Locus 6121

Sequence ID	2L_DroMel_CAF1
Location	17,121,389 – 17,121,617
Length	228
Max. P	0.999346

overview

Window 8

Location	17,121,389 – 17,121,497
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.19
Mean single sequence MFE	-39.74
Consensus MFE	-33.80
Energy contribution	-33.48
Covariance contribution	-0.32
Combinations/Pair	1.13
Mean z-score	-5.05
Structure conservation index	0.85
SVM decision value	3.53
SVM RNA-class probability	0.999346
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17121389 108 + 22407834
ACAUUACACUCGACCGAUUUCCAGGAGAGUCAAAAAGGUAAUUUCUAGAGAAACGGUCACGGAAAAAGAAUU------------UCCGUGACGUUUCUUUGGAGCUUACCAAAGAUUUCU
.......((((..((........)).))))......(((((.(((((((((((((.(((((((((.....))------------)))))))))))))))))))).))))).......... ( -41.80)
>DroSec_CAF1 85245 108 + 1
ACAUGACACUAGACCGAUUUCCAGGAGAGUCCAAAGGGUAAUUUCUAGAGAAACGAUCACGGAGAGUGAAUU------------UCCGUGACGUUUCUUUAGAGCUUACCAAAGAUUUCU
...............((..((..((.....))....(((((.(((((((((((((.(((((((((.....))------------)))))))))))))))))))).)))))...))..)). ( -41.30)
>DroSim_CAF1 101309 108 + 1
ACAUCACACUAGACCGAUUUCCAGGAGAGUCCAAAAGGUAAUUUCUAGAGAAACGAUCACGGAGAGUAAAUU------------UCCGUGACGUUUCUUUAGAGCUUACCAAAGAUUUUU
..(((..(((...((........))..)))......(((((.(((((((((((((.(((((((((.....))------------)))))))))))))))))))).)))))...))).... ( -40.60)
>DroEre_CAF1 87346 120 + 1
ACAUUGCACUAGACCGAUUUGCAGGAGAGUCGAAAAGGUAGUUUCUAGAGAAACCAUCACGGAAAGAAAAUUUUUGACUUAAUCUCCGUGACGUUUCUUUAGAGCUUGCCAAAGUGUUCU
.....(((((....((((((......))))))....(((((.((((((((((((..(((((((.....................))))))).)))))))))))).)))))..)))))... ( -38.90)
>DroYak_CAF1 87050 120 + 1
ACAUGACACUAGACCGAUUUGCAGGAGAAUCGAAAAGGUAAUUUCUAGAGAAACGAUCAAGGAAAUACAAUUUUUGACUUGAUCUCCGUGACGUUUCUUUAGAGCUUGCCUGAGAUUUCU
.............((........)).(((((....((((((.(((((((((((((.(((.(((.((.(((........))))).))).)))))))))))))))).))))))..))))).. ( -36.10)
>consensus
ACAUGACACUAGACCGAUUUCCAGGAGAGUCCAAAAGGUAAUUUCUAGAGAAACGAUCACGGAAAGAAAAUU____________UCCGUGACGUUUCUUUAGAGCUUACCAAAGAUUUCU
...............(((((......))))).....(((((.(((((((((((((.(((((((.....................)))))))))))))))))))).))))).......... (-33.80 = -33.48 +  -0.32)

