Locus 7617

Sequence ID X_DroMel_CAF1
Location 19,002,005 – 19,002,147
Length 142
Max. P 0.933106
window12502 window12503 window12504

overview

Window 2

Location 19,002,005 – 19,002,107
Length 102
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 81.01
Mean single sequence MFE -38.67
Consensus MFE -17.83
Energy contribution -21.19
Covariance contribution 3.36
Combinations/Pair 1.24
Mean z-score -2.85
Structure conservation index 0.46
SVM decision value 0.46
SVM RNA-class probability 0.744245
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19002005 102 + 22224390
UGCAGAA-UACUCCUAUCAGCUG----GUGAGUCACAGCAAGCGGGAUCUCCAACUGAUAUGCCCCACGUGAGUGCGGGGCAU--AUUAAACGCCACACGAAUG----GCUUU
((.(((.-...(((..(..((((----........))))..)..)))))).))..(((((((((((((....))..)))))))--))))...((((......))----))... ( -35.70)
>DroSec_CAF1 24362 102 + 1
UGCAGAA-UUCUUUUAUCAGCUG----GUGAGUCACGGCAAGCGGGUUCUCCAGCUGAUAUGCCCCACGUGAGUGCGGGGCAU--AUUAAACGCCACACGAAUG----GCUUU
.......-........(((((((----(.((..(.((.....)))..)).))))))))((((((((((....))..)))))))--)......((((......))----))... ( -42.10)
>DroSim_CAF1 18948 102 + 1
UGCAGAA-UUCUUUUAUCAGCUG----GUGAGUCACGGCAAGCGGGUUCUCCAGCUGAUAUGCCCCACGUGAGUGCGGGGCAU--AUUAAACGCCACACGAAUG----GCUUU
.......-........(((((((----(.((..(.((.....)))..)).))))))))((((((((((....))..)))))))--)......((((......))----))... ( -42.10)
>DroEre_CAF1 23542 102 + 1
UGUAGCA-UUCCCUUAUCAGCUG----GUGAGUCACUGCGAAGCGGCUCUGCAGCUGAUAUGCCCCACGUGAGUGCAGGGCAU--AUUAAACGCCACACGAAUG----GCUUU
.......-........(((((((----..(((((.((....)).)))))..)))))))((((((((((....)))..))))))--)......((((......))----))... ( -41.20)
>DroYak_CAF1 24682 102 + 1
UGCAGAA-UUCACUUAUCAGCUG----GUGAGUCACUGCAAGCGGGAUAUCCAGCUGAUAUGCCCCACGUGAGUGCUGGGCAU--AUUAAACGCCACACGAAUG----GCUUU
(((((.(-((((((........)----))))))..)))))(((.((....)).)))((((((((((((....)))..))))))--)))....((((......))----))... ( -41.90)
>DroAna_CAF1 28997 106 + 1
AGGGGAACUGCGUUUAUCGGCCGGCAAGUGAGUCACUCUGAGAUGG-------ACUGAUAUCCCCCACGUGAGUGCUGGGCAUGCAUUAAAUGAGUCUCUUCUGUUUCUUUUU
(((((((((.(((((((((((((.((((((...)))).))...)))-------.))))((((((.(((....)))..))).)))...))))))))).)))))).......... ( -29.00)
>consensus
UGCAGAA_UUCUCUUAUCAGCUG____GUGAGUCACUGCAAGCGGGAUCUCCAGCUGAUAUGCCCCACGUGAGUGCGGGGCAU__AUUAAACGCCACACGAAUG____GCUUU
.((...........(((((((((........((........))........)))))))))((((((((....)))..)))))..........................))... (-17.83 = -21.19 +   3.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,002,005 – 19,002,107
Length 102
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 81.01
Mean single sequence MFE -37.85
Consensus MFE -21.58
Energy contribution -22.39
Covariance contribution 0.81
Combinations/Pair 1.18
Mean z-score -3.10
Structure conservation index 0.57
SVM decision value 1.23
SVM RNA-class probability 0.933106
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19002005 102 - 22224390
AAAGC----CAUUCGUGUGGCGUUUAAU--AUGCCCCGCACUCACGUGGGGCAUAUCAGUUGGAGAUCCCGCUUGCUGUGACUCAC----CAGCUGAUAGGAGUA-UUCUGCA
...((----(((....)))))((..(((--(((((((((......))))))).((((((((((.((...(((.....)))..)).)----)))))))))...)))-))..)). ( -43.20)
>DroSec_CAF1 24362 102 - 1
AAAGC----CAUUCGUGUGGCGUUUAAU--AUGCCCCGCACUCACGUGGGGCAUAUCAGCUGGAGAACCCGCUUGCCGUGACUCAC----CAGCUGAUAAAAGAA-UUCUGCA
...((----(((....)))))((..(((--.((((((((......))))))))((((((((((.((...(((.....)))..)).)----))))))))).....)-))..)). ( -43.10)
>DroSim_CAF1 18948 102 - 1
AAAGC----CAUUCGUGUGGCGUUUAAU--AUGCCCCGCACUCACGUGGGGCAUAUCAGCUGGAGAACCCGCUUGCCGUGACUCAC----CAGCUGAUAAAAGAA-UUCUGCA
