Locus 6834

Sequence ID	3L_DroMel_CAF1
Location	18,341,737 – 18,341,870
Length	133
Max. P	0.971053

overview

Window 4

Location	18,341,737 – 18,341,838
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.35
Mean single sequence MFE	-25.05
Consensus MFE	-20.20
Energy contribution	-20.15
Covariance contribution	-0.05
Combinations/Pair	1.06
Mean z-score	-2.17
Structure conservation index	0.81
SVM decision value	1.38
SVM RNA-class probability	0.948131
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18341737 101 + 23771897
UUGUGUUUUAUUU-UUU------------CGCCGGAUUUCGCACAAAUCAAAGCGAAAAUUGCUUUGAUUUGAAAGCUUUUUUUUUUU-G----CCA-CAAGCCCCCGGGGCAGACUGUA
(((((........-...------------.((........)).(((((((((((((...)))))))))))))................-.----.))-)))((((...))))........ ( -25.70)
>DroSec_CAF1 126129 98 + 1
UUGUAUUUUAUUU-UUU------------CGCCGGAUUUCGCACAAAUCAAAGCGAAAAUUGCUUUGAUUUGAAAGCUUUU---UUUU-G----CCA-CAAGCCCGCGGGGCAGACUGUA
.............-(..------------(((.((........(((((((((((((...)))))))))))))...((....---....-)----)..-....)).)))..)......... ( -24.80)
>DroEre_CAF1 121759 97 + 1
UCGUAUUUUAUUU--UU------------CGCCGGAUUUCGCACAAAUCAAAGCGUAAAUUGCUUUGAUUUGAAAGCUUUU---UGUU-G----CCA-CAAGCCCCCGGGGCUGACUGUA
.............--..------------...(((.....((.((((((((((((.....))))))))))))..(((....---.)))-)----)..-..(((((...)))))..))).. ( -25.20)
>DroYak_CAF1 132481 97 + 1
UCGUAUUUUAUUU-UUU------------CGUCGGAUUUCGCACAAAUCAAAGCGUAAAUUUCUUUGAUUUGAAAGCAUAU---U-UU-G----CCA-CAAGCCCCCGGGGCUGACUGUA
.............-...------------.(((((.(..((..((((((((((.(.....).))))))))))...(((...---.-.)-)----)..-........))..)))))).... ( -21.70)
>DroAna_CAF1 122896 87 + 1
UGGUUUUUUAUUU-UU---------------------UUCGCACAAAUCAAAGCGUAAAUUGCUUUGAUUUGAAAGCUUUU---U-AU-G----CG--AAGGCCUCCAGGGCUGACUGUA
.((((........-..---------------------((((((((((((((((((.....)))))))))))).........---.-.)-)----))--))((((.....))))))))... ( -26.60)
>DroPer_CAF1 153300 117 + 1
UCUUUUUUUUUUUUUUUGGUUUUUUAUGCCUCUGCAAUUCGCACAAAUCAAAGCGUAAAUUGCUUUGAUUUGAAAGCUUUU---UAUUUGAAUGUUUUAAGGCCUUCCGGGCUGACUGUA
...............(..((((.....((((.(((.....)))((((((((((((.....))))))))))))(((((.(((---.....))).))))).)))).....))))..)..... ( -26.30)
>consensus
UCGUAUUUUAUUU_UUU____________CGCCGGAUUUCGCACAAAUCAAAGCGUAAAUUGCUUUGAUUUGAAAGCUUUU___U_UU_G____CCA_CAAGCCCCCGGGGCUGACUGUA
........................................((.((((((((((((.....))))))))))))...))........................((((...))))........ (-20.20 = -20.15 +  -0.05)