alignment

secondary structure

dotplot

Window 9

Location	17,121,389 – 17,121,497
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.19
Mean single sequence MFE	-33.74
Consensus MFE	-24.80
Energy contribution	-26.08
Covariance contribution	1.28
Combinations/Pair	1.07
Mean z-score	-3.58
Structure conservation index	0.74
SVM decision value	2.84
SVM RNA-class probability	0.997323
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17121389 108 - 22407834
AGAAAUCUUUGGUAAGCUCCAAAGAAACGUCACGGA------------AAUUCUUUUUCCGUGACCGUUUCUCUAGAAAUUACCUUUUUGACUCUCCUGGAAAUCGGUCGAGUGUAAUGU
..........(((((..((...((((((((((((((------------((.....))))))))).)))))))...))..)))))......((((..(((.....)))..))))....... ( -34.80)
>DroSec_CAF1 85245 108 - 1
AGAAAUCUUUGGUAAGCUCUAAAGAAACGUCACGGA------------AAUUCACUCUCCGUGAUCGUUUCUCUAGAAAUUACCCUUUGGACUCUCCUGGAAAUCGGUCUAGUGUCAUGU
..........(((((..((((.((((((((((((((------------.........))))))).))))))).))))..))))).....(((....(((((......))))).))).... ( -35.60)
>DroSim_CAF1 101309 108 - 1
AAAAAUCUUUGGUAAGCUCUAAAGAAACGUCACGGA------------AAUUUACUCUCCGUGAUCGUUUCUCUAGAAAUUACCUUUUGGACUCUCCUGGAAAUCGGUCUAGUGUGAUGU
.....(((..(((((..((((.((((((((((((((------------.........))))))).))))))).))))..)))))....))).((.((((((......))))).).))... ( -36.00)
>DroEre_CAF1 87346 120 - 1
AGAACACUUUGGCAAGCUCUAAAGAAACGUCACGGAGAUUAAGUCAAAAAUUUUCUUUCCGUGAUGGUUUCUCUAGAAACUACCUUUUCGACUCUCCUGCAAAUCGGUCUAGUGCAAUGU
....((((..(((....((((.((((((((((((((((..((((.....))))..)))))))))).)))))).))))...........(((............)))))).))))...... ( -30.60)
>DroYak_CAF1 87050 120 - 1
AGAAAUCUCAGGCAAGCUCUAAAGAAACGUCACGGAGAUCAAGUCAAAAAUUGUAUUUCCUUGAUCGUUUCUCUAGAAAUUACCUUUUCGAUUCUCCUGCAAAUCGGUCUAGUGUCAUGU
.((...((.((((....((((.((((((((((.(((((((((........))).)))))).))).))))))).))))...........(((((........)))))))))))..)).... ( -31.70)
>consensus
AGAAAUCUUUGGUAAGCUCUAAAGAAACGUCACGGA____________AAUUCUCUUUCCGUGAUCGUUUCUCUAGAAAUUACCUUUUCGACUCUCCUGGAAAUCGGUCUAGUGUAAUGU
..........(((((..((((.((((((((((((((.....................))))))).))))))).))))..)))))..(((((((............)))))))........ (-24.80 = -26.08 +   1.28)

alignment

secondary structure

dotplot

Window 0

Location	17,121,429 – 17,121,537
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.13
Mean single sequence MFE	-36.56
Consensus MFE	-27.76
Energy contribution	-29.16
Covariance contribution	1.40
Combinations/Pair	1.06
Mean z-score	-3.29
Structure conservation index	0.76
SVM decision value	2.97
SVM RNA-class probability	0.997941
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17121429 108 + 22407834
AUUUCUAGAGAAACGGUCACGGAAAAAGAAUU------------UCCGUGACGUUUCUUUGGAGCUUACCAAAGAUUUCUGGCUCUUUGCGAUCGUUGGUAAAAUGGCCUGGGAUGGAAC
..(((((((((((((.(((((((((.....))------------))))))))))))))))))))....(((....(..(.((((.(((((.(....).)))))..)))).)..))))... ( -41.20)
>DroSec_CAF1 85285 108 + 1
AUUUCUAGAGAAACGAUCACGGAGAGUGAAUU------------UCCGUGACGUUUCUUUAGAGCUUACCAAAGAUUUCUGGCUCUUUACGAUCGUUGGUAAAAUGGCUUGGGAUGGAAC
..(((((((((((((.(((((((((.....))------------))))))))))))))))))))....(((....(..(.((((.(((((.(....).)))))..)))).)..))))... ( -40.50)
>DroSim_CAF1 101349 108 + 1
AUUUCUAGAGAAACGAUCACGGAGAGUAAAUU------------UCCGUGACGUUUCUUUAGAGCUUACCAAAGAUUUUUGGCUCUUUACGAUCGUUGGUAAAAUGGCUUGGGAUGGAAC
..(((((((((((((.(((((((((.....))------------))))))))))))))))))))....(((....(((..((((.(((((.(....).)))))..))))..))))))... ( -39.00)
>DroEre_CAF1 87386 120 + 1
GUUUCUAGAGAAACCAUCACGGAAAGAAAAUUUUUGACUUAAUCUCCGUGACGUUUCUUUAGAGCUUGCCAAAGUGUUCUCUUUCCUUUCGAUCGGUCGUAGAAUGGCUUGGGAUGAAAC
..((((((((((((..(((((((.....................))))))).))))))))))))....((((..((((((....((........))....))))))..))))........ ( -31.20)
>DroYak_CAF1 87090 120 + 1
AUUUCUAGAGAAACGAUCAAGGAAAUACAAUUUUUGACUUGAUCUCCGUGACGUUUCUUUAGAGCUUGCCUGAGAUUUCUCUCUCUUUUUGAUAGAUGGUAAAAUGGCAUGGGAUGGAAC
...((((((((((((.(((.(((.((.(((........))))).))).)))))))))))))))(((((((.((((....))))(((.......))).))))....)))............ ( -30.90)
>consensus
AUUUCUAGAGAAACGAUCACGGAAAGAAAAUU____________UCCGUGACGUUUCUUUAGAGCUUACCAAAGAUUUCUGGCUCUUUACGAUCGUUGGUAAAAUGGCUUGGGAUGGAAC
...((((((((((((.(((((((.....................)))))))))))))))))))(((((((((.((((.............)))).))))))....)))............ (-27.76 = -29.16 +   1.40)

