Locus 6507

Sequence ID 2R_DroMel_CAF1
Location 20,335,477 – 20,335,567
Length 90
Max. P 0.990617
window10363 window10364

overview

Window 3

Location 20,335,477 – 20,335,567
Length 90
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 79.19
Mean single sequence MFE -37.47
Consensus MFE -16.74
Energy contribution -17.43
Covariance contribution 0.70
Combinations/Pair 1.21
Mean z-score -2.92
Structure conservation index 0.45
SVM decision value 1.15
SVM RNA-class probability 0.923471
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20335477 90 + 20766785
U--------ACUUUGCAUCCCAAUG---------UCCACUGGG----------CUCCACUGGGGCUCAGUGAACUUUGAAAUGCCGGUGGAGCAGCACCAGUAGCUCCGAUGAGCAU
(--------(((..((((..(((.(---------(.(((((((----------((((...))))))))))).)).)))..)))).((((......))))))))((((....)))).. ( -37.50)
>DroSec_CAF1 52052 90 + 1
U--------ACUUUGCAUCCCAAUG---------UCCACUGGG----------CUCCACUGGGGCUCAGUGAACUUUGAAAUGCGGCUGGAGCAGCAGCAGUAGCUCCGAUGAGCGU
.--------....(((((..(((.(---------(.(((((((----------((((...))))))))))).)).)))..)))))((((((((.((....)).)))))....))).. ( -38.40)
>DroSim_CAF1 53638 90 + 1
U--------ACUUUGCAUCCCAAUG---------UCCACUGGG----------CUCCACUGGGGCUCAGUGAACUUUGAAAUGCGGCUGGAGCAGCAGCAGUAGCUCCGAUGAGCGU
.--------....(((((..(((.(---------(.(((((((----------((((...))))))))))).)).)))..)))))((((((((.((....)).)))))....))).. ( -38.40)
>DroEre_CAF1 54688 90 + 1
U--------ACUUUGCAUCCCAAUG---------UCCACUGGG----------CUCCACUGGGGCUCAGUGAACUUUGAAAUGCGGCUGGGGCAGCAGCAGUAGCUCCGAUGAGCGU
(--------(((.(((((..(((.(---------(.(((((((----------((((...))))))))))).)).)))..)))))((((......))))))))((((....)))).. ( -38.30)
>DroYak_CAF1 53302 100 + 1
U--------ACUUUGCAUCCCAAUG---------UCCACUGGGCUCCAAUGGGCUCCACUGGGGCUCAGUGAACUUUGAAAUGCGGCUGGCGCGGCGGCAGUAGCUGCGAUGAGCGU
.--------....(((((..(((.(---------(.((((((((((((.(((...))).)))))))))))).)).)))..)))))(((.(((((((.......)))))).).))).. ( -47.90)
>DroAna_CAF1 51048 101 + 1
UAGCUGCAUGCUUUGCAUCCCAAUGCCACUGAGCUCCACUGGG----------CUCCAGUGAGGCCCACUGAACUUUGAAGUUCCAUUU----CGCAUCAAGAGC--CACUUAAUAC
..((((((.....)))......((((...((.((..((((((.----------..))))))..)).))..(((((....))))).....----.))))....)))--.......... ( -24.30)
>consensus
U________ACUUUGCAUCCCAAUG_________UCCACUGGG__________CUCCACUGGGGCUCAGUGAACUUUGAAAUGCGGCUGGAGCAGCAGCAGUAGCUCCGAUGAGCGU
.............(((..((((.((...........)).)))).............((.((((((((((......))))..(((.((((......)))).))))))))).)).))). (-16.74 = -17.43 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 20,335,477 – 20,335,567
Length 90
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 79.19
Mean single sequence MFE -39.80
Consensus MFE -22.12
Energy contribution -22.85
Covariance contribution 0.73
Combinations/Pair 1.15
Mean z-score -3.76
Structure conservation index 0.56
SVM decision value 2.22
SVM RNA-class probability 0.990617
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20335477 90 - 20766785
AUGCUCAUCGGAGCUACUGGUGCUGCUCCACCGGCAUUUCAAAGUUCACUGAGCCCCAGUGGAG----------CCCAGUGGA---------CAUUGGGAUGCAAAGU--------A
..((((....))))((((((((......)))).((((..(((.((((((((.((((....)).)----------).)))))))---------).)))..))))..)))--------) ( -38.90)
>DroSec_CAF1 52052 90 - 1
ACGCUCAUCGGAGCUACUGCUGCUGCUCCAGCCGCAUUUCAAAGUUCACUGAGCCCCAGUGGAG----------CCCAGUGGA---------CAUUGGGAUGCAAAGU--------A
..((((....))))((((((((......)))).((((..(((.((((((((.((((....)).)----------).)))))))---------).)))..))))..)))--------) ( -38.60)
>DroSim_CAF1 53638 90 - 1
ACGCUCAUCGGAGCUACUGCUGCUGCUCCAGCCGCAUUUCAAAGUUCACUGAGCCCCAGUGGAG----------CCCAGUGGA---------CAUUGGGAUGCAAAGU--------A
..((((....))))((((((((......)))).((((..(((.((((((((.((((....)).)----------).)))))))---------).)))..))))..)))--------) ( -38.60)
>DroEre_CAF1 54688 90 - 1
ACGCUCAUCGGAGCUACUGCUGCUGCCCCAGCCGCAUUUCAAAGUUCACUGAGCCCCAGUGGAG----------CCCAGUGGA---------CAUUGGGAUGCAAAGU--------A
..((((....))))((((((((......)))).((((..(((.((((((((.((((....)).)----------).)))))))---------).)))..))))..)))--------) ( -38.60)
>DroYak_CAF1 53302 100 - 1
ACGCUCAUCGCAGCUACUGCCGCCGCGCCAGCCGCAUUUCAAAGUUCACUGAGCCCCAGUGGAGCCCAUUGGAGCCCAGUGGA---------CAUUGGGAUGCAAAGU--------A
..(((...(((.((.......)).)))..))).((((..(((.((((((((.((.(((((((...))))))).)).)))))))---------).)))..)))).....--------. ( -45.30)
>DroAna_CAF1 51048 101 - 1
GUAUUAAGUG--GCUCUUGAUGCG----AAAUGGAACUUCAAAGUUCAGUGGGCCUCACUGGAG----------CCCAGUGGAGCUCAGUGGCAUUGGGAUGCAAAGCAUGCAGCUA
........((--(((((..((((.----.....(((((....)))))(.(((((..((((((..----------.))))))..))))).).))))..)))((((.....)))))))) ( -38.80)
>consensus
ACGCUCAUCGGAGCUACUGCUGCUGCUCCAGCCGCAUUUCAAAGUUCACUGAGCCCCAGUGGAG__________CCCAGUGGA_________CAUUGGGAUGCAAAGU________A
..((((....))))....((((......)))).((((.......(((((((.....)))))))...........(((((((...........))))))))))).............. (-22.12 = -22.85 +   0.73)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:31 2006