Locus 691

Sequence ID 2R_DroMel_CAF1
Location 3,405,808 – 3,405,942
Length 134
Max. P 0.991442
window1215 window1216 window1217 window1218

overview

Window 5

Location 3,405,808 – 3,405,917
Length 109
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 77.78
Mean single sequence MFE -36.38
Consensus MFE -20.78
Energy contribution -24.00
Covariance contribution 3.22
Combinations/Pair 1.08
Mean z-score -2.00
Structure conservation index 0.57
SVM decision value 0.85
SVM RNA-class probability 0.867028
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3405808 109 + 20766785
GCGGCCAGGCCCCAAAUUGAUUGGGUGACCGACCGACUGGUUUCGGGCCUCGGGGU-UUCCCUCUGUCGCUCACGGCCAAUUAAUUGGCCAUUUCUCGUUGGCCCAAAUA-
(.(((((((..(((..(((.((((....)))).))).)))..))((((..(((((.-....)))))..))))..((((((....)))))).........)))))).....- ( -41.90)
>DroSec_CAF1 36042 109 + 1
GCGGCCAGGCCCCAAAUUGAUUGGGUGACCGACCGACUGGUUUCGGGCCUCGGGGU-UUCCCUCUGUCGCUUACGGCCAAUUAAUUGGCCAUUUCUCGCUUGCCCAAAUA-
(((((.((((((.(((((..((((........))))..))))).)))))).((((.-...)))).)))))....((((((....))))))....................- ( -40.40)
>DroSim_CAF1 35345 109 + 1
GCGGCCAGGCCCCAAAUUGAUUGGGUGACCGACCGACUGGUUUCGGGCCUCGGGGU-UUCCCUCUGUCGCUUACGGCCAAUUAAUUGGCCAUUUCUCGCUGGCCCAAAUA-
(.(((((((((((.......((((....))))((((......)))).....)))))-.................((((((....))))))........))))))).....- ( -42.60)
>DroEre_CAF1 36512 102 + 1
GCGGCCAGCCCCCAAAUUGAUUGGGUUA--------CUGGUUUCGGGCCUCUGGGUUUUUCCUCUGUCGCUUACUGCCAAUUAAUUGGCCAUUUCUCGCUGGCCCAAAUA-
(..(((((..(((((.....)))))...--------)))))..)(((((...(((....))).............(((((....)))))...........))))).....- ( -32.20)
>DroYak_CAF1 39613 102 + 1
GCGGCCAGGCCCCAAAUUGAUUGGGUUA--------CUGGUUGCGGGCCUCUGGGUUUUCCCUCUGUCGCUUACGGCCAAUUAAUUGGCCAUUUCUCGCUGGCCCAAAUA-
((((((((..(((((.....)))))...--------))))))))(((((...(((....)))............((((((....))))))..........))))).....- ( -45.40)
>DroPer_CAF1 37720 90 + 1
GCAGCC------------GACUGGUUUG--------CUCUUGUCCAAUUUUCGGGU-UUCCCGCUUUCCAUUGUCUGCAUUUAAUAUGUAAUUCUCCGCCUGCCCAAAAAG
((((.(------------((((((...(--------(......((........)).-.....))...)))..)))(((((.....))))).......).))))........ ( -15.80)
>consensus
GCGGCCAGGCCCCAAAUUGAUUGGGUGA________CUGGUUUCGGGCCUCGGGGU_UUCCCUCUGUCGCUUACGGCCAAUUAAUUGGCCAUUUCUCGCUGGCCCAAAUA_
(..(((((..(((((.....)))))...........)))))..)(((((...(((....)))............((((((....))))))..........)))))...... (-20.78 = -24.00 +   3.22)

