Locus 13

Sequence ID sy_ha.0
Location 95 – 1,232,408
Length 1232313
Max. P 0.929297
window84 window85 window86

overview

Window 4

Location 1,232,332 – 1,232,408
Length 76
Sequences 5
Columns 87
Reading direction forward
Mean pairwise identity 62.24
Mean single sequence MFE -14.85
Consensus MFE -10.08
Energy contribution -9.84
Covariance contribution -0.24
Combinations/Pair 1.43
Mean z-score -1.51
Structure conservation index 0.68
SVM decision value 0.97
SVM RNA-class probability 0.892748
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1232332 76 - 2685015
CUGCCGGUUGGGAAUUGCACCCUACCCCGAAGAUG-------AAUUAU--AUAAUUGAUUAAUUUAAUUU-UUAU-AUUACCUUAUA
.....(((.(((.......))).)))..(((((((-------(((((.--.........)))))).))))-))..-........... ( -10.30)
>sy_sa.0 1211975 74 - 2516575
CUGCCGGUUGGGAAUUGCACCCUACCCCGAAGAUG-------AAUUUC--UUAAAU--UUUAUAAAUUUA-UCAU-AGCUUAUUAGU
..((.(((.(((.......))).))).....((((-------(((((.--(.....--...).)))))))-))..-.))........ ( -13.30)
>sy_au.0 1565451 76 + 2809422
CUGCCGGUUGGGAAUUACACCCGACCCCGAAGAUG-------AAUUUU--ACA-UUAUUAAAUUUAAUUC-UCAUUAAUUUUAUACU
.....(((((((.......)))))))..(((..((-------(((((.--...-.....))))))).)))-................ ( -13.90)
>sp_ag.0 1420944 80 - 2160267
CCGCCGGUUAGGAUUUUCACCUGACCCCGAAGAAA----UUCUAUUU--GACAGUUAUUUUACUAAACUC-AUUUUUAUUUGUCAAU
.....(((((((.......)))))))..(((....----)))...((--(((((................-........))))))). ( -16.06)
>sp_pn.0 173968 87 + 2038615
CCACCGGUAGGGAAUUGCACCCUGCCCUGAAGAUAGUUAUUCAAUUACAGAUGAUUAUAGUACUUAAUUUUGAAUAUGUCAACAGAU
.....(((((((.......)))))))(((..((((..(((((((........(((((.......))))))))))))))))..))).. ( -20.70)
>consensus
CUGCCGGUUGGGAAUUGCACCCUACCCCGAAGAUG_______AAUUUC__AUAAUUAUUUUAUUUAAUUC_UCAU_AAUUUAUUAAU
.....(((((((.......)))))))............................................................. (-10.08 =  -9.84 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,232,332 – 1,232,408
Length 76
Sequences 5
Columns 87
Reading direction forward
Mean pairwise identity 62.24
Mean single sequence MFE -14.85
Consensus MFE -10.08
Energy contribution -9.84
Covariance contribution -0.24
Combinations/Pair 1.43
Mean z-score -1.51
Structure conservation index 0.68
SVM decision value 0.97
SVM RNA-class probability 0.892748
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1232332 76 - 2685015/0-87
CUGCCGGUUGGGAAUUGCACCCUACCCCGAAGAUG-------AAUUAU--AUAAUUGAUUAAUUUAAUUU-UUAU-AUUACCUUAUA
.....(((.(((.......))).)))..(((((((-------(((((.--.........)))))).))))-))..-........... ( -10.30)
>sy_sa.0 1211975 74 - 2516575/0-87
CUGCCGGUUGGGAAUUGCACCCUACCCCGAAGAUG-------AAUUUC--UUAAAU--UUUAUAAAUUUA-UCAU-AGCUUAUUAGU
..((.(((.(((.......))).))).....((((-------(((((.--(.....--...).)))))))-))..-.))........ ( -13.30)
>sy_au.0 1565451 76 + 2809422/0-87
CUGCCGGUUGGGAAUUACACCCGACCCCGAAGAUG-------AAUUUU--ACA-UUAUUAAAUUUAAUUC-UCAUUAAUUUUAUACU
.....(((((((.......)))))))..(((..((-------(((((.--...-.....))))))).)))-................ ( -13.90)
>sp_ag.0 1420944 80 - 2160267/0-87
CCGCCGGUUAGGAUUUUCACCUGACCCCGAAGAAA----UUCUAUUU--GACAGUUAUUUUACUAAACUC-AUUUUUAUUUGUCAAU
.....(((((((.......)))))))..(((....----)))...((--(((((................-........))))))). ( -16.06)
>sp_pn.0 173968 87 + 2038615/0-87
CCACCGGUAGGGAAUUGCACCCUGCCCUGAAGAUAGUUAUUCAAUUACAGAUGAUUAUAGUACUUAAUUUUGAAUAUGUCAACAGAU
.....(((((((.......)))))))(((..((((..(((((((........(((((.......))))))))))))))))..))).. ( -20.70)
>consensus
CUGCCGGUUGGGAAUUGCACCCUACCCCGAAGAUG_______AAUUUC__AUAAUUAUUUUAUUUAAUUC_UCAU_AAUUUAUUAAU
.....(((((((.......)))))))............................................................. (-10.08 =  -9.84 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 95 – 214
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 72.63
Mean single sequence MFE -27.13
Consensus MFE -14.30
Energy contribution -14.53
Covariance contribution 0.23
Combinations/Pair 1.19
Mean z-score -2.22
Structure conservation index 0.53
SVM decision value 1.20
SVM RNA-class probability 0.929297
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 95 119 + 2685015/280-400
GUGUGAAUAAAUCAUAGCAUAUAUAAAGUUAUCCACUGAAUGUUAUUAACUUGUGGAUAAUUAUUAACAUGCUGUGAUUAUUU-UUAUCCACUUGUCUAAAUGUCUGUGUAUAAGUCCUA
(..((((..(((((((((((......((((((((((................))))))))))......)))))))))))...)-)))..)(((((((...........).)))))).... ( -27.69)
>sy_au.0 123 119 + 2809422/280-400
CUGUGCAUAACUAAUAAGCAAGAUAAAGUUAUCCACCGAUUGUUAUUAACUUGUGGAUAAUUAUUAACAUGGUGUGUUUAGAAGUUAUCCACGGCUGUUAUU-UUUGUGUAUAACUUAAA
.(((((((((.(((((.((......((((((...((.....))...))))))((((((((((...(((((...)))))....)))))))))).)))))))..-.)))))))))....... ( -27.60)
>sy_sa.0 85 118 + 2516575/280-400
CUGUGUAUAAAUCACAGUUAGGUAAUAGUUAUCCACUGAUUGUGCGUAACUUGUGGAUAAUUAUCAACAGCCUGUGAUUCUUU-UUAUUUGUACCUGUUGUU-UUUGUGUAUAACUUUAA
....(((((((((((((....((.((((((((((((.....((.....))..))))))))))))..))...))))))).....-....))))))..(((((.-.......)))))..... ( -26.10)
>consensus
CUGUGAAUAAAUCAUAGCAAAGAUAAAGUUAUCCACUGAUUGUUAUUAACUUGUGGAUAAUUAUUAACAUGCUGUGAUUAUUU_UUAUCCACACCUGUUAUU_UUUGUGUAUAACUUAAA
.((((((((.................((((((((((.....((.....))..))))))))))..((((((...(((..((.....))..)))..)))))).....))))))))....... (-14.30 = -14.53 +   0.23)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:51:37 2006