Locus 5239

Sequence ID	3R_DroMel_CAF1
Location	13,692,597 – 13,692,797
Length	200
Max. P	0.999892

overview

Window 6

Location	13,692,597 – 13,692,717
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.50
Mean single sequence MFE	-42.48
Consensus MFE	-40.64
Energy contribution	-40.88
Covariance contribution	0.24
Combinations/Pair	1.02
Mean z-score	-1.10
Structure conservation index	0.96
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13692597 120 + 27905053
UUGCAGCUCUUGUCGGUGUGACACACCUGCUGCUAUGGAUUGUCAUCUGGCUCUGCCUGACCAUCAAGCGGCGCUGGCACUUUAAGCUGCCUCCAUUGGACAGCACUUACGGUGGACUGC
..((((((..((((((((.....)))).((((((...(((.((((...(((...))))))).))).))))))...)))).....)))))).(((((((...........))))))).... ( -42.60)
>DroSec_CAF1 2498 120 + 1
UUGCAGCUCUGGUCGGAGUGACACACCUGCUGCUAUGGAUUGUCAUCUGGCUCUGCCUGACCAUCAAGCGGCGCUGGCACUUUAAGCUGCCUCCAUUGGACAGCACUUACGGCGGACUAC
....((.((((.((((((((...((.(.((((((...(((.((((...(((...))))))).))).))))))).)).)))))...((((((......)).)))).....))))))))).. ( -39.00)
>DroSim_CAF1 2513 120 + 1
UUGCAGCUCUUGUCGGAGUGACACACCUGCUGCUAUGGAUUGUCAUCUGGCUCUGCCUGACCAUCAAGCGGCGCUGGCACUUUAAGCUGCCUCCAUUGGACAGCACUUACGGCGGACUGC
..((((.(((.(((((((((...((.(.((((((...(((.((((...(((...))))))).))).))))))).)).)))))...((((((......)).)))).....))))))))))) ( -44.00)
>DroEre_CAF1 2519 120 + 1
UUGCAGCUCUUGUCGGAGUGACACACCUGCUGCUAUGGAUUGUCAUCUGGCUCUGCCUGACCAUCAAGCGGCGCUGGCACUUUAAGCUGCCCCCGCUGGACAGCACUUACGGCGGACUGC
..((((.(((.(((((((((...((.(.((((((...(((.((((...(((...))))))).))).))))))).)).)))))...((((((......)).)))).....))))))))))) ( -42.80)
>DroYak_CAF1 2561 120 + 1
UUGCAGCUCUUGUCGGAGUGACACACCUGCUGCUAUGGAUUGUCAUCUGGCUCUGCCUGACCAUCAAGCGGCGCUGGCACUUUAAGCUGCCUCCACUGGACAGCACUUACGGCGGACUGC
..((((.(((.(((((((((...((.(.((((((...(((.((((...(((...))))))).))).))))))).)).)))))...((((((......)).)))).....))))))))))) ( -44.00)
>consensus
UUGCAGCUCUUGUCGGAGUGACACACCUGCUGCUAUGGAUUGUCAUCUGGCUCUGCCUGACCAUCAAGCGGCGCUGGCACUUUAAGCUGCCUCCAUUGGACAGCACUUACGGCGGACUGC
..((((.(((.(((((((((...((.(.((((((...(((.((((...(((...))))))).))).))))))).)).)))))...((((((......)).)))).....))))))))))) (-40.64 = -40.88 +   0.24)

