Locus 1924

Sequence ID 2R_DroMel_CAF1
Location 7,247,764 – 7,247,908
Length 144
Max. P 0.989954
window3179 window3180 window3181

overview

Window 9

Location 7,247,764 – 7,247,873
Length 109
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 70.36
Mean single sequence MFE -18.04
Consensus MFE -12.90
Energy contribution -12.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.72
SVM decision value 2.19
SVM RNA-class probability 0.989954
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7247764 109 + 20766785
UCUCGAAUGUGAUAUUCUCAGACCCCUCAAACUCCUCCCCGCC--CCCCGUAAAAAAAAAAAAACUUAGGUGUCAAUAUUCCGUUCUAUUGACGCCCUCGAACAAUAACCC
..((((.(.(((.....))).).....................--.......................((((((((((........)))))))))).)))).......... ( -16.20)
>DroPse_CAF1 37748 85 + 1
---------GGGGUUUGUCGCCCCCCUCCUCCUACCCCCUCGU---CCC--------------AGUGAGGUGUCAAUAUCCCGUUCUAUUGACGCCCUCGAACAAUGGCCC
---------(((((.....)))))...................---.((--------------(.(((((((((((((........)))))))).))))).....)))... ( -24.60)
>DroSec_CAF1 43286 103 + 1
UCUCGAAUGUGAUAUUCUCAGACCCCUACCAUUUCCCUCUCCC---CCC-----AAAAAAAAGACUGAGGUGUCAAUAUUCCGUUCUAUUGACGCCCUCGAACAAUAACCC
..((((...........((((......................---...-----..........))))((((((((((........)))))))))).)))).......... ( -16.55)
>DroSim_CAF1 45880 106 + 1
UCUCGAAUGUGAUAUUCUCAGACCCCUACCAUUUCCCUCUCCCCCCCCC-----AAAAAAAAGACUGAGGUGUCAAUAUUCCGUUCUAUUGACGCCCUCGAACAAUAACCC
..((((...........((((............................-----..........))))((((((((((........)))))))))).)))).......... ( -16.46)
>DroYak_CAF1 44961 94 + 1
UCUCGAAUGCGAUAUUCUCAGACCCCUACCUUUUU-----UC----CCC--------AAAACGACUAAGGUGUCAAUAUUCCGUUCUAUUGACGCCCUCGAACAAUAACCC
..((((..((.................(((((...-----((----...--------.....))..)))))(((((((........)))))))))..)))).......... ( -16.50)
>DroAna_CAF1 41183 94 + 1
-CCCCAAGUCGAAAUUCUUAACCCCCUCCA---UC-----GC----GCCAAUACCUAAUAUAAUGUGAGGUGUCAAUAUUCCGUUCUAUUGACGCCCUCGAACAAUG----
-.......((((..................---((-----((----(...(((.....)))..)))))((((((((((........)))))))))).))))......---- ( -17.90)
>consensus
UCUCGAAUGUGAUAUUCUCAGACCCCUACCAUUUCCC_CUCCC___CCC_____AAAAAAAAGACUGAGGUGUCAAUAUUCCGUUCUAUUGACGCCCUCGAACAAUAACCC
....................................................................((((((((((........))))))))))............... (-12.90 = -12.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,247,796 – 7,247,908
Length 112
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 80.58
Mean single sequence MFE -18.55
Consensus MFE -15.13
Energy contribution -15.30
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.82
SVM decision value 1.06
SVM RNA-class probability 0.908041
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7247796 112 + 20766785
UCCUCCCCGCC--CCCCGUAAAAAAAAAAAAACUUAGGUGUCAAUAUUCCGUUCUAUUGACGCCCUCGAACAAUAACCCGAAACA--AACUUCAACAACUUGUCCCCGGCACUCGA
........(((--.......................((((((((((........))))))))))...............(((...--...)))..............)))...... ( -18.50)
>DroSec_CAF1 43318 106 + 1
UUCCCUCUCCC---CCC-----AAAAAAAAGACUGAGGUGUCAAUAUUCCGUUCUAUUGACGCCCUCGAACAAUAACCCGAAACA--AACUUCAAAAACUUGUCCCCGGCACUCGA
...........---...-----........((((((((((((((((........)))))))).)))))...........(((...--...)))........)))............ ( -17.00)
>DroSim_CAF1 45912 109 + 1
UUCCCUCUCCCCCCCCC-----AAAAAAAAGACUGAGGUGUCAAUAUUCCGUUCUAUUGACGCCCUCGAACAAUAACCCGAAACA--AACUUCAAAAACUUGUCCCCGGCACUCGA
.................-----........((((((((((((((((........)))))))).)))))...........(((...--...)))........)))............ ( -17.00)
