Locus 7362

Sequence ID 3R_DroMel_CAF1
Location 19,522,305 – 19,522,447
Length 142
Max. P 0.950007
window11899 window11900 window11901

overview

Window 9

Location 19,522,305 – 19,522,419
Length 114
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 79.53
Mean single sequence MFE -31.52
Consensus MFE -20.80
Energy contribution -21.83
Covariance contribution 1.03
Combinations/Pair 1.41
Mean z-score -1.86
Structure conservation index 0.66
SVM decision value 0.79
SVM RNA-class probability 0.851548
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19522305 114 + 27905053
CAGUACAGCUUAUUCCACAUCCAUGGAGUUGUAAAGUUGUUUAUACCUAGAUCCCCGCCCGCUGCUUUGGAGCAGCAUAUCAUUAUGCUGUUCCCUAAGGGCCUGUUAAAAAAA
(((.(((((((((((((......))))))....)))))))................((((........(((((((((((....)))))))))))....)))))))......... ( -35.10)
>DroGri_CAF1 15949 110 + 1
CAGU---GUUUAUUCCAAGUCCAUGGAGUUGUAGAGCUGCUUAUAGCGGGAGCCACGUCCACUGGAUUGCAUAAGCAAAUUAUUUUGAUGCUCCCUCAGCCUCUGUUAAUGAA-
....---....((((((......))))))..(((((((((.....))((((((....(((...)))((((....))))...........))))))..)).)))))........- ( -26.60)
>DroSim_CAF1 17275 114 + 1
CAGUACAGCUUAUUCCACAUCCAUGGAGUUGUAAAGUUGUUUAUUUUUUUAUCCCCGCCCGCUGCUUUGGAGCACCAUAUCAUUAUGCUGUUCCCUCAGGGCCUGUUAAAUAAA
(((.(((((((((((((......))))))....)))))))................((((........((((((.((((....)))).))))))....)))))))......... ( -28.50)
>DroEre_CAF1 17225 114 + 1
CAGUACAGCUUAUUCCACAUCCAUGGAGUUGUAAAGUUGCUUAUACCUAGAUCCCCGCCCGCUGCUUUGGAGCAGCAUAUCGUUAUGCCGCUCCCUCAGCGCCUGUGGAACAAA
.....((((((((((((......))))))....))))))...............((((.(((((....(((((.(((((....))))).)))))..)))))...))))...... ( -36.10)
>DroYak_CAF1 17308 114 + 1
CAGUACAGCUUAUUCCACAUCCAUGGAGUUGUACAGUUGCUUAUACCUAGAUCCUCGCCCGCUGCUCUGGAGCAGCAUAUCGUUAUGCCGUUCCCUCAGGGCCUGUAAAACCAA
..(((((((....((((......)))))))))))......................((((........(((((.(((((....))))).)))))....))))............ ( -30.50)
>DroAna_CAF1 15545 111 + 1
--GUAUA-UUUACUCCACGUCCAUGGAAUUGUAUAGCUGCUUGUAUCGGGAUCCCUGUCCGCUGGUUUGGAGCAACAUGUCAUUGUGUUGCUCCCUCAGGGCCUGUAAAGAAAU
--.((((-(....((((......))))...)))))....(((....((((..(((((.((...))...((((((((((......))))))))))..)))))))))..))).... ( -32.30)
>consensus
CAGUACAGCUUAUUCCACAUCCAUGGAGUUGUAAAGUUGCUUAUACCUAGAUCCCCGCCCGCUGCUUUGGAGCAGCAUAUCAUUAUGCUGCUCCCUCAGGGCCUGUUAAAAAAA
.....((((((((((((......))))))....)))))).................((((........(((((((((((....)))))))))))....))))............ (-20.80 = -21.83 +   1.03)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,522,345 – 19,522,447
Length 102
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 78.28
Mean single sequence MFE -24.75
Consensus MFE -18.45
Energy contribution -18.62
Covariance contribution 0.17
Combinations/Pair 1.33
Mean z-score -1.99
Structure conservation index 0.75
SVM decision value 1.40
SVM RNA-class probability 0.950007
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19522345 102 + 27905053
UUAUACCUAGAUCCCCGCCCGCUGCUUUGGAGCAGCAUAUCAUUAUGCUGUUCCCUAAGGGCCUGUUAAAAAAAAAAACACAUA--UAAAUAGUG----ACGGCUUAA
................(((.(((.(((.(((((((((((....)))))))))))..))))))................(((...--......)))----..))).... ( -27.30)
>DroSec_CAF1 17126 98 + 1
UUAUACCUAGAUCCCCGCCCGCUGCUUUGGAGCAGCAUAUCAUUAUGCUGUUCCCUCAGGGCCUGUUAAAUAAAA----ACAUA--UAAAUAGAG----GAAGUUUAA
.......(((((..((((((........(((((((((((....)))))))))))....))))(((((........----.....--..))))).)----)..))))). ( -28.46)
>DroSim_CAF1 17315 98 + 1
UUAUUUUUUUAUCCCCGCCCGCUGCUUUGGAGCACCAUAUCAUUAUGCUGUUCCCUCAGGGCCUGUUAAAUAAAA----ACAUA--UAAAUAGAG----GAAGUUUAA