alignment

secondary structure

dotplot

Window 7

Location	13,692,637 – 13,692,757
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.92
Mean single sequence MFE	-49.36
Consensus MFE	-47.62
Energy contribution	-46.94
Covariance contribution	-0.68
Combinations/Pair	1.13
Mean z-score	-1.94
Structure conservation index	0.96
SVM decision value	2.99
SVM RNA-class probability	0.998031
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13692637 120 + 27905053
UGUCAUCUGGCUCUGCCUGACCAUCAAGCGGCGCUGGCACUUUAAGCUGCCUCCAUUGGACAGCACUUACGGUGGACUGCUGGGAAAGUCCAGUGCCCAGCCGCUCCUGAUGUCCAGUGG
.(((....)))....((((..(((((((((((...(((((.....((((((......)).))))........((((((........)))))))))))..))))))..)))))..))).). ( -49.10)
>DroSec_CAF1 2538 120 + 1
UGUCAUCUGGCUCUGCCUGACCAUCAAGCGGCGCUGGCACUUUAAGCUGCCUCCAUUGGACAGCACUUACGGCGGACUACUGGGAAAGUCCAGUGCCCAGCCGCUCCUGAUGUCCAGUGG
.(((....)))....((((..(((((((((((...((((((....((((((......)).)))).........(((((........)))))))))))..))))))..)))))..))).). ( -48.20)
>DroSim_CAF1 2553 120 + 1
UGUCAUCUGGCUCUGCCUGACCAUCAAGCGGCGCUGGCACUUUAAGCUGCCUCCAUUGGACAGCACUUACGGCGGACUGCUGGGAAAGUCCAGUGCCCAGCCGCUCCUGAUGUCCAGUGG
.(((....)))....((((..(((((((((((...((((((....((((((......)).)))).........(((((........)))))))))))..))))))..)))))..))).). ( -49.10)
>DroEre_CAF1 2559 120 + 1
UGUCAUCUGGCUCUGCCUGACCAUCAAGCGGCGCUGGCACUUUAAGCUGCCCCCGCUGGACAGCACUUACGGCGGACUGCUGGGCAAGUCCAGCGCCCAGCCGCUCCUGAUGUCCAGUGG
........(((.((((.((.....)).)))).)))((((........)))).((((((((((.((....((((((..(((((((....))))))).)).))))....)).)))))))))) ( -51.90)
>DroYak_CAF1 2601 120 + 1
UGUCAUCUGGCUCUGCCUGACCAUCAAGCGGCGCUGGCACUUUAAGCUGCCUCCACUGGACAGCACUUACGGCGGACUGCUGGGGAAGUCAAGUGCCCAGCCGCUCCUGAUGUCCAGUGG
.(((....)))....((((..(((((((((((...(((((((...((((((......)).))))((((.((((.....))))...)))).)))))))..))))))..)))))..))).). ( -48.50)
>consensus
UGUCAUCUGGCUCUGCCUGACCAUCAAGCGGCGCUGGCACUUUAAGCUGCCUCCAUUGGACAGCACUUACGGCGGACUGCUGGGAAAGUCCAGUGCCCAGCCGCUCCUGAUGUCCAGUGG
........(((.((((.((.....)).)))).)))((((........)))).((((((((((.((....((((((.(.((((((....))))))).)).))))....)).)))))))))) (-47.62 = -46.94 +  -0.68)

