Locus 10164

Sequence ID 3R_DroMel_CAF1
Location 27,295,525 – 27,295,741
Length 216
Max. P 0.812468
window16171 window16172

overview

Window 1

Location 27,295,525 – 27,295,639
Length 114
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 90.76
Mean single sequence MFE -42.20
Consensus MFE -29.42
Energy contribution -29.42
Covariance contribution 0.00
Combinations/Pair 1.09
Mean z-score -2.10
Structure conservation index 0.70
SVM decision value 0.09
SVM RNA-class probability 0.577501
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27295525 114 - 27905053
CAGCCCUGAGCGCCAACUGCACC---ACCAUUGUGGUGCCCUUGCGGCACCAGUGGUUCCGCUGGUCCGUCGGCCAAGUGAGUGACAGCCAUCACACUGAGCUGAAAUACUCGAACA
..((.....))(((....(((((---((....)))))))....((((.(((((((....))))))))))).)))....((((((.((((((......)).))))...)))))).... ( -45.00)
>DroSec_CAF1 597 114 - 1
CAGCACGGAGCGCCAACUGCACC---GCCAUUGUGGUGCCCUUGCGCCACCAGUGGUGCCGCUGUUCCGUCGGCCAAGUGAGUGACAGCCAUCACACCGAACUGAAAUACUCUAAUA
(((..((((((((.....(((((---((....(((((((....)))))))..))))))).)).))))))((((....((((.((.....)))))).)))).)))............. ( -41.20)
>DroSim_CAF1 1005 114 - 1
CAGCACGGAGCGCCAACUGCACC---ACCAUUGUGGUGCCCUUGCGCCACCAGUGGUGCCGCUGGUCCGUCGGCCAAGUGAGUGACAGCCAUCACACCGAACUGAAAUACUCGAAUA
(((..((((((((.((..(((((---((....)))))))..))))))..((((((....))))))))))((((....((((.((.....)))))).)))).)))............. ( -41.90)
>DroEre_CAF1 744 112 - 1
CAGCCCUGAGCGCCAACUGCACCACCACCAUUGUGGUGCCCUUGCGCCACCAGUGGUUCCGCUGGUCUGUCGGUCGAGUGAGUGACAGCCAUCACAC-----UGAAAUACUCGAAUA
.....((((((((.((..(((((((.......)))))))..)))))).(((((((....)))))))...))))(((((((((((..........)))-----)....)))))))... ( -40.70)
>consensus
CAGCACGGAGCGCCAACUGCACC___ACCAUUGUGGUGCCCUUGCGCCACCAGUGGUGCCGCUGGUCCGUCGGCCAAGUGAGUGACAGCCAUCACACCGAACUGAAAUACUCGAAUA
.......(((......((((((....(((((((((((((....)))))).)))))))..((((((((....))))).))).))).)))...(((........)))....)))..... (-29.42 = -29.42 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 27,295,639 – 27,295,741
Length 102
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 84.32
Mean single sequence MFE -23.35
Consensus MFE -16.75
Energy contribution -16.62
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -1.92
Structure conservation index 0.72
SVM decision value 0.65
SVM RNA-class probability 0.812468
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27295639 102 + 27905053
CCCGAGUCACUGGGUCAACUUGGUGAAGGCAAUGCAAUGCAGAGGGAGACAGCCAAAUCGGAUCCAAAAA-UUCAGAUAAAA-AUAU--------UUAA-----AAAUGGACAUAAA
.((((.((((..((....))..)))).(((..(((...)))...(....).)))...)))).((((....-...(((((...-.)))--------))..-----...))))...... ( -24.40)
>DroSec_CAF1 711 102 + 1
CCCGAGUCACUGGGUCAACUGAGUGAAGGCAAUGCAAUAUAGAGGGAGACAGCCAAAUCGGAUCCAAAAA-UGCAGGUAAAA-AUAG--------UUAC-----AAAUGCACAUAAA
.((((.(((((.((....)).))))).(((....(......)..(....).)))...)))).........-((((.((((..-....--------))))-----...))))...... ( -24.40)
>DroSim_CAF1 1119 102 + 1
CCCGAGUCACUGGGUCAACUGGGUGAAGGCAAUGCAAUGCAGAGGGAGACAGCCAAAUCGGAUCCAAAAA-UUCAGAUAAAA-AUAG--------UUAA-----AAAUGCACAUAAA
.((((.(((((.((....)).))))).(((..(((...)))...(....).)))...)))).........-...........-....--------....-----............. ( -21.40)
>DroEre_CAF1 856 112 + 1
CCCGAGUCACUGGGUCAACUGGGUGAAGGCAAUG-----CAGAGGGAGAGAGCCAAAUCGGACCCAAAAAGUUCAAAUAAAAAAUAGGUGUAGCUUUAAAAAUAAAAUGUAUGUAAA
.((...(((((.((....)).))))).))..(((-----((..(((...((......))...)))..((((((((..((.....))..)).))))))..........)))))..... ( -23.20)
>consensus
CCCGAGUCACUGGGUCAACUGGGUGAAGGCAAUGCAAUGCAGAGGGAGACAGCCAAAUCGGAUCCAAAAA_UUCAGAUAAAA_AUAG________UUAA_____AAAUGCACAUAAA
.((((.(((((.((....)).))))).(((..((.....))...(....).)))...))))........................................................ (-16.75 = -16.62 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:50:14 2006