Locus 4619

Sequence ID	3R_DroMel_CAF1
Location	12,147,402 – 12,147,492
Length	90
Max. P	0.977599

overview

Window 2

Location	12,147,402 – 12,147,492
Length	90
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.41
Mean single sequence MFE	-33.48
Consensus MFE	-29.58
Energy contribution	-29.58
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.98
Structure conservation index	0.88
SVM decision value	1.80
SVM RNA-class probability	0.977599
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12147402 90 + 27905053
--------CCAUCACGU------GUUUCCGUGGUGUAGUGGUUAUCACAUCCGCCUAACACGCGGAAGGCCCCCGGUUCAAUCCCGGGCGGAAACAUUG--------G-A-------AAU
--------(((....((------(((((((.(((.(.(((.....))).(((((.......)))))).)))(((((.......))))))))))))))))--------)-.-------... ( -33.60)
>DroVir_CAF1 70070 89 + 1
-----------------------GUUUCCGUGGUGUAGUGGUUAUCACAUCCGCCUAACACGCGGAAGGCCCCCGGUUCAAUCCCGGGCGGAAACAUCA--------UCUAAUCAAGACU
-----------------------(((((((.(((.(.(((.....))).(((((.......)))))).)))(((((.......))))))))))))....--------............. ( -29.90)
>DroPse_CAF1 61357 91 + 1
--------CUCGAGGAU------GUUUCCGUGGUGUAGCGGUUAUCACAUCCGCCUAACACGCGGAAGGCCCCCGGUUCAAUCCCGGGCGGAAACAUGG--------GGA-------AAU
--------((((.(...------.((((((((((...((((.........))))...)).)))))))).(((((((.......))))).))...).)))--------)..-------... ( -32.20)
>DroGri_CAF1 71564 114 + 1
UUCUAAGAACUUAAUGU------GUUUCCGUGGUGUAGUGGUUAUCACAUCCGCCUAACACGCGGAAGGCCCCCGGUUCAAUCCCGGGCGGAAACAUUCGGCCCAAUCCUCAUUUGGAGU
(((((((..........------..(((((((((...((((.........))))...)).)))))))(((((((((.......))))).(....)....)))).........))))))). ( -36.90)
>DroMoj_CAF1 68936 104 + 1
-CCUA--AACUAAAUUUGACCAAGUUUCCGUGGUGUAGUGGUUAUCACAUCCGCCUAACACGCGGAACGCCCCCGGUUCAAUCCCGGGCGGAAACAUAU--------UGUUAUU-----U
-....--................(((((((.(((((.(((.....))).(((((.......))))))))))(((((.......))))))))))))....--------.......-----. ( -33.30)
>DroAna_CAF1 55648 91 + 1
--------CUCUCAAGA------GUUUCCGUGGUGUAGUGGUUAUCACAUCCGCCUAACACGCGGAAGGCCCCCGGUUCAAUCCCGGGCGGAAACAUUU--------GGG-------UUU
--------..((((((.------(((((((.(((.(.(((.....))).(((((.......)))))).)))(((((.......)))))))))))).)))--------)))-------... ( -35.00)
>consensus
________CCCUAAUGU______GUUUCCGUGGUGUAGUGGUUAUCACAUCCGCCUAACACGCGGAAGGCCCCCGGUUCAAUCCCGGGCGGAAACAUUG________GGU_______AAU
.......................((((((((((((.......)))))).(((((.......)))))..((((..((......)).))))))))))......................... (-29.58 = -29.58 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	12,147,402 – 12,147,492
Length	90
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.41
Mean single sequence MFE	-32.32
Consensus MFE	-29.17
Energy contribution	-29.03
Covariance contribution	-0.14
Combinations/Pair	1.05
Mean z-score	-1.34
Structure conservation index	0.90
SVM decision value	1.27
SVM RNA-class probability	0.939045
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12147402 90 - 27905053
AUU-------U-C--------CAAUGUUUCCGCCCGGGAUUGAACCGGGGGCCUUCCGCGUGUUAGGCGGAUGUGAUAACCACUACACCACGGAAAC------ACGUGAUGG--------
...-------.-.--------((.(((((((((((((.......)))))((...(((((.......))))).(((.....)))....)).)))))))------)..))....-------- ( -31.40)
>DroVir_CAF1 70070 89 - 1
AGUCUUGAUUAGA--------UGAUGUUUCCGCCCGGGAUUGAACCGGGGGCCUUCCGCGUGUUAGGCGGAUGUGAUAACCACUACACCACGGAAAC-----------------------
.((((.....)))--------)...((((((((((((.......)))))((...(((((.......))))).(((.....)))....)).)))))))----------------------- ( -30.50)
>DroPse_CAF1 61357 91 - 1
AUU-------UCC--------CCAUGUUUCCGCCCGGGAUUGAACCGGGGGCCUUCCGCGUGUUAGGCGGAUGUGAUAACCGCUACACCACGGAAAC------AUCCUCGAG--------
...-------...--------..((((((((((((((.......)))))........(.((((..(((((.........)))))))))).)))))))------)).......-------- ( -31.90)
>DroGri_CAF1 71564 114 - 1
ACUCCAAAUGAGGAUUGGGCCGAAUGUUUCCGCCCGGGAUUGAACCGGGGGCCUUCCGCGUGUUAGGCGGAUGUGAUAACCACUACACCACGGAAAC------ACAUUAAGUUCUUAGAA
........((((((((........(((((((((((((.......)))))((...(((((.......))))).(((.....)))....)).)))))))------).....))))))))... ( -36.22)
>DroMoj_CAF1 68936 104 - 1
A-----AAUAACA--------AUAUGUUUCCGCCCGGGAUUGAACCGGGGGCGUUCCGCGUGUUAGGCGGAUGUGAUAACCACUACACCACGGAAACUUGGUCAAAUUUAGUU--UAGG-
.-----.......--------....((((((((((((.......)))))((.(((((((.......))))).(((.....))).)).)).)))))))................--....- ( -31.60)
>DroAna_CAF1 55648 91 - 1
AAA-------CCC--------AAAUGUUUCCGCCCGGGAUUGAACCGGGGGCCUUCCGCGUGUUAGGCGGAUGUGAUAACCACUACACCACGGAAAC------UCUUGAGAG--------
...-------..(--------((..((((((((((((.......)))))((...(((((.......))))).(((.....)))....)).)))))))------..)))....-------- ( -32.30)
>consensus
AUU_______ACC________AAAUGUUUCCGCCCGGGAUUGAACCGGGGGCCUUCCGCGUGUUAGGCGGAUGUGAUAACCACUACACCACGGAAAC______ACAUUAAGG________
.........................((((((((((((.......)))))((...(((((.......))))).(((.....)))....)).)))))))....................... (-29.17 = -29.03 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:49 2006