alignment

secondary structure

dotplot

Window 5

Location	18,341,737 – 18,341,838
Length	101
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.35
Mean single sequence MFE	-24.93
Consensus MFE	-20.08
Energy contribution	-20.25
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-3.02
Structure conservation index	0.81
SVM decision value	1.67
SVM RNA-class probability	0.971053
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18341737 101 - 23771897
UACAGUCUGCCCCGGGGGCUUG-UGG----C-AAAAAAAAAAAGCUUUCAAAUCAAAGCAAUUUUCGCUUUGAUUUGUGCGAAAUCCGGCG------------AAA-AAAUAAAACACAA
....(((((((.(((....)))-.))----)-)..........((...(((((((((((.......))))))))))).)).......))).------------...-............. ( -25.30)
>DroSec_CAF1 126129 98 - 1
UACAGUCUGCCCCGCGGGCUUG-UGG----C-AAAA---AAAAGCUUUCAAAUCAAAGCAAUUUUCGCUUUGAUUUGUGCGAAAUCCGGCG------------AAA-AAAUAAAAUACAA
((((((((((...)))))).))-))(----(-....---....((...(((((((((((.......))))))))))).))........)).------------...-............. ( -27.89)
>DroEre_CAF1 121759 97 - 1
UACAGUCAGCCCCGGGGGCUUG-UGG----C-AACA---AAAAGCUUUCAAAUCAAAGCAAUUUACGCUUUGAUUUGUGCGAAAUCCGGCG------------AA--AAAUAAAAUACGA
........(((..(..(((((.-((.----.-..))---..)))))..)((((((((((.......))))))))))...........))).------------..--............. ( -28.10)
>DroYak_CAF1 132481 97 - 1
UACAGUCAGCCCCGGGGGCUUG-UGG----C-AA-A---AUAUGCUUUCAAAUCAAAGAAAUUUACGCUUUGAUUUGUGCGAAAUCCGACG------------AAA-AAAUAAAAUACGA
....((((((((...)))))..-...----.-..-.---...(((...((((((((((.........)))))))))).)))......))).------------...-............. ( -22.60)
>DroAna_CAF1 122896 87 - 1
UACAGUCAGCCCUGGAGGCCUU--CG----C-AU-A---AAAAGCUUUCAAAUCAAAGCAAUUUACGCUUUGAUUUGUGCGAA---------------------AA-AAAUAAAAAACCA
........(((.....))).((--((----(-(.-.---.........(((((((((((.......)))))))))))))))))---------------------..-............. ( -21.60)
>DroPer_CAF1 153300 117 - 1
UACAGUCAGCCCGGAAGGCCUUAAAACAUUCAAAUA---AAAAGCUUUCAAAUCAAAGCAAUUUACGCUUUGAUUUGUGCGAAUUGCAGAGGCAUAAAAAACCAAAAAAAAAAAAAAAGA
....(((((.((....)).))...............---....((...(((((((((((.......))))))))))).))..........)))........................... ( -24.10)
>consensus
UACAGUCAGCCCCGGGGGCUUG_UGG____C_AA_A___AAAAGCUUUCAAAUCAAAGCAAUUUACGCUUUGAUUUGUGCGAAAUCCGGCG____________AAA_AAAUAAAAUACGA
.....((.(((.....)))........................((...(((((((((((.......))))))))))).))))...................................... (-20.08 = -20.25 +   0.17)

alignment

secondary structure

dotplot

Window 6

Location	18,341,764 – 18,341,870
Length	106
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	81.35
Mean single sequence MFE	-29.53
Consensus MFE	-21.35
Energy contribution	-21.38
Covariance contribution	0.03
Combinations/Pair	1.06
Mean z-score	-2.29
Structure conservation index	0.72
SVM decision value	0.93
SVM RNA-class probability	0.884271
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18341764 106 + 23771897
GCACAAAUCAAAGCGAAAAUUGCUUUGAUUUGAAAGCUUUUUUUUUUUGCCACAAGCCCCCGGGGCAGACUGUACCUCUCAGCCAAAUGAACGAA--AGGAAUUGGAG
...(((((((((((((...)))))))))))))....((..(((((((((......((((...)))).(.(((.......))).).......))))--)))))..)).. ( -29.10)
>DroSec_CAF1 126156 93 + 1
GCACAAAUCAAAGCGAAAAUUGCUUUGAUUUGAAAGCUUUU---UUUUGCCACAAGCCCGCGGGGCAGACUGUACCUCUCAGCCA------------AAGAAGCGGAG
...(((((((((((((...)))))))))))))...((((((---((.........((((...)))).(.(((.......))).))------------))))))).... ( -29.70)
>DroSim_CAF1 136365 104 + 1
GCACAAAUCAAAGCGAAAAUUGCUUUGAUUUGAAAGCUUUU--UUUUUGCCACAAGCCCGCGGGGCAGACUGUACCUCUCAGCGAAAUGAACGAA--AAGAAGCGGAG
...(((((((((((((...)))))))))))))...((((((--((((........((((...)))).(.(((.......)))).........)))--))))))).... ( -31.90)
>DroEre_CAF1 121785 103 + 1
GCACAAAUCAAAGCGUAAAUUGCUUUGAUUUGAAAGCUUUU---UGUUGCCACAAGCCCCCGGGGCUGACUGUACCUCUCAGCCAAAUGAACGCA--GAGAAGUGGAG
((.((((((((((((.....))))))))))))...))....---.....((((.(((((...))))).........((((.((.........)).--)))).)))).. ( -32.80)
>DroYak_CAF1 132508 104 + 1
GCACAAAUCAAAGCGUAAAUUUCUUUGAUUUGAAAGCAUAU---U-UUGCCACAAGCCCCCGGGGCUGACUGUACCUUUCAGCCAAAUGAACGAGAGUAGAAGUGGAG
((.((((((((((.(.....).))))))))))...))....---.-...((((.(((((...)))))...(.(((((((((......)))..))).))).).)))).. ( -26.90)
>DroAna_CAF1 122914 83 + 1
GCACAAAUCAAAGCGUAAAUUGCUUUGAUUUGAAAGCUUUU---U-AUGCG-AAGGCCUCCAGGGCUGACUGUACCCGCCAGCCAAAU--------------------
...((((((((((((.....))))))))))))...((((((---.-....)-)))))......(((((.(.......).)))))....-------------------- ( -26.80)
>consensus
GCACAAAUCAAAGCGAAAAUUGCUUUGAUUUGAAAGCUUUU___UUUUGCCACAAGCCCCCGGGGCAGACUGUACCUCUCAGCCAAAUGAACGAA__AAGAAGUGGAG
((.((((((((((((.....)))))))))))).......................((((...))))...............))......................... (-21.35 = -21.38 +   0.03)