alignment

secondary structure

dotplot

Window 1

Location	17,121,429 – 17,121,537
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.13
Mean single sequence MFE	-32.52
Consensus MFE	-22.31
Energy contribution	-22.87
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-4.08
Structure conservation index	0.69
SVM decision value	3.27
SVM RNA-class probability	0.998884
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17121429 108 - 22407834
GUUCCAUCCCAGGCCAUUUUACCAACGAUCGCAAAGAGCCAGAAAUCUUUGGUAAGCUCCAAAGAAACGUCACGGA------------AAUUCUUUUUCCGUGACCGUUUCUCUAGAAAU
.(((.......((....((((((((.(((..(.........)..))).))))))))..))..((((((((((((((------------((.....))))))))).)))))))...))).. ( -31.50)
>DroSec_CAF1 85285 108 - 1
GUUCCAUCCCAAGCCAUUUUACCAACGAUCGUAAAGAGCCAGAAAUCUUUGGUAAGCUCUAAAGAAACGUCACGGA------------AAUUCACUCUCCGUGAUCGUUUCUCUAGAAAU
............((..((((((........)))))).((((((....))))))..))((((.((((((((((((((------------.........))))))).))))))).))))... ( -30.90)
>DroSim_CAF1 101349 108 - 1
GUUCCAUCCCAAGCCAUUUUACCAACGAUCGUAAAGAGCCAAAAAUCUUUGGUAAGCUCUAAAGAAACGUCACGGA------------AAUUUACUCUCCGUGAUCGUUUCUCUAGAAAU
............((..((((((........)))))).((((((....))))))..))((((.((((((((((((((------------.........))))))).))))))).))))... ( -30.80)
>DroEre_CAF1 87386 120 - 1
GUUUCAUCCCAAGCCAUUCUACGACCGAUCGAAAGGAAAGAGAACACUUUGGCAAGCUCUAAAGAAACGUCACGGAGAUUAAGUCAAAAAUUUUCUUUCCGUGAUGGUUUCUCUAGAAAC
............((((((((....((........))....)))).....))))....((((.((((((((((((((((..((((.....))))..)))))))))).)))))).))))... ( -33.70)
>DroYak_CAF1 87090 120 - 1
GUUCCAUCCCAUGCCAUUUUACCAUCUAUCAAAAAGAGAGAGAAAUCUCAGGCAAGCUCUAAAGAAACGUCACGGAGAUCAAGUCAAAAAUUGUAUUUCCUUGAUCGUUUCUCUAGAAAU
...........((((.........(((.......)))((((....)))).))))...((((.((((((((((.(((((((((........))).)))))).))).))))))).))))... ( -35.70)
>consensus
GUUCCAUCCCAAGCCAUUUUACCAACGAUCGAAAAGAGCCAGAAAUCUUUGGUAAGCUCUAAAGAAACGUCACGGA____________AAUUCUCUUUCCGUGAUCGUUUCUCUAGAAAU
............((((............((.....))............))))....((((.((((((((((((((.....................))))))).))))))).))))... (-22.31 = -22.87 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	17,121,461 – 17,121,577
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.77
Mean single sequence MFE	-28.49
Consensus MFE	-21.24
Energy contribution	-21.88
Covariance contribution	0.64
Combinations/Pair	1.12
Mean z-score	-2.35
Structure conservation index	0.75
SVM decision value	1.26
SVM RNA-class probability	0.936917
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17121461 116 - 22407834
AAAUAAACCACGUAAAGUGGCUAAAAAGCCUCAACAGGCGGUUCCAUCCCAGGCCAUUUUACCAACGAUCGCAAAGAGCCAGAAAUCUUUGGUAAGCUCCAAAGAAACGUCACGGA----
.......((..(((((((((((.....((((....))))((......))..)))))))))))..(((...((.....))......(((((((......)))))))..)))...)).---- ( -33.50)
>DroSec_CAF1 85317 116 - 1
AAAUAAACCACGUAAAGUGGUUAAAAAGCCUCAAAAGACGGUUCCAUCCCAAGCCAUUUUACCAACGAUCGUAAAGAGCCAGAAAUCUUUGGUAAGCUCUAAAGAAACGUCACGGA----
.....((((((.....))))))..............((((((((.............(((((........)))))))))).....(((((((......)))))))...))).....---- ( -23.51)
>DroSim_CAF1 101381 116 - 1
AAAUAAACCACGUAAAGUGGUUAAAAAGCCUCAAAAGGCGGUUCCAUCCCAAGCCAUUUUACCAACGAUCGUAAAGAGCCAAAAAUCUUUGGUAAGCUCUAAAGAAACGUCACGGA----
.......((..(((((((((((.....((((....))))((......))..)))))))))))....((.(((.....((((((....))))))....((....)).)))))..)).---- ( -28.20)
>DroEre_CAF1 87426 120 - 1
AAAUAAGCCACGUAAAGUGGCCAAAAAGCCACAAAAGGAGGUUUCAUCCCAAGCCAUUCUACGACCGAUCGAAAGGAAAGAGAACACUUUGGCAAGCUCUAAAGAAACGUCACGGAGAUU
......((((((((..(((((......)))))....((((((((......))))).))))))).....((....)).............))))...((((...((....))..))))... ( -26.30)
>DroYak_CAF1 87130 120 - 1
AAAUAAGUCACGUAAAGUGGCCACAAAGCCCCGAGAGGCGGUUCCAUCCCAUGCCAUUUUACCAUCUAUCAAAAAGAGAGAGAAAUCUCAGGCAAGCUCUAAAGAAACGUCACGGAGAUC
......(((..((((((((((.....((((((....)).)))).........))))))))))...............((((....)))).)))...((((...((....))..))))... ( -30.94)
>consensus
AAAUAAACCACGUAAAGUGGCUAAAAAGCCUCAAAAGGCGGUUCCAUCCCAAGCCAUUUUACCAACGAUCGAAAAGAGCCAGAAAUCUUUGGUAAGCUCUAAAGAAACGUCACGGA____
.......((..((((((((((......(((......)))((......))...)))))))))).......................(((((((......)))))))........))..... (-21.24 = -21.88 +   0.64)

