Locus 2270

Sequence ID	2R_DroMel_CAF1
Location	8,366,026 – 8,366,159
Length	133
Max. P	0.844171

overview

Window 4

Location	8,366,026 – 8,366,140
Length	114
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	80.75
Mean single sequence MFE	-41.07
Consensus MFE	-30.77
Energy contribution	-30.25
Covariance contribution	-0.52
Combinations/Pair	1.33
Mean z-score	-1.39
Structure conservation index	0.75
SVM decision value	0.32
SVM RNA-class probability	0.685988
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8366026 114 - 20766785
UUCAGCGCCUGUGGUGGUGACCUCCGCCACCCACACGGCUCCCGGCGGAUAUCCGGUCACACAGCUGCCUCCGCCGGGCUAUCCAUCGAGCAAUGCCUACGUAACUGCGACCUC
....(((((((((((((((.....))))).))))).))).(((((((((....((((......))))..)))))))))...........))........(((....)))..... ( -45.20)
>DroPse_CAF1 4716 108 - 1
UGCAGCUCCAGUAGUGGUGACUUCUGCUACACACACAGCCCCUGGAGGUUAUCCUGUUACACAAUUGCCCCCGCCUGGCUAUCCGGCUGGAAAUGCCUACGCCGCU------CC
.(((..((((((.((((((..........))).)))((((..(((.(((.....((.....))...))).)))...)))).....))))))..)))..........------.. ( -28.80)
>DroEre_CAF1 4616 114 - 1
UGCAGCGCCCGUGGUGGUGACUUCCGCCACGCACACAGCUCCCGGCGGAUAUCCGGUCACACAGCUGCCUCCGCCAGGCUAUCCGGCGGGCAAUGCCUACGUAACUUCACCCUC
.(((..(((((((((((......)))))))((....((((...((((((....((((......))))..)))))).)))).....))))))..))).................. ( -44.50)
>DroYak_CAF1 4633 114 - 1
UGCAGCGCCCGUGGUGGUGACCUCCGCCACGCACACGGCUCCCGGCGGAUAUCCGGUCACACAGCUGCCUCCGCCGGGCUAUCCGGCGGGCAAUGCCUACGUAACUUCAACCUC
.(((..(((((((((((......)))))))((...(((..(((((((((....((((......))))..)))))))))....)))))))))..))).................. ( -51.30)
>DroAna_CAF1 14631 114 - 1
UGCAGCACCCGUGGUGGUGACUUCCGCCACCCACGCAGCACCCGGCGGCUAUCCGGUCACCCAGCUGCCUCCGCCUGGCUAUCCGGCGCCCAAUUCCUACACAACGGUGGCCGC
.((.((...((((((((((.....))))).)))))...((((.(((((((....((....)))))))))..((((.((....)))))).................)))))).)) ( -41.80)
>DroPer_CAF1 4688 108 - 1
UGCAGCUCCAGUAGUGGUGACUUCCGCUACACACACAGCCCCUGGCGGUUAUCCUGUUACGCAACUGCCCCCGCCUGGCUAUCCGGCUGGAAAUGCCUACGCCGCU------CC
.(((..((((((.((((((.....))))))......((((...(((((.......(((....))).....))))).)))).....))))))..)))..........------.. ( -34.80)
>consensus
UGCAGCGCCCGUGGUGGUGACUUCCGCCACACACACAGCUCCCGGCGGAUAUCCGGUCACACAGCUGCCUCCGCCUGGCUAUCCGGCGGGCAAUGCCUACGCAACU_C__CCUC
.(((..(((((((((((......)))))))......((((...(((((.....((((......))))...))))).)))).......))))..))).................. (-30.77 = -30.25 +  -0.52)

