Locus 397

Sequence ID	X_DroMel_CAF1
Location	1,172,221 – 1,172,419
Length	198
Max. P	0.967328

overview

Window 0

Location	1,172,221 – 1,172,341
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.90
Mean single sequence MFE	-32.20
Consensus MFE	-23.26
Energy contribution	-24.02
Covariance contribution	0.76
Combinations/Pair	1.11
Mean z-score	-1.86
Structure conservation index	0.72
SVM decision value	0.05
SVM RNA-class probability	0.560339
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1172221 120 - 22224390
CUUUAAUCGGCCGAUUGAUUAGCAUCUCCAUGCUAAUUAUGGUAUUCCCUUAUCUUUGGCGAUGAUCAGCCGCGGAACUUUUGUUUUUGGUAUGCUGGCCGGCCAAUAGACAGCGAAAAC
......((((((...((((((((((....)))))))))).(((((.((....(((.((((........)))).)))((....))....)).))))))))))).................. ( -32.50)
>DroSec_CAF1 8287 116 - 1
CUUUAAUCGGCCGAUUGAUUAGCAUCUCCAUGCUAAUUAUGGUAUUCCCUUAUAUUUGGCAAUGAUCAGCCGCGGAACUCUUGUUUUUGGCCUGCUGG----CCAAUAGACAGCGAAAAC
.......((((.(((((((((((((....))))))))))...((((.((........)).))))))).))))......((((((((((((((....))----)))).)))))).)).... ( -33.70)
>DroSim_CAF1 9040 116 - 1
CUUUAAUCGGCCGAUUGAUUAGCAUCUCCAUGCUAAUUAUGGUAUUCCCUUAUCUUUGGCGAUGAUCAGCCGCGGAACUUUUGUUUUUGGCCUGCUGG----CCAAUAGACAGCGAAAAC
......(((((((..((((((((((....)))))))))))))).........(((.((((........)))).)))....((((((((((((....))----)))).))))))))).... ( -36.30)
>DroEre_CAF1 7395 116 - 1
CUUUAAGCGGCCGAUUGAUUAGCAUCUUCAUGCUAAUUAUGGUAUUUCCCUAUCUUUGGCGAUGAUCAGCCGCGGAACUUUUGUUUUUAGUCUGCUAG----CCACUAAAUAGCGAAAAC
......(((((....((((((((((....))))))))))((((...((((.......)).))..))))))))).....(((((((((((((..(....----).)))))).))))))).. ( -31.20)
>DroYak_CAF1 10305 115 - 1
CUUUAAUCGGCCGAUUGAUUAGCAUCUCCGCGCUAAUUAUGGUAUUUCCCUAUCUCUGGCGAUGAUCAGCCGCGAAACUUUUGUU-UUAGUCUGCUUG----CCAAUAAAUAGCGAAAAC
.........((((..((((((((........)))))))))))).((((.((((...((((((....(((.(..(((((....)))-)).).))).)))----)))....)))).)))).. ( -27.30)
>consensus
CUUUAAUCGGCCGAUUGAUUAGCAUCUCCAUGCUAAUUAUGGUAUUCCCUUAUCUUUGGCGAUGAUCAGCCGCGGAACUUUUGUUUUUGGUCUGCUGG____CCAAUAGACAGCGAAAAC
........((((((.((((((((((....)))))))))).............(((.((((........)))).)))..........))))))(((((.............)))))..... (-23.26 = -24.02 +   0.76)

