Locus 8525

Sequence ID 3L_DroMel_CAF1
Location 22,311,332 – 22,311,645
Length 313
Max. P 0.889796
window13961 window13962 window13963 window13964

overview

Window 1

Location 22,311,332 – 22,311,449
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.32
Mean single sequence MFE -29.82
Consensus MFE -18.85
Energy contribution -19.85
Covariance contribution 1.00
Combinations/Pair 1.08
Mean z-score -2.02
Structure conservation index 0.63
SVM decision value 0.61
SVM RNA-class probability 0.797394
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22311332 117 + 23771897
AAAAGUGGUCAACAUGACAUGGUUGACAUGCGACAUUAGCAAAGGCA--CAACACAAGGCUUCCUUGGGA-CCCCUAACCCUUCCCUCUUUGUGCGCCAACCCAAGAACCCAGCUACCCA
...(((.((((((........)))))).(((.......)))..(((.--...(((((((.......(((.-.......)))......))))))).)))..............)))..... ( -25.12)
>DroSec_CAF1 70037 119 + 1
AAAAGUGGUCAACAUGACAACGUUGACAUGCGACAUUAGCAGAGGCACACAACACAAGGCUUCCUUGGGA-CCCCUAACCCUUCCCUCUCUGUGUGCCAACCCAAGAACCCAGCUAACCG
....(((((((((........)))))).)))....(((((...((((((((....((((...))))((((-...........))))....)))))))).......(....).)))))... ( -31.20)
>DroEre_CAF1 68460 94 + 1
AAAAGUGGUCAACAUGACAACGUUGACAUGCGACAUUAGCAGAGGCA--CAACACAGGGGUUCCUUGAGGUCCCCCAACCCU------------------------AGCCCAGCUACCCA
....(((((((((........)))))).))).....((((.(.(((.--.......((((..((....))..))))......------------------------.)))).)))).... ( -26.76)
>DroYak_CAF1 48526 117 + 1
AAAAGUGGUCAACAUGACAACGUUGACAUGCGACAUUAGCAGAGGUA--CAACACAGGGGUUCCUUGGGAUCCCCUUACACUUCCCUCUCUGUGU-CCAACACAAGAACCCAGCUACCCA
....(((((((((........)))))).((.(((((.((.(((((..--......(((((.(((...))).)))))........)))))))))))-))).)))................. ( -36.19)
>consensus
AAAAGUGGUCAACAUGACAACGUUGACAUGCGACAUUAGCAGAGGCA__CAACACAAGGCUUCCUUGGGA_CCCCUAACCCUUCCCUCUCUGUGU_CCAACCCAAGAACCCAGCUACCCA
....(((((((((........)))))).(((.......)))...........)))..((((((.(((((....))))).............((......))....))))))......... (-18.85 = -19.85 +   1.00)

