((((.........(((((......)))))........)))))........((......)).---))-)). ( -21.33)
>DroSec_CAF1 34813 116 - 1
CAAAUGCAGAGACUACA-ACUACAGUGCUGCAGAAUGCGAGUCAACAAAGGCUCACAAUCUAUAAAGUACAAUCACUUUCAACAACAAAGCCAACAGACAGGACUGGGCCG---UCUGCC
.....(((((.......-......(((((..(((.((.(((((......))))).)).)))....)))))...................(((..(((......))))))..---))))). ( -27.80)
>DroSim_CAF1 33055 116 - 1
CAAAUGCAUAGACUACA-ACUACAGUGCUGCAGAAUUCGAGUCAACAAAGGCUCACAAUCUAUAAAGUACAAUCACUUUCAACAACAAAGCCAACAGACAGGACUGGGCCG---UCUGCC
........(((((....-......(((((..(((....(((((......)))))....)))....)))))...................(((..(((......)))))).)---)))).. ( -22.20)
>DroEre_CAF1 38317 117 - 1
CAAAUGCAGAGGCUACACGCUACAGUGUUGCAGAAUGCGAGUCAACAAAGGCUCACAAUCUAUAAAGUACAAUCACUUUCAACAACAAAGCCAACAGACUGGACUGGGCCG---UCUGCC
.....(((((((((....(((....(((((.(((.((.(((((......))))).)).)))..(((((......))))))))))....)))...(((......))))))).---))))). ( -34.00)
>DroYak_CAF1 34023 119 - 1
CAAAUGAGGAGACUGCA-ACUACAGUGCUGCAGAAUGCGAGUCAACAAAGGCUCACAAUCUAUAAAGUACAAUCACUUUCAACAACAAAGCCAACAGACAGGACUGGGCCGUCGUCUGCC
......((..(((.((.-....((((.(((((((.((.(((((......))))).)).)))..(((((......))))).................).))).)))).)).)))..))... ( -29.50)
>consensus
CAAAUGCAGAGACUACA_ACUACAGUGCUGCAGAAUGCGAGUCAACAAAGGCUCACAAUCUAUAAAGUACAAUCACUUUCAACAACAAAGCCAACAGACAGGACUGGGCCG___UCUGCC
.....(((((..............(((((..(((.((.(((((......))))).)).)))....)))))...................(((..(((......)))))).....))))). (-20.86 = -21.26 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	13,183,288 – 13,183,407
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.98
Mean single sequence MFE	-28.36
Consensus MFE	-25.14
Energy contribution	-25.26
Covariance contribution	0.12
Combinations/Pair	1.10
Mean z-score	-1.89
Structure conservation index	0.89
SVM decision value	2.03
SVM RNA-class probability	0.986024
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13183288 119 - 23771897
CUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGGCAAAUGCAGAGACUACA-ACUACAGUGCUGCAGAAUGCGAAUCAACAAAGGCUUACAAUCUAUAAAGUACAAUCACUUUC
..(((...(((....((((....(((((....))))).))))..)))..))).....-......(((((..(((.((..(..(......)..)..)).)))....))))).......... ( -22.90)
>DroSec_CAF1 34850 119 - 1
CUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGGCAAAUGCAGAGACUACA-ACUACAGUGCUGCAGAAUGCGAGUCAACAAAGGCUCACAAUCUAUAAAGUACAAUCACUUUC
..(((...(((....((((....(((((....))))).))))..)))..))).....-......(((((..(((.((.(((((......))))).)).)))....))))).......... ( -30.10)
>DroSim_CAF1 33092 119 - 1
CUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGGCAAAUGCAUAGACUACA-ACUACAGUGCUGCAGAAUUCGAGUCAACAAAGGCUCACAAUCUAUAAAGUACAAUCACUUUC
..((((..(((....((((....(((((....))))).))))..))).)))).....-......(((((..(((....(((((......)))))....)))....))))).......... ( -26.00)
>DroEre_CAF1 38354 120 - 1
CUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGGCAAAUGCAGAGGCUACACGCUACAGUGUUGCAGAAUGCGAGUCAACAAAGGCUCACAAUCUAUAAAGUACAAUCACUUUC
...((...(((....((((....(((((....))))).))))..)))..))((.((((......)))).))(((.((.(((((......))))).)).)))..(((((......))))). ( -31.10)
>DroYak_CAF1 34063 119 - 1
CUUCUAAGGCAAACAUGCCCGACACGUUGCACAACGUUGGCAAAUGAGGAGACUGCA-ACUACAGUGCUGCAGAAUGCGAGUCAACAAAGGCUCACAAUCUAUAAAGUACAAUCACUUUC
.......((((....)))).((...(((((....((((....))))((....)))))-))....(((((..(((.((.(((((......))))).)).)))....)))))..))...... ( -31.70)
>consensus
CUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGGCAAAUGCAGAGACUACA_ACUACAGUGCUGCAGAAUGCGAGUCAACAAAGGCUCACAAUCUAUAAAGUACAAUCACUUUC
..(((...(((....((((....(((((....))))).))))..)))..)))............(((((..(((.((.(((((......))))).)).)))....))))).......... (-25.14 = -25.26 +   0.12)

