Locus 4453

Sequence ID 2L_DroMel_CAF1
Location 12,791,507 – 12,791,621
Length 114
Max. P 0.976877
window7000 window7001 window7002

overview

Window 0

Location 12,791,507 – 12,791,599
Length 92
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 79.17
Mean single sequence MFE -15.08
Consensus MFE -9.50
Energy contribution -9.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.43
Structure conservation index 0.63
SVM decision value 1.78
SVM RNA-class probability 0.976877
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12791507 92 + 22407834
AGAAUUUUGCCUUUUCAACAGAAGUGCAAAAAUGCAUUUCGAUGCACAAAACUAAAAAAGAAAAAC--AAAAAAGACGCGUCAUUUCACAUUAU
.(((................((((((((....))))))))(((((.....................--.........)))))..)))....... ( -14.81)
>DroSec_CAF1 60988 85 + 1
AGAAUUUUGCCUUUUCAACAGAAGUGCAAAAAUGCAUUUCGAUGCACAAAACAA-------AAAGC--AAAAAAGGCGCGUCAUUUCACAUUAU
.((....((((((((.....((((((((....))))))))..(((.........-------...))--).))))))))..))............ ( -19.60)
>DroSim_CAF1 63127 70 + 1
AGAAUUCUGCCUUUUCAACAGAAGUGCAAAAAUGCAUUUCGU----------------------AC--AAAAAAGACGCGUCAUUUCACAUUAU
.(((...((((((((.....((((((((....))))))))..----------------------..--..)))))..)))....)))....... ( -13.50)
>DroEre_CAF1 62972 86 + 1
AGAGUUCUGCAAUUUUAACAGAAGUGCAA-AUUGCAUUUCGUUGCACAAAACAA-------AACACAAAAAAAAAACGCGUCAUUGCACAUUAU
...(((.((((((.......(((((((..-...)))))))))))))...)))..-------................(((....)))....... ( -15.01)
>DroYak_CAF1 63583 82 + 1
AGAGUUCUGCCAUUUUAACAGAAGUGCAA-AAUGCAUUUCAAUGUACAAAACAA-----------CAAAAAAAAAACGCGUCAUUGCACAUUAU
....(((((.........)))))((((((-.((((.(((...(((........)-----------))......))).))))..))))))..... ( -12.50)
>consensus
AGAAUUCUGCCUUUUCAACAGAAGUGCAAAAAUGCAUUUCGAUGCACAAAACAA_______AA_AC__AAAAAAGACGCGUCAUUUCACAUUAU
....................((((((((....))))))))...................................................... ( -9.50 =  -9.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,791,507 – 12,791,599
Length 92
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 79.17
Mean single sequence MFE -18.48
Consensus MFE -11.48
Energy contribution -11.54
Covariance contribution 0.06
Combinations/Pair 1.20
Mean z-score -2.05
Structure conservation index 0.62
SVM decision value 0.93
SVM RNA-class probability 0.884739
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12791507 92 - 22407834
AUAAUGUGAAAUGACGCGUCUUUUUU--GUUUUUCUUUUUUAGUUUUGUGCAUCGAAAUGCAUUUUUGCACUUCUGUUGAAAAGGCAAAAUUCU
...(((((......)))))...((((--((((((..((..(((....(((((..((......))..)))))..)))..)))))))))))).... ( -15.30)
>DroSec_CAF1 60988 85 - 1
AUAAUGUGAAAUGACGCGCCUUUUUU--GCUUU-------UUGUUUUGUGCAUCGAAAUGCAUUUUUGCACUUCUGUUGAAAAGGCAAAAUUCU
.....(((......)))((((((((.--((...-------.(((...((((((....))))))....))).....)).))))))))........ ( -20.60)