>DroEre_CAF1 42548 94 + 1
CUC-----GC----ACC--------AAAA---CUGAGGUGUCAAUAUGCCGUUCUAUUGACGCCCUCGAACAAUAACCCGAAACA--AACUUCAAAAACUUGUGCCCGGCACUCGA
...-----((----((.--------....---.(((((((((((((........)))))))).)))))...........(((...--...)))........))))........... ( -19.80)
>DroYak_CAF1 44993 99 + 1
UUU-----UC----CCC--------AAAACGACUAAGGUGUCAAUAUUCCGUUCUAUUGACGCCCUCGAACAAUAACCCGAAACAAAAACUUCAAAAACUUGUCCCCGGCACUCGA
...-----..----...--------....(((....((((((((((........)))))))))).............(((..((((.............))))...)))...))). ( -17.12)
>DroPer_CAF1 37662 94 + 1
UACCCCCUCGU---CCC--------------AGUGAGGUGUCAAUAUCCCGUUCUAUUGACGCCCUCGAACAAUGGCCCGAA-CA--UA-UUCA-AAUCCAGUCUCCGGCACUCGU
.......(((.---.((--------------(.(((((((((((((........)))))))).))))).....)))..))).-..--..-....-......((.....))...... ( -21.90)
>consensus
UUCCC_CUCCC___CCC________AAAAAGACUGAGGUGUCAAUAUUCCGUUCUAUUGACGCCCUCGAACAAUAACCCGAAACA__AACUUCAAAAACUUGUCCCCGGCACUCGA
....................................((((((((((........)))))))))).((((..........(((........)))........((.....))..)))) (-15.13 = -15.30 +   0.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,247,796 – 7,247,908
Length 112
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 80.58
Mean single sequence MFE -29.28
Consensus MFE -21.74
Energy contribution -22.53
Covariance contribution 0.79
Combinations/Pair 1.08
Mean z-score -1.16
Structure conservation index 0.74
SVM decision value 0.05
SVM RNA-class probability 0.560148
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7247796 112 - 20766785
UCGAGUGCCGGGGACAAGUUGUUGAAGUU--UGUUUCGGGUUAUUGUUCGAGGGCGUCAAUAGAACGGAAUAUUGACACCUAAGUUUUUUUUUUUUUACGGGG--GGCGGGGAGGA
(((((.(((.(..((((..(.....)..)--)))..).))).....)))))(((.(((((((........))))))).)))..........(((((..((...--..))..))))) ( -29.50)
>DroSec_CAF1 43318 106 - 1
UCGAGUGCCGGGGACAAGUUUUUGAAGUU--UGUUUCGGGUUAUUGUUCGAGGGCGUCAAUAGAACGGAAUAUUGACACCUCAGUCUUUUUUUU-----GGG---GGGAGAGGGAA
.(((..(((.(..((((..(.....)..)--)))..).)))..)))...((((..(((((((........))))))).))))..(((((((((.-----...---.))))))))). ( -31.10)
>DroSim_CAF1 45912 109 - 1
UCGAGUGCCGGGGACAAGUUUUUGAAGUU--UGUUUCGGGUUAUUGUUCGAGGGCGUCAAUAGAACGGAAUAUUGACACCUCAGUCUUUUUUUU-----GGGGGGGGGAGAGGGAA
.(((..(((.(..((((..(.....)..)--)))..).)))..)))...((((..(((((((........))))))).))))..((((((((((-----......)))))))))). ( -31.50)
>DroEre_CAF1 42548 94 - 1
UCGAGUGCCGGGCACAAGUUUUUGAAGUU--UGUUUCGGGUUAUUGUUCGAGGGCGUCAAUAGAACGGCAUAUUGACACCUCAG---UUUU--------GGU----GC-----GAG
....(..(((((.((((...(((((((..--..)))))))...)))).)((((..(((((((........))))))).))))..---..))--------)).----.)-----... ( -27.90)
>DroYak_CAF1 44993 99 - 1
UCGAGUGCCGGGGACAAGUUUUUGAAGUUUUUGUUUCGGGUUAUUGUUCGAGGGCGUCAAUAGAACGGAAUAUUGACACCUUAGUCGUUUU--------GGG----GA-----AAA
(((((.(((.(..(((((...........)))))..).))).....)))))....(((((((........))))))).((((((.....))--------)))----).-----... ( -26.50)
>DroPer_CAF1 37662 94 - 1
ACGAGUGCCGGAGACUGGAUU-UGAA-UA--UG-UUCGGGCCAUUGUUCGAGGGCGUCAAUAGAACGGGAUAUUGACACCUCACU--------------GGG---ACGAGGGGGUA
.(..((.((((....(((.((-((((-..--..-)))))))))......((((..(((((((........))))))).)))).))--------------)).---))..)...... ( -29.20)
>consensus
UCGAGUGCCGGGGACAAGUUUUUGAAGUU__UGUUUCGGGUUAUUGUUCGAGGGCGUCAAUAGAACGGAAUAUUGACACCUCAGUCUUUUU________GGG___GGGAG_GGGAA
.......((..((((((...(((((((......)))))))...))))))((((..(((((((........))))))).)))).................))............... (-21.74 = -22.53 +   0.79)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:28 2006