Locus 2088

Sequence ID X_DroMel_CAF1
Location 5,692,301 – 5,692,434
Length 133
Max. P 0.989306
window3394 window3395 window3396

overview

Window 4

Location 5,692,301 – 5,692,394
Length 93
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 63.26
Mean single sequence MFE -18.16
Consensus MFE -9.90
Energy contribution -10.43
Covariance contribution 0.53
Combinations/Pair 1.50
Mean z-score -2.49
Structure conservation index 0.55
SVM decision value 2.16
SVM RNA-class probability 0.989306
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5692301 93 + 22224390
GGUACCGCAAAAAGA--------------AAAAC----AAUGCCAAAACCACCUCCGUUUUAUGCAGUGAAAUUAAAACCACUGCGUAAUGGAAUAUGAAUAUCAAAUUCA
(((...(((......--------------.....----..)))....)))...(((((..(((((((((..........))))))))))))))...(((((.....))))) ( -20.12)
>DroPse_CAF1 56838 93 + 1
AGCACUGAGAGACAGAU------------AUAUCGAUGGUUGCCAUUCGCAUUCCCGUUCCACCCACUGAACUUAUACGC-UUCUCUAACGGGAUACAUGUAGCCA-----
....(((.....)))..------------.......(((((((.............((((........))))......(.-.((((....))))..)..)))))))----- ( -16.50)
>DroSec_CAF1 13349 92 + 1
GGUACCGCAAAAA-A--------------AAAAC----AAUGCCAAAACCACCUCCGUUUUAUGCAGUGAAAUUAAAACCACUGCAUAAUCGAAUAUGAAUAUCAAAUUCA
(((...(((....-.--------------.....----..)))....))).........((((((((((..........))))))))))..((((.((.....)).)))). ( -18.80)
>DroSim_CAF1 16155 91 + 1
GGUACCGCAAAAA----------------AAAAC----AAUGCCAAAACCACCUCCGUUUUAUGCAGUGAAAUUAAAACCACUGCAUAAUGGAAUAUGAAUAUCAAAUUCA
(((...(((....----------------.....----..)))....)))...(((((..(((((((((..........))))))))))))))...(((((.....))))) ( -20.70)
>DroEre_CAF1 12708 102 + 1
GGCACCGCAAAACAAAAAACAAAAAACAAAAAAC----AA-----AAACCGCCUCCAUUUUAUGUAGUGCUAUUAAAACCACUGCGUAAUGGAAUAUGAAUAUCAAAUUCA
(((...............................----..-----.....)))(((((..(((((((((..........))))))))))))))...(((((.....))))) ( -16.36)
>DroPer_CAF1 60194 93 + 1
AGCACUGAGAGACAGAU------------AUAUCGAUGGUUGCCAUUCGCAUUUCCGUUCCACACAUUGAACUUAUACGC-UUCUCUAACGGGAUACAUGUAGCCA-----
....(((.....)))..------------.......(((((((.............((((........))))......(.-.((((....))))..)..)))))))----- ( -16.50)
>consensus
GGCACCGCAAAAAAA______________AAAAC____AAUGCCAAAACCACCUCCGUUUUAUGCAGUGAAAUUAAAACCACUGCAUAAUGGAAUAUGAAUAUCAAAUUCA
.....................................................((((((..((((((((..........)))))))))))))).................. ( -9.90 = -10.43 +   0.53)