alignment

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secondary structure

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Window 6

Location 3,405,808 – 3,405,917
Length 109
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 77.78
Mean single sequence MFE -40.54
Consensus MFE -23.37
Energy contribution -26.07
Covariance contribution 2.70
Combinations/Pair 1.15
Mean z-score -3.13
Structure conservation index 0.58
SVM decision value 2.27
SVM RNA-class probability 0.991442
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3405808 109 - 20766785
-UAUUUGGGCCAACGAGAAAUGGCCAAUUAAUUGGCCGUGAGCGACAGAGGGAA-ACCCCGAGGCCCGAAACCAGUCGGUCGGUCACCCAAUCAAUUUGGGGCCUGGCCGC
-..((((((((..((....((((((((....))))))))...))...(.((...-.)).)..))))))))......(((((((.(.(((((.....)))))).))))))). ( -50.70)
>DroSec_CAF1 36042 109 - 1
-UAUUUGGGCAAGCGAGAAAUGGCCAAUUAAUUGGCCGUAAGCGACAGAGGGAA-ACCCCGAGGCCCGAAACCAGUCGGUCGGUCACCCAAUCAAUUUGGGGCCUGGCCGC
-..(((((((..((.....((((((((....))))))))..))....(.((...-.)).)...)))))))......(((((((.(.(((((.....)))))).))))))). ( -46.40)
>DroSim_CAF1 35345 109 - 1
-UAUUUGGGCCAGCGAGAAAUGGCCAAUUAAUUGGCCGUAAGCGACAGAGGGAA-ACCCCGAGGCCCGAAACCAGUCGGUCGGUCACCCAAUCAAUUUGGGGCCUGGCCGC
-..((((((((.((.....((((((((....))))))))..))....(.((...-.)).)..))))))))......(((((((.(.(((((.....)))))).))))))). ( -49.90)
>DroEre_CAF1 36512 102 - 1
-UAUUUGGGCCAGCGAGAAAUGGCCAAUUAAUUGGCAGUAAGCGACAGAGGAAAAACCCAGAGGCCCGAAACCAG--------UAACCCAAUCAAUUUGGGGGCUGGCCGC
-..((((((((.((........(((((....))))).....))......((......))...)))))))).((((--------(..(((((.....))))).))))).... ( -37.22)
>DroYak_CAF1 39613 102 - 1
-UAUUUGGGCCAGCGAGAAAUGGCCAAUUAAUUGGCCGUAAGCGACAGAGGGAAAACCCAGAGGCCCGCAACCAG--------UAACCCAAUCAAUUUGGGGCCUGGCCGC
-.....(((((.((.....((((((((....))))))))..))......(((....)))...)))))((..((((--------...(((((.....)))))..))))..)) ( -42.40)
>DroPer_CAF1 37720 90 - 1
CUUUUUGGGCAGGCGGAGAAUUACAUAUUAAAUGCAGACAAUGGAAAGCGGGAA-ACCCGAAAAUUGGACAAGAG--------CAAACCAGUC------------GGCUGC
........(((((((...(((.....)))...))).(((..(((...((((...-.))(((...))).......)--------)...))))))------------..)))) ( -16.60)
>consensus
_UAUUUGGGCCAGCGAGAAAUGGCCAAUUAAUUGGCCGUAAGCGACAGAGGGAA_ACCCCGAGGCCCGAAACCAG________UAACCCAAUCAAUUUGGGGCCUGGCCGC
...((((((((..((....((((((((....))))))))...)).....(((....)))...))))))))................(((((.....))))).......... (-23.37 = -26.07 +   2.70)

