Locus 6707

Sequence ID	3L_DroMel_CAF1
Location	17,904,167 – 17,904,279
Length	112
Max. P	0.955935

overview

Window 5

Location	17,904,167 – 17,904,279
Length	112
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	85.64
Mean single sequence MFE	-34.40
Consensus MFE	-28.00
Energy contribution	-28.67
Covariance contribution	0.67
Combinations/Pair	1.16
Mean z-score	-3.37
Structure conservation index	0.81
SVM decision value	1.46
SVM RNA-class probability	0.955935
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17904167 112 + 23771897
CAGCGCAGGUUAUUGACUUCCCCA-AGUAGCCUCACGUGAGGCUGCGAAUUAAAAAUCCAAACAUUUAUAAUUGCUG----UUCAUUAACCGAACGAA-AAACGGCCUAAAGCACU--GA
(((.((.(((((.(((........-.((((((((....)))))))).(((((.((((......)))).)))))....----.))).)))))(..((..-...))..)....)).))--). ( -30.70)
>DroSec_CAF1 27971 112 + 1
CAGCGCAGGUUAUUGACUUCCCCA-AGUAGCCUCACGUGAGGCUGCGAAUUAAAAAUCCAAACAUUUAUAAUUGCUG----UUCAUUAACCGGCCGAA-AAACGGCCUAAAGCACC--GA
....((.(((((.(((........-.((((((((....)))))))).(((((.((((......)))).)))))....----.))).)))))(((((..-...)))))....))...--.. ( -36.20)
>DroSim_CAF1 28228 113 + 1
CAGCGCAGGUUAUUGACUUCCCCAAAGUAGCCUCACGUGAGGCUGCGAAUUAAAAAUCCAAACAUUUAUAAUUGCUG----UUCAUUAAACGGCCGAA-AAACGGCCUAAAGCACC--GA
..((((((..................((((((((....)))))))).(((((.((((......)))).))))).)))----).........(((((..-...)))))....))...--.. ( -31.10)
>DroEre_CAF1 29192 114 + 1
CGGCGCAGGUUAUUGACUCCCCGA-AAUAGCCUCACGUGAGGCUGUGAAUUACCAGUCCAAACAUUUGUAAUUGCUG----UUCAUUAACCGGCCGAA-AAGCGGCCUAAAGCGCCUCCA
.(((((.(((((.(((........-.((((((((....)))))))).((((((.(((......))).))))))....----.))).)))))(((((..-...)))))....))))).... ( -44.40)
>DroYak_CAF1 29796 112 + 1
AAGCGCAGGUUAUUGACUCCCCGA-AAUAGCCUCACGUGAGGCUGUGAAUUAAAAAUACAAACAUUUAUAAUUGCUG----UUCACUAACCGGCCGAA-AAGCGGCCUAAAGCACC--AA
....((.(((((.(((........-.((((((((....)))))))).(((((.((((......)))).)))))....----.))).)))))(((((..-...)))))....))...--.. ( -33.60)
>DroAna_CAF1 26877 114 + 1
---UUCAGGUUAUUGACUUCCCGA-AAUAGCCUCACGUGAGGCUGUGAAUUAAAAAGCCAAAUAAUUAUGAUGGCUAUUUGCUCAUUAAACGGUUGAAAAAACGGCCUAAGCCUCG--AA
---.((((((((((..........-)))))))).....((((((((((..((((.(((((...........))))).)))).)))).....(((((......)))))..)))))))--). ( -30.40)
>consensus
CAGCGCAGGUUAUUGACUUCCCCA_AAUAGCCUCACGUGAGGCUGCGAAUUAAAAAUCCAAACAUUUAUAAUUGCUG____UUCAUUAACCGGCCGAA_AAACGGCCUAAAGCACC__GA
....((.(((((.(((..........((((((((....)))))))).(((((.((((......)))).))))).........))).)))))(((((......)))))....))....... (-28.00 = -28.67 +   0.67)