...(((((((((....((((........((((((.((((....)))).))))))....)))).((((.......)----)))..--...))))))----)))...... ( -20.80)
>DroEre_CAF1 17265 99 + 1
UUAUACCUAGAUCCCCGCCCGCUGCUUUGGAGCAGCAUAUCGUUAUGCCGCUCCCUCAGCGCCUGUGGAACAAAA----GCAUA--UAAAUAGUU---AAUAGUUUCA
..............((((.(((((....(((((.(((((....))))).)))))..)))))...)))).......----.....--.........---.......... ( -27.10)
>DroYak_CAF1 17348 99 + 1
UUAUACCUAGAUCCUCGCCCGCUGCUCUGGAGCAGCAUAUCGUUAUGCCGUUCCCUCAGGGCCUGUAAAACCAAA----ACAUA--UAAAUAGUU---CACAGUUUCA
.........((..((.((((........(((((.(((((....))))).)))))....))))((((.........----.....--...))))..---...))..)). ( -20.03)
>DroPer_CAF1 14987 101 + 1
UUAUAACGGGACCCACGACCACUGCUUUGGAGCAGCAUGUCAUUAUGUUGUUCUCUUAGGAUCUGCGGAUACGAA----AGAUAGUUAAGCAAAGGUU---UGUUUUA
.......(((((....((((..(((((.(((((((((((....)))))))))))......((((.((....))..----))))....)))))..))))---.))))). ( -24.80)
>consensus
UUAUACCUAGAUCCCCGCCCGCUGCUUUGGAGCAGCAUAUCAUUAUGCUGUUCCCUCAGGGCCUGUUAAAAAAAA____ACAUA__UAAAUAGAG____AAAGUUUAA
................((((........(((((((((((....)))))))))))....)))).............................................. (-18.45 = -18.62 +   0.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,522,345 – 19,522,447
Length 102
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 78.28
Mean single sequence MFE -27.38
Consensus MFE -14.28
Energy contribution -15.08
Covariance contribution 0.81
Combinations/Pair 1.12
Mean z-score -1.82
Structure conservation index 0.52
SVM decision value 0.02
SVM RNA-class probability 0.543440
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19522345 102 - 27905053
UUAAGCCGU----CACUAUUUA--UAUGUGUUUUUUUUUUUAACAGGCCCUUAGGGAACAGCAUAAUGAUAUGCUGCUCCAAAGCAGCGGGCGGGGAUCUAGGUAUAA
....(((..----(((......--...)))..............(((((((...(((.(((((((....))))))).)))...((.....)))))).))).))).... ( -25.20)
>DroSec_CAF1 17126 98 - 1
UUAAACUUC----CUCUAUUUA--UAUGU----UUUUAUUUAACAGGCCCUGAGGGAACAGCAUAAUGAUAUGCUGCUCCAAAGCAGCGGGCGGGGAUCUAGGUAUAA
.......((----(((......--..(((----(.......))))(.(((((..(((.(((((((....))))))).)))....))).)).))))))........... ( -28.80)
>DroSim_CAF1 17315 98 - 1
UUAAACUUC----CUCUAUUUA--UAUGU----UUUUAUUUAACAGGCCCUGAGGGAACAGCAUAAUGAUAUGGUGCUCCAAAGCAGCGGGCGGGGAUAAAAAAAUAA
.......((----(((......--..(((----(.......))))(.(((((..(((.((.((((....)))).)).)))....))).)).))))))........... ( -24.30)
>DroEre_CAF1 17265 99 - 1
UGAAACUAUU---AACUAUUUA--UAUGC----UUUUGUUCCACAGGCGCUGAGGGAGCGGCAUAACGAUAUGCUGCUCCAAAGCAGCGGGCGGGGAUCUAGGUAUAA
..........---.........--(((((----((..(((((.....(((((..(((((((((((....)))))))))))....)))))....)))))..))))))). ( -39.80)
>DroYak_CAF1 17348 99 - 1
UGAAACUGUG---AACUAUUUA--UAUGU----UUUGGUUUUACAGGCCCUGAGGGAACGGCAUAACGAUAUGCUGCUCCAGAGCAGCGGGCGAGGAUCUAGGUAUAA
.....(((((---(((((....--.....----..))).)))))))((((((..(((.(((((((....))))))).)))....))..))))................ ( -27.80)
>DroPer_CAF1 14987 101 - 1
UAAAACA---AACCUUUGCUUAACUAUCU----UUCGUAUCCGCAGAUCCUAAGAGAACAACAUAAUGACAUGCUGCUCCAAAGCAGUGGUCGUGGGUCCCGUUAUAA
...(((.---.((((...((((...((((----..((....)).))))..))))...........(((((.(((((((....))))))))))))))))...))).... ( -18.40)
>consensus
UUAAACUGU____CACUAUUUA__UAUGU____UUUUAUUUAACAGGCCCUGAGGGAACAGCAUAAUGAUAUGCUGCUCCAAAGCAGCGGGCGGGGAUCUAGGUAUAA
.............................................(.(((((..(((.(((((((....))))))).)))....))).)).)................ (-14.28 = -15.08 +   0.81)

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 12:44:01 2006