alignment

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secondary structure

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Window 5

Location 5,692,318 – 5,692,434
Length 116
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 87.72
Mean single sequence MFE -28.17
Consensus MFE -20.86
Energy contribution -21.74
Covariance contribution 0.88
Combinations/Pair 1.13
Mean z-score -2.55
Structure conservation index 0.74
SVM decision value 1.38
SVM RNA-class probability 0.948340
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5692318 116 + 22224390
AACAAUGCCAAAACCACCUCCGUUUUAUGCAGUGAAAUUAAAACCACUGCGUAAUGGAAUAUGAAUAUCAAAUUCAGACUCAGUGGCUAGCAAAGUGUUUCACCUCCAGUUGGAUG
((((.(((.....((((.(((((..(((((((((..........))))))))))))))...(((((.....)))))......))))...)))...)))).....(((....))).. ( -28.20)
>DroSec_CAF1 13365 113 + 1
AACAAUGCCAAAACCACCUCCGUUUUAUGCAGUGAAAUUAAAACCACUGCAUAAUCGAAUAUGAAUAUCAAAUUCAGACUCAGUGGUUGGCAAAGUGUUUCCCCUCCAUUUGG---
((((.(((((..(((((.......((((((((((..........))))))))))..((...(((((.....)))))...)).))))))))))...))))..............--- ( -31.20)
>DroSim_CAF1 16170 113 + 1
AACAAUGCCAAAACCACCUCCGUUUUAUGCAGUGAAAUUAAAACCACUGCAUAAUGGAAUAUGAAUAUCAAAUUCAGACUCAGUGGCUGGCAAAGUGUUUCCCCUCCAUUUGG---
((((.(((((...((((.(((((..(((((((((..........))))))))))))))...(((((.....)))))......)))).)))))...))))..............--- ( -31.80)
>DroEre_CAF1 12739 110 + 1
AACAA-----AAACCGCCUCCAUUUUAUGUAGUGCUAUUAAAACCACUGCGUAAUGGAAUAUGAAUAUCAAAUUCAGACUCAGUGGCCAGAAAAGUGUUU-CCCUCCAAUUAGAUG
((((.-----.....((((((((..(((((((((..........))))))))))))))...(((((.....)))))........)))........)))).-............... ( -20.34)
>DroYak_CAF1 13675 115 + 1
AACAAUGC-AAACCCACCUCCGGUUGAUGCAGUGAAAUGAAAACCACUGCGUAAUGGAAUAUGAAUAUCAUAUGCAGACUCAGUGGCUAGCAAAGUGCUGCCCCUCCAUUUUGAUG
..((((((-.........((((....((((((((..........))))))))..))))(((((.....)))))))).....((.(((.(((.....)))))).)).....)))... ( -29.30)
>consensus
AACAAUGCCAAAACCACCUCCGUUUUAUGCAGUGAAAUUAAAACCACUGCGUAAUGGAAUAUGAAUAUCAAAUUCAGACUCAGUGGCUAGCAAAGUGUUUCCCCUCCAUUUGGAUG
((((.(((.....((((.(((((..(((((((((..........))))))))))))))...(((((.....)))))......))))...)))...))))................. (-20.86 = -21.74 +   0.88)

alignment

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secondary structure

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Window 6

Location 5,692,318 – 5,692,434
Length 116
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 87.72
Mean single sequence MFE -33.28
Consensus MFE -23.64
Energy contribution -25.12
Covariance contribution 1.48
Combinations/Pair 1.13
Mean z-score -2.41
Structure conservation index 0.71
SVM decision value 0.86
SVM RNA-class probability 0.868684
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5692318 116 - 22224390
CAUCCAACUGGAGGUGAAACACUUUGCUAGCCACUGAGUCUGAAUUUGAUAUUCAUAUUCCAUUACGCAGUGGUUUUAAUUUCACUGCAUAAAACGGAGGUGGUUUUGGCAUUGUU
..(((....)))........((..(((((((((((((((.(((((.....))))).))))......(((((((........)))))))..........))))))..)))))..)). ( -33.50)
>DroSec_CAF1 13365 113 - 1
---CCAAAUGGAGGGGAAACACUUUGCCAACCACUGAGUCUGAAUUUGAUAUUCAUAUUCGAUUAUGCAGUGGUUUUAAUUUCACUGCAUAAAACGGAGGUGGUUUUGGCAUUGUU
---((....))...(....)((..(((((((((((((((.(((((.....))))).))))..(((((((((((........)))))))))))......))))))..)))))..)). ( -40.00)
>DroSim_CAF1 16170 113 - 1
---CCAAAUGGAGGGGAAACACUUUGCCAGCCACUGAGUCUGAAUUUGAUAUUCAUAUUCCAUUAUGCAGUGGUUUUAAUUUCACUGCAUAAAACGGAGGUGGUUUUGGCAUUGUU
---((....))...(....)((..(((((((((((((((.(((((.....))))).))))..(((((((((((........)))))))))))......))))))..)))))..)). ( -39.40)
>DroEre_CAF1 12739 110 - 1
CAUCUAAUUGGAGGG-AAACACUUUUCUGGCCACUGAGUCUGAAUUUGAUAUUCAUAUUCCAUUACGCAGUGGUUUUAAUAGCACUACAUAAAAUGGAGGCGGUUU-----UUGUU
..........((.((-((((........((((((((.((..((((.((.....)).))))....)).))))))))......((.((.(((...))).)))).))))-----)).)) ( -22.00)
>DroYak_CAF1 13675 115 - 1
CAUCAAAAUGGAGGGGCAGCACUUUGCUAGCCACUGAGUCUGCAUAUGAUAUUCAUAUUCCAUUACGCAGUGGUUUUCAUUUCACUGCAUCAACCGGAGGUGGGUUU-GCAUUGUU
((((..((((((((((((((.....))).))).))........(((((.....)))))))))))..(((((((........)))))))..........)))).....-........ ( -31.50)
>consensus
CAUCCAAAUGGAGGGGAAACACUUUGCUAGCCACUGAGUCUGAAUUUGAUAUUCAUAUUCCAUUACGCAGUGGUUUUAAUUUCACUGCAUAAAACGGAGGUGGUUUUGGCAUUGUU
.................((((...(((((((((((((((.(((((.....))))).))))......(((((((........)))))))..........)))))))..)))).)))) (-23.64 = -25.12 +   1.48)

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 10:25:58 2006