Locus 4671

Sequence ID 2R_DroMel_CAF1
Location 15,244,102 – 15,244,222
Length 120
Max. P 0.979247
window7511 window7512 window7513

overview

Window 1

Location 15,244,102 – 15,244,197
Length 95
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 68.50
Mean single sequence MFE -24.55
Consensus MFE -16.09
Energy contribution -15.62
Covariance contribution -0.47
Combinations/Pair 1.27
Mean z-score -1.04
Structure conservation index 0.66
SVM decision value 0.31
SVM RNA-class probability 0.681884
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15244102 95 - 20766785
ACCUGGGCCUCCCGGGUGAGAGCCGGGUAGCCUAACCACUAGACAAUAUGGGAUAUAUCGC----GGGAC-CACAUAAAAUAAAUUUUUGGAUACCAUUC-----------
.(((((((..(((((.(....))))))..)))...(((.((.....))))).........)----))).(-((...............))).........----------- ( -23.66)
>DroGri_CAF1 76633 104 - 1
ACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUACAGAGU----AAUGUCCACCAGAAAUCAGUUAUGU--UAUA-UUCACUACAAAUCG
....((((.((((((((....)))...(((((((..............)))))))))))).----...))))...........((..((.--....-..))..))...... ( -20.24)
>DroEre_CAF1 67803 95 - 1
ACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCACUAGACAAUAUGGGAUAUGAAUG----GGUAU-CACACAAAAUCAUAUUUCAGAUACCAACA-----------
(((((((...)))))))........(((((((((.....)))......((..((((((.(.----.((..-...))..).))))))..))))))))....----------- ( -29.80)
>DroWil_CAF1 168494 99 - 1
ACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUAUGUUCUU---GCCGU-UGCCAAAAAUUAUUUUU--GUUAUCAGGA-CACCA-----
.....((..(((((((..(..((.((((((((((..............)))))))...))).---))..)-..)).((((....))))--.....)))))-..)).----- ( -22.14)
>DroYak_CAF1 71192 95 - 1
ACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCACUAGACAAUAUGGGAUAUAAUGG----UCAAA-CGCUCAAUAUCAAAUUUCCGAUACCAAUU-----------
(((((((...)))))))(((.((((.((((((((..............))))))))..)))----)....-..)))..((((........))))......----------- ( -25.24)
>DroAna_CAF1 61209 94 - 1
ACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUAUGGUUACUGAGGUGU-CA---AAAAUCGAUUUUAU--UACAAGGG-----------
.(((.(((.(((.....))).))).(((((((((((((.((..((....))..))))))))..).)))))-).---..............--.....)))----------- ( -26.20)
>consensus
ACCCGGGCCUCCCGGGUGAAAGCCAGAUAUCCUAACCACUAGACAAUAUGGGAUAUAAUGG____GGUAU_CACAAAAAAUCAAUUUUCUGAUACCAAUA___________
(((((((...))))))).........((((((((..............))))))))....................................................... (-16.09 = -15.62 +  -0.47)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,244,126 – 15,244,222
Length 96
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 75.15
Mean single sequence MFE -31.82
Consensus MFE -24.42
Energy contribution -23.92
Covariance contribution -0.50
Combinations/Pair 1.11
Mean z-score -1.37
Structure conservation index 0.77
SVM decision value 1.26
SVM RNA-class probability 0.937869
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15244126 96 + 20766785
AUGUG-GUCCC-GCGAU----AUAUCCCAUAUUGUCUAGUGGUUAGGCUACCCGGCUCUCACCCGGGAGGCCCAGGUUCAGUUCCCUGUAUAGGAAAUGUGC----
.((((-....)-)))..----......((((((..(((.......((((.(((((.......))))).))))((((........))))..)))..)))))).---- ( -29.30)
>DroGri_CAF1 76665 101 + 1
UGGUGGACAUU-ACUCU----GUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAGUAAUUUUUU
........(((-(((..----...((((((((((((....)))).........(((((((.....)))))))((((.......))))))))))))))))))..... ( -31.50)
>DroEre_CAF1 67827 95 + 1
