Locus 6257

Sequence ID	3L_DroMel_CAF1
Location	16,670,409 – 16,670,668
Length	259
Max. P	0.996177

overview

Window 5

Location	16,670,409 – 16,670,529
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.67
Mean single sequence MFE	-37.64
Consensus MFE	-33.60
Energy contribution	-33.80
Covariance contribution	0.20
Combinations/Pair	1.07
Mean z-score	-1.19
Structure conservation index	0.89
SVM decision value	0.10
SVM RNA-class probability	0.581627
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16670409 120 - 23771897
CCCCCCUCGGAAUUGCCGCUAGUGGAGCCUCCUGCUGCUCCAUCAAUGGAAUUUCGGCGAUUCCGGCGCUUCACCACCACCGUCGUGGAUCUCGAUUUUGGACCCGCCAGUUUAGUAUUA
........((((((((((((((((((((........)))))))...))).....))))))))))((((..((....((((....))))..(........)))..))))............ ( -37.60)
>DroSec_CAF1 38025 120 - 1
CCCCCCUCGGAAUUGCCGCUAGUGGAGCCUCCAGCUGCUCCAUCAAUGCAAUUUCGGCGAUUCCGGCGCUUCACCACCACCGCCGUGGCUCUCGAUUUUGGACCCGCCAGUUUAGUAUUA
........((((((((.....(((((((........)))))))....))))))))((((..(((((.......)).((((....))))...........)))..))))............ ( -36.20)
>DroSim_CAF1 38103 120 - 1
CCCCCCUCGGAAUUGCCGCUAGUGGAGCCUCCAGCUGCUCCAUCAAUGCAAUUUCGGCGAUUCCGGCGCUUCACCACCACCGCCGUGGAUUUCGAUUUUGGACCCGCCAGUUUAGUAUUA
........((((((((.....(((((((........)))))))....))))))))((((..(((((.......)).((((....))))...........)))..))))............ ( -36.90)
>DroEre_CAF1 38113 120 - 1
CCCCCGUCGGAAUUGCCGCCUGUGGAGCCUUCGGCUGCUCCAUUAAUGCGAUUUCGGCGAUUUCGGCGCUUCACCACCACCGUAGUGGAUCUCGAUUUUGGACCCGCCAGUUUACUAUUC
....((((((((((((.....((((((((....)..)))))))....)))))))))))).....((((..((....((((....))))..(........)))..))))............ ( -40.70)
>DroYak_CAF1 39300 120 - 1
CCCACGUCGGCAUUGCCGCCUGUGGCGCCUCCGGCUGCUCCAUCAGUGCGAUUUCGGCGAUUCCGGCGCUUCACCACCACCGUAGUGGAUCUCGAUCUUGGACCCGCCAGUUUACUAUUC
.(((((((((.((((((((((((((.((........)).))).))).))(....))))))).))))))........((((....))))..........)))................... ( -36.80)
>consensus
CCCCCCUCGGAAUUGCCGCUAGUGGAGCCUCCAGCUGCUCCAUCAAUGCAAUUUCGGCGAUUCCGGCGCUUCACCACCACCGUCGUGGAUCUCGAUUUUGGACCCGCCAGUUUAGUAUUA
........((((((((.....(((((((........)))))))....))))))))((((..(((((.......)).((((....))))...........)))..))))............ (-33.60 = -33.80 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	16,670,449 – 16,670,569
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.08
Mean single sequence MFE	-40.86
Consensus MFE	-31.10
Energy contribution	-32.14
Covariance contribution	1.04
Combinations/Pair	1.03
Mean z-score	-2.70
Structure conservation index	0.76
SVM decision value	1.77
SVM RNA-class probability	0.976245
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16670449 120 - 23771897
UGCCGAAUAACCACUUCCGGAGAAAGCUGCUCUGGAAUUACCCCCCUCGGAAUUGCCGCUAGUGGAGCCUCCUGCUGCUCCAUCAAUGGAAUUUCGGCGAUUCCGGCGCUUCACCACCAC
.(((..........((((((((.......))))))))...........((((((((((((((((((((........)))))))...))).....)))))))))))))............. ( -42.30)
>DroSec_CAF1 38065 120 - 1
UGUCGAAUUACCACUUCCGGAGAAAACUGCUCUGGAAUUACCCCCCUCGGAAUUGCCGCUAGUGGAGCCUCCAGCUGCUCCAUCAAUGCAAUUUCGGCGAUUCCGGCGCUUCACCACCAC
.(((((((..((..((((((((.......))))))))...........((((((((.....(((((((........)))))))....))))))))))..))).))))............. ( -40.00)
>DroSim_CAF1 38143 120 - 1
UGUCGAAUUACCACUUCCGGAGAAAGCUGCUCUGGAAUUACCCCCCUCGGAAUUGCCGCUAGUGGAGCCUCCAGCUGCUCCAUCAAUGCAAUUUCGGCGAUUCCGGCGCUUCACCACCAC
.(((((((..((..((((((((.......))))))))...........((((((((.....(((((((........)))))))....))))))))))..))).))))............. ( -40.00)
>DroEre_CAF1 38153 120 - 1
UCUUGAAAUACCGCCUCCGCAGAAACCUGCUCUGGAUUUACCCCCGUCGGAAUUGCCGCCUGUGGAGCCUUCGGCUGCUCCAUUAAUGCGAUUUCGGCGAUUUCGGCGCUUCACCACCAC
...((((....(((((((((((....))))...)))........((((((((((((.....((((((((....)..)))))))....)))))))))))).....)))).))))....... ( -43.10)
>DroYak_CAF1 39340 120 - 1
UCUGGAAUUUCCACCUCCGCAGAAACCUGCGCUGCAUUUACCCACGUCGGCAUUGCCGCCUGUGGCGCCUCCGGCUGCUCCAUCAGUGCGAUUUCGGCGAUUCCGGCGCUUCACCACCAC
..(((............(((((....))))).............((((((.((((((((((((((.((........)).))).))).))(....))))))).)))))).....))).... ( -38.90)
>consensus
UGUCGAAUUACCACUUCCGGAGAAACCUGCUCUGGAAUUACCCCCCUCGGAAUUGCCGCUAGUGGAGCCUCCAGCUGCUCCAUCAAUGCAAUUUCGGCGAUUCCGGCGCUUCACCACCAC
....(((...((...(((((((.......)))))))............((((((((((...(((((((........)))))))...........))))))))))))...)))........ (-31.10 = -32.14 +   1.04)

