Locus 7135

Sequence ID	3R_DroMel_CAF1
Location	18,803,389 – 18,803,527
Length	138
Max. P	0.853377

overview

Window 3

Location	18,803,389 – 18,803,500
Length	111
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	80.07
Mean single sequence MFE	-50.92
Consensus MFE	-32.97
Energy contribution	-33.28
Covariance contribution	0.31
Combinations/Pair	1.27
Mean z-score	-1.39
Structure conservation index	0.65
SVM decision value	0.06
SVM RNA-class probability	0.563353
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18803389 111 - 27905053
UUCCCGACAGCGACCACGAUGGUCGGGCAGAUAGCCGGGCUGGCAGGGGAAGUCGAUCAUGGCCACCAUCAUGGUCUUCUCGGUGGUGGUUUGGCCGGCGACCGGA--GGC---UC
(((((..((((((((.....)))).(((.....)))..))))...))))).((((....(((((((((((((.(......).))))))))..))))).))))....--...---.. ( -50.10)
>DroSec_CAF1 28784 111 - 1
UUCCCGACAACGACCACGAUGGUCGGGCAGAUAGCCCGGCUGGCAGGGGAAGUCGAUCAUGGCCACCAUCAUGGUCUUCUCGGUGGUGGUUUGGCCGGCGACCGUG--GGC---UC
.............(((((..((((((((.....))))))))..........((((....(((((((((((((.(......).))))))))..))))).))))))))--)..---.. ( -48.80)
>DroEre_CAF1 28014 105 - 1
UUCCCGACAGCGACCGCGAUGGUCGGGCAGAUAGCCCGGCUGGCAGGGGAAGUCGAUCAUGGCCACCAUCAUGGGCUUCUCGGUGGUGGC------GGCGCCCGGA--GAC---GC
.(((((...(((.((((.((((((((((.....)))))))).((..((((((((.((.((((...)))).)).)))))))).)).)).))------))))).))).--)).---.. ( -49.30)
>DroYak_CAF1 30919 111 - 1
UUCCCGACAGCGACCACGAUGGUCGGGCAGAUAGCCCGGCUGGCAGGGAAAGUCGAUCAUGGCCACCAUCAUGGGCUUCUCGGUGGUGGCAUUGCCGUCGCCCUGG--GAC---UC
(((((..((((((((.....))))((((.....)))).))))...)))))((((.((.((((...)))).)).))))((((((.((((((......))))))))))--)).---.. ( -52.50)
>DroMoj_CAF1 30774 108 - 1
CUCGCGGCACCGUCCGCGACUGUCGGGCAGGUAGCCCGGCUGGCAGGGGAAGUCGAUCAUGGCCACCUCCAUGAUCUUCUCGGUGGUGGCUGC-----UGAG-GAG--GGUCGCAC
...(((((.((.(((.(..(((((((((.....))))))).))..).)))....((((((((......))))))))(((((((..(...)..)-----))))-)))--)))))).. ( -52.80)
>DroAna_CAF1 29881 114 - 1
UUCCCGGCACCGACCACGGUGGUCGGGCAGGUAGCCCGGCUGGCAGGGGAAGUCUAUCAUGGCCACCUCCAUGAUUUUCUCGGUAACGGGCUGUCCGCUGGCAGGCUUGAC--UGU
...(((((.((((((.....))))))...(((((((((....((..((((((...(((((((......))))))))))))).))..))))))).)))))))(((......)--)). ( -52.00)
>consensus
UUCCCGACAGCGACCACGAUGGUCGGGCAGAUAGCCCGGCUGGCAGGGGAAGUCGAUCAUGGCCACCAUCAUGGUCUUCUCGGUGGUGGCUUGGCCGGCGACCGGG__GAC___UC
.........((.((((((.(((((((((.....))))))))).)..((((((...(((((((......))))))))))))).))))).)).......................... (-32.97 = -33.28 +   0.31)

