Locus 1689

Sequence ID 2R_DroMel_CAF1
Location 6,403,499 – 6,403,631
Length 132
Max. P 0.784219
window2814 window2815 window2816 window2817

overview

Window 4

Location 6,403,499 – 6,403,605
Length 106
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 81.37
Mean single sequence MFE -30.59
Consensus MFE -18.92
Energy contribution -20.35
Covariance contribution 1.42
Combinations/Pair 1.28
Mean z-score -1.68
Structure conservation index 0.62
SVM decision value 0.03
SVM RNA-class probability 0.549078
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6403499 106 + 20766785
UCC----AGAGGGUCUUUCAUACAACUGCAAGUUGUGCAGCUUCACGUCGUUGAAGCAACGAACUUUGUUCGAGCACUAUGUGACCAUGCACAACAUGCCCCUUAGCCAG
...----.(((((..............(((.((((((((((((((......))))))..(((((...)))))...............)))))))).))))))))...... ( -32.03)
>DroSec_CAF1 756 106 + 1
UCC----AGAGGGUCUUUCGUACAACUGCAAGUUGUGCAGCUUCACGUCGUUGAAGCAACGCGUUUUGUUUGAGCACUAUGUGACCAUGCACAACAUGCCCCUCAGUCAG
...----.(((((......(.....).(((.((((((((((((((......))))))..(((((..(((....)))..)))))....)))))))).))))))))...... ( -37.20)
>DroSim_CAF1 670 106 + 1
UCC----AGAGGGUCUUUCGUACAACUGCAAGUUGUGCAGCUUCACGUCGUUAAAGCAACGCGUUUUGUUUGAGCACUAUGUGACCAUGCACAACAUGCCCCUCAGUCAG
...----.(((((......(.....).(((.((((((((...((((((.(((.((((((......)))))).)))...))))))...)))))))).))))))))...... ( -34.30)
>DroEre_CAF1 740 106 + 1
UGC----AGAGGGUCUGUCGUACAAUUGCAAGCUAUGCAGCUUCACAUCGUUGAAGCAACGUGUUUUGUUUGAACACUAUGUGACCAUGCAUAACAUGCCCCUUAGCCAG
.((----.(((((..((.....))...(((.(.((((((...((((((.((((...))))((((((.....)))))).))))))...)))))).).)))))))).))... ( -32.00)
>DroYak_CAF1 671 106 + 1
UCC----AGAGGGUCUGUCGUACAACUGCAAGCUGUGCAGUUUCACAUCGUUGAAGCAACGAGUUUUGUUCGAGCACUAUGUUACCAUGCAUAACAUGCCCCUUAGCCAG
...----.(((((....(((.(((((((((.....))))))......((((((...))))))....))).)))(((.(((((......)))))...))))))))...... ( -27.40)
>DroAna_CAF1 620 110 + 1
UCCUAUUAGAUGGACUUGCUUAUCACUGCAAAAUGUGCAGCUAUACCACACUGAAGCAGCGUCUGUUGCACGAUCACUAUCGUUCGACCCACAACCAAACCCCUGCCCAG
......(((..((((((((((....(((((.....)))))......(.....))))))).))))((((.(((((....))))).))))..............)))..... ( -20.60)
>consensus
UCC____AGAGGGUCUUUCGUACAACUGCAAGUUGUGCAGCUUCACGUCGUUGAAGCAACGAGUUUUGUUCGAGCACUAUGUGACCAUGCACAACAUGCCCCUUAGCCAG
........(((((..............(((.(.((((((...((((((.(((..(((((......)))))..)))...))))))...)))))).).))))))))...... (-18.92 = -20.35 +   1.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 6,403,499 – 6,403,605
Length 106
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 81.37
Mean single sequence MFE -35.20
Consensus MFE -23.05
Energy contribution -22.87
Covariance contribution -0.19
Combinations/Pair 1.44
Mean z-score -2.07
Structure conservation index 0.65
SVM decision value 0.57
SVM RNA-class probability 0.784219
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6403499 106 - 20766785
CUGGCUAAGGGGCAUGUUGUGCAUGGUCACAUAGUGCUCGAACAAAGUUCGUUGCUUCAACGACGUGAAGCUGCACAACUUGCAGUUGUAUGAAAGACCCUCU----GGA
(..(...(((((((.((((((((...((((...((......))...((.(((((...)))))))))))...)))))))).))).......(....).))))).----.). ( -32.90)
