Locus 2819

Sequence ID X_DroMel_CAF1
Location 7,545,318 – 7,545,487
Length 169
Max. P 0.977074
window4627 window4628 window4629

overview

Window 7

Location 7,545,318 – 7,545,413
Length 95
Sequences 3
Columns 101
Reading direction forward
Mean pairwise identity 82.27
Mean single sequence MFE -20.20
Consensus MFE -17.81
Energy contribution -17.70
Covariance contribution -0.11
Combinations/Pair 1.11
Mean z-score -2.25
Structure conservation index 0.88
SVM decision value 1.78
SVM RNA-class probability 0.977074
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7545318 95 + 22224390
AAAAAA---AAUCAAAAAAA---GAAGAAGAAAAACCAGCAAUCGCUGAUAACAGCGGGAACGAUGUGCAUCGGUGGCGUAUACGUGAUGCGGCUUAAUAA
......---...........---..............(((..((((((((.(((.((....)).)))..))))))))(((((.....))))))))...... ( -20.50)
>DroSec_CAF1 38402 89 + 1
AAAAGAAA---------AAA---CAAGAAGAAAAACCAGCAAUCGCUGAUAAGAGCGGGAACGAUGUGCAUCGGUGGCGUAUACGUGAUGCGGCUUUAUAA
........---------...---.............((((....))))...((((((....)....((((((((((.....))).)))))))))))).... ( -19.30)
>DroEre_CAF1 49320 99 + 1
AAAAACAUAAGUCAAAAAAAUGUAGAGAAGAAAAACCAGCAAUCGCUGAUAACAGCGAGAACGA--UGCAUCGGUGGCGUAUACGUGAUGUGGCUAAAUAA
.........(((((.....(((((.....(....(((.(((.((((((....))))))......--)))...)))..)...)))))....)))))...... ( -20.80)
>consensus
AAAAAAA__A_UCAAAAAAA___AAAGAAGAAAAACCAGCAAUCGCUGAUAACAGCGGGAACGAUGUGCAUCGGUGGCGUAUACGUGAUGCGGCUUAAUAA
.....................................(((..((((((....)))))).........(((((((((.....))).)))))).)))...... (-17.81 = -17.70 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 7,545,318 – 7,545,413
Length 95
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 82.27
Mean single sequence MFE -16.80
Consensus MFE -13.27
Energy contribution -14.27
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.65
Structure conservation index 0.79
SVM decision value 0.30
SVM RNA-class probability 0.677213
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7545318 95 - 22224390
UUAUUAAGCCGCAUCACGUAUACGCCACCGAUGCACAUCGUUCCCGCUGUUAUCAGCGAUUGCUGGUUUUUCUUCUUC---UUUUUUUGAUU---UUUUUU
.....((((((((((.((....)).....))))).....((...(((((....)))))...)).))))).........---...........---...... ( -17.80)
>DroSec_CAF1 38402 89 - 1
UUAUAAAGCCGCAUCACGUAUACGCCACCGAUGCACAUCGUUCCCGCUCUUAUCAGCGAUUGCUGGUUUUUCUUCUUG---UUU---------UUUCUUUU
....(((((((((((.((....)).....))))).....((...((((......))))...)).))))))........---...---------........ ( -15.40)
>DroEre_CAF1 49320 99 - 1
UUAUUUAGCCACAUCACGUAUACGCCACCGAUGCA--UCGUUCUCGCUGUUAUCAGCGAUUGCUGGUUUUUCUUCUCUACAUUUUUUUGACUUAUGUUUUU
......(((((......((((.((....)))))).--..((..((((((....))))))..)))))))................................. ( -17.20)
>consensus
UUAUUAAGCCGCAUCACGUAUACGCCACCGAUGCACAUCGUUCCCGCUGUUAUCAGCGAUUGCUGGUUUUUCUUCUUC___UUUUUUUGA_U__UUUUUUU
.....((((((((((.((....)).....))))).....((...(((((....)))))...)).)))))................................ (-13.27 = -14.27 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 7,545,379 – 7,545,487
Length 108
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 90.94
Mean single sequence MFE -28.64
Consensus MFE -25.88
Energy contribution -26.16
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -1.16
Structure conservation index 0.90
SVM decision value -0.01
SVM RNA-class probability 0.526333
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7545379 108 + 22224390
GCAUCGGUGGCGUAUACGUGAUGCGGCUUAAUAAGGGAGCAUACUUGUACCCUAACUGAAAUC------UGAAUGCCACAAUUGCAUCUCACACAGCCCACCAAAGUGUCACCA
.....(((((((......((.((.((((.....((((.(((....))).))))..........------(((((((.......)))).)))...)))))).))...))))))). ( -28.90)
>DroSec_CAF1 38457 108 + 1
GCAUCGGUGGCGUAUACGUGAUGCGGCUUUAUAAGGGAGCAUACUUGUCCCCUAAAUGAAAUC------UGAAUGCCACAAUUGCAUUUCACACAGCCCACCAAAGUGUCACCA
.....(((((((......((.((.((((.....((((..((....))..))))..........------.((((((.......)))))).....)))))).))...))))))). ( -29.80)
>DroSim_CAF1 38846 108 + 1
GCAUCGGUGGCGUAUACGUGAUGCGGCUUAAUAAGGGAGCAUACUUGUCCCCUAACUGAAAUC------UGAAUGCCACAAUUGCAUUUCACACAGCCCACCAAAGUGUCACCA
.....(((((((......((.((.((((.....((((..((....))..))))..........------.((((((.......)))))).....)))))).))...))))))). ( -29.80)
>DroEre_CAF1 49385 108 + 1
GCAUCGGUGGCGUAUACGUGAUGUGGCUAAAUAAGGGAGCAUACUUGUCCACUAACCAACAUG------CGAAUGCGACAAUUGCAUUUCACACAGCCCACCAAAGUGUCACCA
.....(((((((......((.((.((((.....(((((.((....))))).))........((------.((((((((...))))))))))...)))))).))...))))))). ( -27.30)
>DroYak_CAF1 39218 114 + 1
GCAUCGGUGGCGUAUACGUGAUGUGGCUAAAUAAGGGAGCAUACUUGUCCACUAACUAAAAUCUGAAUCUGAAUGCCACAAAUGCAUUUCACGCAGUCCACCAAAGUGUCGCCA
.....(((((((.....(((.((((((......(((((.((....))))).))........((.......))..))))))..(((.......)))...))).....))))))). ( -27.40)
>consensus
GCAUCGGUGGCGUAUACGUGAUGCGGCUUAAUAAGGGAGCAUACUUGUCCCCUAACUGAAAUC______UGAAUGCCACAAUUGCAUUUCACACAGCCCACCAAAGUGUCACCA
.....(((((((......((.((.((((.....((((..((....))..)))).................((((((.......)))))).....)))))).))...))))))). (-25.88 = -26.16 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:20 2006