Locus 5111

Sequence ID	3R_DroMel_CAF1
Location	13,457,398 – 13,457,497
Length	99
Max. P	0.985861

overview

Window 3

Location	13,457,398 – 13,457,497
Length	99
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.52
Mean single sequence MFE	-33.13
Consensus MFE	-31.97
Energy contribution	-31.97
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.71
Structure conservation index	0.96
SVM decision value	1.13
SVM RNA-class probability	0.920426
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13457398 99 + 27905053
GAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCC-----------UUGU------UUAAAA-UUUU-UGCUCUCUUUU--
(((((..(((.(..(((((((..(((((((((.......)))))).)))(((((.......)))))....))))-----------))).------.)...)-))..-.)).)))....-- ( -32.70)
>DroVir_CAF1 4622 103 + 1
GCGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCC-----------UUAUAUUUUUUUCUU------UAACUUUUUGCCGC
(((((.....(((..(((((.....(((((((.......)))))))..)))((((((((.......))))))))-----------............)).------..)))....))))) ( -36.60)
>DroPse_CAF1 14433 95 + 1
GCGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCC-----------UUAA------CUCAAC-UUUU-UACUCAU------
..((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).-----------....------......-....-.......------ ( -32.00)
>DroGri_CAF1 4991 99 + 1
GCGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCC-----------GUAU------CUCCAA-UUUUUUUUGUGCUCU---
((((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).-----------....------...(((-......))).))...--- ( -33.30)
>DroWil_CAF1 7830 101 + 1
GAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCC-----------U-GU------CUAAUUUUUUU-UGCUUUCUGUUGU
..((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).-----------.-..------...........-............. ( -31.90)
>DroMoj_CAF1 3814 116 + 1
GCGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGUUGUGCAUUCUUUUACUUAUUUCUUA-UUUGUUACUUUUUUU---
...((.((((.......(((.....(((((((.......)))))))..)))((((((((.......)))))))))))).))....................-...............--- ( -32.30)
>consensus
GCGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCC___________UUAU______CUCAAA_UUUU_UACUUUCUGU___
..((((((((.......(((.....(((((((.......)))))))..)))(((.......))).))))))))............................................... (-31.97 = -31.97 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	13,457,398 – 13,457,497
Length	99
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.52
Mean single sequence MFE	-30.43
Consensus MFE	-29.93
Energy contribution	-29.93
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.19
Structure conservation index	0.98
SVM decision value	2.02
SVM RNA-class probability	0.985861
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13457398 99 - 27905053
--AAAAGAGAGCA-AAAA-UUUUAA------ACAA-----------GGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUC
--...........-....-......------....-----------(((((((((((((.......)))))((..((((((.......)))))).))..............)))))))). ( -30.40)
>DroVir_CAF1 4622 103 - 1
GCGGCAAAAAGUUA------AAGAAAAAAAUAUAA-----------GGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCGC
(((((.....(((.------........)))...(-----------(((.....(((((.......)))))((..((((((.......)))))).))....))))..........))))) ( -30.50)
>DroPse_CAF1 14433 95 - 1
------AUGAGUA-AAAA-GUUGAG------UUAA-----------GGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCGC
------.......-....-......------....-----------.((((((((((((.......)))))((..((((((.......)))))).))..............))))))).. ( -30.10)
>DroGri_CAF1 4991 99 - 1
---AGAGCACAAAAAAAA-UUGGAG------AUAC-----------GGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCGC
---...((.(((......-)))...------....-----------.((((((((((((.......)))))((..((((((.......)))))).))..............))))))))) ( -30.80)
>DroWil_CAF1 7830 101 - 1
ACAACAGAAAGCA-AAAAAAAUUAG------AC-A-----------GGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUC
.............-...........------..-.-----------(((((((((((((.......)))))((..((((((.......)))))).))..............)))))))). ( -30.40)
>DroMoj_CAF1 3814 116 - 1
---AAAAAAAGUAACAAA-UAAGAAAUAAGUAAAAGAAUGCACAACGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCGC
---...............-..........(((......)))......((((((((((((.......)))))((..((((((.......)))))).))..............))))))).. ( -30.40)
>consensus
___AAAAAAAGUA_AAAA_UAUGAA______AUAA___________GGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCGC
...............................................((((((((((((.......)))))((..((((((.......)))))).))..............))))))).. (-29.93 = -29.93 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:29 2006