>DroSim_CAF1 63127 70 - 1
AUAAUGUGAAAUGACGCGUCUUUUUU--GU----------------------ACGAAAUGCAUUUUUGCACUUCUGUUGAAAAGGCAGAAUUCU
.....(((......)))((((((((.--..----------------------(((((.((((....)))).))).)).))))))))........ ( -16.20)
>DroEre_CAF1 62972 86 - 1
AUAAUGUGCAAUGACGCGUUUUUUUUUUGUGUU-------UUGUUUUGUGCAACGAAAUGCAAU-UUGCACUUCUGUUAAAAUUGCAGAACUCU
.....((((((....(((((((....(((..(.-------.......)..))).)))))))...-))))))((((((.......)))))).... ( -20.50)
>DroYak_CAF1 63583 82 - 1
AUAAUGUGCAAUGACGCGUUUUUUUUUUG-----------UUGUUUUGUACAUUGAAAUGCAUU-UUGCACUUCUGUUAAAAUGGCAGAACUCU
.....((((((....(((((((.....((-----------(........)))..)))))))...-))))))(((((((.....))))))).... ( -19.80)
>consensus
AUAAUGUGAAAUGACGCGUCUUUUUU__GU_UU_______UUGUUUUGUGCAUCGAAAUGCAUUUUUGCACUUCUGUUGAAAAGGCAGAAUUCU
.....(((......)))((((((((.................((.....))...(((.((((....)))).)))....))))))))........ (-11.48 = -11.54 +   0.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,791,523 – 12,791,621
Length 98
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 82.81
Mean single sequence MFE -16.20
Consensus MFE -12.50
Energy contribution -12.90
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.77
SVM decision value 1.14
SVM RNA-class probability 0.921757
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12791523 98 + 22407834
AACAGAAGUGCAAAAAUGCAUUUCGAUGCACAAAACUAAAAAAGAAAAAC--AAAAAAGACGCGUCAUUUCACAUUAUAUCGCUGAUAGAGUAAUGCAUU
....((((((((....))))))))(((((.....................--.........)))))......((((((.((.......)))))))).... ( -17.11)
>DroSec_CAF1 61004 91 + 1
AACAGAAGUGCAAAAAUGCAUUUCGAUGCACAAAACAA-------AAAGC--AAAAAAGGCGCGUCAUUUCACAUUAUAUUGCUGAUAGAGUAAUGCAUU
....((((((((....))))))))(((((.(.......-------.....--.......).)))))...........(((((((.....))))))).... ( -18.71)
>DroSim_CAF1 63143 76 + 1
AACAGAAGUGCAAAAAUGCAUUUCGU----------------------AC--AAAAAAGACGCGUCAUUUCACAUUAUAUCGCUGAUAGAGUAAUGCAUU
....((((((((....))))))))..----------------------..--.........((((.((((...((((......)))).)))).))))... ( -13.50)
>DroEre_CAF1 62988 92 + 1
AACAGAAGUGCAA-AUUGCAUUUCGUUGCACAAAACAA-------AACACAAAAAAAAAACGCGUCAUUGCACAUUAUAUUGCUGAUAGAGUAAUGCAUU
....(((((((..-...)))))))..(((.........-------................(((....))).......((((((.....))))))))).. ( -17.20)
>DroYak_CAF1 63599 88 + 1
AACAGAAGUGCAA-AAUGCAUUUCAAUGUACAAAACAA-----------CAAAAAAAAAACGCGUCAUUGCACAUUAUAUCGCUGAUAGAGUAAUGCAUU
....(((((((..-...)))))))((((((........-----------............(((....)))..........(((.....)))..)))))) ( -14.50)
>consensus
AACAGAAGUGCAAAAAUGCAUUUCGAUGCACAAAACAA_______AA_AC__AAAAAAGACGCGUCAUUUCACAUUAUAUCGCUGAUAGAGUAAUGCAUU
....((((((((....)))))))).....................................((((.((((...((((......)))).)))).))))... (-12.50 = -12.90 +   0.40)

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 11:18:05 2006