Locus 7777

Sequence ID	2L_DroMel_CAF1
Location	21,925,461 – 21,925,666
Length	205
Max. P	0.541469

overview

Window 1

Location	21,925,461 – 21,925,572
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	85.96
Mean single sequence MFE	-31.60
Consensus MFE	-24.67
Energy contribution	-24.92
Covariance contribution	0.25
Combinations/Pair	1.10
Mean z-score	-1.92
Structure conservation index	0.78
SVM decision value	0.02
SVM RNA-class probability	0.541469
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21925461 111 + 22407834
AAAAAAGAUGCCU---------GGAAGCCAAAGAGACAGCACUGGUAAAUGCACAACACGUGAACCAGGGCCACGUCAGUCAGCAAUAAAUAAAUGCAAGCUGGCAGUCAUUUGGUCGUC
.............---------((..((((((..(((.((.(((((.....(((.....))).))))).))...((((((..(((.........)))..)))))).))).))))))..)) ( -31.00)
>DroSec_CAF1 212992 111 + 1
AAAAAAGAUGCCU---------GGAAGCCAAAGAGACAGCACUGGUAAAUGCACAACACGUGAACCAGGGCCACGUCAGUCAGCAAUAAAUAAAUGCAAGCUGGCAGUCAUUUGGUCGUC
.............---------((..((((((..(((.((.(((((.....(((.....))).))))).))...((((((..(((.........)))..)))))).))).))))))..)) ( -31.00)
>DroSim_CAF1 157327 111 + 1
AAAAAAGAUGCCU---------GGAAGCCAAAGAGACAGCACUGGUAAAUGCACAACACGUGAACCAGGGCCACGUCAGUCAGCAAUAAAUAAAUGCAAGCUGGCAGUCAUUUGGUCGUC
.............---------((..((((((..(((.((.(((((.....(((.....))).))))).))...((((((..(((.........)))..)))))).))).))))))..)) ( -31.00)
>DroEre_CAF1 180031 120 + 1
AAAAAAUAUGCCGGAGCUACGAGGAAGCCAAAGAUACAGCACUGGUAAAUGCACAACAUGUGAACCAGGGCCACGUCAGUCAGCAAUAAAUAAAUGCAAGCUGGCAGUCAUUUGGUCGUC
...........((......)).((..(((((((((...((.(((((.....(((.....))).))))).))...((((((..(((.........)))..)))))).))).))))))..)) ( -30.20)
>DroYak_CAF1 175508 120 + 1
AAAAGCGAUGCCGGGGUUACGCGGAAGCCAAAGAAACAGCACUGGUAAAUGCACAACAUGUGAACCAGGGCCACGUCAGUCAGCAAUAAAUAAAUGCAAGCUGGCAGUCAUUUGGUCGUC
....(((...(((.(....).)))..((((((...((.((.(((((.....(((.....))).))))).))...((((((..(((.........)))..)))))).))..))))))))). ( -34.50)
>DroAna_CAF1 155327 117 + 1
CAA---UUUAAAGCAGCCAUAAAACAGCUAGAAGUACAGCACUUGGAGAGGCCCUACACGUGAGCCAGGGCCACGUCAGUCAGCAAUAAAUAAAUGCAAGCUGGCAGUCAUUUGGUCGUC
...---......((.((((....((..((..((((.....))))..)).((((((...(....)..))))))..((((((..(((.........)))..)))))).))....)))).)). ( -31.90)
>consensus
AAAAAAGAUGCCG_________GGAAGCCAAAGAGACAGCACUGGUAAAUGCACAACACGUGAACCAGGGCCACGUCAGUCAGCAAUAAAUAAAUGCAAGCUGGCAGUCAUUUGGUCGUC
......................((..((((((...((.((.(((((.....(((.....))).))))).))...((((((..(((.........)))..)))))).))..))))))..)) (-24.67 = -24.92 +   0.25)

alignment

secondary structure

dotplot

Window 2

Location	21,925,572 – 21,925,666
Length	94
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	73.96
Mean single sequence MFE	-33.52
Consensus MFE	-12.24
Energy contribution	-12.35
Covariance contribution	0.11
Combinations/Pair	1.22
Mean z-score	-1.99
Structure conservation index	0.37
SVM decision value	-0.04
SVM RNA-class probability	0.513165
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21925572 94 + 22407834
ACACGUCCUGACAGUCCGACGACCGUGG-------AGGAAUG-----GCCACAAAGGGAAGAGUUCUAGCAGGGCUACGGCU-------------GGGAUUCGGGACU-GAGGGAGGGAA
...(.((((..((((((.......((((-------.......-----.))))........((((((((((.(.....).)))-------------))))))).)))))-).)))).)... ( -37.40)
>DroSec_CAF1 213103 94 + 1
ACACGUCCUGACAGUCCGACGACCGUGG-------AGGAAUG-----GCCACAAAGGGAAGAGUUUUAGCAGGGCUACGGCU-------------GGGAUUCGGGACU-GAGGGAGGGAA
...(.((((..((((((.......((((-------.......-----.))))........((((((((((.(.....).)))-------------))))))).)))))-).)))).)... ( -34.80)
>DroSim_CAF1 157438 94 + 1
ACACGUCCUGACAGUCCGACGACCGUGG-------AGGAAUG-----GCCACAAAGGGAAGAGUUUUAGCAGGGCUACGGCU-------------GGGAUUCGGGACU-GAGGAAGGGAA
.(...((((..((((((.......((((-------.......-----.))))........((((((((((.(.....).)))-------------))))))).)))))-)))))...).. ( -31.60)
>DroEre_CAF1 180151 108 + 1
ACACGUCCUGACAGUCGGACGACCGUGU-------AGGAAUG-----GCCACAAAGGGAAGAGUUCCAGCAGGGCUACGGCUGGGAAUGGGAAACGGGAAUCGGGAAUCGGGAAUGGGAA
.(...((((((((((((...(.((.(((-------.(((((.-----.((......))....))))).))).)))..)))))).((.(.(....).)...)).....))))))...)... ( -34.90)
>DroYak_CAF1 175628 88 + 1
ACACGUCCUGACAGUCGGACGACCGUAG-------AGGAAUG-----GUCACAAAGGGAAGAGUUCCAGCAGGGCU-------------------GGGAGUCAGGACU-GGGAAUUGGAA
.((.((((((((........((((((..-------....)))-----))).............(((((((...)))-------------------)))))))))))))-).......... ( -32.50)
>DroAna_CAF1 155444 98 + 1
ACACGGCCAGACAGGCGGACGACUUUCGGGUGGUGGGGCAUGGCGGGGCAAUAAAGUGGAAAGGUCCUGCAGGGCUUCGAAU-------------CAGGAUCAGGA--------UCGGA-
...(.(((.....))).).((((((((.(((..((((((...(((((((..............)))))))...)))))).))-------------)..))..))).--------)))..- ( -29.94)
>consensus
ACACGUCCUGACAGUCCGACGACCGUGG_______AGGAAUG_____GCCACAAAGGGAAGAGUUCCAGCAGGGCUACGGCU_____________GGGAUUCGGGACU_GAGGAAGGGAA
....((((((((.(((....))).))..........(((((.......((......))....)))))..))))))............................................. (-12.24 = -12.35 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:44:41 2006