Locus 6489

Sequence ID	X_DroMel_CAF1
Location	16,265,109 – 16,265,266
Length	157
Max. P	0.917209

overview

Window 9

Location	16,265,109 – 16,265,226
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.09
Mean single sequence MFE	-54.68
Consensus MFE	-26.64
Energy contribution	-25.42
Covariance contribution	-1.22
Combinations/Pair	1.48
Mean z-score	-2.12
Structure conservation index	0.49
SVM decision value	0.85
SVM RNA-class probability	0.865187
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16265109 117 + 22224390
CUUUGGCUGCCGCCUUGGAAAUGCAACGGGCAGCGGCUG---CGGCGGCCACCGCUGAGGCAAAUCGGGCAGCGGGCGCCGCUGGCGGGAAUAUCUCCACGCAAAAGUACCGCCAGGUGG
...((((((((((..(.(...(((.....))).).)..)---)))))))))(((((..(((........((((((...))))))((((((.....))).))).........))).))))) ( -53.10)
>DroVir_CAF1 9572 114 + 1
CAUUGGCAGCCGCGCUGGAGAUACAGCGUGCAGCUGCCGCGGCAGCGGCCACCGCGGAGGCAACAAAAGC------UGCCGCUGGUGGCAACAUAUCAGCGCAAAAGUAUCGCCAGGUGG
.........((((.((((.(((((...((((.(((((....))))).((((((((((.(((.......))------).)))).)))))).........))))....))))).)))))))) ( -57.30)
>DroGri_CAF1 9753 114 + 1
CCCUCGCCGCCGCCUUGGAAAUACAGCGUGCAGCGGCGGCGGCAGCGGCAACCGCUGAGGCAACGCGUGC------CGCUGCCGGUGGCAAUAUAUCGGCGCAAAAGUAUCGACAGGUGG
....(((((((((((((......))).(.((((((((((((.((((((...))))))......))).)))------)))))))))))))......(((..((....))..)))..)))). ( -54.80)
>DroEre_CAF1 2292 117 + 1
CACUAGCUGCCGCCUUGGAGAUCCAACGGGCAGCGGCGG---CAGCGGCCACUGCGGAGGCAAAUCGGGCAGCGGGCGCUGCUGGCGGGAAUAUCUCCACGCAAAAGUACCGUCAGGUGG
((((.((((((.(.((((....)))).)))))))(((((---(((((.((.((((.((......))..)))).)).))))))))((((((.....))).))).......))....)))). ( -57.90)
>DroMoj_CAF1 6320 114 + 1
CCCUGGCCGCCGCUCUGGAAAUUCAGCGUGCCGCAGCGGCGGCAGCAGCCACCGCAGAGGCAACCAAAGC------CGCCGCCGGCGGCAACAUAUCAGCGCAAAAGUAUCGCCAGGUGG
.((((((..((.....)).......(((((((...((((.(((....))).))))...))).......((------((((...)))))).........)))).........))))))... ( -49.40)
>DroAna_CAF1 8481 117 + 1
CUUUGGCCGCCGCCUUGGAGAUCCAGCGGGCAGCGGCGG---AGGCAGCCACUGCAGAGGCCAACAGGGCAGCCGGAGCGGCGGGCGGGAAUAUAUCCACCCAGAAGUACCGGCAGGUUG
((((.(((((.(((((((....)))..)))).))))).)---)))(((((.........(((.....))).(((((.((..((((.(((......))).))).)..)).))))).))))) ( -55.60)
>consensus
CACUGGCCGCCGCCUUGGAAAUACAGCGGGCAGCGGCGG___CAGCGGCCACCGCAGAGGCAAACAGGGC______CGCCGCUGGCGGCAAUAUAUCCACGCAAAAGUACCGCCAGGUGG
.....(((((.((((((......)))..))).))))).......((((...))))....((.......))........((((((((((.....................))))).))))) (-26.64 = -25.42 +  -1.22)