alignment

secondary structure

dotplot

Window 7

Location	18,341,764 – 18,341,870
Length	106
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	81.35
Mean single sequence MFE	-30.74
Consensus MFE	-24.62
Energy contribution	-25.50
Covariance contribution	0.88
Combinations/Pair	1.04
Mean z-score	-2.48
Structure conservation index	0.80
SVM decision value	1.22
SVM RNA-class probability	0.932821
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18341764 106 - 23771897
CUCCAAUUCCU--UUCGUUCAUUUGGCUGAGAGGUACAGUCUGCCCCGGGGGCUUGUGGCAAAAAAAAAAAGCUUUCAAAUCAAAGCAAUUUUCGCUUUGAUUUGUGC
........(((--((((..(....)..)))))))....(((.((((...))))....)))...........((...(((((((((((.......))))))))))).)) ( -30.90)
>DroSec_CAF1 126156 93 - 1
CUCCGCUUCUU------------UGGCUGAGAGGUACAGUCUGCCCCGCGGGCUUGUGGCAAAA---AAAAGCUUUCAAAUCAAAGCAAUUUUCGCUUUGAUUUGUGC
(((.(((....------------.))).))).(.((((((((((...)))))).)))).)....---....((...(((((((((((.......))))))))))).)) ( -32.30)
>DroSim_CAF1 136365 104 - 1
CUCCGCUUCUU--UUCGUUCAUUUCGCUGAGAGGUACAGUCUGCCCCGCGGGCUUGUGGCAAAAA--AAAAGCUUUCAAAUCAAAGCAAUUUUCGCUUUGAUUUGUGC
..(((((((((--..((.......))..)))))))(((((((((...)))))).)))))......--....((...(((((((((((.......))))))))))).)) ( -32.20)
>DroEre_CAF1 121785 103 - 1
CUCCACUUCUC--UGCGUUCAUUUGGCUGAGAGGUACAGUCAGCCCCGGGGGCUUGUGGCAACA---AAAAGCUUUCAAAUCAAAGCAAUUUACGCUUUGAUUUGUGC
....(((((((--.((.........)).)))))))...((((((((...))))...))))....---....((...(((((((((((.......))))))))))).)) ( -33.80)
>DroYak_CAF1 132508 104 - 1
CUCCACUUCUACUCUCGUUCAUUUGGCUGAAAGGUACAGUCAGCCCCGGGGGCUUGUGGCAA-A---AUAUGCUUUCAAAUCAAAGAAAUUUACGCUUUGAUUUGUGC
..((((.....((((((.....(((((((.......)))))))...))))))...))))...-.---....((...((((((((((.........)))))))))).)) ( -27.60)
>DroAna_CAF1 122914 83 - 1
--------------------AUUUGGCUGGCGGGUACAGUCAGCCCUGGAGGCCUU-CGCAU-A---AAAAGCUUUCAAAUCAAAGCAAUUUACGCUUUGAUUUGUGC
--------------------....(((((((.......)))))))..((((((...-.....-.---....))))))((((((((((.......)))))))))).... ( -27.62)
>consensus
CUCCACUUCUU__UUCGUUCAUUUGGCUGAGAGGUACAGUCAGCCCCGGGGGCUUGUGGCAAAA___AAAAGCUUUCAAAUCAAAGCAAUUUACGCUUUGAUUUGUGC
..((((..................(((((.......))))).(((.....)))..))))............((...(((((((((((.......))))))))))).)) (-24.62 = -25.50 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:30:55 2006