Locus 4643

Sequence ID 2L_DroMel_CAF1
Location 13,293,121 – 13,293,313
Length 192
Max. P 0.985463
window7332 window7333 window7334 window7335 window7336 window7337

overview

Window 2

Location 13,293,121 – 13,293,241
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -39.22
Consensus MFE -32.68
Energy contribution -33.68
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.83
SVM decision value 1.19
SVM RNA-class probability 0.927716
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13293121 120 + 22407834
CCAAGAAGGACUCGAAGAAUCUAGACGAGGAGGACAUGGCCUUCAAACAGAAGCAGAAGGAGCAGCAGAAGGCUAUGGAGGCGGCCAAGGCAGGUGCCUCCAAGAAGGGACCUCUUCUUG
.((((((...((((...........))))((((..(((((((((.....(..((.......))..).)))))))))(((((((.((......))))))))).........)))))))))) ( -40.80)
>DroSec_CAF1 5990 120 + 1
CAAAGAAGGACUCGAAGAAUCUAGACGAGGAGGACAUGGCCUUCAAGCAGAAGCAGAAGGAGCAGCAGAAGGCUCUGGAGGCGGCCAAGGCAGGUGCCGCCAAGAAGGGACCUCUUCUCG
.......................((.(((((((.....((((((..((....))....(((((........)))))))))))(((...(((....)))))).........))))))))). ( -38.80)
>DroSim_CAF1 5975 120 + 1
CCAAGAAGGACUCAAAGAAUCUAGACGAGGAGGACAUGGCCUUCAAGCAAAAGCAGAAGGAGCAGCAGAAGGCUCUGGAGGCGGCCAAGGCAGGUGCCGCCAAGAAGGGACCUCUUCUCG
((.....))..............((.(((((((.....((((((..((....))....(((((........)))))))))))(((...(((....)))))).........))))))))). ( -39.10)
>DroEre_CAF1 7015 120 + 1
CGAAGAAGGACUCGAAGAAUCUAGACGAGGAGGACAUGGCCUUCAAGCAGAAGCAGAAGGAGCAGAAGAAGGCUCUGGAGGCAGCCAAGGCAGGUGCCUCCAAGAAGGGACCUCUUGUUG
..((((.((.(((......((.....))(((((.(((.((((((..((....))....(((((........))))))))))).((....))..)))))))).....))).)))))).... ( -39.10)
>DroYak_CAF1 6148 120 + 1
CAAAGAAGGACUCGAAGAAUCUAGACGAGGAGGACAUGGCCUUCAAGCAGAAGCAGAAGGAGCAGCAGAAGGCUCUGGAGGCAGCCAAGGCUGGUGCCUCCAAGAAGGGACCACUUGUUG
..........((((...........))))...((((((((((((..((....))....(((((........)))))(((((((.(((....))))))))))..)))))..)))..)))). ( -38.30)
>consensus
CAAAGAAGGACUCGAAGAAUCUAGACGAGGAGGACAUGGCCUUCAAGCAGAAGCAGAAGGAGCAGCAGAAGGCUCUGGAGGCGGCCAAGGCAGGUGCCUCCAAGAAGGGACCUCUUCUUG