alignment

secondary structure

dotplot

Window 1

Location	1,172,261 – 1,172,379
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.46
Mean single sequence MFE	-36.80
Consensus MFE	-29.68
Energy contribution	-29.76
Covariance contribution	0.08
Combinations/Pair	1.12
Mean z-score	-2.17
Structure conservation index	0.81
SVM decision value	1.61
SVM RNA-class probability	0.967328
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1172261 118 + 22224390
AAGUUCCGCGGCUGAUCAUCGCCAAAGAUAAGGGAAUACCAUAAUUAGCAUGGAGAUGCUAAUCAAUCGGCCGAUUAAAGCCGC--CUGCCUCAAAAGUUGGCCGCCUAUGGAUAACUUU
(((((((((((((....((((((........((.....))...((((((((....)))))))).....)).))))...))))))--..(((.........))).......)))..)))). ( -34.80)
>DroSec_CAF1 8323 118 + 1
GAGUUCCGCGGCUGAUCAUUGCCAAAUAUAAGGGAAUACCAUAAUUAGCAUGGAGAUGCUAAUCAAUCGGCCGAUUAAAGCCGC--CUGCUCCAAAAGUUGGCGGCCUAUGGAUCACUGU
.(((((((((((((((.(((.((........)).)))......((((((((....))))))))..))))))))......(((((--(.(((.....))).))))))...))))..))).. ( -41.20)
>DroSim_CAF1 9076 118 + 1
AAGUUCCGCGGCUGAUCAUCGCCAAAGAUAAGGGAAUACCAUAAUUAGCAUGGAGAUGCUAAUCAAUCGGCCGAUUAAAGCCGC--CUGCUCCAAAAGUUGGCGGCCUAUUGAUCACUGU
.(((.....(((((((.(((......)))..((.....))...((((((((....))))))))..)))))))((((((.(((((--(.(((.....))).))))))...))))))))).. ( -39.70)
>DroEre_CAF1 7431 118 + 1
AAGUUCCGCGGCUGAUCAUCGCCAAAGAUAGGGAAAUACCAUAAUUAGCAUGAAGAUGCUAAUCAAUCGGCCGCUUAAAGCCGCCCCUGCCA-CAAAGUUGCCGGCCUACGGAUCACUU-
..(.((((((((((((.(((......))).((......))...((((((((....))))))))..))))))))).....(((((..((....-...))..).))))....))).)....- ( -35.50)
>DroYak_CAF1 10340 116 + 1
AAGUUUCGCGGCUGAUCAUCGCCAGAGAUAGGGAAAUACCAUAAUUAGCGCGGAGAUGCUAAUCAAUCGGCCGAUUAAAGCCGC--CUGCUC-AAAAGUCUGUGGCCUACGGAUCACUU-
.(((...((((((....((((((.......((......))...(((((((......))))))).....)).))))...))))))--..))).-........(((..(....)..)))..- ( -32.80)
>consensus
AAGUUCCGCGGCUGAUCAUCGCCAAAGAUAAGGGAAUACCAUAAUUAGCAUGGAGAUGCUAAUCAAUCGGCCGAUUAAAGCCGC__CUGCUCCAAAAGUUGGCGGCCUAUGGAUCACUUU
.(((((((((((((((...............((.....))...((((((((....))))))))..))))))))......(((((..((........))...)))))...))))..))).. (-29.68 = -29.76 +   0.08)

alignment

secondary structure

dotplot

Window 2

Location	1,172,261 – 1,172,379
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.46
Mean single sequence MFE	-37.02
Consensus MFE	-27.54
Energy contribution	-27.90
Covariance contribution	0.36
Combinations/Pair	1.10
Mean z-score	-1.63
Structure conservation index	0.74
SVM decision value	0.08
SVM RNA-class probability	0.572215
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1172261 118 - 22224390
AAAGUUAUCCAUAGGCGGCCAACUUUUGAGGCAG--GCGGCUUUAAUCGGCCGAUUGAUUAGCAUCUCCAUGCUAAUUAUGGUAUUCCCUUAUCUUUGGCGAUGAUCAGCCGCGGAACUU
.((((..(((.......(((.........)))..--((((((...((((.((((.((((((((((....)))))))))).((((......)))).))))))))....))))))))))))) ( -38.50)
>DroSec_CAF1 8323 118 - 1
ACAGUGAUCCAUAGGCCGCCAACUUUUGGAGCAG--GCGGCUUUAAUCGGCCGAUUGAUUAGCAUCUCCAUGCUAAUUAUGGUAUUCCCUUAUAUUUGGCAAUGAUCAGCCGCGGAACUC
.......(((..((((((((..(((...)))..)--)))))))....((((.(((((((((((((....))))))))))...((((.((........)).))))))).)))).))).... ( -37.40)
>DroSim_CAF1 9076 118 - 1
ACAGUGAUCAAUAGGCCGCCAACUUUUGGAGCAG--GCGGCUUUAAUCGGCCGAUUGAUUAGCAUCUCCAUGCUAAUUAUGGUAUUCCCUUAUCUUUGGCGAUGAUCAGCCGCGGAACUU
....((((((..((((((((..(((...)))..)--)))))))......(((((.((((((((((....)))))))))).((((......)))).)))))..))))))............ ( -38.00)
>DroEre_CAF1 7431 118 - 1
-AAGUGAUCCGUAGGCCGGCAACUUUG-UGGCAGGGGCGGCUUUAAGCGGCCGAUUGAUUAGCAUCUUCAUGCUAAUUAUGGUAUUUCCCUAUCUUUGGCGAUGAUCAGCCGCGGAACUU
-((((..(((((.(((((((..(((.(-(.((....)).))...)))..))))..((((((((((....))))))))))((((...((((.......)).))..)))))))))))))))) ( -40.80)
>DroYak_CAF1 10340 116 - 1
-AAGUGAUCCGUAGGCCACAGACUUUU-GAGCAG--GCGGCUUUAAUCGGCCGAUUGAUUAGCAUCUCCGCGCUAAUUAUGGUAUUUCCCUAUCUCUGGCGAUGAUCAGCCGCGAAACUU
-..(((..(....)..)))........-......--((((((...((((((((..((((((((........)))))))))))).....((.......))))))....))))))....... ( -30.40)
>consensus
AAAGUGAUCCAUAGGCCGCCAACUUUUGGAGCAG__GCGGCUUUAAUCGGCCGAUUGAUUAGCAUCUCCAUGCUAAUUAUGGUAUUCCCUUAUCUUUGGCGAUGAUCAGCCGCGGAACUU
...(((..(....)..))).................((((((...((((.((((.((((((((((....)))))))))).((.....))......))))))))....))))))....... (-27.54 = -27.90 +   0.36)