alignment

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secondary structure

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Window 2

Location 22,311,449 – 22,311,568
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.03
Mean single sequence MFE -44.60
Consensus MFE -35.79
Energy contribution -35.72
Covariance contribution -0.06
Combinations/Pair 1.06
Mean z-score -2.30
Structure conservation index 0.80
SVM decision value 0.96
SVM RNA-class probability 0.889796
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22311449 119 - 23771897
CUUU-UCUUGCUCGUGUGCUCACGCACAUGCUGAGAUUUGAAUGCGCUGCGAUUUUUUGCGUGUGCUGUGGGUAUUUUUCUUAGGCGAGGAGCACGCAAGGAGCUCAGAAAGGAGGUGGC
((((-(((..(((((((((((((((((((((.((((.(((.........))).)))).)))))))).)))))))).........)))))((((.(....)..)))))))))))....... ( -44.80)
>DroSec_CAF1 70156 120 - 1
CUUUUUCUUGCUCGUGUGCUCACGCACAUGCUGAGAUUUGAAUGCGCUGCGAUUUUUUGCGUGUGCUGUGGGCAUUUUUCUUGGGCGAAGAGCACGCAAGGAGCUCGGAAAGAAGAUGGC
.(((((((((((((.((((((((((((((((.((((.(((.........))).)))).)))))))).))))))))......))))))).((((.(....)..)))).))))))....... ( -46.40)
>DroEre_CAF1 68554 117 - 1
CUUU-UCUUGCUCGUGUGCUCACGCACAUGCUGAGAUUUGAAUGCGCUGCGAUUUUUUGCGUGUGCUGCGGGCAUUUUUCAUAGGCGAGGAGCACGCAAGGAGCUCGGAAAGGAA--GGC
((((-(((.((((((((((((.(((...((.(((((..((..((((((((((....)))))...)).)))..))..))))))).)))..))))))))...))))..)))))))..--... ( -45.00)
>DroYak_CAF1 48643 116 - 1
CUGU-UCUUGCUCGUGUGCUCACGCACAUGCUGAGAUUUAAAUGCGCUGCGAUUUUUUGCGUGUGCUGCGCGCAUUUUUCAUAGGCGAGGAGCACGCAAUGAGCUCGGAAAGGAA---CC
((.(-(((.((((((((((((.(((...((.(((((....(((((((.((((....))))((.....)))))))))))))))).)))..))))))))...))))..)))).))..---.. ( -42.20)
>consensus
CUUU_UCUUGCUCGUGUGCUCACGCACAUGCUGAGAUUUGAAUGCGCUGCGAUUUUUUGCGUGUGCUGCGGGCAUUUUUCAUAGGCGAGGAGCACGCAAGGAGCUCGGAAAGGAA__GGC
.....(((.((((((((((((.(((.......((((..((...(((((((((....))))).))))......))..))))....)))..))))))))...))))..)))........... (-35.79 = -35.72 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,311,489 – 22,311,608
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.84
Mean single sequence MFE -38.38
Consensus MFE -34.59
Energy contribution -34.65
Covariance contribution 0.06
Combinations/Pair 1.06
Mean z-score -1.58
Structure conservation index 0.90
SVM decision value 0.28
SVM RNA-class probability 0.666010
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22311489 119 - 23771897
GGAGCAUUUGAUAACAUGUUUUGCCAACCGGCCCGCACUGCUUU-UCUUGCUCGUGUGCUCACGCACAUGCUGAGAUUUGAAUGCGCUGCGAUUUUUUGCGUGUGCUGUGGGUAUUUUUC
.(((((...((.(((((((...(((....)))..))).)).)).-)).)))))..((((((((((((((((.((((.(((.........))).)))).)))))))).))))))))..... ( -39.20)
>DroSec_CAF1 70196 120 - 1
GGAGCAUUUGAUAACAUGUUUUGCCAACCGGCCCGCAUCGCUUUUUCUUGCUCGUGUGCUCACGCACAUGCUGAGAUUUGAAUGCGCUGCGAUUUUUUGCGUGUGCUGUGGGCAUUUUUC
.(((((...((....((((...(((....)))..)))).....))...)))))..((((((((((((((((.((((.(((.........))).)))).)))))))).))))))))..... ( -40.40)
>DroEre_CAF1 68592 119 - 1
GGAGCAUUUGAUAACAUGUUUUGCCAGCCGGCCCGAACCGCUUU-UCUUGCUCGUGUGCUCACGCACAUGCUGAGAUUUGAAUGCGCUGCGAUUUUUUGCGUGUGCUGCGGGCAUUUUUC
.(((((...((......((((.(((....)))..))))......-)).)))))..((((((.(((((((((.((((.(((.........))).)))).)))))))).).))))))..... ( -37.20)
>DroYak_CAF1 48680 119 - 1
GGAGCAUUUGAUAACAUGUUUUGGCAACCAGCCCGCACCGCUGU-UCUUGCUCGUGUGCUCACGCACAUGCUGAGAUUUAAAUGCGCUGCGAUUUUUUGCGUGUGCUGCGCGCAUUUUUC
.(((((...((((.(.(((...(((.....))).)))..).)))-)..)))))((((((.((.((((((((.((((((............))))))..)))))))))).))))))..... ( -36.70)
>consensus
GGAGCAUUUGAUAACAUGUUUUGCCAACCGGCCCGCACCGCUUU_UCUUGCUCGUGUGCUCACGCACAUGCUGAGAUUUGAAUGCGCUGCGAUUUUUUGCGUGUGCUGCGGGCAUUUUUC
(((((((........)))))))........(((((((........((((...(((((((....)))))))..)))).......(((((((((....))))).)))))))))))....... (-34.59 = -34.65 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,311,529 – 22,311,645
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.53
Mean single sequence MFE -39.98
Consensus MFE -27.66
Energy contribution -31.10
Covariance contribution 3.44
Combinations/Pair 1.11
Mean z-score -2.50
Structure conservation index 0.69
SVM decision value 0.07
SVM RNA-class probability 0.566553
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22311529 116 + 23771897
CAAAUCUCAGCAUGUGCGUGAGCACACGAGCAAGA-AAAGCAGUGCGGGCCGGUUGGCAAAACAUGUUAUCAAAUGCUCCGACGCACCGCAAAUUGCCAGC-CGGACCACGACCACGA--
....(((..((.(((((....)))))...)).)))-......((((((((((((((((((....((....))..(((......))).......))))))))-))).)).))..)))..-- ( -40.10)
>DroSec_CAF1 70236 111 + 1
CAAAUCUCAGCAUGUGCGUGAGCACACGAGCAAGAAAAAGCGAUGCGGGCCGGUUGGCAAAACAUGUUAUCAAAUGCUCCGACGCACCGCAAAUUGCCAGC-CGGACCA------CGA--
.........((((((((....))))....((........)).))))((.(((((((((((....((....))..(((......))).......))))))))-))).)).------...-- ( -39.90)
>DroEre_CAF1 68632 118 + 1
CAAAUCUCAGCAUGUGCGUGAGCACACGAGCAAGA-AAAGCGGUUCGGGCCGGCUGGCAAAACAUGUUAUCAAAUGCUCCGACGCACCGCAAAUUUGCAGC-CGGACCACGACCACGACC
....(((..((.(((((....)))))...)).)))-...(.(((.(((((((((((.((((...((....))..(((......))).......))))))))-))).)).))))).).... ( -39.30)
>DroYak_CAF1 48720 117 + 1
UAAAUCUCAGCAUGUGCGUGAGCACACGAGCAAGA-ACAGCGGUGCGGGCUGGUUGCCAAAACAUGUUAUCAAAUGCUCCGACGCACCGCAAAUUGCCAGCCCGGACCACGACCACGA--
....(((..((.(((((....)))))...)).)))-...(.(((.((((((((((((.......((....))..(((......)))..)))....))))))))).))).)........-- ( -40.60)
>consensus
CAAAUCUCAGCAUGUGCGUGAGCACACGAGCAAGA_AAAGCGGUGCGGGCCGGUUGGCAAAACAUGUUAUCAAAUGCUCCGACGCACCGCAAAUUGCCAGC_CGGACCACGACCACGA__
.........((((((((....))))....((........)).))))((.(((((((((((....((....))..(((......))).......)))))))).))).))............ (-27.66 = -31.10 +   3.44)

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 13:18:02 2006