Locus 9130

Sequence ID	3R_DroMel_CAF1
Location	24,374,597 – 24,374,784
Length	187
Max. P	0.623291

overview

Window 7

Location	24,374,597 – 24,374,687
Length	90
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	85.48
Mean single sequence MFE	-15.69
Consensus MFE	-12.45
Energy contribution	-12.82
Covariance contribution	0.36
Combinations/Pair	1.06
Mean z-score	-1.94
Structure conservation index	0.79
SVM decision value	0.18
SVM RNA-class probability	0.623291
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24374597 90 - 27905053
GCCCCCUCCCCACAGGAUUUC------------UUCGAUGUGUUU-UUUCUC-CCUUUUUUUUGCAUCUCGCGGAUGCUUGCAUCUCGAAAUCAAUCAACUCAA
...............((((((------------...((((((...-...)..-..........(((((.....)))))..)))))..))))))........... ( -14.70)
>DroSec_CAF1 196804 101 - 1
GCCCCCUCCCCACAGGAUUUCUUCCCCCACCUCUUCGAUGUGUUU-UUUCUC-CCUUU-UUUUGCAUCUCGCGGAUGCUUGCAUCUCGAAAUCAAUCAACUCAA
..............(((.....)))........(((((.((((..-......-.....-....(((((.....)))))..)))).))))).............. ( -14.71)
>DroSim_CAF1 205408 101 - 1
GCCCCCUCCCCACAGGAUUUCUUCCCCCACCUCUUCGAUGUGUUU-UUUCUC-CCUUU-UUUUGCAUCUCGCGGAUGCUUGCAUCUCGAAAUCAAUCAACUCAA
..............(((.....)))........(((((.((((..-......-.....-....(((((.....)))))..)))).))))).............. ( -14.71)
>DroEre_CAF1 210829 100 - 1
ACCCCCUCCCCACAGGAUUUCUUCC-CCGCCUCUUCGACGUGUUG-UUUCUC-CCUUU-UUUUGCAUCUCGCGGAUGCUUGCAUCUCGAAAUCAAUCAACUCAA
..............(((.....)))-.......(((((.((((..-......-.....-....(((((.....)))))..)))).))))).............. ( -14.71)
>DroYak_CAF1 204229 103 - 1
GCCCCCUCCACACAGGAUUUCUUCCCCCACCUCUGCGAUGUGUUUUUUUCUC-CCUUUUUUUUGCAUCUCGCGGAUGCUUGCAUCUCGAAAUCAAUCAACUCAA
...............((((((.............((((.((((.........-..........)))).))))(((((....))))).))))))........... ( -18.51)
>DroAna_CAF1 199879 95 - 1
ACCCCAACCCCCGAUGAUUUCUCUGUCCC-------GCUUUGCUU-CUUCGUUUAUUU-UUUUGCAUCUCGCGGAUGCUUGCAUCUCGAAAUCAAUCAACUCAA
............(((((((((.......(-------((..(((..-............-....)))....)))((((....))))..)))))).)))....... ( -16.77)
>consensus
GCCCCCUCCCCACAGGAUUUCUUCCCCCACCUCUUCGAUGUGUUU_UUUCUC_CCUUU_UUUUGCAUCUCGCGGAUGCUUGCAUCUCGAAAUCAAUCAACUCAA
...............((((((..............(((.((((....................)))).))).(((((....))))).))))))........... (-12.45 = -12.82 +   0.36)