alignment

secondary structure

dotplot

Window 3

Location	1,172,301 – 1,172,419
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.21
Mean single sequence MFE	-40.60
Consensus MFE	-28.96
Energy contribution	-29.72
Covariance contribution	0.76
Combinations/Pair	1.10
Mean z-score	-2.80
Structure conservation index	0.71
SVM decision value	1.12
SVM RNA-class probability	0.918357
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1172301 118 + 22224390
AUAAUUAGCAUGGAGAUGCUAAUCAAUCGGCCGAUUAAAGCCGC--CUGCCUCAAAAGUUGGCCGCCUAUGGAUAACUUUUUCCCUGCAUACUUGUGGGGGAGCCGAAAAUUGUAUGGCU
...((((((((....))))))))....((((........)))).--..(((.(((...(((((..((...))........(((((..((....))..))))))))))...)))...))). ( -35.90)
>DroSec_CAF1 8363 118 + 1
AUAAUUAGCAUGGAGAUGCUAAUCAAUCGGCCGAUUAAAGCCGC--CUGCUCCAAAAGUUGGCGGCCUAUGGAUCACUGUUUCCCUGCAUACUUGUGGGGGAACCGAAAAUUUUAUGGCU
...((((((((....)))))))).....((((((((...(((((--(.(((.....))).)))))).....)))).(.(((((((..((....))..))))))).)..........)))) ( -46.20)
>DroSim_CAF1 9116 118 + 1
AUAAUUAGCAUGGAGAUGCUAAUCAAUCGGCCGAUUAAAGCCGC--CUGCUCCAAAAGUUGGCGGCCUAUUGAUCACUGUUUCCCUGCAUACUUGUGGGGGAACCGAAAAUUGUAUGGCU
...((((((((....)))))))).....((((((((((.(((((--(.(((.....))).))))))...)))))).(.(((((((..((....))..))))))).)..........)))) ( -47.60)
>DroEre_CAF1 7471 118 + 1
AUAAUUAGCAUGAAGAUGCUAAUCAAUCGGCCGCUUAAAGCCGCCCCUGCCA-CAAAGUUGCCGGCCUACGGAUCACUU-UUUCCUGCAUACUUGUGGGGGAACAGAAAAUUGUGUGGCA
...((((((((....)))))))).....(((.((.....)).)))...((((-((.((((.(((.....)))....(((-(..((..((....))..))..)).))..)))).)))))). ( -40.10)
>DroYak_CAF1 10380 116 + 1
AUAAUUAGCGCGGAGAUGCUAAUCAAUCGGCCGAUUAAAGCCGC--CUGCUC-AAAAGUCUGUGGCCUACGGAUCACUU-UUCCCUGCAUACUUGUGGGCGAACGGAAAAUUGUGUGGCA
...(((((((......))))))).....(((........)))((--(.((.(-((...(((((.(((((((((......-.)))..........))))))..)))))...))).))))). ( -33.20)
>consensus
AUAAUUAGCAUGGAGAUGCUAAUCAAUCGGCCGAUUAAAGCCGC__CUGCUCCAAAAGUUGGCGGCCUAUGGAUCACUUUUUCCCUGCAUACUUGUGGGGGAACCGAAAAUUGUAUGGCU
...((((((((....))))))))......(((((((...(((((..((........))...))))).....)))).....(((((..((....))..)))))..............))). (-28.96 = -29.72 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:31 2006