..((((.((.(((......((.....))(((((.(((.((((((..((....))....(((((........))))))))))).((....))..)))))))).....))).)))))).... (-32.68 = -33.68 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,293,121 – 13,293,241
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -37.72
Consensus MFE -31.00
Energy contribution -31.88
Covariance contribution 0.88
Combinations/Pair 1.09
Mean z-score -2.39
Structure conservation index 0.82
SVM decision value 2.01
SVM RNA-class probability 0.985463
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13293121 120 - 22407834
CAAGAAGAGGUCCCUUCUUGGAGGCACCUGCCUUGGCCGCCUCCAUAGCCUUCUGCUGCUCCUUCUGCUUCUGUUUGAAGGCCAUGUCCUCCUCGUCUAGAUUCUUCGAGUCCUUCUUGG
((((((((((.(......(((((((.((......))..)))))))..((((((.((.((.......))....))..))))))...).))))((((...........))))...)))))). ( -40.20)
>DroSec_CAF1 5990 120 - 1
CGAGAAGAGGUCCCUUCUUGGCGGCACCUGCCUUGGCCGCCUCCAGAGCCUUCUGCUGCUCCUUCUGCUUCUGCUUGAAGGCCAUGUCCUCCUCGUCUAGAUUCUUCGAGUCCUUCUUUG
((((..((((.(...(((.((((((..........))))))...)))((((((.((.((.......))....))..))))))...).))))))))....(((((...)))))........ ( -37.40)
>DroSim_CAF1 5975 120 - 1
CGAGAAGAGGUCCCUUCUUGGCGGCACCUGCCUUGGCCGCCUCCAGAGCCUUCUGCUGCUCCUUCUGCUUUUGCUUGAAGGCCAUGUCCUCCUCGUCUAGAUUCUUUGAGUCCUUCUUGG
((((((((((.........((((((..........))))))..((..((((((.((.((.......))....))..))))))..))....)))).....(((((...))))).)))))). ( -39.20)
>DroEre_CAF1 7015 120 - 1
CAACAAGAGGUCCCUUCUUGGAGGCACCUGCCUUGGCUGCCUCCAGAGCCUUCUUCUGCUCCUUCUGCUUCUGCUUGAAGGCCAUGUCCUCCUCGUCUAGAUUCUUCGAGUCCUUCUUCG
......((((.(...(((.(((((((((......)).))))))))))((((((....((.............))..))))))...).))))((((...........)))).......... ( -36.72)
>DroYak_CAF1 6148 120 - 1
CAACAAGUGGUCCCUUCUUGGAGGCACCAGCCUUGGCUGCCUCCAGAGCCUUCUGCUGCUCCUUCUGCUUCUGCUUGAAGGCCAUGUCCUCCUCGUCUAGAUUCUUCGAGUCCUUCUUUG
......(.((.(...(((.(((((((((......)).))))))))))((((((.((.((.......))....))..))))))...).)).)((((...........)))).......... ( -35.10)
>consensus
CAAGAAGAGGUCCCUUCUUGGAGGCACCUGCCUUGGCCGCCUCCAGAGCCUUCUGCUGCUCCUUCUGCUUCUGCUUGAAGGCCAUGUCCUCCUCGUCUAGAUUCUUCGAGUCCUUCUUGG
.(((((((((.(.....((((((((....((....)).)))))))).((((((.((.((.......))....))..))))))...).))))((((...........))))...))))).. (-31.00 = -31.88 +   0.88)