alignment

secondary structure

dotplot

Window 4

Location	18,803,423 – 18,803,527
Length	104
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	79.91
Mean single sequence MFE	-43.12
Consensus MFE	-26.70
Energy contribution	-26.70
Covariance contribution	0.00
Combinations/Pair	1.23
Mean z-score	-2.09
Structure conservation index	0.62
SVM decision value	0.79
SVM RNA-class probability	0.851936
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18803423 104 + 27905053
AGACCAUGAUGGUGGCCAUGAUCGACUUCCCCUGCCAGCCCGGCUAUCUGCCCGACCAUCGUGGUCGCUGUCGGGAAAUCUGGUGAUUC--------GAUG-GCU-UCGUGACA
.(((((((((((((((...((......))....))).....(((.....)))..))))))))))))((((((((...(((....)))))--------))))-)).-........ ( -39.90)
>DroSec_CAF1 28818 107 + 1
AGACCAUGAUGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGUGGUCGUUGUCGGGAAAUCUGGUGAUCCGA-----CGAUG-GCU-UCGUGACA
.(((((((((((((((...((......))....)))...(((((.....)))))))))))))))))((((((((...(((....)))))))-----)))).-...-........ ( -46.90)
>DroEre_CAF1 28042 104 + 1
AGCCCAUGAUGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGCGGUCGCUGUCGGGAAAUCUGGUGAUUC--------GAUG-GCUUUCGUGAC-
....(((((....((((((((((.(((...((((.((((.((((.....))))((((.....)))))))).))))......))))))).--------.)))-))).)))))..- ( -41.80)
>DroYak_CAF1 30953 106 + 1
AGCCCAUGAUGGUGGCCAUGAUCGACUUUCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGUGGUCGCUGUCGGGAAAUCUGGUGAUUC--------CGUGGGCUGCCGUGACA
((((((((..(((.((((.(((.....(((((.(.((((.((((.....))))((((.....)))))))).))))))))))))).))).--------))))))))......... ( -47.90)
>DroMoj_CAF1 30805 90 + 1
AGAUCAUGGAGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUACCUGCCCGACAGUCGCGGACGGUGCCGCGAGAUAUGGUAAACCC------------------------
.((((((((......)))))))).........((((((.(((((.....))))).)..((((((......))))))....))))).....------------------------ ( -38.20)
>DroAna_CAF1 29918 112 + 1
AAAUCAUGGAGGUGGCCAUGAUAGACUUCCCCUGCCAGCCGGGCUACCUGCCCGACCACCGUGGUCGGUGCCGGGAAAUCUGGUAAACGGCAAAACCACUU-UCU-UCGUGAUA
..(((((((((((.(((....((((.(((((..((..(((((((.....))))((((.....))))))))).))))).))))......)))...)))....-..)-))))))). ( -44.00)
>consensus
AGACCAUGAUGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGUGGUCGCUGUCGGGAAAUCUGGUGAUCC________GAUG_GCU_UCGUGACA
...(((((((((((((...((......))....)))...(((((.....)))))))))))))))....((((((.....))))))............................. (-26.70 = -26.70 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	18,803,423 – 18,803,527
Length	104
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	79.91
Mean single sequence MFE	-41.32
Consensus MFE	-29.60
Energy contribution	-30.52
Covariance contribution	0.92
Combinations/Pair	1.11
Mean z-score	-1.76
Structure conservation index	0.72
SVM decision value	0.80
SVM RNA-class probability	0.853377
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18803423 104 - 27905053
UGUCACGA-AGC-CAUC--------GAAUCACCAGAUUUCCCGACAGCGACCACGAUGGUCGGGCAGAUAGCCGGGCUGGCAGGGGAAGUCGAUCAUGGCCACCAUCAUGGUCU
.....(((-...-..))--------)........((((((((..((((((((.....)))).(((.....)))..))))....))))))))((((((((......)))))))). ( -38.80)
>DroSec_CAF1 28818 107 - 1
UGUCACGA-AGC-CAUCG-----UCGGAUCACCAGAUUUCCCGACAACGACCACGAUGGUCGGGCAGAUAGCCCGGCUGGCAGGGGAAGUCGAUCAUGGCCACCAUCAUGGUCU
........-.((-(((.(-----((((....)).((((((((.....((....))..((((((((.....)))))))).....))))))))))).))))).(((.....))).. ( -40.40)
>DroEre_CAF1 28042 104 - 1
-GUCACGAAAGC-CAUC--------GAAUCACCAGAUUUCCCGACAGCGACCGCGAUGGUCGGGCAGAUAGCCCGGCUGGCAGGGGAAGUCGAUCAUGGCCACCAUCAUGGGCU
-........(((-(...--------.........((((((((..((((((((.....))))((((.....)))).))))....))))))))...(((((......))))))))) ( -40.90)
>DroYak_CAF1 30953 106 - 1
UGUCACGGCAGCCCACG--------GAAUCACCAGAUUUCCCGACAGCGACCACGAUGGUCGGGCAGAUAGCCCGGCUGGCAGGGAAAGUCGAUCAUGGCCACCAUCAUGGGCU
(((....)))(((((.(--------(.....)).((((((((..((((((((.....))))((((.....)))).))))...))).)))))....((((...))))..))))). ( -42.30)
>DroMoj_CAF1 30805 90 - 1
------------------------GGGUUUACCAUAUCUCGCGGCACCGUCCGCGACUGUCGGGCAGGUAGCCCGGCUGGCAGGGGAAGUCGAUCAUGGCCACCUCCAUGAUCU
------------------------((.((..((.....((((((......))))))(.(((((((.....))))))).)...))..)).))((((((((......)))))))). ( -39.90)
>DroAna_CAF1 29918 112 - 1
UAUCACGA-AGA-AAGUGGUUUUGCCGUUUACCAGAUUUCCCGGCACCGACCACGGUGGUCGGGCAGGUAGCCCGGCUGGCAGGGGAAGUCUAUCAUGGCCACCUCCAUGAUUU
.(((((..-...-..))))).............(((((((((.((((((....))))((((((((.....)))))))).))..)))))))))(((((((......))))))).. ( -45.60)
>consensus
UGUCACGA_AGC_CAUC________GAAUCACCAGAUUUCCCGACAGCGACCACGAUGGUCGGGCAGAUAGCCCGGCUGGCAGGGGAAGUCGAUCAUGGCCACCAUCAUGGUCU
..................................((((((((.....((....)).(((((((((.....)))))))))....))))))))((((((((......)))))))). (-29.60 = -30.52 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:18 2006