alignment

secondary structure

dotplot

Window 8

Location	13,692,637 – 13,692,757
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.92
Mean single sequence MFE	-50.08
Consensus MFE	-47.08
Energy contribution	-47.12
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.76
Structure conservation index	0.94
SVM decision value	2.21
SVM RNA-class probability	0.990399
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13692637 120 - 27905053
CCACUGGACAUCAGGAGCGGCUGGGCACUGGACUUUCCCAGCAGUCCACCGUAAGUGCUGUCCAAUGGAGGCAGCUUAAAGUGCCAGCGCCGCUUGAUGGUCAGGCAGAGCCAGAUGACA
...(((..(((((..((((((..(((((((((((........))))).........(((((((....).))))))....))))))...)))))))))))..)))................ ( -48.10)
>DroSec_CAF1 2538 120 - 1
CCACUGGACAUCAGGAGCGGCUGGGCACUGGACUUUCCCAGUAGUCCGCCGUAAGUGCUGUCCAAUGGAGGCAGCUUAAAGUGCCAGCGCCGCUUGAUGGUCAGGCAGAGCCAGAUGACA
(((.((((((.((...(((((.(((((((((......))))).)))))))))...)).)))))).))).(((........(((....))).(((((.....)))))...)))........ ( -50.40)
>DroSim_CAF1 2553 120 - 1
CCACUGGACAUCAGGAGCGGCUGGGCACUGGACUUUCCCAGCAGUCCGCCGUAAGUGCUGUCCAAUGGAGGCAGCUUAAAGUGCCAGCGCCGCUUGAUGGUCAGGCAGAGCCAGAUGACA
...(((..(((((..((((((..(((((((((((........))))).........(((((((....).))))))....))))))...)))))))))))..)))................ ( -48.10)
>DroEre_CAF1 2559 120 - 1
CCACUGGACAUCAGGAGCGGCUGGGCGCUGGACUUGCCCAGCAGUCCGCCGUAAGUGCUGUCCAGCGGGGGCAGCUUAAAGUGCCAGCGCCGCUUGAUGGUCAGGCAGAGCCAGAUGACA
((.(((((((.((...(((((.(((((((((......))))).)))))))))...)).))))))).)).(((........(((....))).(((((.....)))))...)))........ ( -54.00)
>DroYak_CAF1 2601 120 - 1
CCACUGGACAUCAGGAGCGGCUGGGCACUUGACUUCCCCAGCAGUCCGCCGUAAGUGCUGUCCAGUGGAGGCAGCUUAAAGUGCCAGCGCCGCUUGAUGGUCAGGCAGAGCCAGAUGACA
((((((((((...(((...((((((...........))))))..)))(((....).)))))))))))).(((........(((....))).(((((.....)))))...)))........ ( -49.80)
>consensus
CCACUGGACAUCAGGAGCGGCUGGGCACUGGACUUUCCCAGCAGUCCGCCGUAAGUGCUGUCCAAUGGAGGCAGCUUAAAGUGCCAGCGCCGCUUGAUGGUCAGGCAGAGCCAGAUGACA
...(((..(((((..((((((..(((((((((((........))))).........((((((.......))))))....))))))...)))))))))))..)))................ (-47.08 = -47.12 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	13,692,677 – 13,692,797
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.25
Mean single sequence MFE	-52.88
Consensus MFE	-52.50
Energy contribution	-51.82
Covariance contribution	-0.68
Combinations/Pair	1.13
Mean z-score	-2.33
Structure conservation index	0.99
SVM decision value	4.41
SVM RNA-class probability	0.999892
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13692677 120 + 27905053
UUUAAGCUGCCUCCAUUGGACAGCACUUACGGUGGACUGCUGGGAAAGUCCAGUGCCCAGCCGCUCCUGAUGUCCAGUGGCCAGCGUACGGGGAGCAACUCGAGCAGCAGUGGCUGCAAC
.....((((...((((((((((.((....((((((.(.((((((....))))))).))).)))....)).)))))))))).))))...((((......)))).(((((....)))))... ( -50.50)
>DroSec_CAF1 2578 120 + 1
UUUAAGCUGCCUCCAUUGGACAGCACUUACGGCGGACUACUGGGAAAGUCCAGUGCCCAGCCGCUCCUGAUGUCCAGUGGCCAGCGCACGGGGAGCAACUCGAGCAGCAGUGGCUGCAAC
.....((((...((((((((((.((....((((((..(((((((....))))))).)).))))....)).)))))))))).))))...((((......)))).(((((....)))))... ( -52.50)
>DroSim_CAF1 2593 120 + 1
UUUAAGCUGCCUCCAUUGGACAGCACUUACGGCGGACUGCUGGGAAAGUCCAGUGCCCAGCCGCUCCUGAUGUCCAGUGGCCAGCGCACGGGGAGCAACUCGAGCAGCAGUGGCUGCAAC
.....((((...((((((((((.((....((((((.(.((((((....))))))).)).))))....)).)))))))))).))))...((((......)))).(((((....)))))... ( -52.00)
>DroEre_CAF1 2599 120 + 1
UUUAAGCUGCCCCCGCUGGACAGCACUUACGGCGGACUGCUGGGCAAGUCCAGCGCCCAGCCGCUCCUGAUGUCCAGUGGCCAGCGCACGGGAAGCAACUCGAGCAGCAGUGGCUGCAAC
.....((((...((((((((((.((....((((((..(((((((....))))))).)).))))....)).)))))))))).))))...((((......)))).(((((....)))))... ( -55.90)
>DroYak_CAF1 2641 120 + 1
UUUAAGCUGCCUCCACUGGACAGCACUUACGGCGGACUGCUGGGGAAGUCAAGUGCCCAGCCGCUCCUGAUGUCCAGUGGCCAGCGCACGGGGAGCAACUCGAGCAGCAGUGGCUGCAAC
.....((((...((((((((((((.......))((((.((((((.(.......).)))))).).)))...)))))))))).))))...((((......)))).(((((....)))))... ( -53.50)
>consensus
UUUAAGCUGCCUCCAUUGGACAGCACUUACGGCGGACUGCUGGGAAAGUCCAGUGCCCAGCCGCUCCUGAUGUCCAGUGGCCAGCGCACGGGGAGCAACUCGAGCAGCAGUGGCUGCAAC
.....((((...((((((((((.((....((((((.(.((((((....))))))).)).))))....)).)))))))))).))))...((((......)))).(((((....)))))... (-52.50 = -51.82 +  -0.68)

