Locus 7535

Sequence ID	3L_DroMel_CAF1
Location	20,236,708 – 20,236,840
Length	132
Max. P	0.969127

overview

Window 7

Location	20,236,708 – 20,236,800
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	97.50
Mean single sequence MFE	-18.72
Consensus MFE	-17.38
Energy contribution	-17.66
Covariance contribution	0.28
Combinations/Pair	1.04
Mean z-score	-1.32
Structure conservation index	0.93
SVM decision value	0.53
SVM RNA-class probability	0.770457
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20236708 92 + 23771897
UCUGGUAGACACACAUAUAUCGACCAUAUAUAUACUAUAGCCACUAUAUGUAUACCGCGAUGUCCUGUGCAUCCCGUGAAACCUCUUCGCUG
...((.(..((((...((((((...(((((((((..........)))))))))....))))))..))))..).))(((((.....))))).. ( -18.90)
>DroSec_CAF1 6269 92 + 1
UCUGGUAGACACACAUAUAUCGACCAUAUAUAUACUAUAGCCACUAUAUGUAUACCGCGAUGUCCUGUGCAUCCCGUGAAACCUCUUCGCUG
...((.(..((((...((((((...(((((((((..........)))))))))....))))))..))))..).))(((((.....))))).. ( -18.90)
>DroSim_CAF1 7513 92 + 1
UCUGGUAGACACACAUAUAUCGACCAUAUAUAUACUAUAGCCACUAUAUGUAUACCGCGAUGUCCUGUGCAUCCCGUGAAACCUCUUCGCUG
...((.(..((((...((((((...(((((((((..........)))))))))....))))))..))))..).))(((((.....))))).. ( -18.90)
>DroEre_CAF1 7058 89 + 1
UCUGGUAGACA--CAUAUAUCGACCAUAUAUAUACUAUAGCCACUAUAUGUAUACCGCGAUGUCCUGUGCAUUCCGUGAAACCU-UUCGCUG
...((....((--((.((((((...(((((((((..........)))))))))....))))))..))))....))(((((....-))))).. ( -18.80)
>DroYak_CAF1 11577 91 + 1
UCUGGUAGACACGCAUAUAUCGACCAUAUAUAUACUAUAGCCACUAUAUGUAUACCGCGAUGUCCUGUGCAUUCCGUGAAACCU-UUCGCUG
...((....((((...((((((...(((((((((..........)))))))))....))))))..))))....))(((((....-))))).. ( -18.10)
>consensus
UCUGGUAGACACACAUAUAUCGACCAUAUAUAUACUAUAGCCACUAUAUGUAUACCGCGAUGUCCUGUGCAUCCCGUGAAACCUCUUCGCUG
...((.(..((((...((((((...(((((((((..........)))))))))....))))))..))))..).))(((((.....))))).. (-17.38 = -17.66 +   0.28)

alignment

secondary structure

dotplot

Window 8

Location	20,236,708 – 20,236,800
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	97.50
Mean single sequence MFE	-25.76
Consensus MFE	-22.26
Energy contribution	-23.26
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.88
Structure conservation index	0.86
SVM decision value	1.29
SVM RNA-class probability	0.938337
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20236708 92 - 23771897
CAGCGAAGAGGUUUCACGGGAUGCACAGGACAUCGCGGUAUACAUAUAGUGGCUAUAGUAUAUAUAUGGUCGAUAUAUGUGUGUCUACCAGA
.........(((.....(.(((((....).)))).)(..(((((((((.((((((((.......)))))))).)))))))))..).)))... ( -26.90)
>DroSec_CAF1 6269 92 - 1
CAGCGAAGAGGUUUCACGGGAUGCACAGGACAUCGCGGUAUACAUAUAGUGGCUAUAGUAUAUAUAUGGUCGAUAUAUGUGUGUCUACCAGA
.........(((.....(.(((((....).)))).)(..(((((((((.((((((((.......)))))))).)))))))))..).)))... ( -26.90)
>DroSim_CAF1 7513 92 - 1
CAGCGAAGAGGUUUCACGGGAUGCACAGGACAUCGCGGUAUACAUAUAGUGGCUAUAGUAUAUAUAUGGUCGAUAUAUGUGUGUCUACCAGA
.........(((.....(.(((((....).)))).)(..(((((((((.((((((((.......)))))))).)))))))))..).)))... ( -26.90)
>DroEre_CAF1 7058 89 - 1
CAGCGAA-AGGUUUCACGGAAUGCACAGGACAUCGCGGUAUACAUAUAGUGGCUAUAGUAUAUAUAUGGUCGAUAUAUG--UGUCUACCAGA
..((((.-..((((.............)))).))))((((.(((((((.((((((((.......))))))))...))))--))).))))... ( -25.62)
>DroYak_CAF1 11577 91 - 1
CAGCGAA-AGGUUUCACGGAAUGCACAGGACAUCGCGGUAUACAUAUAGUGGCUAUAGUAUAUAUAUGGUCGAUAUAUGCGUGUCUACCAGA
.......-.(((..((((..((((...(.....)...)))).((((((.((((((((.......)))))))).))))))))))...)))... ( -22.50)
>consensus
CAGCGAAGAGGUUUCACGGGAUGCACAGGACAUCGCGGUAUACAUAUAGUGGCUAUAGUAUAUAUAUGGUCGAUAUAUGUGUGUCUACCAGA
.........(((.....(.(((((....).)))).)(..(((((((((.((((((((.......)))))))).)))))))))..).)))... (-22.26 = -23.26 +   1.00)

