Locus 89

Sequence ID	2R_DroMel_CAF1
Location	1,338,505 – 1,338,620
Length	115
Max. P	0.898642

overview

Window 9

Location	1,338,505 – 1,338,620
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.60
Mean single sequence MFE	-39.43
Consensus MFE	-21.84
Energy contribution	-22.96
Covariance contribution	1.12
Combinations/Pair	1.15
Mean z-score	-2.35
Structure conservation index	0.55
SVM decision value	1.00
SVM RNA-class probability	0.898642
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1338505 115 + 20766785
GCUCCCAUUCGGAAUUUCGGGGGGCAACCA-AGCCGCAGCCAAAGUCAAAGGCAUUUGCAAGAUUUGUGUUUGGCCAAAAAGGAACUGGCCGA-GGCAAAGGAUGCUGCGACCCCCG---
..(((.....)))....((((((((.....-.))((((((....(((....((....))....(((((.((((((((.........)))))))-)))))).))))))))).))))))--- ( -40.70)
>DroSec_CAF1 56941 103 + 1
GCUCCCAUUUGG---------GAGCAA-----CCCGCAGCCAAAGUCAAAGGAAUUUGCAAGAUUUGUGUUCGGCCAAAAAGGAACUGGCCGAAGGCAAAGGAUGCUGCGACCCCCG---
((((((....))---------))))..-----..((((((((((.((....)).)))).....(((((.((((((((.........)))))))).)))))....)))))).......--- ( -43.80)
>DroSim_CAF1 35157 102 + 1
GCUCCCAUUCGG---------GAGCAA-----CCCGCAGCCAAAGUCAAAGGCAUUUGCAAGAUUUGAGUUCGGCCAAAAAGGAACUGGCCGA-GCCAAAGGAUGCUGCGACCCCCG---
((((((....))---------))))..-----..((((((....(((....((....))....((((.(((((((((.........)))))))-)))))).))))))))).......--- ( -43.10)
>DroEre_CAF1 38411 119 + 1
ACUUCCCUCCGGGAUCUCGGAGGGCAACCAAAGCCGCAGCCAAAGUCAAAGGCAUUUGCAAGAUUUCUGUUUGGCCAAAAGGGAACUGGCCGA-GAAAGAGGAUGCUGCGACCCCCGGUG
....((((((((....))))))))..(((...(.((((((((((((.....)).)))).....(((((.((((((((...(....))))))))-)..)))))..)))))).)....))). ( -41.30)
>DroYak_CAF1 25556 116 + 1
ACUGAUAUUCGGGAUUUCGGAGGGCAACCAAAGCCGCAGUCAAAGUCAAAGGCAUUUGCAAAAUUUAUGUUUGGUAAAAAAAGAACUGCCCGA-CGAAAAGGAUGCUGCGACCCCCA---
..........(((.(((((..(((((......(((...............))).(((((.((((....)))).)))))........)))))..-))))).((.........))))).--- ( -28.26)
>consensus
GCUCCCAUUCGG_AU_UCGG_GGGCAACCA_AGCCGCAGCCAAAGUCAAAGGCAUUUGCAAGAUUUGUGUUUGGCCAAAAAGGAACUGGCCGA_GGCAAAGGAUGCUGCGACCCCCG___
..........((.........((....)).....((((((....(.((((....)))))....(((((..(((((((.........)))))))..)))))....))))))....)).... (-21.84 = -22.96 +   1.12)

alignment

secondary structure

dotplot

Window 0

Location	1,338,505 – 1,338,620
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.60
Mean single sequence MFE	-39.25
Consensus MFE	-22.10
Energy contribution	-23.18
Covariance contribution	1.08
Combinations/Pair	1.09
Mean z-score	-1.88
Structure conservation index	0.56
SVM decision value	0.10
SVM RNA-class probability	0.581210
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1338505 115 - 20766785
---CGGGGGUCGCAGCAUCCUUUGCC-UCGGCCAGUUCCUUUUUGGCCAAACACAAAUCUUGCAAAUGCCUUUGACUUUGGCUGCGGCU-UGGUUGCCCCCCGAAAUUCCGAAUGGGAGC
---((((((..(((((.......(((-..((((((.......)))))).............(((...(((.........))))))))).-..)))))))))))...((((.....)))). ( -41.70)
>DroSec_CAF1 56941 103 - 1
---CGGGGGUCGCAGCAUCCUUUGCCUUCGGCCAGUUCCUUUUUGGCCGAACACAAAUCUUGCAAAUUCCUUUGACUUUGGCUGCGGG-----UUGCUC---------CCAAAUGGGAGC
---...((.(((((((....((((..(((((((((.......)))))))))..)))).....((((.((....)).))))))))))).-----))((((---------((....)))))) ( -41.60)
>DroSim_CAF1 35157 102 - 1
---CGGGGGUCGCAGCAUCCUUUGGC-UCGGCCAGUUCCUUUUUGGCCGAACUCAAAUCUUGCAAAUGCCUUUGACUUUGGCUGCGGG-----UUGCUC---------CCGAAUGGGAGC
---...((.((((((((...(((((.-((((((((.......)))))))).).))))...)))....(((.........)))))))).-----))((((---------((....)))))) ( -39.90)
>DroEre_CAF1 38411 119 - 1
CACCGGGGGUCGCAGCAUCCUCUUUC-UCGGCCAGUUCCCUUUUGGCCAAACAGAAAUCUUGCAAAUGCCUUUGACUUUGGCUGCGGCUUUGGUUGCCCUCCGAGAUCCCGGAGGGAAGU
.(((((((.(((((((..........-..((((((.......))))))...((((..((..((....))....)).))))))))))))))))))..(((((((......))))))).... ( -46.40)
>DroYak_CAF1 25556 116 - 1
---UGGGGGUCGCAGCAUCCUUUUCG-UCGGGCAGUUCUUUUUUUACCAAACAUAAAUUUUGCAAAUGCCUUUGACUUUGACUGCGGCUUUGGUUGCCCUCCGAAAUCCCGAAUAUCAGU
---.(((((((((((((......(((-..(((((........((((.......)))).........))))).)))...)).)))))))(((((.......))))).)))).......... ( -26.63)
>consensus
___CGGGGGUCGCAGCAUCCUUUGCC_UCGGCCAGUUCCUUUUUGGCCAAACACAAAUCUUGCAAAUGCCUUUGACUUUGGCUGCGGCU_UGGUUGCCC_CCGA_AU_CCGAAUGGGAGC
....((((((((((((.............((((((.......))))))..............((((....))))......)))))).........))))))................... (-22.10 = -23.18 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:26:28 2006