Locus 10348

Sequence ID 3R_DroMel_CAF1
Location 27,862,271 – 27,862,430
Length 159
Max. P 0.999722
window16469 window16470 window16471 window16472

overview

Window 9

Location 27,862,271 – 27,862,390
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.99
Mean single sequence MFE -37.38
Consensus MFE -32.52
Energy contribution -32.28
Covariance contribution -0.24
Combinations/Pair 1.03
Mean z-score -3.12
Structure conservation index 0.87
SVM decision value 3.34
SVM RNA-class probability 0.999047
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27862271 119 + 27905053
UUUGAAUUAUUAAUUUUUAAACUUUU-CGCAACACAAAAAGAAUGACCCAAAGGCCUUUGAUUUGGCCUAUGGGUCAGUGAAGCUUAAGUAAUAGGGUGAUGCGAGCUUGGUACCCUUGC
.........................(-((((.(((........(((((((.(((((........))))).)))))))......((((.....))))))).)))))((..((...))..)) ( -35.70)
>DroSec_CAF1 171521 119 + 1
UUUGAAUUAUUAAUUUUUAAACUUUU-CGCAACACAAAAAGAAUGACCCAAAGGCCUUUGAUUUGGCCUAUGGGUCAGUGAAGCUUAAGUAAUAGGGUGAUGCGAGCUUGGUACCCUUGC
.........................(-((((.(((........(((((((.(((((........))))).)))))))......((((.....))))))).)))))((..((...))..)) ( -35.70)
>DroSim_CAF1 173738 119 + 1
UUUGAAUUAUUAAUUUUUAAACUUUU-CGCAACACAAAAAGAAUGACCCAAAGGCCUUUGAUUUGGCCUAUGGGUCAGUGAAGCUUAAGUAAUAGGGUGAUGCGAGCUUGGUACCCUUGC
.........................(-((((.(((........(((((((.(((((........))))).)))))))......((((.....))))))).)))))((..((...))..)) ( -35.70)
>DroEre_CAF1 201597 120 + 1
UUUGAAUUAUUAAUUUUUAAGCUUUUCCGCAGCACAAAAAGAAUGACCCAAAGGCCUUUGAUUUGGCCUAUGGGUCAGUGAAGCUAAAGUAAUAGGGUGAUGCGAGGGUGGUACCCUUGC
............(((((...(((((...((..(((........(((((((.(((((........))))).))))))))))..)).)))))...)))))...(((((((.....))))))) ( -39.90)
>DroYak_CAF1 175373 120 + 1
UUUGAAUUAUUAAUUUUUAAGCUUUUCCGCAGCACAAAAAGAAUGACCCAAAGGCCUUUGAUUUGGCCUAUGGGUCAGUGAAGCUAAAGUAAUAGGGUGAUGCGAGGGUGGUACCCUUGC
............(((((...(((((...((..(((........(((((((.(((((........))))).))))))))))..)).)))))...)))))...(((((((.....))))))) ( -39.90)
>consensus
UUUGAAUUAUUAAUUUUUAAACUUUU_CGCAACACAAAAAGAAUGACCCAAAGGCCUUUGAUUUGGCCUAUGGGUCAGUGAAGCUUAAGUAAUAGGGUGAUGCGAGCUUGGUACCCUUGC
....................((((....((..(((........(((((((.(((((........))))).))))))))))..))..))))...((((((...((....)).))))))... (-32.52 = -32.28 +  -0.24)

