Locus 1067

Sequence ID 3L_DroMel_CAF1
Location 3,129,220 – 3,129,470
Length 250
Max. P 0.668094
window1649 window1650 window1651

overview

Window 9

Location 3,129,220 – 3,129,319
Length 99
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 82.20
Mean single sequence MFE -32.58
Consensus MFE -22.62
Energy contribution -23.48
Covariance contribution 0.86
Combinations/Pair 1.19
Mean z-score -1.42
Structure conservation index 0.69
SVM decision value -0.01
SVM RNA-class probability 0.526886
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3129220 99 - 23771897
UCUCGCACGCCGAUUCAAUUGGUGUUGAGGAUGCUGCCCCCGCUGCGAAUUCAUCAGCUGCAGCGGCCUCCUCGACGCCAA---AUAAGACCAACUACCGCG
...(((............(((((((((((((.(((((..(.((((.(....)..)))).)..))))).)))))))))))))---...((.....))...))) ( -37.00)
>DroSec_CAF1 18163 99 - 1
UCUCGCACGCCGAUUCAAUUAGUGUCGAGGAAGCUGCCCCCGCUUCAAAUUCAUCAGCUGCAGCGGCGUCCUCGGCGCCCA---AUAAGACCGACUACCGCG
...(((...............((((((((((.(((((..(.(((...........))).)..))))).))))))))))...---...((.....))...))) ( -29.70)
>DroSim_CAF1 16461 99 - 1
UCUCGCACGCCGAUUCAAUUAGUGUCGAGGAAGCUGUCCCCGCUGAAAAUUCAUCAGCUGCAGCGGCGUCCUCGGCGCCCA---AUAAGACCGACUACCGCG
...(((...............((((((((((.(((((..(.(((((.......))))).)..))))).))))))))))...---...((.....))...))) ( -33.80)
>DroEre_CAF1 16848 99 - 1
UCUCGCAUGCCGAUUCUAUUGGUGUUGAGGAAGUUGCCCCCGCUUCGAAUUCAUCAGCUGCAGCGGCUUCCUCGGCGCCCA---AUAAGACCGACUACCGCG
...(((..(.((.(..(((((((((((((((((((((..(.(((..((.....))))).)..))))))))))))))).)))---)))..).)).)....))) ( -36.80)
>DroYak_CAF1 19488 99 - 1
UCUCACACGCCGAUUCCAUUGGUGUUGAGGAAGUUGCCCCCGCAUCGAAUUCAUCAGCUGCAGCGGCUUCCUCGGCGCCCA---AUAAGACCGACUACCGCG
.......(((((.((..((((((((((((((((((((....(((.(..........).))).))))))))))))))).)))---))..)).))......))) ( -31.90)
>DroAna_CAF1 16003 93 - 1
UCUCGCACGCCGAUUCCAUUGGCGUGGAAGAAGUCGCACCCGCCC---------CCGCUGCGCCAGCCUCGUCAGCCGGAAAUAGUAAGACCAACUAUAGAG
(((..(((((((((...)))))))))..))).(((((....)).(---------(.((((((.......)).)))).)).........)))........... ( -26.30)
>consensus
UCUCGCACGCCGAUUCAAUUGGUGUUGAGGAAGCUGCCCCCGCUUCGAAUUCAUCAGCUGCAGCGGCCUCCUCGGCGCCCA___AUAAGACCGACUACCGCG
...(((..((((((...))))))((((((((.(((((..(.(((...........))).)..))))).)))))))).......................))) (-22.62 = -23.48 +   0.86)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,129,319 – 3,129,438
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.41
Mean single sequence MFE -47.47
Consensus MFE -32.49
Energy contribution -33.43
Covariance contribution 0.95
Combinations/Pair 1.22
Mean z-score -2.29
Structure conservation index 0.68
SVM decision value 0.28
SVM RNA-class probability 0.668094
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3129319 119 + 23771897
AGAUCCAGUCGGUGGCGCGCUCCACAUUGCCAUCGGUCGCUUUCAGAGCAGCCACCGCCUGUCUUUCGUCGAAGCCCAUGCUCAUGAGCAUGGCCAGGCUCUCGGGAUUGGCCACAAAC-
....((((((((((((..((((......((........)).....)))).))))))(((((.((((....)))).(((((((....))))))).)))))......))))))........- ( -45.70)
>DroVir_CAF1 35506 120 + 1
AUAUCCAGUCGGUGGCACGUUCCACGUUGCCAUCUGUGGCUUUUAGAGCGGCGACCGCCUGGCGCUCGUCAAAGCCCAUGCUCAUGAGCAUGGCCAGGCUUUCGGGAUUGGCAGCAAAAU
....(((((((((.((.(((((......((((....)))).....))))))).)))((((((((((......))).((((((....)))))))))))))......))))))......... ( -53.70)
>DroPse_CAF1 14452 119 + 1
AGAUCCAGUCUGUGGCACGCUCCACAUUCCCAUCGGUGGCCUUGAGGGCGGCCACGGCCUGGCGUUCAUCGAAUCCCAUGCUCAUGAGCAUAGCCAGGCUUUCCGGAUUGGCCACAAAC-
....((((((((((((.(((.((.((...(((....)))...)).))))))))))((((((((((((...))))...(((((....))))).))))))))....)))))))........- ( -49.80)