GUGUG-AUACC-CAUUC----AUAUCCCAUAUUGUCUAGUGGUUAGGAUACCCGGCUCUCACCCGGGAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUGU-U----
.((((-(....-...))----)))((((((((((......((....((.(((((((((((....)))))..))))))))....)))))))))))).....-.---- ( -33.40)
>DroWil_CAF1 168521 101 + 1
UGGCA-ACGGCAAGAAC----AUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAGUAACUUUUU
.(...-.).........----...((((((((((((....)))).........(((((((.....)))))))((((.......))))))))))))........... ( -30.60)
>DroYak_CAF1 71216 95 + 1
GAGCG-UUUGA-CCAUU----AUAUCCCAUAUUGUCUAGUGGUUAGGAUACCCGGCUCUCACCCGGGAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUGA-C----
((((.-..(((-(((((----(.((........)).)))))))))((....)).))))..(((((((...)))))))(((.(((((.....))))).)))-.---- ( -35.50)
>DroMoj_CAF1 93414 104 + 1
-AAUGGCUACU-CUUCUAGAAGUGUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAGUAAAUUUUU
-....(((.(.-(((....))).)((((((((((((....)))).........(((((((.....)))))))((((.......)))))))))))))))........ ( -30.60)
>consensus
GAGUG_AUACC_CCUAU____AUAUCCCAUAUGGUCUAGUGGCUAGGAUACCCGGCUCUCACCCAGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUAA_U____
........................((((((((.............((...(((((.......)))))...))((((.......))))))))))))........... (-24.42 = -23.92 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,244,126 – 15,244,222
Length 96
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 75.15
Mean single sequence MFE -30.33
Consensus MFE -26.11
Energy contribution -25.00
Covariance contribution -1.11
Combinations/Pair 1.22
Mean z-score -1.92
Structure conservation index 0.86
SVM decision value 1.83
SVM RNA-class probability 0.979247
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15244126 96 - 20766785
----GCACAUUUCCUAUACAGGGAACUGAACCUGGGCCUCCCGGGUGAGAGCCGGGUAGCCUAACCACUAGACAAUAUGGGAUAU----AUCGC-GGGAC-CACAU
----((.....((((((((((....)))....(((((..(((((.(....))))))..)))))............)))))))...----...))-.....-..... ( -32.10)
>DroGri_CAF1 76665 101 - 1
AAAAAAUUACUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUAC----AGAGU-AAUGUCCACCA
.....((((((((((((((((((.......)))))....(((((.(....))))))....((((...))))....)))))))...----..)))-)))........ ( -28.50)
>DroEre_CAF1 67827 95 - 1
----A-ACAUUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCACUAGACAAUAUGGGAUAU----GAAUG-GGUAU-CACAC
----.-......(((((.((((...((..(((((((...)))))))..)).))))((((((((..............))))))))----..)))-))...-..... ( -34.24)
>DroWil_CAF1 168521 101 - 1
AAAAAGUUACUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUAU----GUUCUUGCCGU-UGCCA
...(((..((.((((((((((((.......)))))....(((((.(....))))))....((((...))))....)))))))...----)).))).....-..... ( -27.10)
>DroYak_CAF1 71216 95 - 1
----G-UCAUUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCACUAGACAAUAUGGGAUAU----AAUGG-UCAAA-CGCUC
----.-(((.(((((.....))))).)))(((((((...)))))))..((.(((.((((((((..............))))))))----..)))-))...-..... ( -32.44)
>DroMoj_CAF1 93414 104 - 1
AAAAAUUUACUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGACACUUCUAGAAG-AGUAGCCAUU-
......(((((((((((((((((.......)))))....(((((.(....))))))....((((...))))....)))))))..(((....)))-))))).....- ( -27.60)
>consensus
____A_UCACUUCCCAUACCGGGAAUCGAACCCGGGCCUCCCGGGUGAAAGCCAGAUAUCCUAACCACUAGACAAUAUGGGAUAU____AAAGG_GGUAU_CACAA
...........((((((((((((.......)))))....(((((.(....))))))...................)))))))........................ (-26.11 = -25.00 +  -1.11)

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 11:26:18 2006