Locus 4945

Sequence ID	2R_DroMel_CAF1
Location	16,120,916 – 16,121,030
Length	114
Max. P	0.943390

overview

Window 2

Location	16,120,916 – 16,121,030
Length	114
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	82.54
Mean single sequence MFE	-33.07
Consensus MFE	-25.93
Energy contribution	-25.63
Covariance contribution	-0.30
Combinations/Pair	1.10
Mean z-score	-3.24
Structure conservation index	0.78
SVM decision value	1.33
SVM RNA-class probability	0.943390
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16120916 114 + 20766785
UUGGUCCUCCUGGGAGUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUUUGGUAA---UAACAAUAAAUCCCUUGUCUUCUUACGGCGUGCAUUUG-UGCUCUUCAUUC-
.....((....))((((((((.(((((.(((((((.((.(((((.((((((....(....)...---.))))))))))).)).)))))))))))).)))))))).-............- ( -36.10)
>DroVir_CAF1 12116 110 + 1
---GUCGU-CUCCAAAUGCUUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUCUGCUAA---UAACAAUAAAUCCCUUGUCUUCUUAUGGCGCGCAUU-C-UGCUCUUCAUUUA
---.....-.....(((((...(((((.(((((((.((.((((((((((((.(((....)))))---)))))..))))).)).))))))))))))...)))))-.-............. ( -28.40)
>DroGri_CAF1 11925 108 + 1
---AUCGG-UUU-AAAUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUUUGUUAA---UAACAAUAAAUCCCUUGUCUCCUAACGGCGCGCAUU-G-UGCUCUUCAUUA-
---...((-(..-.(((((...((((..(((.(((.((.((((((((((((...........))---)))))..))))).)).))))))..))))...)))))-.-.)))........- ( -27.10)
>DroWil_CAF1 13120 117 + 1
UUGUGUGUGG-UGGAAUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUUUAAUAAAAUUAACAAUAAAUCCCUUGUCUUCUUAUGGCGUGUAUUUAAAGCUCUUCAUUU-
..(((...((-(.((((((((.(((((.(((((((.((.(((((.((((((.................))))))))))).)).)))))))))))).))))))))...)))...)))..- ( -33.73)
>DroMoj_CAF1 12885 111 + 1
UC-GUCGU-AUC-GAGUGCUUGCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUCUGCUAA---UAACAAUAAAUCCCUUGUCUUCUUAUGGCUCGCAUU-G-AGCUCUUCAUUUC
..-...((-.((-.(((((..((((((.(((((((.((.((((((((((((.(((....)))))---)))))..))))).)).)))))))))))))..)))))-)-))).......... ( -34.90)
>DroAna_CAF1 10616 112 + 1
GGAGUCCU-GUGGAAGUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUUUAUGGUAA---UAACAAUAAAUCCCUUGUCUUCUUACGGCGUGCAUUCG--GCUCAUCACUC-
.((((...-((.(((.(((((.(((((.(((((((.((.((((((((((((...........))---)))))..))))).)).)))))))))))).)))))))).--)).....))))- ( -38.20)
>consensus
U__GUCGU_CUCGAAAUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUUUGCUAA___UAACAAUAAAUCCCUUGUCUUCUUACGGCGCGCAUU_G_UGCUCUUCAUUU_
..............(((((...(((((.(((((((.((.(((((.((((((.................))))))))))).)).))))))))))))...)))))................ (-25.93 = -25.63 +  -0.30)

alignment

secondary structure

dotplot

Window 3

Location	16,120,916 – 16,121,030
Length	114
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	82.54
Mean single sequence MFE	-25.02
Consensus MFE	-16.62
Energy contribution	-16.90
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-2.25
Structure conservation index	0.66
SVM decision value	0.43
SVM RNA-class probability	0.731431
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16120916 114 - 20766785
-GAAUGAAGAGCA-CAAAUGCACGCCGUAAGAAGACAAGGGAUUUAUUGUUA---UUACCAAAGACCAAACAACAAAAUCACUAGUCUUCCAUACGGAAUGCACUCCCAGGAGGACCAA
-............-....((((..(((((.((((((.((.(((((.(((((.---.............)))))..))))).)).))))))..)))))..))))(((....)))...... ( -29.34)
>DroVir_CAF1 12116 110 - 1
UAAAUGAAGAGCA-G-AAUGCGCGCCAUAAGAAGACAAGGGAUUUAUUGUUA---UUAGCAGAGACCAAACAACAAAAUCACUAGUCUUCCAUACGGAAAGCAUUUGGAG-ACGAC---
.............-(-(((((...((.((.((((((.((.(((((.(((((.---.............)))))..))))).)).))))))..)).))...))))))(...-.)...--- ( -23.64)
>DroGri_CAF1 11925 108 - 1
-UAAUGAAGAGCA-C-AAUGCGCGCCGUUAGGAGACAAGGGAUUUAUUGUUA---UUAACAAAGACCAAACAACAAAAUCACUAGUCUUCCAUACGGAAUGCAUUU-AAA-CCGAU---
-............-.-((((((..((((..((((((.((.(((((.(((((.---.............)))))..))))).)).))))))...))))..)))))).-...-.....--- ( -25.44)
>DroWil_CAF1 13120 117 - 1
-AAAUGAAGAGCUUUAAAUACACGCCAUAAGAAGACAAGGGAUUUAUUGUUAAUUUUAUUAAAGACCAAACAACAAAAUCACUAGUCUUCCAUACGGAAUGCAUUCCA-CCACACACAA
-..(((..(.((...........)))....((((((.((.(((((.(((((..((((....))))...)))))..))))).)).)))))))))..((((....)))).-.......... ( -16.80)
>DroMoj_CAF1 12885 111 - 1
GAAAUGAAGAGCU-C-AAUGCGAGCCAUAAGAAGACAAGGGAUUUAUUGUUA---UUAGCAGAGACCAAACAACAAAAUCACUAGUCUUCCAUACGGCAAGCACUC-GAU-ACGAC-GA
........(((..-.-..(((..(((.((.((((((.((.(((((.(((((.---.............)))))..))))).)).))))))..)).)))..))))))-...-.....-.. ( -23.14)
>DroAna_CAF1 10616 112 - 1
-GAGUGAUGAGC--CGAAUGCACGCCGUAAGAAGACAAGGGAUUUAUUGUUA---UUACCAUAAACCAAACAACAAAAUCACUAGUCUUCCAUACGGAAUGCACUUCCAC-AGGACUCC
-((((..((...--.(((((((..(((((.((((((.((.(((((.(((((.---.............)))))..))))).)).))))))..)))))..)))).)))..)-)..)))). ( -31.74)
>consensus
_AAAUGAAGAGCA_C_AAUGCACGCCAUAAGAAGACAAGGGAUUUAUUGUUA___UUACCAAAGACCAAACAACAAAAUCACUAGUCUUCCAUACGGAAUGCACUCCAAC_ACGAC__A
..................((((..((....((((((.((.(((((.(((((.................)))))..))))).)).)))))).....))..))))................ (-16.62 = -16.90 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:53 2006