Locus 6252

Sequence ID X_DroMel_CAF1
Location 15,919,917 – 15,920,113
Length 196
Max. P 0.789537
window10185 window10186 window10187 window10188

overview

Window 5

Location 15,919,917 – 15,920,037
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.30
Mean single sequence MFE -36.23
Consensus MFE -32.26
Energy contribution -31.82
Covariance contribution -0.44
Combinations/Pair 1.15
Mean z-score -1.48
Structure conservation index 0.89
SVM decision value 0.28
SVM RNA-class probability 0.666063
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15919917 120 + 22224390
CACUGCAUUCGGGAAUGAAACUGGAGCACAGCUGAGCGCUAGGCCGAAGUGGGACGAAACACCCACAUAAAGGUAAUGGGCGCUAUCGAGAGAGCGGGAGAGUAAGACCACGUUCUAAUC
...(((.(((((........))))))))......((((((..(((...(((((........))))).....)))....))))))......((((((((.........)).)))))).... ( -36.90)
>DroSec_CAF1 18467 118 + 1
CACUGCAUUCGGGAACGAAACUGGAGCACAGCUGAGUGCUAGGCCAAAGUGGGACGA-ACACCCACAUAACGGUAACGGGCGCUAUCGAGAGAGUGGGAGAGCAAGACCAUGUUCUAAA-
((((...((((....)))).((.((((((......))))((((((...(((((....-...)))))....((....))))).))))).))..))))..((((((......))))))...- ( -37.70)
>DroSim_CAF1 3283 118 + 1
CACUGCAUUCGGGAAUGAAACUGGAGCACAGCUGAGUGCUAGGCCGAAGUGGGACGA-ACACCCACAUAACGGUAACGGGCGCUAUCGAGAGAGUGGGAGAGUAAGACCAUGUUCUAAA-
...(((.(((((........))))))))......((((((..((((..(((((....-...)))))....))))....))))))....((((.((((..........)))).))))...- ( -34.90)
>DroYak_CAF1 3308 118 + 1
CAAUGCAUUCGGGAGUGAAACUGGAGCACAGCUGAGCGGUAGGCCGAAGUGGGACGA-ACACCCACAUAACGGUAACGGCCGCUAUCGAGAGAGUGGAAGAGUAAGACAAUAUUCUAAA-
...(((.(((((........))))))))......((((((..((((..(((((....-...)))))....))))....)))))).((....)).....((((((......))))))...- ( -35.40)
>consensus
CACUGCAUUCGGGAAUGAAACUGGAGCACAGCUGAGCGCUAGGCCGAAGUGGGACGA_ACACCCACAUAACGGUAACGGGCGCUAUCGAGAGAGUGGGAGAGUAAGACCAUGUUCUAAA_
...(((.(((((........))))))))..((..((((((..((((..(((((........)))))....))))....)))))).((....))))...((((((......)))))).... (-32.26 = -31.82 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,919,957 – 15,920,073
Length 116
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 88.53
Mean single sequence MFE -39.55
Consensus MFE -28.92
Energy contribution -29.18
Covariance contribution 0.25
Combinations/Pair 1.12
Mean z-score -2.02
Structure conservation index 0.73
SVM decision value 0.58
SVM RNA-class probability 0.789537
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15919957 116 + 22224390
AGGCCGAAGUGGGACGAAACACCCACAUAAAGGUAAUGGGCGCUAUCGAGAGAGCGGGAGAGUAAGACCACGUUCUAAUCCGCUCUCCACGC--UCCACGCUCUACGCAGCUGAUCCG
..(((...(((((........))))).....))).((.(((((....(((.((((((((((((.(((......))).....))))))).)))--))....)))...)).))).))... ( -37.60)
>DroSec_CAF1 18507 107 + 1
AGGCCAAAGUGGGACGA-ACACCCACAUAACGGUAACGGGCGCUAUCGAGAGAGUGGGAGAGCAAGACCAUGUUCUAAA-CGCUCUC---------CACGCUCUACGCAGCUGAUCCG
..(((...(((((....-...)))))....((....)))))(((..((..(((((((((((((.(((......)))...-.))))))---------).)))))).)).)))....... ( -39.50)
>DroSim_CAF1 3323 107 + 1
AGGCCGAAGUGGGACGA-ACACCCACAUAACGGUAACGGGCGCUAUCGAGAGAGUGGGAGAGUAAGACCAUGUUCUAAA-CGCUCUC---------CACGCUCUACGCAGCUGAUCCG
..((((..(((((....-...)))))....))))..((((((((..((..(((((((((((((.(((......)))...-.))))))---------).)))))).)).))).).)))) ( -38.80)
>DroYak_CAF1 3348 116 + 1
AGGCCGAAGUGGGACGA-ACACCCACAUAACGGUAACGGCCGCUAUCGAGAGAGUGGAAGAGUAAGACAAUAUUCUAAA-CGCUCUCCACGCUCUCCACGCUUUACGCAGCUGGUCCG
..((((..(((((....-...)))))....))))..((((((((...(((((.(((((.((((.(((......)))...-.))))))))).)))))...((.....))))).)).))) ( -42.30)
>consensus
AGGCCGAAGUGGGACGA_ACACCCACAUAACGGUAACGGGCGCUAUCGAGAGAGUGGGAGAGUAAGACCAUGUUCUAAA_CGCUCUC_________CACGCUCUACGCAGCUGAUCCG
..((((..(((((........)))))....))))..((((((((.....(((((((..((((((......))))))....)))))))............((.....))))).).)))) (-28.92 = -29.18 +   0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,919,957 – 15,920,073