alignment

secondary structure

dotplot

Window 5

Location	13,183,328 – 13,183,447
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.72
Mean single sequence MFE	-48.92
Consensus MFE	-44.04
Energy contribution	-43.96
Covariance contribution	-0.08
Combinations/Pair	1.08
Mean z-score	-3.38
Structure conservation index	0.90
SVM decision value	4.65
SVM RNA-class probability	0.999934
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13183328 119 + 23771897
UCGCAUUCUGCAGCACUGUAGU-UGUAGUCUCUGCAUUUGCCAACGUUGUGCAACGUGUCAGGCAUGUUUGCCUUAGAAGCCGCCACUCUGGUGGCUUUUGGCCACGGGAUGCAGAAUGU
..((((((((((((((.((((.-(((((...))))).)))).......))))..((((.((((((....)))))(((((((((((.....)))))))))))).))))...)))))))))) ( -51.90)
>DroSec_CAF1 34890 119 + 1
UCGCAUUCUGCAGCACUGUAGU-UGUAGUCUCUGCAUUUGCCAACGUUGUGCAACGUGUCAGGCAUGUUUGCCUUAGAAGCCGCCAUUCUGGUGGCUUUUGGCCACGGGAUGCAGAAAGU
.......(((((((......))-)))))..(((((((((((((....)).))..((((.((((((....)))))(((((((((((.....)))))))))))).))))))))))))).... ( -48.40)
>DroSim_CAF1 33132 119 + 1
UCGAAUUCUGCAGCACUGUAGU-UGUAGUCUAUGCAUUUGCCAACGUUGUGCAACGUGUCAGGCAUGUUUGCCUUAGAAGCCGCCACUCUGGUGGCUUUUGGCCACGGGAUGCAGAAAGU
.....(((((((((((....((-(((((.........))).))))...))))..((((.((((((....)))))(((((((((((.....)))))))))))).))))...)))))))... ( -46.50)
>DroEre_CAF1 38394 120 + 1
UCGCAUUCUGCAACACUGUAGCGUGUAGCCUCUGCAUUUGCCAACGUUGUGCAACGUGUCAGGCAUGUUUGCCUUAGAAGCCGCCACUCUGGUGGCUUUUGGCCACGGGAUGCGGAAAGU
((((((((((((.((.(((.((((((((...))))))..))..))).)))))).((((.((((((....)))))(((((((((((.....)))))))))))).))))))))))))..... ( -49.20)
>DroYak_CAF1 34103 119 + 1
UCGCAUUCUGCAGCACUGUAGU-UGCAGUCUCCUCAUUUGCCAACGUUGUGCAACGUGUCGGGCAUGUUUGCCUUAGAAGCCGCCACUCUGGUGGCUUUUGGCCACGGGAUGCAGAGCUU
..((..((((((((((....((-(((((.........))).))))...))))..((((.((((((....)))))(((((((((((.....)))))))))))).))))...)))))))).. ( -48.60)
>consensus
UCGCAUUCUGCAGCACUGUAGU_UGUAGUCUCUGCAUUUGCCAACGUUGUGCAACGUGUCAGGCAUGUUUGCCUUAGAAGCCGCCACUCUGGUGGCUUUUGGCCACGGGAUGCAGAAAGU
.....(((((((...((((....((((.....))))...(((.(((((....)))))...(((((....))))).((((((((((.....))))))))))))).))))..)))))))... (-44.04 = -43.96 +  -0.08)