alignment

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secondary structure

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Window 4

Location 13,293,161 – 13,293,281
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.58
Mean single sequence MFE -41.80
Consensus MFE -32.28
Energy contribution -33.44
Covariance contribution 1.16
Combinations/Pair 1.03
Mean z-score -1.84
Structure conservation index 0.77
SVM decision value 0.39
SVM RNA-class probability 0.717661
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13293161 120 + 22407834
CUUCAAACAGAAGCAGAAGGAGCAGCAGAAGGCUAUGGAGGCGGCCAAGGCAGGUGCCUCCAAGAAGGGACCUCUUCUUGGCGGCGGUAUCAAAAAGUCCGGCAAAAAGUGAUCCAUUGC
((((.....)))).....(((...((.....((((((((((((.((......))))))))))((((((....))))))))))(.(((...........))).).....))..)))..... ( -37.30)
>DroSec_CAF1 6030 120 + 1
CUUCAAGCAGAAGCAGAAGGAGCAGCAGAAGGCUCUGGAGGCGGCCAAGGCAGGUGCCGCCAAGAAGGGACCUCUUCUCGGCGGCGGAAUCAAGAAGUCCGGCAAAAAGUGAUCCAUAGC
((((..((....)).))))((((........))))((((.((.(((.........((((((.((((((....)))))).))))))(((.........)))))).....))..)))).... ( -41.50)
>DroSim_CAF1 6015 120 + 1
CUUCAAGCAAAAGCAGAAGGAGCAGCAGAAGGCUCUGGAGGCGGCCAAGGCAGGUGCCGCCAAGAAGGGACCUCUUCUCGGCGGCGGGAUCAAGAAGUCCGGCAAAAAGUGAUCCAUAGC
((((..((....)).))))((((........))))((((.((.(((........(((((((.((((((....)))))).)))))))((((......))))))).....))..)))).... ( -43.70)
>DroEre_CAF1 7055 120 + 1
CUUCAAGCAGAAGCAGAAGGAGCAGAAGAAGGCUCUGGAGGCAGCCAAGGCAGGUGCCUCCAAGAAGGGACCUCUUGUUGGCGGCGGGAUCAAAAAGUCGGGCAAAAAGUGAUCCCUAGC
((((..((....)).))))((((........))))((((((((.((......))))))))))...(((((.(.(((.(((.((((...........))).).))).))).).)))))... ( -40.80)
>DroYak_CAF1 6188 120 + 1
CUUCAAGCAGAAGCAGAAGGAGCAGCAGAAGGCUCUGGAGGCAGCCAAGGCUGGUGCCUCCAAGAAGGGACCACUUGUUGGCGGCGGGAUCAAAAAGUCGGGCAAAAAGUGAUCCCUAGC
((((..((....)).))))((((........))))((((((((.(((....)))))))))))...(((((.(((((.(((.((((...........))).).))).))))).)))))... ( -45.70)
>consensus
CUUCAAGCAGAAGCAGAAGGAGCAGCAGAAGGCUCUGGAGGCGGCCAAGGCAGGUGCCUCCAAGAAGGGACCUCUUCUUGGCGGCGGGAUCAAAAAGUCCGGCAAAAAGUGAUCCAUAGC
((((..............(((((........)))))(((((((.((......)))))))))..))))(((.(.(((.(((.((((...........).))).))).))).).)))..... (-32.28 = -33.44 +   1.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,293,161 – 13,293,281
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.58
Mean single sequence MFE -40.31
Consensus MFE -32.56
Energy contribution -33.56
Covariance contribution 1.00
Combinations/Pair 1.06
Mean z-score -2.15
Structure conservation index 0.81
SVM decision value 1.53
SVM RNA-class probability 0.962020
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13293161 120 - 22407834
GCAAUGGAUCACUUUUUGCCGGACUUUUUGAUACCGCCGCCAAGAAGAGGUCCCUUCUUGGAGGCACCUGCCUUGGCCGCCUCCAUAGCCUUCUGCUGCUCCUUCUGCUUCUGUUUGAAG
((...(((((.(((((((.(((..............))).))))))).))))).....(((((((.((......))..)))))))..))((((.((.((.......))....))..)))) ( -37.04)