alignment

secondary structure

dotplot

Window 0

Location	13,692,677 – 13,692,797
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.25
Mean single sequence MFE	-54.16
Consensus MFE	-48.08
Energy contribution	-48.68
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.26
Structure conservation index	0.89
SVM decision value	2.84
SVM RNA-class probability	0.997343
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13692677 120 - 27905053
GUUGCAGCCACUGCUGCUCGAGUUGCUCCCCGUACGCUGGCCACUGGACAUCAGGAGCGGCUGGGCACUGGACUUUCCCAGCAGUCCACCGUAAGUGCUGUCCAAUGGAGGCAGCUUAAA
...(((((....)))))..((((((((.((.(....).))(((.((((((.((...((((.(((((.((((......))))..)))))))))...)).)))))).))).))))))))... ( -49.70)
>DroSec_CAF1 2578 120 - 1
GUUGCAGCCACUGCUGCUCGAGUUGCUCCCCGUGCGCUGGCCACUGGACAUCAGGAGCGGCUGGGCACUGGACUUUCCCAGUAGUCCGCCGUAAGUGCUGUCCAAUGGAGGCAGCUUAAA
...(((((....)))))..(((((((..((.(((.(....))))((((((.((...(((((.(((((((((......))))).)))))))))...)).))))))..))..)))))))... ( -54.80)
>DroSim_CAF1 2593 120 - 1
GUUGCAGCCACUGCUGCUCGAGUUGCUCCCCGUGCGCUGGCCACUGGACAUCAGGAGCGGCUGGGCACUGGACUUUCCCAGCAGUCCGCCGUAAGUGCUGUCCAAUGGAGGCAGCUUAAA
...(((((....)))))..(((((((..((.(((.(....))))((((((.((...(((((.((((.((((......))))..)))))))))...)).))))))..))..)))))))... ( -52.20)
>DroEre_CAF1 2599 120 - 1
GUUGCAGCCACUGCUGCUCGAGUUGCUUCCCGUGCGCUGGCCACUGGACAUCAGGAGCGGCUGGGCGCUGGACUUGCCCAGCAGUCCGCCGUAAGUGCUGUCCAGCGGGGGCAGCUUAAA
...(((((....)))))..((((((((.((((.((....))..(((((((.((...(((((.(((((((((......))))).)))))))))...)).)))))))))))))))))))... ( -60.90)
>DroYak_CAF1 2641 120 - 1
GUUGCAGCCACUGCUGCUCGAGUUGCUCCCCGUGCGCUGGCCACUGGACAUCAGGAGCGGCUGGGCACUUGACUUCCCCAGCAGUCCGCCGUAAGUGCUGUCCAGUGGAGGCAGCUUAAA
...(((((....)))))..((((((((.((.(....).))((((((((((...(((...((((((...........))))))..)))(((....).)))))))))))).))))))))... ( -53.20)
>consensus
GUUGCAGCCACUGCUGCUCGAGUUGCUCCCCGUGCGCUGGCCACUGGACAUCAGGAGCGGCUGGGCACUGGACUUUCCCAGCAGUCCGCCGUAAGUGCUGUCCAAUGGAGGCAGCUUAAA
...(((((....)))))..(((((((..((.(((.(....))))((((((.((...(((((.((((.((((......))))..)))))))))...)).))))))..))..)))))))... (-48.08 = -48.68 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:55 2006