alignment

secondary structure

dotplot

Window 0

Location	16,265,109 – 16,265,226
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.09
Mean single sequence MFE	-55.57
Consensus MFE	-23.67
Energy contribution	-23.40
Covariance contribution	-0.27
Combinations/Pair	1.53
Mean z-score	-2.43
Structure conservation index	0.43
SVM decision value	1.11
SVM RNA-class probability	0.917209
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16265109 117 - 22224390
CCACCUGGCGGUACUUUUGCGUGGAGAUAUUCCCGCCAGCGGCGCCCGCUGCCCGAUUUGCCUCAGCGGUGGCCGCCG---CAGCCGCUGCCCGUUGCAUUUCCAAGGCGGCAGCCAAAG
.....(((((((......(((.((((...)))))))..((((((.(((((((..((......)).))))))).)))))---).)))((((((..(((......))))))))).))))... ( -53.10)
>DroVir_CAF1 9572 114 - 1
CCACCUGGCGAUACUUUUGCGCUGAUAUGUUGCCACCAGCGGCA------GCUUUUGUUGCCUCCGCGGUGGCCGCUGCCGCGGCAGCUGCACGCUGUAUCUCCAGCGCGGCUGCCAAUG
.....((((((((..((......))..))))))))...((((((------((....((..((.....))..)).))))))))(((((((((..((((......))))))))))))).... ( -57.10)
>DroGri_CAF1 9753 114 - 1
CCACCUGUCGAUACUUUUGCGCCGAUAUAUUGCCACCGGCAGCG------GCACGCGUUGCCUCAGCGGUUGCCGCUGCCGCCGCCGCUGCACGCUGUAUUUCCAAGGCGGCGGCGAGGG
...(((((((............)))))..(((((...(((((((------((((.(((((...)))))).))))))))))((((((((.....))((......)).))))))))))))). ( -52.70)
>DroEre_CAF1 2292 117 - 1
CCACCUGACGGUACUUUUGCGUGGAGAUAUUCCCGCCAGCAGCGCCCGCUGCCCGAUUUGCCUCCGCAGUGGCCGCUG---CCGCCGCUGCCCGUUGGAUCUCCAAGGCGGCAGCUAGUG
.(((.....(((......(((.((((...)))))))..((((((.(((((((..((......)).))))))).)))))---).)))(((((((.((((....)))).).))))))..))) ( -53.60)
>DroMoj_CAF1 6320 114 - 1
CCACCUGGCGAUACUUUUGCGCUGAUAUGUUGCCGCCGGCGGCG------GCUUUGGUUGCCUCUGCGGUGGCUGCUGCCGCCGCUGCGGCACGCUGAAUUUCCAGAGCGGCGGCCAGGG
...((((((((.....)).(((((......((((((.(((((((------((..((((..((.....))..))))..)))))))))))))))..(((......)))..))))))))))). ( -62.00)
>DroAna_CAF1 8481 117 - 1
CAACCUGCCGGUACUUCUGGGUGGAUAUAUUCCCGCCCGCCGCUCCGGCUGCCCUGUUGGCCUCUGCAGUGGCUGCCU---CCGCCGCUGCCCGCUGGAUCUCCAAGGCGGCGGCCAAAG
......(((((......(((((((........))))))).....))))).......((((((...((((((((.....---..))))))))(((((((....))..))))).)))))).. ( -54.90)
>consensus
CCACCUGGCGAUACUUUUGCGCGGAUAUAUUCCCGCCAGCGGCG______GCCCGAGUUGCCUCAGCGGUGGCCGCUG___CCGCCGCUGCACGCUGGAUCUCCAAGGCGGCGGCCAAAG
.......((((.....))))((((............))))((((......(((....((((....)))).)))))))......((((((((...(((......))).))))))))..... (-23.67 = -23.40 +  -0.27)

alignment

secondary structure

dotplot

Window 1

Location	16,265,148 – 16,265,266
Length	118
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.27
Mean single sequence MFE	-45.60
Consensus MFE	-26.21
Energy contribution	-25.43
Covariance contribution	-0.78
Combinations/Pair	1.30
Mean z-score	-1.78
Structure conservation index	0.57
SVM decision value	0.41
SVM RNA-class probability	0.723498
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16265148 118 + 22224390
--CGGCGGCCACCGCUGAGGCAAAUCGGGCAGCGGGCGCCGCUGGCGGGAAUAUCUCCACGCAAAAGUACCGCCAGGUGGUGAUGAACGCGUUCAUUAAGUGCGAGGGCGGCGGCUACGA
--(((((((..((((((.((....))...))))))..)))))))((((((.....))).)))....((((((((......(((((((....)))))))...((....))))))).))).. ( -52.90)
>DroVir_CAF1 9612 114 + 1
GGCAGCGGCCACCGCGGAGGCAACAAAAGC------UGCCGCUGGUGGCAACAUAUCAGCGCAAAAGUAUCGCCAGGUGGUCAUGAACACGUUCAUCAAGUGCGAGAACGGCGGCUUCGA
(((.(((((((((((((.((((........------))))(((((((....)))..)))).........))))..))))))).......(((((.((......))))))))).))).... ( -43.80)
>DroGri_CAF1 9793 114 + 1
GGCAGCGGCAACCGCUGAGGCAACGCGUGC------CGCUGCCGGUGGCAAUAUAUCGGCGCAAAAGUAUCGACAGGUGGUGAUGAACACGUUCAUCAAAUGCGAAAACGGUGGCUUCGA
((((((((((..(((...(....)))))))------))))))).(.(((....(((((.((((....((((....)))).(((((((....)))))))..))))....)))))))).).. ( -45.30)
>DroEre_CAF1 2331 118 + 1
--CAGCGGCCACUGCGGAGGCAAAUCGGGCAGCGGGCGCUGCUGGCGGGAAUAUCUCCACGCAAAAGUACCGUCAGGUGGUGAUGAACGCGUUCAUUAAGUGCGAAGGCGGCGGCUACGA
--(((((((..((((....((.......)).))))..)))))))((((((.....))).)))....((((((((......(((((((....)))))))...((....))))))).))).. ( -47.10)
>DroMoj_CAF1 6360 114 + 1
GGCAGCAGCCACCGCAGAGGCAACCAAAGC------CGCCGCCGGCGGCAACAUAUCAGCGCAAAAGUAUCGCCAGGUGGUAAUGAAUACAUUCAUCAAAUGCGAAAACGGCGGCUUCGA
(((....)))......(((((..((...((------((((...))))))..........((((....((((((...))))))(((((....)))))....)))).....))..))))).. ( -37.30)
>DroAna_CAF1 8520 118 + 1
--AGGCAGCCACUGCAGAGGCCAACAGGGCAGCCGGAGCGGCGGGCGGGAAUAUAUCCACCCAGAAGUACCGGCAGGUUGUGAUGAACGCGUUCAUAAAGUGCGAGGGCGGUGGCUACGA
--..(.(((((((((....(((..((.(((.(((((.((..((((.(((......))).))).)..)).)))))..))).))(((((....)))))...).))....))))))))).).. ( -47.20)
>consensus
__CAGCGGCCACCGCAGAGGCAAACAGGGC______CGCCGCUGGCGGCAAUAUAUCCACGCAAAAGUACCGCCAGGUGGUGAUGAACACGUUCAUCAAGUGCGAAAACGGCGGCUACGA
....(.((((.(((.....(((...............(((((((((((.....................))))).)))))).(((((....)))))....))).....))).)))).).. (-26.21 = -25.43 +  -0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:09 2006