>DroSec_CAF1 6030 120 - 1
GCUAUGGAUCACUUUUUGCCGGACUUCUUGAUUCCGCCGCCGAGAAGAGGUCCCUUCUUGGCGGCACCUGCCUUGGCCGCCUCCAGAGCCUUCUGCUGCUCCUUCUGCUUCUGCUUGAAG
(((.((((.........((((((.........)))((((((((((((......)))))))))))).........)))....)))).)))((((.((.((.......))....))..)))) ( -41.32)
>DroSim_CAF1 6015 120 - 1
GCUAUGGAUCACUUUUUGCCGGACUUCUUGAUCCCGCCGCCGAGAAGAGGUCCCUUCUUGGCGGCACCUGCCUUGGCCGCCUCCAGAGCCUUCUGCUGCUCCUUCUGCUUUUGCUUGAAG
(((.((((.........(((((((.....).))).((((((((((((......)))))))))))).........)))....)))).)))((((.((.((.......))....))..)))) ( -41.42)
>DroEre_CAF1 7055 120 - 1
GCUAGGGAUCACUUUUUGCCCGACUUUUUGAUCCCGCCGCCAACAAGAGGUCCCUUCUUGGAGGCACCUGCCUUGGCUGCCUCCAGAGCCUUCUUCUGCUCCUUCUGCUUCUGCUUGAAG
((..(((((((.................)))))))...))(((..((((((.......((((((((((......)).))))))))((((........)))).....))))))..)))... ( -39.23)
>DroYak_CAF1 6188 120 - 1
GCUAGGGAUCACUUUUUGCCCGACUUUUUGAUCCCGCCGCCAACAAGUGGUCCCUUCUUGGAGGCACCAGCCUUGGCUGCCUCCAGAGCCUUCUGCUGCUCCUUCUGCUUCUGCUUGAAG
...(((((((((((.(((..((...............)).))).)))))))))))...((((((((((......)).))))))))((((........))))((((.((....))..)))) ( -42.56)
>consensus
GCUAUGGAUCACUUUUUGCCGGACUUUUUGAUCCCGCCGCCAAGAAGAGGUCCCUUCUUGGAGGCACCUGCCUUGGCCGCCUCCAGAGCCUUCUGCUGCUCCUUCUGCUUCUGCUUGAAG
.....(((((.(((((((.(((..............))).))))))).))))).....(((((((....((....)).)))))))((((........))))((((.((....))..)))) (-32.56 = -33.56 +   1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,293,201 – 13,293,313
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.81
Mean single sequence MFE -38.27
Consensus MFE -26.12
Energy contribution -27.00
Covariance contribution 0.88
Combinations/Pair 1.04
Mean z-score -1.84
Structure conservation index 0.68
SVM decision value 0.36
SVM RNA-class probability 0.702408
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13293201 112 + 22407834
GCGGCCAAGGCAGGUGCCUCCAAGAAGGGACCUCUUCUUGGCGGCGGUAUCAAAAAGUCCGGCAAAAAGUGAUCCAUUGCCACACCUUCAUCUGUAUAU--------CUUGGCAUAUUCA
...(((((((((((((((.(((((((((....))))))))).)))...............(((((...........)))))........))))))....--------))))))....... ( -39.50)
>DroSec_CAF1 6070 112 + 1
GCGGCCAAGGCAGGUGCCGCCAAGAAGGGACCUCUUCUCGGCGGCGGAAUCAAGAAGUCCGGCAAAAAGUGAUCCAUAGCCACACUUUCAUAUGCAUUC--------CUUAGCAUAUUCA
((.(((......)))((((((.((((((....)))))).))))))(((((((.(((((..(((...............)))..)))))....)).))))--------)...))....... ( -35.96)
>DroSim_CAF1 6055 112 + 1
GCGGCCAAGGCAGGUGCCGCCAAGAAGGGACCUCUUCUCGGCGGCGGGAUCAAGAAGUCCGGCAAAAAGUGAUCCAUAGCCACACUUUCAUAUGAAUUC--------CUUAGCAUAUUCA
...((.((((..(((((((((.((((((....)))))).)))))).((((((....(.....)......))))))...))).....(((....)))..)--------))).))....... ( -37.00)
>DroEre_CAF1 7095 112 + 1
GCAGCCAAGGCAGGUGCCUCCAAGAAGGGACCUCUUGUUGGCGGCGGGAUCAAAAAGUCGGGCAAAAAGUGAUCCCUAGCCGCGGCUUCAUCUGUUUUC--------CUUAACUGAAUUA