alignment

secondary structure

dotplot

Window 6

Location	13,183,328 – 13,183,447
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.72
Mean single sequence MFE	-38.96
Consensus MFE	-32.32
Energy contribution	-32.72
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.07
Structure conservation index	0.83
SVM decision value	1.66
SVM RNA-class probability	0.970615
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13183328 119 - 23771897
ACAUUCUGCAUCCCGUGGCCAAAAGCCACCAGAGUGGCGGCUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGGCAAAUGCAGAGACUACA-ACUACAGUGCUGCAGAAUGCGA
.(((((((((...(((((((....(((((....)))))))).....(((((....)))))..))))..((((...((((((....))((...)).))-))....)))))))))))))... ( -41.10)
>DroSec_CAF1 34890 119 - 1
ACUUUCUGCAUCCCGUGGCCAAAAGCCACCAGAAUGGCGGCUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGGCAAAUGCAGAGACUACA-ACUACAGUGCUGCAGAAUGCGA
......((((...((((.....(((((.((.....)).)))))...(((((....)))))..)))).))))........(((..(((((..(((...-.....))).)))))...))).. ( -36.20)
>DroSim_CAF1 33132 119 - 1
ACUUUCUGCAUCCCGUGGCCAAAAGCCACCAGAGUGGCGGCUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGGCAAAUGCAUAGACUACA-ACUACAGUGCUGCAGAAUUCGA
...(((((((...(((((((....(((((....)))))))).....(((((....)))))..))))..((((...((((................))-))....)))))))))))..... ( -37.29)
>DroEre_CAF1 38394 120 - 1
ACUUUCCGCAUCCCGUGGCCAAAAGCCACCAGAGUGGCGGCUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGGCAAAUGCAGAGGCUACACGCUACAGUGUUGCAGAAUGCGA
......(((((.(.((((((..(((((.((.....)).))))).....(((....((((....(((((....))))).))))..)))...))))))((((....))))....).))))). ( -40.20)
>DroYak_CAF1 34103 119 - 1
AAGCUCUGCAUCCCGUGGCCAAAAGCCACCAGAGUGGCGGCUUCUAAGGCAAACAUGCCCGACACGUUGCACAACGUUGGCAAAUGAGGAGACUGCA-ACUACAGUGCUGCAGAAUGCGA
..((((((((((((((.((((.(((((.((.....)).)))))....((((....))))....(((((....)))))))))..))).))).((((..-....))))..))))))..)).. ( -40.00)
>consensus
ACUUUCUGCAUCCCGUGGCCAAAAGCCACCAGAGUGGCGGCUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGGCAAAUGCAGAGACUACA_ACUACAGUGCUGCAGAAUGCGA
...(((((((.((.((((((..(((((.((.....)).)))))....))).....((((....(((((....))))).))))..................))).).).)))))))..... (-32.32 = -32.72 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	13,183,367 – 13,183,487
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.42
Mean single sequence MFE	-48.62
Consensus MFE	-46.26
Energy contribution	-45.94
Covariance contribution	-0.32
Combinations/Pair	1.06
Mean z-score	-1.57
Structure conservation index	0.95
SVM decision value	1.59
SVM RNA-class probability	0.965830
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13183367 120 + 23771897
CCAACGUUGUGCAACGUGUCAGGCAUGUUUGCCUUAGAAGCCGCCACUCUGGUGGCUUUUGGCCACGGGAUGCAGAAUGUGGCAGAUGCCUCGGGAGGUGGUUGAGUCAUGCAUGGCAGC
((((((((.((((.((((.((((((....)))))(((((((((((.....)))))))))))).))))...)))).))))).(((((((((((....)).)))...))).))).))).... ( -48.90)
>DroSec_CAF1 34929 120 + 1
CCAACGUUGUGCAACGUGUCAGGCAUGUUUGCCUUAGAAGCCGCCAUUCUGGUGGCUUUUGGCCACGGGAUGCAGAAAGUGGCAGAUGCCUCGGGAGGUGGUUGAGUCAUGCAUGGCAGC
.....((..((((.......(((((....)))))....(((((((.((((((.(((.((((.((((............)))))))).))))))))))))))))......))))..))... ( -47.70)
>DroSim_CAF1 33171 120 + 1
CCAACGUUGUGCAACGUGUCAGGCAUGUUUGCCUUAGAAGCCGCCACUCUGGUGGCUUUUGGCCACGGGAUGCAGAAAGUGGCAGAUGCCUCGGGAGGUGGUUGAGUCAUGCAUGGCAGC
.....((..((((..((((((((((....)))))(((((((((((.....)))))))))))(((((............))))).)))))(((((.......)))))...))))..))... ( -47.30)
>DroEre_CAF1 38434 120 + 1
CCAACGUUGUGCAACGUGUCAGGCAUGUUUGCCUUAGAAGCCGCCACUCUGGUGGCUUUUGGCCACGGGAUGCGGAAAGUGGCAGAUGCCUCGGGAGGUGGUUGAGUCAUGCAUGGCAGC
.....((..(((..(((((((((((....)))))(((((((((((.....))))))))))).......))))))....(((((....(((((....)).)))...))))))))..))... ( -48.70)
>DroYak_CAF1 34142 120 + 1
CCAACGUUGUGCAACGUGUCGGGCAUGUUUGCCUUAGAAGCCGCCACUCUGGUGGCUUUUGGCCACGGGAUGCAGAGCUUGGCAGAUGCCUCGGGAGGUGGUUGAGUCAUGCAUGACAGC
.....(((((....((((.((((((....)))))(((((((((((.....)))))))))))).))))..(((((..(((..((....((((....)))).))..)))..))))).))))) ( -50.50)
>consensus
CCAACGUUGUGCAACGUGUCAGGCAUGUUUGCCUUAGAAGCCGCCACUCUGGUGGCUUUUGGCCACGGGAUGCAGAAAGUGGCAGAUGCCUCGGGAGGUGGUUGAGUCAUGCAUGGCAGC
.....((..((((.((((.((((((....)))))(((((((((((.....)))))))))))).))))............((((....(((((....)).)))...))))))))..))... (-46.26 = -45.94 +  -0.32)