Length 116
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 88.53
Mean single sequence MFE -41.42
Consensus MFE -30.00
Energy contribution -30.50
Covariance contribution 0.50
Combinations/Pair 1.09
Mean z-score -1.60
Structure conservation index 0.72
SVM decision value 0.12
SVM RNA-class probability 0.594137
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15919957 116 - 22224390
CGGAUCAGCUGCGUAGAGCGUGGA--GCGUGGAGAGCGGAUUAGAACGUGGUCUUACUCUCCCGCUCUCUCGAUAGCGCCCAUUACCUUUAUGUGGGUGUUUCGUCCCACUUCGGCCU
.((.((.(((......)))(((((--(((.((((((.((((((.....))))))..)))))))))))...(((.(((((((((.........))))))))))))...)))...)))). ( -44.00)
>DroSec_CAF1 18507 107 - 1
CGGAUCAGCUGCGUAGAGCGUG---------GAGAGCG-UUUAGAACAUGGUCUUGCUCUCCCACUCUCUCGAUAGCGCCCGUUACCGUUAUGUGGGUGU-UCGUCCCACUUUGGCCU
(((....((((((.((((.(((---------(((((((-...(((......))))))))).)))).)))))).))))..)))...(((....(((((...-....)))))..)))... ( -39.80)
>DroSim_CAF1 3323 107 - 1
CGGAUCAGCUGCGUAGAGCGUG---------GAGAGCG-UUUAGAACAUGGUCUUACUCUCCCACUCUCUCGAUAGCGCCCGUUACCGUUAUGUGGGUGU-UCGUCCCACUUCGGCCU
(((....((((((.((((.(((---------(.(((.(-(..(((......))).)).))))))).)))))).))))..)))...(((....(((((...-....)))))..)))... ( -39.20)
>DroYak_CAF1 3348 116 - 1
CGGACCAGCUGCGUAAAGCGUGGAGAGCGUGGAGAGCG-UUUAGAAUAUUGUCUUACUCUUCCACUCUCUCGAUAGCGGCCGUUACCGUUAUGUGGGUGU-UCGUCCCACUUCGGCCU
(((.((.(((((.....))((.(((((.((((((((..-...(((......)))..))).))))).))))).))))))))))...(((....(((((...-....)))))..)))... ( -42.70)
>consensus
CGGAUCAGCUGCGUAGAGCGUG_________GAGAGCG_UUUAGAACAUGGUCUUACUCUCCCACUCUCUCGAUAGCGCCCGUUACCGUUAUGUGGGUGU_UCGUCCCACUUCGGCCU
.((....((((((.((((.((((........(((((......(((......)))..))))))))).)))))).))))..))....(((....(((((........)))))..)))... (-30.00 = -30.50 +   0.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,919,997 – 15,920,113
Length 116
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 90.32
Mean single sequence MFE -40.62
Consensus MFE -30.40
Energy contribution -30.77
Covariance contribution 0.38
Combinations/Pair 1.06
Mean z-score -1.62
Structure conservation index 0.75
SVM decision value 0.08
SVM RNA-class probability 0.572206
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15919997 116 - 22224390
UUCCACAUCCGAAGGCCAAGAAAUGCGCUUCGUGUGUCCUCGGAUCAGCUGCGUAGAGCGUGGA--GCGUGGAGAGCGGAUUAGAACGUGGUCUUACUCUCCCGCUCUCUCGAUAGCG
......((((((.(((((.(((......))).)).))).))))))..((((((.((((((.(((--(.(((((..(((........)))..)).))).))))))))))..)).)))). ( -45.00)
>DroSec_CAF1 18546 108 - 1
UUCCACAUCCGAAGGCCAAGAAAUGCGCUUCGUGUGUCCUCGGAUCAGCUGCGUAGAGCGUG---------GAGAGCG-UUUAGAACAUGGUCUUGCUCUCCCACUCUCUCGAUAGCG
......((((((.(((((.(((......))).)).))).))))))..((((((.((((.(((---------(((((((-...(((......))))))))).)))).)))))).)))). ( -40.80)
>DroSim_CAF1 3362 108 - 1
UUCCACAUCCGAAGGCCAAGAAAUGCGCUUCGUGUGUCCUCGGAUCAGCUGCGUAGAGCGUG---------GAGAGCG-UUUAGAACAUGGUCUUACUCUCCCACUCUCUCGAUAGCG
......((((((.(((((.(((......))).)).))).))))))..((((((.((((.(((---------(.(((.(-(..(((......))).)).))))))).)))))).)))). ( -38.50)
>DroYak_CAF1 3387 117 - 1
UUCCACAUCCGAAGGCCAAGAACUGCGCUUCGUGUGUCCUCGGACCAGCUGCGUAAAGCGUGGAGAGCGUGGAGAGCG-UUUAGAAUAUUGUCUUACUCUUCCACUCUCUCGAUAGCG
...(((.(((((.(((((.(((......))).)).))).)))))...(((......))))))(((((.((((((((..-...(((......)))..))).))))).)))))....... ( -38.20)
>consensus
UUCCACAUCCGAAGGCCAAGAAAUGCGCUUCGUGUGUCCUCGGAUCAGCUGCGUAGAGCGUG_________GAGAGCG_UUUAGAACAUGGUCUUACUCUCCCACUCUCUCGAUAGCG
.......(((((.(((((.(((......))).)).))).)))))...((((((.((((.((((........(((((......(((......)))..))))))))).)))))).)))). (-30.40 = -30.77 +   0.38)

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 12:08:28 2006