(.((((..(((....(((.((((.((((....)))).)))).)))(((((((....(.....)......)))))))..)))..)))).).((.(((...--------...))).)).... ( -38.60)
>DroYak_CAF1 6228 120 + 1
GCAGCCAAGGCUGGUGCCUCCAAGAAGGGACCACUUGUUGGCGGCGGGAUCAAAAAGUCGGGCAAAAAGUGAUCCCUAGCCACGCCUUCAUCUUCUUUUAAAUCGCACCCAUGUGGAUUA
......((((((((((((.((((.(((......))).)))).)))(((((((....(.....)......)))))))..)))).)))))............((((.(((....))))))). ( -40.30)
>consensus
GCGGCCAAGGCAGGUGCCUCCAAGAAGGGACCUCUUCUUGGCGGCGGGAUCAAAAAGUCCGGCAAAAAGUGAUCCAUAGCCACACCUUCAUCUGCAUUC________CUUAGCAUAUUCA
...(((((((.((((.((........)).))))..)))))))(((.((((((....(.....)......))))))...)))....................................... (-26.12 = -27.00 +   0.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,293,201 – 13,293,313
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.81
Mean single sequence MFE -42.13
Consensus MFE -28.29
Energy contribution -28.33
Covariance contribution 0.04
Combinations/Pair 1.17
Mean z-score -2.40
Structure conservation index 0.67
SVM decision value 1.21
SVM RNA-class probability 0.931522
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13293201 112 - 22407834
UGAAUAUGCCAAG--------AUAUACAGAUGAAGGUGUGGCAAUGGAUCACUUUUUGCCGGACUUUUUGAUACCGCCGCCAAGAAGAGGUCCCUUCUUGGAGGCACCUGCCUUGGCCGC
.......((((((--------.....(((..((((((.((((((.((....))..)))))).)))))).......(((.((((((((......)))))))).)))..))).))))))... ( -41.60)
>DroSec_CAF1 6070 112 - 1
UGAAUAUGCUAAG--------GAAUGCAUAUGAAAGUGUGGCUAUGGAUCACUUUUUGCCGGACUUCUUGAUUCCGCCGCCGAGAAGAGGUCCCUUCUUGGCGGCACCUGCCUUGGCCGC
.......((((((--------((((.((...(((.((.((((...((....))....)))).))))).)))))))((((((((((((......)))))))))))).......)))))... ( -44.30)
>DroSim_CAF1 6055 112 - 1
UGAAUAUGCUAAG--------GAAUUCAUAUGAAAGUGUGGCUAUGGAUCACUUUUUGCCGGACUUCUUGAUCCCGCCGCCGAGAAGAGGUCCCUUCUUGGCGGCACCUGCCUUGGCCGC
.......((((((--------(...(((...(((.((.((((...((....))....)))).))))).)))....((((((((((((......)))))))))))).....)))))))... ( -45.10)
>DroEre_CAF1 7095 112 - 1
UAAUUCAGUUAAG--------GAAAACAGAUGAAGCCGCGGCUAGGGAUCACUUUUUGCCCGACUUUUUGAUCCCGCCGCCAACAAGAGGUCCCUUCUUGGAGGCACCUGCCUUGGCUGC
.....((((((((--------(....(((.....((((((((..(((((((.................))))))))))))...(((((((...)))))))..)))..)))))))))))). ( -40.73)
>DroYak_CAF1 6228 120 - 1
UAAUCCACAUGGGUGCGAUUUAAAAGAAGAUGAAGGCGUGGCUAGGGAUCACUUUUUGCCCGACUUUUUGAUCCCGCCGCCAACAAGUGGUCCCUUCUUGGAGGCACCAGCCUUGGCUGC
.(((((((....))).)))).......((.(.((((((((((..(((((((.................)))))))))))).......((((.((((....)))).))))))))).))).. ( -38.93)
>consensus
UGAAUAUGCUAAG________GAAUACAGAUGAAGGUGUGGCUAUGGAUCACUUUUUGCCGGACUUUUUGAUCCCGCCGCCAAGAAGAGGUCCCUUCUUGGAGGCACCUGCCUUGGCCGC
.....................................(((((((.((((((.................)))))).(((.((((((((......)))))))).)))........))))))) (-28.29 = -28.33 +   0.04)

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 11:23:27 2006