Locus 1627

Sequence ID	2R_DroMel_CAF1
Location	6,095,681 – 6,095,805
Length	124
Max. P	0.743042

overview

Window 3

Location	6,095,681 – 6,095,784
Length	103
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	81.77
Mean single sequence MFE	-18.78
Consensus MFE	-8.52
Energy contribution	-8.92
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.45
Structure conservation index	0.45
SVM decision value	0.45
SVM RNA-class probability	0.743042
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6095681 103 + 20766785
AAGAAGUGCAGCAAAAGCAAAUGUACUGAAAGC------GAGGAAUACAUUCUUCUUCUUCAAAAAAAAAUACCAUCAAAAAGAAAGUAAGAAA-----AAGUU-U-UUUCUGCAA
......(((((.((((((........((((...------((((((....))))))...))))........(((..((.....))..))).....-----..)))-)-)).))))). ( -18.90)
>DroSec_CAF1 113455 101 + 1
AAGAAGUGCAGCCAAAGCAAAUGUACUGAAAGCAAGAAGGAGGAAUACGUUCUUCU------GAAA-AAAUACCAUCAA-AAGAAAGUAAGAAA-----AAGUU-U-UUACUGCCA
....((((((((....))...))))))....((.(((((((.(....).)))))))------....-............-.....((((((((.-----...))-)-))))))).. ( -18.80)
>DroSim_CAF1 118091 103 + 1
AAGAAGUGCAGCCAAAGCAAAUGUACUGAAAGGAAGACGAAGGAAUACGUUCUUCU------GAAAAAAAUACCAUCAA-AAGAAAGUAAGAAA-----AAGUU-UUUUGCUGCAA
......((((((.(((((.............((((((((........)).))))))------........(((..((..-..))..))).....-----..)))-))..)))))). ( -20.00)
>DroEre_CAF1 117306 109 + 1
AAGAAGUGCAGCAAAAGCAAAUGUACUGAAAGCAACACGGAGGAAUACAUUCUUCU------GAAAGAAAUACCAGCAU-AAGAAAUCAAGAAAGAGAAAAGUUAUUUUCGUACAA
......(((.......)))..(((((.(((((.(((.((((((((....)))))))------)................-......((......)).....))).)))))))))). ( -19.40)
>DroYak_CAF1 115326 101 + 1
AAGAAGUGCAGCAAAAGCAAAUGUACUGAAAGCAAGAAUGAUGAAUGCGUUCUUCU------GAAA-AAAUACCAUCAC-AAGAAA---AGAAAGA---AAGUU-UUUUCGCAUAA
....((((((((....))...))))))....((.....(((((......(((....------))).-......))))).-..((((---(((....---...))-))))))).... ( -16.82)
>consensus
AAGAAGUGCAGCAAAAGCAAAUGUACUGAAAGCAAGAAGGAGGAAUACGUUCUUCU______GAAA_AAAUACCAUCAA_AAGAAAGUAAGAAA_____AAGUU_UUUUCCUGCAA
....((((((((....))...))))))............((((((....))))))............................................................. ( -8.52 =  -8.92 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	6,095,714 – 6,095,805
Length	91
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	78.39
Mean single sequence MFE	-11.96
Consensus MFE	-0.08
Energy contribution	-0.04
Covariance contribution	-0.04
Combinations/Pair	1.50
Mean z-score	-1.45
Structure conservation index	0.01
SVM decision value	0.16
SVM RNA-class probability	0.612514
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6095714 91 - 20766785
UCUUUUUUUACUUAAGCUCUCUUGCAGAAA-A-AACUU-----UUUCUUACUUUCUUUUUGAUGGUAUUUUUUUUUGAAGAAGAAGAAUGUAUUCCUC---
(((((((((......((......))(((((-(-....)-----)))))((((.((.....)).))))...........)))))))))...........--- ( -12.60)
>DroSec_CAF1 113491 84 - 1
UU--UUUUUCCUUAAGCUUUCUGGCAGUAA-A-AACUU-----UUUCUUACUUUCUU-UUGAUGGUAUUU-UUUC------AGAAGAACGUAUUCCUCCUU
..--...........(((....))).....-.-.....-----.....(((.(((((-((((..(....)-..))------))))))).)))......... ( -12.80)
>DroSim_CAF1 118127 87 - 1
UCU-UUUUUACUUAAGCUUGCUUGCAGCAAAA-AACUU-----UUUCUUACUUUCUU-UUGAUGGUAUUUUUUUC------AGAAGAACGUAUUCCUUCGU
..(-(((((.((((((....)))).)).))))-))...-----.....(((.(((((-((((..(.....)..))------))))))).)))......... ( -14.10)
>DroEre_CAF1 117342 93 - 1
UCU-UUUUUACUUAAGCUUUCUUGUACGAAAAUAACUUUUCUCUUUCUUGAUUUCUU-AUGCUGGUAUUUCUUUC------AGAAGAAUGUAUUCCUCCGU
...-...........((.(((((....(((((....)))))................-...((((........))------))))))).)).......... (  -8.00)
>DroYak_CAF1 115362 85 - 1
UCU-UUCUUACUUAAGCUUUCUUAUGCGAAAA-AACUU---UCUUUCU---UUUCUU-GUGAUGGUAUUU-UUUC------AGAAGAACGCAUUCAUCAUU
...-...........((.(((((.((.(((((-.(((.---((.....---......-..)).))).)))-)).)------).))))).)).......... ( -12.32)
>consensus
UCU_UUUUUACUUAAGCUUUCUUGCAGGAAAA_AACUU_____UUUCUUACUUUCUU_UUGAUGGUAUUU_UUUC______AGAAGAACGUAUUCCUCCGU
...............((......))............................................................................ ( -0.08 =  -0.04 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:12 2006