alignment

secondary structure

dotplot

Window 5

Location	8,366,060 – 8,366,159
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	80.41
Mean single sequence MFE	-38.62
Consensus MFE	-23.69
Energy contribution	-24.33
Covariance contribution	0.64
Combinations/Pair	1.22
Mean z-score	-1.82
Structure conservation index	0.61
SVM decision value	0.34
SVM RNA-class probability	0.694550
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8366060 99 + 20766785
AGCCCGGCGGAGGCAGCUGUGUGACCGGAUAUCCGCCGGGAGCCGUGUGGGUGGCGGAGGUCACCACCACAGGCGCUGAAAGUAGAAAGAACGGAAAAA
..(((((((((.....(((......)))...))))))))).((((((..((((((....))))))..))).)))......................... ( -41.30)
>DroPse_CAF1 4744 98 + 1
AGCCAGGCGGGGGCAAUUGUGUAACAGGAUAACCUCCAGGGGCUGUGUGUGUAGCAGAAGUCACCACUACUGGAGCUGCAACGGCAGAGAUUAGAAU-U
..((((..(((((..(((.((...)).)))..))))).((((((.(((.....)))..)))).))....))))..((((....))))..........-. ( -28.50)
>DroEre_CAF1 4650 98 + 1
AGCCUGGCGGAGGCAGCUGUGUGACCGGAUAUCCGCCGGGAGCUGUGUGCGUGGCGGAAGUCACCACCACGGGCGCUGCAAGGAGCAAGAACGGAAA-A
..(((((((((.....(((......)))...))))))))).((.((((.(((((.((......)).))))).)))).))..................-. ( -41.90)
>DroYak_CAF1 4667 98 + 1
AGCCCGGCGGAGGCAGCUGUGUGACCGGAUAUCCGCCGGGAGCCGUGUGCGUGGCGGAGGUCACCACCACGGGCGCUGCAAGGAGCAAGAGCGGAAA-A
..(((((((((.....(((......)))...))))))))).((.((((.(((((.((......)).))))).)))).)).....((....)).....-. ( -45.30)
>DroAna_CAF1 14665 96 + 1
AGCCAGGCGGAGGCAGCUGGGUGACCGGAUAGCCGCCGGGUGCUGCGUGGGUGGCGGAAGUCACCACCACGGGUGCUGCAAUGA--AAAAAAUGAAC-A
.((..(((((......((((....))))....))))).((..((.((((((((((....)))))..)))))))..)))).....--...........-. ( -43.60)
>DroPer_CAF1 4716 98 + 1
AGCCAGGCGGGGGCAGUUGCGUAACAGGAUAACCGCCAGGGGCUGUGUGUGUAGCGGAAGUCACCACUACUGGAGCUGCAACGGCAGAGAUUAGAAU-U
.(((..((....)).(((((((..(((....((.(((...))).))(((.((..(....)..)))))..)))..)).))))))))............-. ( -31.10)
>consensus
AGCCAGGCGGAGGCAGCUGUGUGACCGGAUAUCCGCCGGGAGCUGUGUGCGUGGCGGAAGUCACCACCACGGGCGCUGCAAGGAGAAAGAACGGAAA_A
.(((((((((..((......))..((((.......))))...))))(((.(((((....))))))))..)))))......................... (-23.69 = -24.33 +   0.64)

alignment

secondary structure

dotplot

Window 6

Location	8,366,060 – 8,366,159
Length	99
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	80.41
Mean single sequence MFE	-33.17
Consensus MFE	-24.08
Energy contribution	-23.42
Covariance contribution	-0.66
Combinations/Pair	1.30
Mean z-score	-1.80
Structure conservation index	0.73
SVM decision value	0.76
SVM RNA-class probability	0.844171
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8366060 99 - 20766785
UUUUUCCGUUCUUUCUACUUUCAGCGCCUGUGGUGGUGACCUCCGCCACCCACACGGCUCCCGGCGGAUAUCCGGUCACACAGCUGCCUCCGCCGGGCU
......................((((((((((((((((.....))))).))))).)))..((((((((....((((......))))..))))))))))) ( -41.40)
>DroPse_CAF1 4744 98 - 1
A-AUUCUAAUCUCUGCCGUUGCAGCUCCAGUAGUGGUGACUUCUGCUACACACACAGCCCCUGGAGGUUAUCCUGUUACACAAUUGCCCCCGCCUGGCU
.-..........((((....)))).....((((..(......)..))))......((((..(((.(((.....((.....))...))).)))...)))) ( -21.50)
>DroEre_CAF1 4650 98 - 1
U-UUUCCGUUCUUGCUCCUUGCAGCGCCCGUGGUGGUGACUUCCGCCACGCACACAGCUCCCGGCGGAUAUCCGGUCACACAGCUGCCUCCGCCAGGCU
.-.........((((.....)))).(((((((((((......))))))))............((((((....((((......))))..)))))).))). ( -35.10)
>DroYak_CAF1 4667 98 - 1
U-UUUCCGCUCUUGCUCCUUGCAGCGCCCGUGGUGGUGACCUCCGCCACGCACACGGCUCCCGGCGGAUAUCCGGUCACACAGCUGCCUCCGCCGGGCU
.-.....(((...((.....)))))(((((((((((......)))))))).....))).(((((((((....((((......))))..))))))))).. ( -42.50)
>DroAna_CAF1 14665 96 - 1
U-GUUCAUUUUUU--UCAUUGCAGCACCCGUGGUGGUGACUUCCGCCACCCACGCAGCACCCGGCGGCUAUCCGGUCACCCAGCUGCCUCCGCCUGGCU
.-...........--.....((.((....(((((((((.....))))).))))(((((....((.((((....)))).))..)))))....))...)). ( -30.60)
>DroPer_CAF1 4716 98 - 1
A-AUUCUAAUCUCUGCCGUUGCAGCUCCAGUAGUGGUGACUUCCGCUACACACACAGCCCCUGGCGGUUAUCCUGUUACGCAACUGCCCCCGCCUGGCU
.-..........((((....)))).....(((((((......)))))))......((((...(((((.......(((....))).....))))).)))) ( -27.90)
>consensus
U_UUUCCGUUCUUUCUCCUUGCAGCGCCCGUGGUGGUGACUUCCGCCACACACACAGCUCCCGGCGGAUAUCCGGUCACACAGCUGCCUCCGCCUGGCU
.............................(((((((......)))))))......((((...(((((.....((((......))))...))))).)))) (-24.08 = -23.42 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:15 2006