alignment

secondary structure

dotplot

Window 7

Location	16,670,529 – 16,670,649
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.58
Mean single sequence MFE	-38.80
Consensus MFE	-22.68
Energy contribution	-23.04
Covariance contribution	0.36
Combinations/Pair	1.26
Mean z-score	-2.69
Structure conservation index	0.58
SVM decision value	0.05
SVM RNA-class probability	0.557376
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16670529 120 + 23771897
UAAUUCCAGAGCAGCUUUCUCCGGAAGUGGUUAUUCGGCAGGAAAUAAUUCCGAAGGAGGUACAUCGACUGGACGCAAGUCCAUUGGUAGUAAAUCCAGAGGAACUUAUUUCCGAGCAAG
...((((.(((.......))).))))...........((.((((((((((((...(((..((((((((.(((((....)))))))))).)))..)))...)))).))))))))..))... ( -43.50)
>DroSec_CAF1 38145 120 + 1
UAAUUCCAGAGCAGUUUUCUCCGGAAGUGGUAAUUCGACAGGAAAUAUUUCCGAAGGAGGUACAUCGACUGGACGCAAGUCCAUUGGUAGUAAAUCCAGAGGAACUUAUUCCCGAGCAGG
...(((..(((.((.((((((((((((((....(((....)))..))))))))..(((..((((((((.(((((....)))))))))).)))..))).)))))).)).)))..))).... ( -37.80)
>DroSim_CAF1 38223 120 + 1
UAAUUCCAGAGCAGCUUUCUCCGGAAGUGGUAAUUCGACAGGAAAUAUUUCCGAAGGAGGUAAAUCGACUGGACGCAAGUCCAUUGGUAGUAAAUCCAGAGGAACCUAUUCCCGAGCAGG
..........((.(((((((.((((((((....(((....)))..)))))))).)))))))...(((..(((((....)))))((((........)))).((((....)))))))))... ( -36.40)
>DroEre_CAF1 38233 120 + 1
UAAAUCCAGAGCAGGUUUCUGCGGAGGCGGUAUUUCAAGAGGAAAUAAUUCCGAAGGAGGUAAAUCAACUGGAUGCAAUUCCGGUGGAAGUAAUUCCAAAGGAACUAAUUCCCGGACAGG
...((((((.((((....)))).((.....((((((....((((....))))....))))))..))..)))))).....((((.(((((....)))))..((((....)))))))).... ( -35.80)
>DroYak_CAF1 39420 120 + 1
UAAAUGCAGCGCAGGUUUCUGCGGAGGUGGAAAUUCCAGAGGAAAUAAUUCCGAAGGAGGUAAACCGACUGGAUGCAAUUCCGGUGGAUGUAAUUCCAGAGGAAUUAAUUCCCGAGCAGG
....(((..(((((....)))))....(((.....)))(.((((.(((((((...((((.((..((.((((((......))))))))...)).))))...))))))).)))))..))).. ( -40.50)
>consensus
UAAUUCCAGAGCAGCUUUCUCCGGAAGUGGUAAUUCGACAGGAAAUAAUUCCGAAGGAGGUAAAUCGACUGGACGCAAGUCCAUUGGUAGUAAAUCCAGAGGAACUUAUUCCCGAGCAGG
..................(((.((((..(((..(((....((((....))))...(((..((..((((.(((((....)))))))))...))..))).)))..)))..)))).))).... (-22.68 = -23.04 +   0.36)