alignment

secondary structure

dotplot

Window 9

Location	20,236,726 – 20,236,840
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	98.60
Mean single sequence MFE	-33.60
Consensus MFE	-33.64
Energy contribution	-33.48
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.58
Structure conservation index	1.00
SVM decision value	1.64
SVM RNA-class probability	0.969127
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20236726 114 + 23771897
AUCGACCAUAUAUAUACUAUAGCCACUAUAUGUAUACCGCGAUGUCCUGUGCAUCCCGUGAAACCUCUUCGCUGCAUCCGCGUAUCGGGGGUGGUCGGUCUGCCCGAAAAACUC
(((((((((...((((((((((...))))).)))))((.(((((..(.(((((....(((((.....))))))))))..)..))))).)))))))))))............... ( -34.10)
>DroSec_CAF1 6287 114 + 1
AUCGACCAUAUAUAUACUAUAGCCACUAUAUGUAUACCGCGAUGUCCUGUGCAUCCCGUGAAACCUCUUCGCUGCAUCCGCGUAUCGGGGGUGGUCGGUCUGCCCGAAAAACUC
(((((((((...((((((((((...))))).)))))((.(((((..(.(((((....(((((.....))))))))))..)..))))).)))))))))))............... ( -34.10)
>DroSim_CAF1 7531 114 + 1
AUCGACCAUAUAUAUACUAUAGCCACUAUAUGUAUACCGCGAUGUCCUGUGCAUCCCGUGAAACCUCUUCGCUGCAUCCGCGUAUCGGGGGUGGUCGGUCUGCCCGAAAAACUC
(((((((((...((((((((((...))))).)))))((.(((((..(.(((((....(((((.....))))))))))..)..))))).)))))))))))............... ( -34.10)
>DroEre_CAF1 7074 113 + 1
AUCGACCAUAUAUAUACUAUAGCCACUAUAUGUAUACCGCGAUGUCCUGUGCAUUCCGUGAAACCU-UUCGCUGCAUCCGCGUAUUGGGGGUGGUCGGUCUGCCCGAAAAACUC
(((((((((...((((((((((...))))).)))))((.(((((..(.(((((....(((((....-))))))))))..)..))))).)))))))))))............... ( -31.80)
>DroYak_CAF1 11595 113 + 1
AUCGACCAUAUAUAUACUAUAGCCACUAUAUGUAUACCGCGAUGUCCUGUGCAUUCCGUGAAACCU-UUCGCUGCAUCCGCGUAUCGGGGGUGGUCGGUCUGCCCGAAAAACUC
(((((((((...((((((((((...))))).)))))((.(((((..(.(((((....(((((....-))))))))))..)..))))).)))))))))))............... ( -33.90)
>consensus
AUCGACCAUAUAUAUACUAUAGCCACUAUAUGUAUACCGCGAUGUCCUGUGCAUCCCGUGAAACCUCUUCGCUGCAUCCGCGUAUCGGGGGUGGUCGGUCUGCCCGAAAAACUC
(((((((((...((((((((((...))))).)))))((.(((((..(.(((((....(((((.....))))))))))..)..))))).)))))))))))............... (-33.64 = -33.48 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:39 2006