Locus 3126

Sequence ID X_DroMel_CAF1
Location 8,337,764 – 8,337,976
Length 212
Max. P 0.998184
window5108 window5109 window5110

overview

Window 8

Location 8,337,764 – 8,337,875
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.84
Mean single sequence MFE -21.63
Consensus MFE -19.04
Energy contribution -19.20
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -2.31
Structure conservation index 0.88
SVM decision value 3.03
SVM RNA-class probability 0.998184
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8337764 111 - 22224390
--UUAGCAUAAUGCAAUUAGUGUAAAAAAUCAAA--CAAACUA---UAAAUUAAUACUUAGCAUUACAUUAAUUGCU--GCGAAAUUCCUCUUUACUGCGUUCUAAAAAUAGCGUGCAGC
--...(((....(((((((((((((.........--.......---.................))))))))))))))--))..............(((((..(((....)))..))))). ( -21.51)
>DroSec_CAF1 2638 110 - 1
--UUAGCAUAAUGCAAUUAGUGUAAA-AAUCAAA--CAAACUA---UAAAUUAAUACUUAGCAUUACAUUAAUUGCU--GCGAAAUUCCCCUUUACUGCGUUCUAAAAAUAGCGUGCAGC
--...(((....(((((((((((((.-.......--.......---.................))))))))))))))--))..............(((((..(((....)))..))))). ( -21.55)
>DroSim_CAF1 2721 110 - 1
--UUAGCAUAAUGCAAUUAGUGUAAA-AAUCAAA--CAAACUA---UAAAUUAAUACUUAGCAUUACAUUAAUUGCU--GCGAAAUUCCCCUUUACUGCGUUCUAAAAAUAGCGUGCAGC
--...(((....(((((((((((((.-.......--.......---.................))))))))))))))--))..............(((((..(((....)))..))))). ( -21.55)
>DroEre_CAF1 718 119 - 1
UGUUAGCAUAAUGCAAUUAGUGUAAA-AAUCUAAACUAAACUAUCUAAAAUUAAUACUUAGCAUUACAUUAAUUGCCCCGCGAUAUGCCUCUUUACUGCUCUCUAAAAAUAGCGUGCAGC
.....(((((..(((((((((((((.-...((((.......................))))..))))))))))))).......))))).......((((.(.(((....))).).)))). ( -22.10)
>DroYak_CAF1 1348 112 - 1
UGUUAGCAUAAUGCAAUUAGCGUAAA-AAUCAAA--CAAACAA---AAAAUUAAUACUUAGCAUUACAUUAAUUGCU--GCGGGAUGCCACUUUACUGCGCUCUAAAAAUAGCGUGCAGC
.....((((...((((((((.((((.-.......--.......---.................)))).)))))))).--.....)))).......((((((.(((....))).)))))). ( -21.45)
>consensus
__UUAGCAUAAUGCAAUUAGUGUAAA_AAUCAAA__CAAACUA___UAAAUUAAUACUUAGCAUUACAUUAAUUGCU__GCGAAAUUCCCCUUUACUGCGUUCUAAAAAUAGCGUGCAGC
.....((.....(((((((((((((......................................)))))))))))))...))..............((((((.(((....))).)))))). (-19.04 = -19.20 +   0.16)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,337,839 – 8,337,936
Length 97
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.60
Mean single sequence MFE -31.94
Consensus MFE -18.96
Energy contribution -19.36
Covariance contribution 0.40
Combinations/Pair 1.14
Mean z-score -4.19
Structure conservation index 0.59
SVM decision value 2.46
SVM RNA-class probability 0.994228
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8337839 97 - 22224390
A---CA----------CUGCUUGCACGCUGGCCUUAAACUUUGCGUU-UCAGGGCCACGUUA-GCAAAA-CCAAUUG-----UUAGCAUAAUGCAAUUAGUGUAAAAAAUCAAA--CAAA
(---((----------(((.(((((.(.(((((((((((.....)))-).))))))))((((-((((..-....)))-----)))))....))))).))))))...........--.... ( -32.20)
>DroSec_CAF1 2713 107 - 1
A---CACUGCACUGCACUGCUUGCACGCUGGCCUUAAACUUUGCGUU-UCAGGGCCACGCUA-GCAAAAAAAAAUUG-----UUAGCAUAAUGCAAUUAGUGUAAA-AAUCAAA--CAAA
.---........(((((((.(((((.(.(((((((((((.....)))-).))))))))((((-((((.......)))-----)))))....))))).)))))))..-.......--.... ( -35.60)
>DroSim_CAF1 2796 106 - 1