>DroGri_CAF1 18844 119 + 1
AGAUCCAAUCUGUGGCACGUUCCACGUUGCCAUCGGUGGCUUUGAGUGCGGCCACCGCUUGCAUCUCAUCGAAGCCCAUGCUCAUCAGCAUGGCCAGACUUUCGGGAUUGGCCACAAAU-
....(((((((((((((((.....)).)))))).((((((((((((((((((....)).)))))....))))))))((((((....))))))))).........)))))))........- ( -44.60)
>DroWil_CAF1 25025 119 + 1
AAAUCCAGUCGGUGGCUCGUUCAACGUUGCCAUCAGUGGCUUUGAGGGCAGCAACAGCCUGACGCUCAUCGAAUCCCAUGCUCAUCAACAUGGCCAGACUUUCGGGAUUGGCCACAAAU-
..........((((((.((.....))..)))))).((((((.((((.(((((....).))).).))))...((((((..((.(((....)))))..(.....)))))))))))))....- ( -38.10)
>DroMoj_CAF1 18673 119 + 1
AGAUCCAGUCGGUGGCUCGCUCCACAUUGCCAUCGGUGGCCUUGAGGGCGGCCGUCGCUUGGCGCUCGCCAAAGCCCAUGCUCAUGAGCAUGGCCAGUGACUCGGGAUUGGCAACGAAA-
....((((((...(((.(((.((.((..((((....))))..)).))))))))((((((((((....))))).(.(((((((....))))))).).)))))....))))))........- ( -52.90)
>consensus
AGAUCCAGUCGGUGGCACGCUCCACAUUGCCAUCGGUGGCUUUGAGGGCGGCCACCGCCUGGCGCUCAUCGAAGCCCAUGCUCAUGAGCAUGGCCAGGCUUUCGGGAUUGGCCACAAAA_
.....(((.(((((((.(((((......((((....)))).....)))))))))))).)))...............((((((....))))))(((((.((....)).)))))........ (-32.49 = -33.43 +   0.95)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,129,359 – 3,129,470
Length 111
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 77.96
Mean single sequence MFE -41.70
Consensus MFE -23.26
Energy contribution -23.73
Covariance contribution 0.48
Combinations/Pair 1.33
Mean z-score -1.61
Structure conservation index 0.56
SVM decision value -0.02
SVM RNA-class probability 0.521609
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3129359 111 - 23771897
AACAACAGCAUUGGAGACUGCGCCGCCAACCAGUUUGUGGCCAAUCCCGAGAGCCUGGCCAUGCUCAUGAGCAUGGGCUUCGACGAAAGACAGGCGGUGGCUGCUCUGAAA
.....((((.((((.((.((.(((((.((....)).))))))).))))))..(((((.(((((((....))))))).......(....).)))))....))))........ ( -42.70)
>DroPse_CAF1 14492 111 - 1
AACAAUAGCAUCGGCGACUGCGCCAGCGAGCAGUUUGUGGCCAAUCCGGAAAGCCUGGCUAUGCUCAUGAGCAUGGGAUUCGAUGAACGCCAGGCCGUGGCCGCCCUCAAG
............(((((((((........))))))...(((((...((....(((((((((((((....))))))...(((...))).)))))))))))))))))...... ( -39.80)
>DroGri_CAF1 18884 111 - 1
AACAAUCGCAUUGGCGAUGGCGCCGCCGCAAAAUUUGUGGCCAAUCCCGAAAGUCUGGCCAUGCUGAUGAGCAUGGGCUUCGAUGAGAUGCAAGCGGUGGCCGCACUCAAA
....(((((....))))).((((((((((.......(((((((....(....)..)))))))(((....)))....((.((.....)).))..))))))).)))....... ( -43.10)
>DroWil_CAF1 25065 111 - 1
AAUAACAGUAUUGGCGAUAGUGCGGCCAAUCAAUUUGUGGCCAAUCCCGAAAGUCUGGCCAUGUUGAUGAGCAUGGGAUUCGAUGAGCGUCAGGCUGUUGCUGCCCUCAAA
............((((.....((((((.........(((((((....(....)..)))))))..(((((..(((.(....).)))..)))))))))))...))))...... ( -35.70)
>DroMoj_CAF1 18713 111 - 1
AAUAAUCGCAUUGGUGAUGGCGCCGCCUCCGCUUUCGUUGCCAAUCCCGAGUCACUGGCCAUGCUCAUGAGCAUGGGCUUUGGCGAGCGCCAAGCGACGGCCGCCCUCAAG
....(((((....)))))((((..(((..(((((.(((((((((..(((......)))(((((((....)))))))...))))).))))..)))))..)))))))...... ( -43.10)
>DroAna_CAF1 16136 111 - 1
AACAACCAGAUUGGUGACUGUGCCGCAGAGCAGUUCGUGGCCAAUCCGGAGAGCCUGGCCAUGCUGAUGAGCAUGGGCUUUGAUGAGCGCCAGGCGGUAGCUGCUCUAAAG
.....((.(((((((((((((........))))))....))))))).))((((((((((((((((....)))))).((((....)))))))))((....)).))))).... ( -45.80)
>consensus
AACAACAGCAUUGGCGACUGCGCCGCCGACCAGUUUGUGGCCAAUCCCGAAAGCCUGGCCAUGCUCAUGAGCAUGGGCUUCGAUGAGCGCCAGGCGGUGGCCGCCCUCAAA
............((((....))))............(((((((.........(((((((((((((....)))))))..(((...)))..))))))..)))))))....... (-23.26 = -23.73 +   0.48)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:12 2006