alignment

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secondary structure

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Window 0

Location 27,862,271 – 27,862,390
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.99
Mean single sequence MFE -34.60
Consensus MFE -31.30
Energy contribution -31.06
Covariance contribution -0.24
Combinations/Pair 1.04
Mean z-score -4.15
Structure conservation index 0.90
SVM decision value 3.95
SVM RNA-class probability 0.999722
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27862271 119 - 27905053
GCAAGGGUACCAAGCUCGCAUCACCCUAUUACUUAAGCUUCACUGACCCAUAGGCCAAAUCAAAGGCCUUUGGGUCAUUCUUUUUGUGUUGCG-AAAAGUUUAAAAAUUAAUAAUUCAAA
...(((((..............))))).....((((((.....(((((((.(((((........))))).)))))))...((((((.....))-))))))))))................ ( -32.74)
>DroSec_CAF1 171521 119 - 1
GCAAGGGUACCAAGCUCGCAUCACCCUAUUACUUAAGCUUCACUGACCCAUAGGCCAAAUCAAAGGCCUUUGGGUCAUUCUUUUUGUGUUGCG-AAAAGUUUAAAAAUUAAUAAUUCAAA
...(((((..............))))).....((((((.....(((((((.(((((........))))).)))))))...((((((.....))-))))))))))................ ( -32.74)
>DroSim_CAF1 173738 119 - 1
GCAAGGGUACCAAGCUCGCAUCACCCUAUUACUUAAGCUUCACUGACCCAUAGGCCAAAUCAAAGGCCUUUGGGUCAUUCUUUUUGUGUUGCG-AAAAGUUUAAAAAUUAAUAAUUCAAA
...(((((..............))))).....((((((.....(((((((.(((((........))))).)))))))...((((((.....))-))))))))))................ ( -32.74)
>DroEre_CAF1 201597 120 - 1
GCAAGGGUACCACCCUCGCAUCACCCUAUUACUUUAGCUUCACUGACCCAUAGGCCAAAUCAAAGGCCUUUGGGUCAUUCUUUUUGUGCUGCGGAAAAGCUUAAAAAUUAAUAAUUCAAA
((.((((.....))))((((.(((.(((......)))......(((((((.(((((........))))).)))))))........))).)))).....)).................... ( -37.40)
>DroYak_CAF1 175373 120 - 1
GCAAGGGUACCACCCUCGCAUCACCCUAUUACUUUAGCUUCACUGACCCAUAGGCCAAAUCAAAGGCCUUUGGGUCAUUCUUUUUGUGCUGCGGAAAAGCUUAAAAAUUAAUAAUUCAAA
((.((((.....))))((((.(((.(((......)))......(((((((.(((((........))))).)))))))........))).)))).....)).................... ( -37.40)
>consensus
GCAAGGGUACCAAGCUCGCAUCACCCUAUUACUUAAGCUUCACUGACCCAUAGGCCAAAUCAAAGGCCUUUGGGUCAUUCUUUUUGUGUUGCG_AAAAGUUUAAAAAUUAAUAAUUCAAA
((.(((((..............))))).........((..((((((((((.(((((........))))).)))))))........)))..))......)).................... (-31.30 = -31.06 +  -0.24)

alignment

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secondary structure

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Window 1

Location 27,862,310 – 27,862,430
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.83
Mean single sequence MFE -44.32
Consensus MFE -40.90
Energy contribution -40.90
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.45
Structure conservation index 0.92
SVM decision value 3.29
SVM RNA-class probability 0.998946
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27862310 120 + 27905053
GAAUGACCCAAAGGCCUUUGAUUUGGCCUAUGGGUCAGUGAAGCUUAAGUAAUAGGGUGAUGCGAGCUUGGUACCCUUGCCCCAUAUGUGCUUUCUCGCUUGAGUGCGCAUUGUCAGACC
...(((((((.(((((........))))).)))))))(((..(((((((..(.(((((.(((.(.((..((...))..)).))))....))))).)..))))))).)))........... ( -41.70)
>DroSec_CAF1 171560 120 + 1
GAAUGACCCAAAGGCCUUUGAUUUGGCCUAUGGGUCAGUGAAGCUUAAGUAAUAGGGUGAUGCGAGCUUGGUACCCUUGCCCCAUAUGUGCUUUCUCGCUUGAGUGCGCAUUGUCAGACC
...(((((((.(((((........))))).)))))))(((..(((((((..(.(((((.(((.(.((..((...))..)).))))....))))).)..))))))).)))........... ( -41.70)
>DroSim_CAF1 173777 120 + 1
GAAUGACCCAAAGGCCUUUGAUUUGGCCUAUGGGUCAGUGAAGCUUAAGUAAUAGGGUGAUGCGAGCUUGGUACCCUUGCCCCAUAUGUGCUUUCUCGCUUGAGUGCGCAUUGUCAGACC
...(((((((.(((((........))))).)))))))(((..(((((((..(.(((((.(((.(.((..((...))..)).))))....))))).)..))))))).)))........... ( -41.70)
>DroEre_CAF1 201637 119 + 1
GAAUGACCCAAAGGCCUUUGAUUUGGCCUAUGGGUCAGUGAAGCUAAAGUAAUAGGGUGAUGCGAGGGUGGUACCCUUGCCCCAUAUGUGCU-UCUCGCUUGAGUGCGCAUUGUCAGACC
...(((((((.(((((........))))).))))))).(((.............(((....(((((((.....))))))))))..((((((.-.(((....))).))))))..))).... ( -48.80)
>DroYak_CAF1 175413 120 + 1
GAAUGACCCAAAGGCCUUUGAUUUGGCCUAUGGGUCAGUGAAGCUAAAGUAAUAGGGUGAUGCGAGGGUGGUACCCUUGCUCCAUAUGUGCUUUCUCGCUUGAGUGCGCAUUGUCAGACC
...(((((((.(((((........))))).))))))).................((.(((((((((((.....))))))).....((((((...(((....))).)))))).))))..)) ( -47.70)
>consensus
GAAUGACCCAAAGGCCUUUGAUUUGGCCUAUGGGUCAGUGAAGCUUAAGUAAUAGGGUGAUGCGAGCUUGGUACCCUUGCCCCAUAUGUGCUUUCUCGCUUGAGUGCGCAUUGUCAGACC
...(((((((.(((((........))))).)))))))..................((..(((((((...(((((...((...))...)))))..)))((......))))))..))..... (-40.90 = -40.90 +  -0.00)

