Locus 3995

Sequence ID 2L_DroMel_CAF1
Location 11,627,927 – 11,628,022
Length 95
Max. P 0.899516
window6300 window6301

overview

Window 0

Location 11,627,927 – 11,628,022
Length 95
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 81.27
Mean single sequence MFE -35.43
Consensus MFE -20.00
Energy contribution -21.45
Covariance contribution 1.45
Combinations/Pair 1.14
Mean z-score -2.97
Structure conservation index 0.56
SVM decision value 1.01
SVM RNA-class probability 0.899516
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11627927 95 + 22407834
GCAAAAGCCCUAAGCUAGCACACCCGA-AAGGCGUCUAAAGCCAGCAAAAAUAUGGCCACAGAAGUGGUCGGGG------UUGCGAA-GAACU-------------UGGGGCUU-CC
....((((((((((((.(((.((((..-..(((.......)))..........(((((((....))))))))))------))))..)-)..))-------------))))))))-.. ( -39.40)
>DroSec_CAF1 81279 95 + 1
GCAAAAGCCCUAAGCCAGCACACCCGA-AAGGCGUCUAAAGCCAGCAAAAAUAUGGCCACAGAAGUGGUCGGGG------UUGCGAA-GAACU-------------UGGGGCUU-CC
....((((((((((...(((.((((..-..(((.......)))..........(((((((....))))))))))------))))...-...))-------------))))))))-.. ( -39.10)
>DroSim_CAF1 85051 95 + 1
GCAAAAGCCCUAAGCCAGCACACCCGA-AAGGCGUCUAAAGCCAGCAAAAAUAUGGCCACAGAAGUGGUCGGGG------UUGCGAA-GAACU-------------UGGGGCUU-CC
....((((((((((...(((.((((..-..(((.......)))..........(((((((....))))))))))------))))...-...))-------------))))))))-.. ( -39.10)
>DroEre_CAF1 111558 100 + 1
G-AAAAGCCCUAAGCCAGCACACCCGA-AAGGCGUCUAAAGCCGGCAAAUAUAUGGCCGCAGAAGUGCUCGGGGCACUUCUUGUGAA-GAACU-------------UGGGGCUU-CC
.-..((((((((((....(((((((..-..)).)).....((.(((.........)))))((((((((.....)))))))).)))..-...))-------------))))))))-.. ( -39.60)
>DroYak_CAF1 84683 94 + 1
G-AAAAGCCCUAAGCCAGCACACCCGA-AAGGCGUCUAAAGCCGGCAAAUAUAUGACCACAAAAGUGGUAGGGG------UUGCGAA-GAACU-------------UGGGUCUG-CC
.-...((.((((((...(((..(((..-..(((.......)))............(((((....))))).))).------.)))...-...))-------------)))).)).-.. ( -28.60)
>DroAna_CAF1 94687 107 + 1
G-AAAUGCCUUAAGCCCACGCAGCCAAAAAGACGUCUAAAGCCAGCAAAAAUAUGGCCAUCU---CGGUGGGGG------UAGAGAGAUAGCUUGAAUUCCGGGUGUGGAGCUUCCC
.-.........((((((((((.(((....((....))...((((.........)))).....---.))).((((------(.(((......)))..)))))..)))))).))))... ( -26.80)
>consensus
G_AAAAGCCCUAAGCCAGCACACCCGA_AAGGCGUCUAAAGCCAGCAAAAAUAUGGCCACAGAAGUGGUCGGGG______UUGCGAA_GAACU_____________UGGGGCUU_CC
....((((((((.(....)...(((.....(((.......)))...........((((((....))))))))).................................))))))))... (-20.00 = -21.45 +   1.45)

alignment

Postscript

secondary structure

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dotplot

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Window 1

Location 11,627,927 – 11,628,022
Length 95
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 81.27
Mean single sequence MFE -33.82
Consensus MFE -20.90
Energy contribution -21.82
Covariance contribution 0.92
Combinations/Pair 1.23
Mean z-score -2.12
Structure conservation index 0.62
SVM decision value 0.48
SVM RNA-class probability 0.752055
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11627927 95 - 22407834
GG-AAGCCCCA-------------AGUUC-UUCGCAA------CCCCGACCACUUCUGUGGCCAUAUUUUUGCUGGCUUUAGACGCCUU-UCGGGUGUGCUAGCUUAGGGCUUUUGC
((-((((((.(-------------((((.-...(((.------.(((((...(.((((.(((((((....)).))))).)))).)....-)))))..))).))))).)))))))).. ( -36.50)
>DroSec_CAF1 81279 95 - 1
GG-AAGCCCCA-------------AGUUC-UUCGCAA------CCCCGACCACUUCUGUGGCCAUAUUUUUGCUGGCUUUAGACGCCUU-UCGGGUGUGCUGGCUUAGGGCUUUUGC
((-((((((.(-------------((((.-...(((.------.(((((...(.((((.(((((((....)).))))).)))).)....-)))))..))).))))).)))))))).. ( -36.40)
>DroSim_CAF1 85051 95 - 1
GG-AAGCCCCA-------------AGUUC-UUCGCAA------CCCCGACCACUUCUGUGGCCAUAUUUUUGCUGGCUUUAGACGCCUU-UCGGGUGUGCUGGCUUAGGGCUUUUGC
((-((((((.(-------------((((.-...(((.------.(((((...(.((((.(((((((....)).))))).)))).)....-)))))..))).))))).)))))))).. ( -36.40)
>DroEre_CAF1 111558 100 - 1
GG-AAGCCCCA-------------AGUUC-UUCACAAGAAGUGCCCCGAGCACUUCUGCGGCCAUAUAUUUGCCGGCUUUAGACGCCUU-UCGGGUGUGCUGGCUUAGGGCUUUU-C
((-((((((..-------------.....-......((((((((.....))))))))..............((((((.....(((((..-...)))))))))))...))))))))-. ( -37.80)
>DroYak_CAF1 84683 94 - 1
GG-CAGACCCA-------------AGUUC-UUCGCAA------CCCCUACCACUUUUGUGGUCAUAUAUUUGCCGGCUUUAGACGCCUU-UCGGGUGUGCUGGCUUAGGGCUUUU-C
((-((.((((.-------------.....-...((((------.....(((((....))))).......)))).(((.......)))..-..)))).))))(((.....)))...-. ( -28.20)
>DroAna_CAF1 94687 107 - 1
GGGAAGCUCCACACCCGGAAUUCAAGCUAUCUCUCUA------CCCCCACCG---AGAUGGCCAUAUUUUUGCUGGCUUUAGACGUCUUUUUGGCUGCGUGGGCUUAAGGCAUUU-C
...((((.((((.............((((((((....------........)---))))))).........((.((((..((....))....)))))))))))))).........-. ( -27.60)
>consensus
GG_AAGCCCCA_____________AGUUC_UUCGCAA______CCCCGACCACUUCUGUGGCCAUAUUUUUGCUGGCUUUAGACGCCUU_UCGGGUGUGCUGGCUUAGGGCUUUU_C
...((((((........................................((((....))))..........((((((.....((((((....))))))))))))...)))))).... (-20.90 = -21.82 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:44 2006