alignment

secondary structure

dotplot

Window 3

Location	17,121,497 – 17,121,617
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.97
Mean single sequence MFE	-27.86
Consensus MFE	-20.30
Energy contribution	-21.05
Covariance contribution	0.75
Combinations/Pair	1.17
Mean z-score	-2.69
Structure conservation index	0.73
SVM decision value	1.54
SVM RNA-class probability	0.962645
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17121497 120 - 22407834
AAAAAUCAAAACCUCAAAGGAUUACAAAGACAACGGUUGAAAAUAAACCACGUAAAGUGGCUAAAAAGCCUCAACAGGCGGUUCCAUCCCAGGCCAUUUUACCAACGAUCGCAAAGAGCC
............(((...(((((...........((((.......))))..(((((((((((.....((((....))))((......))..)))))))))))....)))).)...))).. ( -28.20)
>DroSec_CAF1 85353 120 - 1
AAAGAUCAAAAGCUCAAAGGAUUACAAAGACAGUGGUAGAAAAUAAACCACGUAAAGUGGUUAAAAAGCCUCAAAAGACGGUUCCAUCCCAAGCCAUUUUACCAACGAUCGUAAAGAGCC
...........((((..(.((((.........(((((.........)))))(((((((((((....((((((....)).))))........)))))))))))....)))).)...)))). ( -27.20)
>DroSim_CAF1 101417 120 - 1
AAAGAUCAAAACCUCAAAAGAUUACAAAGACACCGGUUGAAAAUAAACCACGUAAAGUGGUUAAAAAGCCUCAAAAGGCGGUUCCAUCCCAAGCCAUUUUACCAACGAUCGUAAAGAGCC
...((((...........................((((.......))))..(((((((((((.....((((....))))((......))..)))))))))))....)))).......... ( -27.70)
>DroYak_CAF1 87170 120 - 1
AAAGACCAAAGGCGCAAGGCGUUACAAAGACUAUGGUUGGAAAUAAGUCACGUAAAGUGGCCACAAAGCCCCGAGAGGCGGUUCCAUCCCAUGCCAUUUUACCAUCUAUCAAAAAGAGAG
...(((((..(.(....).)(((.....)))..))))).............((((((((((.....((((((....)).)))).........)))))))))).................. ( -28.34)
>consensus
AAAGAUCAAAACCUCAAAGGAUUACAAAGACAACGGUUGAAAAUAAACCACGUAAAGUGGCUAAAAAGCCUCAAAAGGCGGUUCCAUCCCAAGCCAUUUUACCAACGAUCGUAAAGAGCC
...((((...........................((((.......))))..(((((((((((.....(((......)))((......))..)))))))))))....)))).......... (-20.30 = -21.05 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:39 2006