Locus 1609

Sequence ID 2L_DroMel_CAF1
Location 4,327,522 – 4,327,670
Length 148
Max. P 0.999883
window2581 window2582 window2583 window2584

overview

Window 1

Location 4,327,522 – 4,327,612
Length 90
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 66.96
Mean single sequence MFE -24.77
Consensus MFE -13.16
Energy contribution -13.60
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -4.34
Structure conservation index 0.53
SVM decision value 4.37
SVM RNA-class probability 0.999883
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4327522 90 + 22407834
AAAUGCAACGGCAUACAUAUAUGUAGUUGUUAUAUCCCAUAUAGCA--------UCAUACUAU-CCAUA-----CUAUGUAAGCCACAUGGACGAAAGUCAAGU
.........(((.((((((((((((((((((((((...))))))))--------....)))).-.))))-----.)))))).))).....(((....))).... ( -24.80)
>DroSec_CAF1 81596 80 + 1
AAAGGC---------------UAUAGAUGCUAUAUCCCAUAUAGCA--------CCACAGCAU-CUAUAGAUAUCCAUGUGAGCCACAUGGACGAAAGUCAAGU
.....(---------------((((((((((...............--------....)))))-)))))).....((((((...))))))(((....))).... ( -24.81)
>DroSim_CAF1 85025 81 + 1
AAAGGCA--------------UAUAGAUGCUAUAUCCCAUAUAGCA--------CCAUAGUAU-CUAUAGAUAUCCAUGUGAGCCACAUGGACGAAAGUCAAGU
...(((.--------------((((((((((((.............--------..)))))))-)))))....((((((((...)))))))).....))).... ( -24.36)
>DroEre_CAF1 77980 93 + 1
AAAUGCCACAGCAUACACACG----UAUGCUAUAUCGCAUAUAGCACACACGUACUAUACU--ACUGGC-----ACAUAUGAGCCACAUAGACGAAAGUCAAGU
...(((((.(((((((....)----))))))........(((((.((....)).)))))..--..))))-----)..((((.....))))(((....))).... ( -25.10)
>consensus
AAAGGCA______________UAUAGAUGCUAUAUCCCAUAUAGCA________CCAUACUAU_CUAUA_____CCAUGUGAGCCACAUGGACGAAAGUCAAGU
...........................((((((((...)))))))).............................((((((...))))))(((....))).... (-13.16 = -13.60 +   0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,327,522 – 4,327,612
Length 90
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 66.96
Mean single sequence MFE -27.55
Consensus MFE -10.60
Energy contribution -10.16
Covariance contribution -0.44
Combinations/Pair 1.26
Mean z-score -3.60
Structure conservation index 0.38
SVM decision value 2.16
SVM RNA-class probability 0.989419
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4327522 90 - 22407834
ACUUGACUUUCGUCCAUGUGGCUUACAUAG-----UAUGG-AUAGUAUGA--------UGCUAUAUGGGAUAUAACAACUACAUAUAUGUAUGCCGUUGCAUUU
............((((((((((...((((.-----((...-.)).)))).--------.))))))))))......((((..((((....))))..))))..... ( -21.10)
>DroSec_CAF1 81596 80 - 1
ACUUGACUUUCGUCCAUGUGGCUCACAUGGAUAUCUAUAG-AUGCUGUGG--------UGCUAUAUGGGAUAUAGCAUCUAUA---------------GCCUUU
...........(((((((((...)))))))))..((((((-((((((((.--------..((.....)).)))))))))))))---------------)..... ( -30.30)
>DroSim_CAF1 85025 81 - 1
ACUUGACUUUCGUCCAUGUGGCUCACAUGGAUAUCUAUAG-AUACUAUGG--------UGCUAUAUGGGAUAUAGCAUCUAUA--------------UGCCUUU
............((((((((((.(.(((((.((((....)-)))))))))--------.)))))))))).....((((....)--------------))).... ( -24.80)
>DroEre_CAF1 77980 93 - 1
ACUUGACUUUCGUCUAUGUGGCUCAUAUGU-----GCCAGU--AGUAUAGUACGUGUGUGCUAUAUGCGAUAUAGCAUA----CGUGUGUAUGCUGUGGCAUUU
....(((....)))((((.....)))).((-----((((.(--((((((.((((((((((((((((...))))))))))----))))))))))))))))))).. ( -34.00)
>consensus
ACUUGACUUUCGUCCAUGUGGCUCACAUGG_____UAUAG_AUACUAUGG________UGCUAUAUGGGAUAUAGCAUCUAUA______________UGCAUUU
...((.((....((((((((((...(((((..............)))))..........))))))))))....))))........................... (-10.60 = -10.16 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,327,553 – 4,327,645
Length 92
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 80.96
Mean single sequence MFE -24.75
Consensus MFE -17.25
Energy contribution -17.12
Covariance contribution -0.12
Combinations/Pair 1.13
Mean z-score -2.63
Structure conservation index 0.70