alignment

secondary structure

dotplot

Window 8

Location	16,670,529 – 16,670,649
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.58
Mean single sequence MFE	-34.71
Consensus MFE	-23.21
Energy contribution	-24.81
Covariance contribution	1.60
Combinations/Pair	1.11
Mean z-score	-2.83
Structure conservation index	0.67
SVM decision value	1.04
SVM RNA-class probability	0.904861
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16670529 120 - 23771897
CUUGCUCGGAAAUAAGUUCCUCUGGAUUUACUACCAAUGGACUUGCGUCCAGUCGAUGUACCUCCUUCGGAAUUAUUUCCUGCCGAAUAACCACUUCCGGAGAAAGCUGCUCUGGAAUUA
...((..((((((((.((((...(((..(((......(((((....)))))......)))..)))...)))))))))))).))...........((((((((.......))))))))... ( -37.30)
>DroSec_CAF1 38145 120 - 1
CCUGCUCGGGAAUAAGUUCCUCUGGAUUUACUACCAAUGGACUUGCGUCCAGUCGAUGUACCUCCUUCGGAAAUAUUUCCUGUCGAAUUACCACUUCCGGAGAAAACUGCUCUGGAAUUA
......((((((....((((...(((..(((......(((((....)))))......)))..)))...))))....))))))............((((((((.......))))))))... ( -35.60)
>DroSim_CAF1 38223 120 - 1
CCUGCUCGGGAAUAGGUUCCUCUGGAUUUACUACCAAUGGACUUGCGUCCAGUCGAUUUACCUCCUUCGGAAAUAUUUCCUGUCGAAUUACCACUUCCGGAGAAAGCUGCUCUGGAAUUA
.......(((((((..((((...(((...........(((((....)))))...........)))...)))).)))))))..............((((((((.......))))))))... ( -32.35)
>DroEre_CAF1 38233 120 - 1
CCUGUCCGGGAAUUAGUUCCUUUGGAAUUACUUCCACCGGAAUUGCAUCCAGUUGAUUUACCUCCUUCGGAAUUAUUUCCUCUUGAAAUACCGCCUCCGCAGAAACCUGCUCUGGAUUUA
...(((((((((.(((((((...(((..((..((.((.(((......))).)).))..))..)))...))))))).))))).................((((....))))...))))... ( -32.00)
>DroYak_CAF1 39420 120 - 1
CCUGCUCGGGAAUUAAUUCCUCUGGAAUUACAUCCACCGGAAUUGCAUCCAGUCGGUUUACCUCCUUCGGAAUUAUUUCCUCUGGAAUUUCCACCUCCGCAGAAACCUGCGCUGCAUUUA
..(((..(((((((((((((..((((......))))..)))))))..(((((..((....))......((((....)))).))))))))))).....(((((....)))))..))).... ( -36.30)
>consensus
CCUGCUCGGGAAUAAGUUCCUCUGGAUUUACUACCAAUGGACUUGCGUCCAGUCGAUUUACCUCCUUCGGAAUUAUUUCCUGUCGAAUUACCACUUCCGGAGAAACCUGCUCUGGAAUUA
.......((((((.((((((...(((...........(((((....)))))...........)))...))))))))))))...............(((((((.......))))))).... (-23.21 = -24.81 +   1.60)