alignment

secondary structure

dotplot

Window 8

Location	13,183,367 – 13,183,487
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.42
Mean single sequence MFE	-37.54
Consensus MFE	-36.40
Energy contribution	-36.28
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-1.34
Structure conservation index	0.97
SVM decision value	0.93
SVM RNA-class probability	0.884181
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13183367 120 - 23771897
GCUGCCAUGCAUGACUCAACCACCUCCCGAGGCAUCUGCCACAUUCUGCAUCCCGUGGCCAAAAGCCACCAGAGUGGCGGCUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGG
(((((((((((.((.((...........))(((....)))....))))).((..(((((.....)))))..)))))))))).....(((((....)))))..((((((....)))).)). ( -37.70)
>DroSec_CAF1 34929 120 - 1
GCUGCCAUGCAUGACUCAACCACCUCCCGAGGCAUCUGCCACUUUCUGCAUCCCGUGGCCAAAAGCCACCAGAAUGGCGGCUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGG
(((((((((((.((.((...........))(((....)))....))))).((..(((((.....)))))..)))))))))).....(((((....)))))..((((((....)))).)). ( -37.40)
>DroSim_CAF1 33171 120 - 1
GCUGCCAUGCAUGACUCAACCACCUCCCGAGGCAUCUGCCACUUUCUGCAUCCCGUGGCCAAAAGCCACCAGAGUGGCGGCUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGG
(((((((((((.((.((...........))(((....)))....))))).((..(((((.....)))))..)))))))))).....(((((....)))))..((((((....)))).)). ( -37.70)
>DroEre_CAF1 38434 120 - 1
GCUGCCAUGCAUGACUCAACCACCUCCCGAGGCAUCUGCCACUUUCCGCAUCCCGUGGCCAAAAGCCACCAGAGUGGCGGCUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGG
((((((((...((.................(((....)))..............(((((.....)))))))..)))))))).....(((((....)))))..((((((....)))).)). ( -37.50)
>DroYak_CAF1 34142 120 - 1
GCUGUCAUGCAUGACUCAACCACCUCCCGAGGCAUCUGCCAAGCUCUGCAUCCCGUGGCCAAAAGCCACCAGAGUGGCGGCUUCUAAGGCAAACAUGCCCGACACGUUGCACAACGUUGG
...((((....))))....(((.....((.(((((.((((((((((..(.((..(((((.....)))))..)))..).)))))....))))...)))))))..(((((....)))))))) ( -37.40)
>consensus
GCUGCCAUGCAUGACUCAACCACCUCCCGAGGCAUCUGCCACUUUCUGCAUCCCGUGGCCAAAAGCCACCAGAGUGGCGGCUUCUAAGGCAAACAUGCCUGACACGUUGCACAACGUUGG
((((((((...((.................(((....)))..............(((((.....)))))))..)))))))).....(((((....)))))..((((((....)))).)). (-36.40 = -36.28 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:25 2006