>DroSec_CAF1 756 106 - 1
CUGACUGAGGGGCAUGUUGUGCAUGGUCACAUAGUGCUCAAACAAAACGCGUUGCUUCAACGACGUGAAGCUGCACAACUUGCAGUUGUACGAAAGACCCUCU----GGA
....(.((((((((.((((((((((..(((...)))..)).......(((((((......)))))))....)))))))).))).......(....).))))).----).. ( -37.90)
>DroSim_CAF1 670 106 - 1
CUGACUGAGGGGCAUGUUGUGCAUGGUCACAUAGUGCUCAAACAAAACGCGUUGCUUUAACGACGUGAAGCUGCACAACUUGCAGUUGUACGAAAGACCCUCU----GGA
....(.((((((((.((((((((((..(((...)))..)).......(((((((......)))))))....)))))))).))).......(....).))))).----).. ( -37.90)
>DroEre_CAF1 740 106 - 1
CUGGCUAAGGGGCAUGUUAUGCAUGGUCACAUAGUGUUCAAACAAAACACGUUGCUUCAACGAUGUGAAGCUGCAUAGCUUGCAAUUGUACGACAGACCCUCU----GCA
...((..(((((((.((((((((...((((((.(((((.......)))))((((...)))).))))))...)))))))).)))..(((.....))).))))..----)). ( -37.80)
>DroYak_CAF1 671 106 - 1
CUGGCUAAGGGGCAUGUUAUGCAUGGUAACAUAGUGCUCGAACAAAACUCGUUGCUUCAACGAUGUGAAACUGCACAGCUUGCAGUUGUACGACAGACCCUCU----GGA
....(((..(((..(((..(((.......((((((......)).....((((((...)))))))))).(((((((.....))))))))))..)))..)))..)----)). ( -31.00)
>DroAna_CAF1 620 110 - 1
CUGGGCAGGGGUUUGGUUGUGGGUCGAACGAUAGUGAUCGUGCAACAGACGCUGCUUCAGUGUGGUAUAGCUGCACAUUUUGCAGUGAUAAGCAAGUCCAUCUAAUAGGA
.(((((....((((((((((((((((........))))).))))))...((((((....(((..(.....)..))).....)))))).)))))..))))).......... ( -33.70)
>consensus
CUGGCUAAGGGGCAUGUUGUGCAUGGUCACAUAGUGCUCAAACAAAACACGUUGCUUCAACGACGUGAAGCUGCACAACUUGCAGUUGUACGAAAGACCCUCU____GGA
.......(((((((.((((((((...((((...((......))......(((((...)))))..))))...)))))))).))).......(....).))))......... (-23.05 = -22.87 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 6,403,525 – 6,403,631
Length 106
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 82.08
Mean single sequence MFE -31.77
Consensus MFE -19.62
Energy contribution -20.43
Covariance contribution 0.81
Combinations/Pair 1.35
Mean z-score -1.87
Structure conservation index 0.62
SVM decision value 0.06
SVM RNA-class probability 0.562129
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6403525 106 + 20766785
AGUUGUGCAGCUUCACGUCGUUGAAGCAACGAACUUUGUUCGAGCACUAUGUGACCAUGCACAACAUGCCCCUUAGCCAGGCAGAGGAGUACGUAAAAUCAAAGCA
.((((((((((((((......))))))..(((((...)))))...............)))))))).(((.((((.((...)).)))).)))............... ( -31.10)
>DroSec_CAF1 782 106 + 1
AGUUGUGCAGCUUCACGUCGUUGAAGCAACGCGUUUUGUUUGAGCACUAUGUGACCAUGCACAACAUGCCCCUCAGUCAGGCAGAGGAGCACGUAAAAUCGAAGCA
.((((((((((((((......))))))..(((((..(((....)))..)))))....)))))))).(((.((((.(.....).)))).)))((......))..... ( -35.70)
>DroSim_CAF1 696 106 + 1
AGUUGUGCAGCUUCACGUCGUUAAAGCAACGCGUUUUGUUUGAGCACUAUGUGACCAUGCACAACAUGCCCCUCAGUCAGGCAGAGGAGCACGUAAAAUCGAAGCA
.((((((((...((((((.(((.((((((......)))))).)))...))))))...)))))))).(((.((((.(.....).)))).)))((......))..... ( -32.80)
>DroEre_CAF1 766 106 + 1
AGCUAUGCAGCUUCACAUCGUUGAAGCAACGUGUUUUGUUUGAACACUAUGUGACCAUGCAUAACAUGCCCCUUAGCCAGGCAGAGGAGCACGUAAAAUCAAAGCA
.((((((((...((((((.((((...))))((((((.....)))))).))))))...))))))((.(((.((((.((...)).)))).))).)).........)). ( -32.30)