alignment

secondary structure

dotplot

Window 9

Location	16,670,569 – 16,670,668
Length	99
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.24
Mean single sequence MFE	-36.02
Consensus MFE	-20.33
Energy contribution	-20.65
Covariance contribution	0.32
Combinations/Pair	1.17
Mean z-score	-3.00
Structure conservation index	0.56
SVM decision value	2.66
SVM RNA-class probability	0.996177
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16670569 99 + 23771897
GGAAAUAAUUCCGAAGGAGGUACAUCGACUGGACGCAAGUCCAUUGGUAGUAAAUCCAGAGGAACUUAUUUCCGAGCAAGUUAUA---------------------CCGGUGCUGGUAGU
((((((((((((...(((..((((((((.(((((....)))))))))).)))..)))...)))).))))))))..........((---------------------(((....))))).. ( -39.50)
>DroSec_CAF1 38185 99 + 1
GGAAAUAUUUCCGAAGGAGGUACAUCGACUGGACGCAAGUCCAUUGGUAGUAAAUCCAGAGGAACUUAUUCCCGAGCAGGUUAUA---------------------CCGGUGCUGGCAGU
((((....((((...(((..((((((((.(((((....)))))))))).)))..)))...))))....))))(.((((((.....---------------------))..)))).).... ( -34.70)
>DroSim_CAF1 38263 99 + 1
GGAAAUAUUUCCGAAGGAGGUAAAUCGACUGGACGCAAGUCCAUUGGUAGUAAAUCCAGAGGAACCUAUUCCCGAGCAGGUUAUA---------------------CCGGUGCUGGCAGU
((((....((((...(((..((.(((((.(((((....))))))))))..))..)))...))))....))))(.((((((.....---------------------))..)))).).... ( -31.10)
>DroEre_CAF1 38273 120 + 1
GGAAAUAAUUCCGAAGGAGGUAAAUCAACUGGAUGCAAUUCCGGUGGAAGUAAUUCCAAAGGAACUAAUUCCCGGACAGGUUAUACCGGUGGAUGUAAUGGUAAUGCCGGUGCUGGUAGU
((((.((.((((...((((.((..((.((((((......)))))).))..)).))))...)))).)).))))(((((.(((..(((((..........)))))..))).)).)))..... ( -34.80)
>DroYak_CAF1 39460 120 + 1
GGAAAUAAUUCCGAAGGAGGUAAACCGACUGGAUGCAAUUCCGGUGGAUGUAAUUCCAGAGGAAUUAAUUCCCGAGCAGGUAAAACCGGUGGAGGUAAUGGUAAUACCGGUGCUGGUAGU
((((.(((((((...((((.((..((.((((((......))))))))...)).))))...))))))).))))............(((((((..((((.......))))..)))))))... ( -40.00)
>consensus
GGAAAUAAUUCCGAAGGAGGUAAAUCGACUGGACGCAAGUCCAUUGGUAGUAAAUCCAGAGGAACUUAUUCCCGAGCAGGUUAUA_____________________CCGGUGCUGGUAGU
((((....((((...(((..((..((((.(((((....)))))))))...))..)))...))))....))))(.((((((..........................))..)))).).... (-20.33 = -20.65 +   0.32)