alignment

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secondary structure

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Window 7

Location 3,405,848 – 3,405,942
Length 94
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 81.35
Mean single sequence MFE -26.35
Consensus MFE -20.87
Energy contribution -20.57
Covariance contribution -0.30
Combinations/Pair 1.42
Mean z-score -1.37
Structure conservation index 0.79
SVM decision value 0.24
SVM RNA-class probability 0.648694
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3405848 94 + 20766785
UUUCGGGCCUCGGGGU-UUCCCUCUGUCGCUCACGGCCAAUUAAUUGGCCAUUUCUCGUUGGCCCAAAUA--CACGGACAUCCGGCCCCUUUGAC--------CG
....((((..(((((.-....)))))..))))..((((........(((((........)))))......--...((....))))))........--------.. ( -30.30)
>DroSec_CAF1 36082 94 + 1
UUUCGGGCCUCGGGGU-UUCCCUCUGUCGCUUACGGCCAAUUAAUUGGCCAUUUCUCGCUUGCCCAAAUA--CACGGACAUCCGGCCCCUUUGAC--------CU
....(((((...((((-........((.....))((((((....))))))...........)))).....--...((....))))))).......--------.. ( -27.10)
>DroSim_CAF1 35385 94 + 1
UUUCGGGCCUCGGGGU-UUCCCUCUGUCGCUUACGGCCAAUUAAUUGGCCAUUUCUCGCUGGCCCAAAUA--CACGGACAUCCGGCCCCUUUGAC--------CU
....(((((..((((.-...))))..........((((((....))))))..........))))).....--..(((....)))...........--------.. ( -29.40)
>DroEre_CAF1 36544 95 + 1
UUUCGGGCCUCUGGGUUUUUCCUCUGUCGCUUACUGCCAAUUAAUUGGCCAUUUCUCGCUGGCCCAAAUA--CACGGACAUCCGGCCCCUUUGAC--------CG
....(((((...(((....)))..((((((.....)).........(((((........)))))......--....))))...))))).......--------.. ( -25.30)
>DroYak_CAF1 39645 95 + 1
UUGCGGGCCUCUGGGUUUUCCCUCUGUCGCUUACGGCCAAUUAAUUGGCCAUUUCUCGCUGGCCCAAAUA--CACGGACAUCCGGCCCCUUUGAC--------UG
..(((((((...(((....)))............((((((....))))))..........))))).....--..(((....))))).........--------.. ( -30.60)
>DroPer_CAF1 37740 104 + 1
UGUCCAAUUUUCGGGU-UUCCCGCUUUCCAUUGUCUGCAUUUAAUAUGUAAUUCUCCGCCUGCCCAAAAAGUCACGGAUGUCCGGCCCCACCGCCACCGCCACCG
.((((..((((.((((-.....((........)).(((((.....)))))...........)))).)))).....))))....(((......))).......... ( -15.40)
>consensus
UUUCGGGCCUCGGGGU_UUCCCUCUGUCGCUUACGGCCAAUUAAUUGGCCAUUUCUCGCUGGCCCAAAUA__CACGGACAUCCGGCCCCUUUGAC________CG
....(((((...(((....)))..((((((.....)).........(((((........)))))............))))...)))))................. (-20.87 = -20.57 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,405,848 – 3,405,942
Length 94
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 81.35
Mean single sequence MFE -33.89
Consensus MFE -22.95
Energy contribution -24.98
Covariance contribution 2.03
Combinations/Pair 1.16
Mean z-score -2.29
Structure conservation index 0.68
SVM decision value 0.81
SVM RNA-class probability 0.857733
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3405848 94 - 20766785
CG--------GUCAAAGGGGCCGGAUGUCCGUG--UAUUUGGGCCAACGAGAAAUGGCCAAUUAAUUGGCCGUGAGCGACAGAGGGAA-ACCCCGAGGCCCGAAA
.(--------(((.....))))((....))...--..((((((((..((....((((((((....))))))))...))...(.((...-.)).)..)))))))). ( -39.70)
>DroSec_CAF1 36082 94 - 1
AG--------GUCAAAGGGGCCGGAUGUCCGUG--UAUUUGGGCAAGCGAGAAAUGGCCAAUUAAUUGGCCGUAAGCGACAGAGGGAA-ACCCCGAGGCCCGAAA
..--------.......(((((...((((((..--....)))))).((.....((((((((....))))))))..))....(.((...-.)).)..))))).... ( -36.20)
>DroSim_CAF1 35385 94 - 1
AG--------GUCAAAGGGGCCGGAUGUCCGUG--UAUUUGGGCCAGCGAGAAAUGGCCAAUUAAUUGGCCGUAAGCGACAGAGGGAA-ACCCCGAGGCCCGAAA
.(--------(((.....))))((....))...--..((((((((.((.....((((((((....))))))))..))....(.((...-.)).)..)))))))). ( -38.80)
>DroEre_CAF1 36544 95 - 1
CG--------GUCAAAGGGGCCGGAUGUCCGUG--UAUUUGGGCCAGCGAGAAAUGGCCAAUUAAUUGGCAGUAAGCGACAGAGGAAAAACCCAGAGGCCCGAAA
.(--------(((.....))))((....))...--..((((((((.((........(((((....))))).....))......((......))...)))))))). ( -30.62)
>DroYak_CAF1 39645 95 - 1
CA--------GUCAAAGGGGCCGGAUGUCCGUG--UAUUUGGGCCAGCGAGAAAUGGCCAAUUAAUUGGCCGUAAGCGACAGAGGGAAAACCCAGAGGCCCGCAA
..--------.........(((((....))).)--)....(((((.((.....((((((((....))))))))..))......(((....)))...))))).... ( -33.60)
>DroPer_CAF1 37740 104 - 1
CGGUGGCGGUGGCGGUGGGGCCGGACAUCCGUGACUUUUUGGGCAGGCGGAGAAUUACAUAUUAAAUGCAGACAAUGGAAAGCGGGAA-ACCCGAAAAUUGGACA
.(((.((((((.(((.....)))..)).)))).)))..........(((...(((.....)))...)))...((((.....(.((...-.)))....)))).... ( -24.40)
>consensus
CG________GUCAAAGGGGCCGGAUGUCCGUG__UAUUUGGGCCAGCGAGAAAUGGCCAAUUAAUUGGCCGUAAGCGACAGAGGGAA_ACCCCGAGGCCCGAAA
.................((((.....)))).......((((((((..((....((((((((....))))))))...)).....(((....)))...)))))))). (-22.95 = -24.98 +   2.03)

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 09:44:45 2006