SVM decision value 2.18
SVM RNA-class probability 0.989692
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4327553 92 + 22407834
AUAUCCCAUAUAGCA--------UCAUACUAU-CCAUA-----CUAUGUAAGCCACAUGGACGAAAGUCAAGUGCGCAAACAAAGCAAGCAUAAAAAUAUAUGUGG
.....((((((((((--------(........-.....-----.(((((.....)))))(((....)))..))))((.......)).............))))))) ( -19.00)
>DroSec_CAF1 81612 97 + 1
AUAUCCCAUAUAGCA--------CCACAGCAU-CUAUAGAUAUCCAUGUGAGCCACAUGGACGAAAGUCAAGUGCGCCAACAAAGCGAGCAUAAAAAUGUGUGUGG
.....((((((((((--------(........-...........((((((...))))))(((....)))..))))(((........).)).........))))))) ( -24.60)
>DroSim_CAF1 85042 97 + 1
AUAUCCCAUAUAGCA--------CCAUAGUAU-CUAUAGAUAUCCAUGUGAGCCACAUGGACGAAAGUCAAGUGCGCCAACAAAGCGAGCAUAAAAAUGUGUGUGG
.....((((((((((--------(....((((-(....))))).((((((...))))))(((....)))..))))(((........).)).........))))))) ( -26.40)
>DroEre_CAF1 78007 99 + 1
AUAUCGCAUAUAGCACACACGUACUAUACU--ACUGGC-----ACAUAUGAGCCACAUAGACGAAAGUCAAGUGCGCAAACAAGGCGAGCAUAAAAAUGUGUGUGG
.............((((((((((((.....--..((((-----........))))....(((....))).)))))((.......))............))))))). ( -29.00)
>consensus
AUAUCCCAUAUAGCA________CCAUACUAU_CUAUA_____CCAUGUGAGCCACAUGGACGAAAGUCAAGUGCGCAAACAAAGCGAGCAUAAAAAUGUGUGUGG
....................................................((((((((((....)))..((.(((.......))).)).........))))))) (-17.25 = -17.12 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,327,577 – 4,327,670
Length 93
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 78.18
Mean single sequence MFE -27.53
Consensus MFE -16.85
Energy contribution -16.68
Covariance contribution -0.17
Combinations/Pair 1.20
Mean z-score -2.13
Structure conservation index 0.61
SVM decision value 1.20
SVM RNA-class probability 0.929907
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4327577 93 + 22407834
CCAUA-----CUAUGUAAGCCACAUGGACGAAAGUCAAGUGCGCAAACAAAGCAAGCAUAAA-AAUAUAUGUGG------------------CAGAGCAAUUAGAAGAGCGGCCAGC
((...-----........(((((((((((....)))..((((((.......))..))))...-....)))))))------------------)...((..........))))..... ( -24.00)
>DroSec_CAF1 81636 98 + 1
CUAUAGAUAUCCAUGUGAGCCACAUGGACGAAAGUCAAGUGCGCCAACAAAGCGAGCAUAAA-AAUGUGUGUGG------------------CAGAGCAAUUAGAAGAGCGGCCAGC
.............(((..(((((...(((....)))..))).))..)))..((..(((((..-..))))).(((------------------(...((..........)).)))))) ( -24.50)
>DroSim_CAF1 85066 98 + 1
CUAUAGAUAUCCAUGUGAGCCACAUGGACGAAAGUCAAGUGCGCCAACAAAGCGAGCAUAAA-AAUGUGUGUGG------------------CAGAGCAAUUAGAAGAGCAACCAGC
.............(((..(((((((.(((....)))..((.(((.......))).)).....-.....))))))------------------)...))).................. ( -23.70)
>DroEre_CAF1 78038 93 + 1
CUGGC-----ACAUAUGAGCCACAUAGACGAAAGUCAAGUGCGCAAACAAGGCGAGCAUAAA-AAUGUGUGUGG------------------CGGGGCAAUUAGAUGAGCGGCCAGC
(((((-----........(((((((((((....)))..((.(((.......))).)).....-....)))))))------------------)...((..........)).))))). ( -32.50)
>DroYak_CAF1 83920 93 + 1
CUAUA-----GCAUAUGAGCCACAUAGACGAAAGUCAAGUGCGCAAACAAAGCGAGCAUAAA-AAUGUGUGUGG------------------CAGAGCAAUUAGAAGAGCGGCCAGC
.....-----((......(((((((((((....)))..((.(((.......))).)).....-....)))))))------------------)...((..........)).)).... ( -25.90)
>DroAna_CAF1 56607 105 + 1
-----------CAACUGCGCC-CAUGGGCGAAAGUCAAGUGCGCCAGCACAGCGAGCAUAAAAAAUAUGUGGGGCUUGUUGUGAUGCCCAGGCCCAGCAAUUAGAGGAUCGAGCAGC
-----------...(((((((-....)))....(((..((((....)))).((..(((((.....))))).(((((((..........))))))).))........)))...)))). ( -34.60)
>consensus
CUAUA_____CCAUGUGAGCCACAUGGACGAAAGUCAAGUGCGCAAACAAAGCGAGCAUAAA_AAUGUGUGUGG__________________CAGAGCAAUUAGAAGAGCGGCCAGC
...................((((((((((....)))..((.(((.......))).))..........)))))))........................................... (-16.85 = -16.68 +  -0.17)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:35 2006