alignment

secondary structure

dotplot

Window 6

Location	17,904,167 – 17,904,279
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	85.64
Mean single sequence MFE	-35.38
Consensus MFE	-26.14
Energy contribution	-27.58
Covariance contribution	1.45
Combinations/Pair	1.17
Mean z-score	-2.16
Structure conservation index	0.74
SVM decision value	-0.05
SVM RNA-class probability	0.508371
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17904167 112 - 23771897
UC--AGUGCUUUAGGCCGUUU-UUCGUUCGGUUAAUGAA----CAGCAAUUAUAAAUGUUUGGAUUUUUAAUUCGCAGCCUCACGUGAGGCUACU-UGGGGAAGUCAAUAACCUGCGCUG
.(--(((((....(..((...-..))..)(((((.(((.----..(((((((.((((......)))).))))).))((((((....))))))...-........))).))))).)))))) ( -32.30)
>DroSec_CAF1 27971 112 - 1
UC--GGUGCUUUAGGCCGUUU-UUCGGCCGGUUAAUGAA----CAGCAAUUAUAAAUGUUUGGAUUUUUAAUUCGCAGCCUCACGUGAGGCUACU-UGGGGAAGUCAAUAACCUGCGCUG
.(--(((((....(((((...-..)))))(((((.(((.----..(((((((.((((......)))).))))).))((((((....))))))...-........))).))))).)))))) ( -40.10)
>DroSim_CAF1 28228 113 - 1
UC--GGUGCUUUAGGCCGUUU-UUCGGCCGUUUAAUGAA----CAGCAAUUAUAAAUGUUUGGAUUUUUAAUUCGCAGCCUCACGUGAGGCUACUUUGGGGAAGUCAAUAACCUGCGCUG
.(--(((((....(((((...-..))))).......(((----((...........))))).(((((((.......((((((....)))))).......)))))))........)))))) ( -33.84)
>DroEre_CAF1 29192 114 - 1
UGGAGGCGCUUUAGGCCGCUU-UUCGGCCGGUUAAUGAA----CAGCAAUUACAAAUGUUUGGACUGGUAAUUCACAGCCUCACGUGAGGCUAUU-UCGGGGAGUCAAUAACCUGCGCCG
....(((((...(((..((((-..(((((((((...(((----((...........))))).))))))).......((((((....))))))...-.))..))))......)))))))). ( -41.10)
>DroYak_CAF1 29796 112 - 1
UU--GGUGCUUUAGGCCGCUU-UUCGGCCGGUUAGUGAA----CAGCAAUUAUAAAUGUUUGUAUUUUUAAUUCACAGCCUCACGUGAGGCUAUU-UCGGGGAGUCAAUAACCUGCGCUU
..--(((((....(((((...-..)))))((((((((((----.......(((((....))))).......)))))((((((....))))))...-............))))).))))). ( -35.44)
>DroAna_CAF1 26877 114 - 1
UU--CGAGGCUUAGGCCGUUUUUUCAACCGUUUAAUGAGCAAAUAGCCAUCAUAAUUAUUUGGCUUUUUAAUUCACAGCCUCACGUGAGGCUAUU-UCGGGAAGUCAAUAACCUGAA---
.(--(.(((.((((((..(((.((((.........)))).)))..)))...........(((((((((..(.....((((((....))))))...-)..))))))))))))))))).--- ( -29.50)
>consensus
UC__GGUGCUUUAGGCCGUUU_UUCGGCCGGUUAAUGAA____CAGCAAUUAUAAAUGUUUGGAUUUUUAAUUCACAGCCUCACGUGAGGCUACU_UCGGGAAGUCAAUAACCUGCGCUG
....(((((....(((((......)))))(((((.(((......................(((((.....))))).((((((....))))))............))).))))).))))). (-26.14 = -27.58 +   1.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:09 2006