...((----(((....)))))((..(((--.((((((((......))))))))((((((((((.((...(((.....)))..)).)----))))))))).....)-))..)). ( -43.10)
>DroEre_CAF1 23542 102 - 1
AAAGC----CAUUCGUGUGGCGUUUAAU--AUGCCCUGCACUCACGUGGGGCAUAUCAGCUGCAGAGCCGCUUCGCAGUGACUCAC----CAGCUGAUAAGGGAA-UGCUACA
.....----......((((((((((...--.(((((..(......)..)))))(((((((((..(((.((((....)))).)))..----)))))))))...)))-))))))) ( -44.60)
>DroYak_CAF1 24682 102 - 1
AAAGC----CAUUCGUGUGGCGUUUAAU--AUGCCCAGCACUCACGUGGGGCAUAUCAGCUGGAUAUCCCGCUUGCAGUGACUCAC----CAGCUGAUAAGUGAA-UUCUGCA
...((----(((....)))))((..(((--.(((((.((......)).)))))((((((((((......(((.....))).....)----))))))))).....)-))..)). ( -35.50)
>DroAna_CAF1 28997 106 - 1
AAAAAGAAACAGAAGAGACUCAUUUAAUGCAUGCCCAGCACUCACGUGGGGGAUAUCAGU-------CCAUCUCAGAGUGACUCACUUGCCGGCCGAUAAACGCAGUUCCCCU
...........................(((...(((..(((....))).))).((((.((-------(.......(((((...)))))...))).))))...)))........ ( -17.60)
>consensus
AAAGC____CAUUCGUGUGGCGUUUAAU__AUGCCCCGCACUCACGUGGGGCAUAUCAGCUGGAGAACCCGCUUGCAGUGACUCAC____CAGCUGAUAAAAGAA_UUCUGCA
...............(((((...........((((((((......))))))))(((((((((............................))))))))).........))))) (-21.58 = -22.39 +   0.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,002,040 – 19,002,147
Length 107
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 80.48
Mean single sequence MFE -33.73
Consensus MFE -15.99
Energy contribution -18.27
Covariance contribution 2.28
Combinations/Pair 1.14
Mean z-score -2.78
Structure conservation index 0.47
SVM decision value 0.65
SVM RNA-class probability 0.812169
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19002040 107 - 22224390
ACUGGCACUCGUUCAGGUGAAUGAAUGUAAAUAUUAUUCAAAAGCCAUUCGUGUGGCGUUUAAUAUGC--CCCGCACU-----CACGUGGGGCAUAUCAGUUGGAGAUCCCGCU
(((((((.((((((....)))))).)))...............(((((....))))).....((((((--(((((...-----...))))))))))))))).((.....))... ( -37.60)
>DroPse_CAF1 24613 111 - 1
UCCCGAACACACUCAUGUGAAUAAAUGUAAAUAUUAUUCAAAACUCAUUCGUGUGGCAUUUUAUAGGCACCCUGCACAUGGUCUUUGUCGGGCAUAUCAGCACACGCACA---C
.(((((....((.((((((......(((..(((..((.(...((......))...).))..)))..))).....)))))))).....))))).......((....))...---. ( -20.70)
>DroSec_CAF1 24397 107 - 1
ACUGGCACUCGUUCAGCUGAAUGAAUGUAAAUAUUAUUCAAAAGCCAUUCGUGUGGCGUUUAAUAUGC--CCCGCACU-----CACGUGGGGCAUAUCAGCUGGAGAACCCGCU
...((...((.(((((((((.((((((.......))))))...(((((....)))))......(((((--(((((...-----...)))))))))))))))))))))..))... ( -44.10)
>DroSim_CAF1 18983 107 - 1
ACUGGCACUCGUUCAGGUGAAUGAAUGUAAAUAUUAUUCAAAAGCCAUUCGUGUGGCGUUUAAUAUGC--CCCGCACU-----CACGUGGGGCAUAUCAGCUGGAGAACCCGCU
...((...((.(((((.(((.((((((.......))))))...(((((....)))))......(((((--(((((...-----...))))))))))))).)))))))..))... ( -39.60)
>DroEre_CAF1 23577 107 - 1
ACUCGCACUCGUUCAGGUGAAUGAAUGUAAAUAUUAUUCAAAAGCCAUUCGUGUGGCGUUUAAUAUGC--CCUGCACU-----CACGUGGGGCAUAUCAGCUGCAGAGCCGCUU
....((.(((...(((.(((.((((((.......))))))...(((((....)))))......(((((--((..(...-----...)..)))))))))).)))..)))..)).. ( -37.80)
>DroPer_CAF1 26818 111 - 1
UCCCGAACACACUCAUGUGAAUAAAUGUAAAUAUUAUUCAAAACUCAUUCGUGUGGCAUUUUAUAGGCACCCUGCACAAUGUCUUCGUCGGGCAUAUCAGCACACGCACA---U
.(((((.(((((..((((((((((((....)).))))))).....)))..)))))(((((.(.((((...)))).).))))).....))))).......((....))...---. ( -22.60)
>consensus
ACUCGCACUCGUUCAGGUGAAUGAAUGUAAAUAUUAUUCAAAAGCCAUUCGUGUGGCGUUUAAUAUGC__CCCGCACU_____CACGUGGGGCAUAUCAGCUGGAGAACCCGCU
...........(((((.(((.((((((.......))))))...(((((....)))))......(((((..(((((...........))))))))))))).)))))......... (-15.99 = -18.27 +   2.28)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:30 2006