alignment

secondary structure

dotplot

Window 8

Location	24,374,659 – 24,374,756
Length	97
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	82.35
Mean single sequence MFE	-35.32
Consensus MFE	-25.72
Energy contribution	-25.96
Covariance contribution	0.24
Combinations/Pair	1.25
Mean z-score	-1.60
Structure conservation index	0.73
SVM decision value	0.11
SVM RNA-class probability	0.590454
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24374659 97 + 27905053
CAUCGAA------------GAAAUCCUGUGGGGAGGGGGCAA-AGAUUCCACUCGGGUGGUCCUCCUAUUGGAAGAUUCACGUUGUAUACCCUAUAGUGAUGAUAUUAUA
.......------------...(((((((((((.(((((...-.....)).)))..((((((.(((....))).)).))))........)))))))).)))......... ( -26.40)
>DroSec_CAF1 196865 110 + 1
CAUCGAAGAGGUGGGGGAAGAAAUCCUGUGGGGAGGGGGCAAGAUAUUCCACUCGGGUGGUCUUCCUUCUGGAAGAUUCACGUUGUAUACCCUAUAGUAAUGGUGUUAUA
((((.....))))............((((((((.(((((.((....)))).)))..((((((((((....)))))).))))........))))))))............. ( -30.90)
>DroSim_CAF1 205469 110 + 1
CAUCGAAGAGGUGGGGGAAGAAAUCCUGUGGGGAGGGGGCAAGAGAUUCCACUCCGGUGGUCUUCCUUCUGGAAGAUUCACGUUGUAUACCCUAUAGUAAUGGUAUUAUA
((((.....))))............((((((((.((((.............)))).((((((((((....)))))).))))........))))))))............. ( -32.02)
>DroEre_CAF1 210890 109 + 1
CGUCGAAGAGGCGG-GGAAGAAAUCCUGUGGGGAGGGGGUGAAAUAUUCCACUCGGGUGGUCUUUCUUCUGGAAGAUCCACGCUGCAUACCCUAUAGCGAUGGCGUUCCA
((((.....))))(-(((.(..(((((((((((...(((((........)))))(.((((((((((....)))))).)))).)......)))))))).)))..).)))). ( -44.80)
>DroYak_CAF1 204292 103 + 1
CAUCGCAGAGGUGGGGGAAGAAAUCCUGUGUGGAGGGGGCGAAAUAUUCCACUCGGGUGGUCUUCCUUCAAGAAGAUCCGCGCUGUAUACCCUAUAGCGAUGG-------
((((((.((..((((((((((...((((.((((((...........)))))).))))...))))))))))......)).))((((((.....)))))))))).------- ( -42.50)
>consensus
CAUCGAAGAGGUGGGGGAAGAAAUCCUGUGGGGAGGGGGCAAAAUAUUCCACUCGGGUGGUCUUCCUUCUGGAAGAUUCACGUUGUAUACCCUAUAGUGAUGGUAUUAUA
((((.....))))............((((((((..(.(((........((....))((((((((((....)))))).))))))).)...))))))))............. (-25.72 = -25.96 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	24,374,687 – 24,374,784
Length	97
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	73.09
Mean single sequence MFE	-22.92
Consensus MFE	-13.76
Energy contribution	-13.45
Covariance contribution	-0.31
Combinations/Pair	1.22
Mean z-score	-1.55
Structure conservation index	0.60
SVM decision value	0.04
SVM RNA-class probability	0.555008
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24374687 97 - 27905053
----------GAUAU--CAUGAUUUUGUAAUCCAAGAAUAUAUAAUAUCAUCACUAUAGGGUAUACAACGUGAAUCUUCCAAUAGGAGGACCACCCGAGUGGAAUCU-UU
----------(((((--.((((((((........))))).))).))))).(((((...((((.(((...)))..((((((....))))))..)))).))))).....-.. ( -22.30)
>DroSec_CAF1 196905 108 - 1
UAAUAUCAUUGAUAU--CCUGAUUUUCUAAUCGAAGAAUAUAUAACACCAUUACUAUAGGGUAUACAACGUGAAUCUUCCAGAAGGAAGACCACCCGAGUGGAAUAUCUU
.....((((((((((--((((.(((((.....))))).....(((.....)))...)))))))).))..)))).((((((....))))))((((....))))........ ( -21.60)
>DroSim_CAF1 205509 110 - 1
UUAUAUCCUGGAUAUUUCUGGAUUUUCUAAUCGAAGAAUAUAUAAUACCAUUACUAUAGGGUAUACAACGUGAAUCUUCCAGAAGGAAGACCACCGGAGUGGAAUCUCUU
.(((((((((.(((((..(.((((....)))).)..)))))...............)))))))))....(.((.((((((....))))))((((....))))..)).).. ( -25.29)
>DroEre_CAF1 210929 95 - 1
AGAUAUGAUAG--------------GAUACUA-CAUACUAUGGAACGCCAUCGCUAUAGGGUAUGCAGCGUGGAUCUUCCAGAAGAAAGACCACCCGAGUGGAAUAUUUC
...((((.(((--------------....)))-))))((.(((((..(((.((((.((.....)).)))))))...)))))..)).....((((....))))........ ( -22.50)
>consensus
U_AUAUCAU_GAUAU__C_UGAUUUUCUAAUCGAAGAAUAUAUAACACCAUCACUAUAGGGUAUACAACGUGAAUCUUCCAGAAGGAAGACCACCCGAGUGGAAUAUCUU
..................................................(((((...((((.(((...)))..((((((....))))))..)))).)))))........ (-13.76 = -13.45 +  -0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:27:15 2006