alignment

secondary structure

dotplot

Window 0

Location	16,670,569 – 16,670,668
Length	99
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.24
Mean single sequence MFE	-28.05
Consensus MFE	-16.69
Energy contribution	-17.49
Covariance contribution	0.80
Combinations/Pair	1.15
Mean z-score	-2.51
Structure conservation index	0.60
SVM decision value	1.82
SVM RNA-class probability	0.978686
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16670569 99 - 23771897
ACUACCAGCACCGG---------------------UAUAACUUGCUCGGAAAUAAGUUCCUCUGGAUUUACUACCAAUGGACUUGCGUCCAGUCGAUGUACCUCCUUCGGAAUUAUUUCC
..((((......))---------------------))..........((((((((.((((...(((..(((......(((((....)))))......)))..)))...)))))))))))) ( -28.00)
>DroSec_CAF1 38185 99 - 1
ACUGCCAGCACCGG---------------------UAUAACCUGCUCGGGAAUAAGUUCCUCUGGAUUUACUACCAAUGGACUUGCGUCCAGUCGAUGUACCUCCUUCGGAAAUAUUUCC
......((((..((---------------------.....)))))).(((((((..((((...(((..(((......(((((....)))))......)))..)))...)))).))))))) ( -26.90)
>DroSim_CAF1 38263 99 - 1
ACUGCCAGCACCGG---------------------UAUAACCUGCUCGGGAAUAGGUUCCUCUGGAUUUACUACCAAUGGACUUGCGUCCAGUCGAUUUACCUCCUUCGGAAAUAUUUCC
......((((..((---------------------.....)))))).(((((((..((((...(((...........(((((....)))))...........)))...)))).))))))) ( -24.75)
>DroEre_CAF1 38273 120 - 1
ACUACCAGCACCGGCAUUACCAUUACAUCCACCGGUAUAACCUGUCCGGGAAUUAGUUCCUUUGGAAUUACUUCCACCGGAAUUGCAUCCAGUUGAUUUACCUCCUUCGGAAUUAUUUCC
..........((((((.((((............)))).....)).))))(((.(((((((...(((..((..((.((.(((......))).)).))..))..)))...))))))).))). ( -27.90)
>DroYak_CAF1 39460 120 - 1
ACUACCAGCACCGGUAUUACCAUUACCUCCACCGGUUUUACCUGCUCGGGAAUUAAUUCCUCUGGAAUUACAUCCACCGGAAUUGCAUCCAGUCGGUUUACCUCCUUCGGAAUUAUUUCC
....((((((..((((..(((............)))..)))))))).))(((.(((((((...(((..((.(((.((.(((......))).)).))).))..)))...))))))).))). ( -32.70)
>consensus
ACUACCAGCACCGG_____________________UAUAACCUGCUCGGGAAUAAGUUCCUCUGGAUUUACUACCAAUGGACUUGCGUCCAGUCGAUUUACCUCCUUCGGAAUUAUUUCC
...............................................((((((.((((((...(((...........(((((....)))))...........)))...)))))))))))) (-16.69 = -17.49 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:02 2006