A---CACUGCACUGCACUGCUUGCACGCUGGCCUUAAACUUUGCGUU-UCAGGGCCACGCUA-GCAAAA-CCAAUUG-----UUAGCAUAAUGCAAUUAGUGUAAA-AAUCAAA--CAAA
.---........(((((((.(((((.(.(((((((((((.....)))-).))))))))((((-((((..-....)))-----)))))....))))).)))))))..-.......--.... ( -36.10)
>DroEre_CAF1 798 106 - 1
G----------CUGCACUGCUUGCACGCUGGCCUUAAACUUUGCGUU-UCAGGGUCACGUUA-ACAAAA-CCAAUUGUUAUGUUAGCAUAAUGCAAUUAGUGUAAA-AAUCUAAACUAAA
.----------.(((((((.(((((.(.(((((((((((.....)))-).))))))))((((-(((.((-(.....))).)))))))....))))).)))))))..-............. ( -31.80)
>DroYak_CAF1 1423 114 - 1
GUUGCACUG--CUGCACUGCUUUCGCGCUGGCCUUAAACUUUGCGUUUUCAGGGUCAUGUUAAACGAAA-CCAAUUGUUAUGUUAGCAUAAUGCAAUUAGCGUAAA-AAUCAAA--CAAA
.((((.(((--.(((..((.(((((.(((((((((((((.....))))..))))))).))....)))))-.))...((((((....)))))))))..))).)))).-.......--.... ( -24.00)
>consensus
A___CACUG__CUGCACUGCUUGCACGCUGGCCUUAAACUUUGCGUU_UCAGGGCCACGUUA_GCAAAA_CCAAUUG_____UUAGCAUAAUGCAAUUAGUGUAAA_AAUCAAA__CAAA
............(((((((.(((((...(((((((.(((.....)))...))))))).((((..(((.......)))......))))....))))).)))))))................ (-18.96 = -19.36 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,337,875 – 8,337,976
Length 101
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.53
Mean single sequence MFE -31.14
Consensus MFE -16.84
Energy contribution -17.00
Covariance contribution 0.16
Combinations/Pair 1.12
Mean z-score -2.31
Structure conservation index 0.54
SVM decision value 0.65
SVM RNA-class probability 0.812126
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8337875 101 - 22224390
AACUCAAGCAAGAAGUUAAACGCCAUUUCGGCGAAGCAGUA---CA----------CUGCUUGCACGCUGGCCUUAAACUUUGCGUU-UCAGGGCCACGUUA-GCAAAA-CCAAUUG---
.......((...........((((.....))))((((((..---..----------))))))))(((.(((((((((((.....)))-).))))))))))..-......-.......--- ( -31.50)
>DroSec_CAF1 2748 103 - 1
AACUCAAGCAAGAAGUUAAACGCCA---------AGCAGUA---CACUGCACUGCACUGCUUGCACGCUGGCCUUAAACUUUGCGUU-UCAGGGCCACGCUA-GCAAAAAAAAAUUG---
.......((............((.(---------((((((.---((......)).)))))))))..(((((((((((((.....)))-).))))))).))..-))............--- ( -30.20)
>DroSim_CAF1 2831 102 - 1
AACUCAAGCAAGAAGUUAAACGCCA---------AGCAGUA---CACUGCACUGCACUGCUUGCACGCUGGCCUUAAACUUUGCGUU-UCAGGGCCACGCUA-GCAAAA-CCAAUUG---
.......((............((.(---------((((((.---((......)).)))))))))..(((((((((((((.....)))-).))))))).))..-))....-.......--- ( -30.20)
>DroEre_CAF1 837 107 - 1
AACUCAAGCAAGAAGUUAAACGGCAUGUCGGCUAAGCAGUG----------CUGCACUGCUUGCACGCUGGCCUUAAACUUUGCGUU-UCAGGGUCACGUUA-ACAAAA-CCAAUUGUUA
.......(((((.(((....((((((....((...)).)))----------))).))).)))))(((.(((((((((((.....)))-).))))))))))((-((((..-....)))))) ( -30.20)
>DroYak_CAF1 1460 117 - 1
AACUCAAGCAAGAAGUUAAACGCCAUGUCGGCUAAGCAGUGUUGCACUG--CUGCACUGCUUUCGCGCUGGCCUUAAACUUUGCGUUUUCAGGGUCAUGUUAAACGAAA-CCAAUUGUUA
......(((((((((((.((.((((((.(((..(((((((((.((...)--).)))))))))))))).)))).)).)))))).(((((.((......))..)))))...-....))))). ( -33.60)
>consensus
AACUCAAGCAAGAAGUUAAACGCCAU_UCGGC_AAGCAGUA___CACUG__CUGCACUGCUUGCACGCUGGCCUUAAACUUUGCGUU_UCAGGGCCACGUUA_GCAAAA_CCAAUUG___
(((((......).))))..................(((((...............)))))((((..(((((((((.(((.....)))...))))))).))...))))............. (-16.84 = -17.00 +   0.16)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:32 2006