Locus 4431

Sequence ID	3R_DroMel_CAF1
Location	11,700,410 – 11,700,500
Length	90
Max. P	0.981357

overview

Window 9

Location	11,700,410 – 11,700,500
Length	90
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	66.71
Mean single sequence MFE	-35.77
Consensus MFE	-8.93
Energy contribution	-10.90
Covariance contribution	1.97
Combinations/Pair	1.12
Mean z-score	-2.97
Structure conservation index	0.25
SVM decision value	1.89
SVM RNA-class probability	0.981357
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11700410 90 + 27905053
CUGUCGAGUUAAC-----------------UUCCCUGCCCCAAAAGGGGGGUGAGGUGGGCAUAUCCCCUUGGGAUAUGUUCACUCGCAUCGAUAGCUUAAACAAUU
(((((((((..((-----------------((((((........))))))))(((.((((((((((((...))))))))))))))))).)))))))........... ( -39.60)
>DroSec_CAF1 36496 107 + 1
CUGCCGAGUUAACCGGGUGAGGGGAACGGCUCCCCUGCCCCAAAAAAGGGGAGGUGGGUGCACAACACCUUGGGAUAUGUUCACUCGCAUCGAUAGCUUAAACCAUU
.....((((((..((((((((..(((((..((((((.((((......))))))..(((((.....))))).))))..))))).))))).))).))))))........ ( -38.70)
>DroSim_CAF1 39319 103 + 1
CUGCCGAGUUAACCGGGUGAGGGGAACGGCUCCACUGCCCCAA---AGGGGGGGUG-UUGCAUCUCCCCUUGGGAUAUGUUCACUCGCAUCGAUAGCUUAAACCAUU
.....((((((..((((((((..(((((((......)))((.(---((((((((((-...))))))))))).))....)))).))))).))).))))))........ ( -41.90)
>DroEre_CAF1 37437 89 + 1
CCGCCGAGUUAUCCGG------GGGAUGGCUCCCCUGCCCCAAA---GGGG---------UCCAUCCCCUUGGGAUAUGUUCACUCGCAUCGGCAGCUUAAACCAUU
..(((((..(((((((------(((((((..(((((.......)---))))---------.)))))))))..)))))(((......))))))))............. ( -41.40)
>DroYak_CAF1 37317 89 + 1
CCGCCGAGUUAUCCGG------GGAACUGCUCCCCCACCCCAAA---GGGG---------UCCAUCCCCUUGGGAUGUGUUCACUCGCAUCGGUAGCUUACCCCAUU
.....((((((((.((------(((.....)))))....((((.---((((---------.....))))))))((((((......))))))))))))))........ ( -34.90)
>DroAna_CAF1 37750 73 + 1
CUGCCGGGAGAU-----------------CUACCCUGCCCUCAG---G--------------CCACCCCUUGGGGAGUGCCCCAACUCAUCGAUAGUUUUAAACAUU
(((.((((((..-----------------....((((....)))---)--------------.......((((((....))))))))).))).)))........... ( -18.10)
>consensus
CUGCCGAGUUAACCGG______GGAACGGCUCCCCUGCCCCAAA___GGGG_________CACAUCCCCUUGGGAUAUGUUCACUCGCAUCGAUAGCUUAAACCAUU
..(.(((((............................((((......))))...........((((((...)))))).....))))))................... ( -8.93 = -10.90 +   1.97)

alignment

secondary structure

dotplot

Window 0

Location	11,700,410 – 11,700,500
Length	90
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	66.71
Mean single sequence MFE	-33.44
Consensus MFE	-12.26
Energy contribution	-12.93
Covariance contribution	0.67
Combinations/Pair	1.29
Mean z-score	-1.73
Structure conservation index	0.37
SVM decision value	0.16
SVM RNA-class probability	0.613906
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11700410 90 - 27905053
AAUUGUUUAAGCUAUCGAUGCGAGUGAACAUAUCCCAAGGGGAUAUGCCCACCUCACCCCCCUUUUGGGGCAGGGAA-----------------GUUAACUCGACAG
...((((...((.......))((((.((((((((((...))))))).....(((..((((......))))..)))..-----------------))).)))))))). ( -28.40)
>DroSec_CAF1 36496 107 - 1
AAUGGUUUAAGCUAUCGAUGCGAGUGAACAUAUCCCAAGGUGUUGUGCACCCACCUCCCCUUUUUUGGGGCAGGGGAGCCGUUCCCCUCACCCGGUUAACUCGGCAG
.(((((....)))))...(((((((((((...((((..((((.....))))...((((((......)))).))))))...)))).((......))...)))).))). ( -33.90)
>DroSim_CAF1 39319 103 - 1
AAUGGUUUAAGCUAUCGAUGCGAGUGAACAUAUCCCAAGGGGAGAUGCAA-CACCCCCCCU---UUGGGGCAGUGGAGCCGUUCCCCUCACCCGGUUAACUCGGCAG
.(((((....)))))...(((((((.(((........(((((((..((..-(((..((((.---..))))..)))..))..)))))))......))).)))).))). ( -35.34)
>DroEre_CAF1 37437 89 - 1
AAUGGUUUAAGCUGCCGAUGCGAGUGAACAUAUCCCAAGGGGAUGGA---------CCCC---UUUGGGGCAGGGGAGCCAUCCC------CCGGAUAACUCGGCGG
...........(((((((.....(....).(((((...((((((((.---------((((---(.......)))))..)))))))------).)))))..))))))) ( -39.90)
>DroYak_CAF1 37317 89 - 1
AAUGGGGUAAGCUACCGAUGCGAGUGAACACAUCCCAAGGGGAUGGA---------CCCC---UUUGGGGUGGGGGAGCAGUUCC------CCGGAUAACUCGGCGG
..............(((...(((((...(.((((((((((((.....---------.)))---)))))))))((((((...))))------)))....))))).))) ( -40.10)
>DroAna_CAF1 37750 73 - 1
AAUGUUUAAAACUAUCGAUGAGUUGGGGCACUCCCCAAGGGGUGG--------------C---CUGAGGGCAGGGUAG-----------------AUCUCCCGGCAG
..((((................(..((.((((((....)))))).--------------)---)..)(((.(((....-----------------.)))))))))). ( -23.00)
>consensus
AAUGGUUUAAGCUAUCGAUGCGAGUGAACAUAUCCCAAGGGGAUGUG_________CCCC___UUUGGGGCAGGGGAGCCGUUCC______CCGGAUAACUCGGCAG
..................(((((((.....((((((...))))))...........((((......))))............................))))).)). (-12.26 = -12.93 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:02 2006