>DroYak_CAF1 697 106 + 1
AGCUGUGCAGUUUCACAUCGUUGAAGCAACGAGUUUUGUUCGAGCACUAUGUUACCAUGCAUAACAUGCCCCUUAGCCAGGCAGAGGAGCACGUUAAAUCAAAGCA
.(((((((.((((((......))))))..((((.....)))).))))..............((((.(((.((((.((...)).)))).))).))))......))). ( -28.90)
>DroAna_CAF1 650 106 + 1
AAAUGUGCAGCUAUACCACACUGAAGCAGCGUCUGUUGCACGAUCACUAUCGUUCGACCCACAACCAAACCCCUGCCCAGGCAGAGGAGCUCUCUAAGGUGAAGCU
........((((.((((.....(((((...((..((((.(((((....))))).))))..)).......((.((((....)))).)).))).))...)))).)))) ( -29.80)
>consensus
AGUUGUGCAGCUUCACGUCGUUGAAGCAACGAGUUUUGUUCGAGCACUAUGUGACCAUGCACAACAUGCCCCUUAGCCAGGCAGAGGAGCACGUAAAAUCAAAGCA
...((((((...((((((.(((..(((((......)))))..)))...))))))...))))))((.(((.((((.((...)).)))).))).))............ (-19.62 = -20.43 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 6,403,525 – 6,403,631
Length 106
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 82.08
Mean single sequence MFE -34.77
Consensus MFE -24.61
Energy contribution -24.28
Covariance contribution -0.33
Combinations/Pair 1.43
Mean z-score -1.96
Structure conservation index 0.71
SVM decision value 0.49
SVM RNA-class probability 0.756274
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6403525 106 - 20766785
UGCUUUGAUUUUACGUACUCCUCUGCCUGGCUAAGGGGCAUGUUGUGCAUGGUCACAUAGUGCUCGAACAAAGUUCGUUGCUUCAACGACGUGAAGCUGCACAACU
.................(((((..((...))..)))))...((((((((...((((...((......))...((.(((((...)))))))))))...)))))))). ( -29.60)
>DroSec_CAF1 782 106 - 1
UGCUUCGAUUUUACGUGCUCCUCUGCCUGACUGAGGGGCAUGUUGUGCAUGGUCACAUAGUGCUCAAACAAAACGCGUUGCUUCAACGACGUGAAGCUGCACAACU
..............(((((((((.........)))))))))((((((((((..(((...)))..)).......(((((((......)))))))....)))))))). ( -36.50)
>DroSim_CAF1 696 106 - 1
UGCUUCGAUUUUACGUGCUCCUCUGCCUGACUGAGGGGCAUGUUGUGCAUGGUCACAUAGUGCUCAAACAAAACGCGUUGCUUUAACGACGUGAAGCUGCACAACU
..............(((((((((.........)))))))))((((((((((..(((...)))..)).......(((((((......)))))))....)))))))). ( -36.50)
>DroEre_CAF1 766 106 - 1
UGCUUUGAUUUUACGUGCUCCUCUGCCUGGCUAAGGGGCAUGUUAUGCAUGGUCACAUAGUGUUCAAACAAAACACGUUGCUUCAACGAUGUGAAGCUGCAUAGCU
.((.........((((((((((..((...))..))))))))))((((((...((((((.(((((.......)))))((((...)))).))))))...)))))))). ( -36.90)
>DroYak_CAF1 697 106 - 1
UGCUUUGAUUUAACGUGCUCCUCUGCCUGGCUAAGGGGCAUGUUAUGCAUGGUAACAUAGUGCUCGAACAAAACUCGUUGCUUCAACGAUGUGAAACUGCACAGCU
((((.((...((((((((((((..((...))..))))))))))))..)).)))).....((((....(((....((((((...)))))))))......)))).... ( -35.00)
>DroAna_CAF1 650 106 - 1
AGCUUCACCUUAGAGAGCUCCUCUGCCUGGGCAGGGGUUUGGUUGUGGGUCGAACGAUAGUGAUCGUGCAACAGACGCUGCUUCAGUGUGGUAUAGCUGCACAUUU
((((..(((..........(((((((....)))))))....(((((((((((........))))).))))))..((((((...)))))))))..))))........ ( -34.10)
>consensus
UGCUUCGAUUUUACGUGCUCCUCUGCCUGGCUAAGGGGCAUGUUGUGCAUGGUCACAUAGUGCUCAAACAAAACACGUUGCUUCAACGACGUGAAGCUGCACAACU
..............((((((((..(.....)..))))))))((((((((...((((...((......))......(((((...)))))..))))...)))))))). (-24.61 = -24.28 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:43 2006