alignment

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secondary structure

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Window 2

Location 27,862,310 – 27,862,430
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.83
Mean single sequence MFE -38.62
Consensus MFE -35.76
Energy contribution -35.60
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -2.69
Structure conservation index 0.93
SVM decision value 3.70
SVM RNA-class probability 0.999536
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27862310 120 - 27905053
GGUCUGACAAUGCGCACUCAAGCGAGAAAGCACAUAUGGGGCAAGGGUACCAAGCUCGCAUCACCCUAUUACUUAAGCUUCACUGACCCAUAGGCCAAAUCAAAGGCCUUUGGGUCAUUC
............(((......))).(((.((....((((((...((((.....))))......)))))).......)))))..(((((((.(((((........))))).)))))))... ( -37.10)
>DroSec_CAF1 171560 120 - 1
GGUCUGACAAUGCGCACUCAAGCGAGAAAGCACAUAUGGGGCAAGGGUACCAAGCUCGCAUCACCCUAUUACUUAAGCUUCACUGACCCAUAGGCCAAAUCAAAGGCCUUUGGGUCAUUC
............(((......))).(((.((....((((((...((((.....))))......)))))).......)))))..(((((((.(((((........))))).)))))))... ( -37.10)
>DroSim_CAF1 173777 120 - 1
GGUCUGACAAUGCGCACUCAAGCGAGAAAGCACAUAUGGGGCAAGGGUACCAAGCUCGCAUCACCCUAUUACUUAAGCUUCACUGACCCAUAGGCCAAAUCAAAGGCCUUUGGGUCAUUC
............(((......))).(((.((....((((((...((((.....))))......)))))).......)))))..(((((((.(((((........))))).)))))))... ( -37.10)
>DroEre_CAF1 201637 119 - 1
GGUCUGACAAUGCGCACUCAAGCGAGA-AGCACAUAUGGGGCAAGGGUACCACCCUCGCAUCACCCUAUUACUUUAGCUUCACUGACCCAUAGGCCAAAUCAAAGGCCUUUGGGUCAUUC
............(((......))).((-(((....(((((((.((((.....)))).)).....))))).......)))))..(((((((.(((((........))))).)))))))... ( -42.70)
>DroYak_CAF1 175413 120 - 1
GGUCUGACAAUGCGCACUCAAGCGAGAAAGCACAUAUGGAGCAAGGGUACCACCCUCGCAUCACCCUAUUACUUUAGCUUCACUGACCCAUAGGCCAAAUCAAAGGCCUUUGGGUCAUUC
(((....(((((.((.(((....)))...)).))).))((((.((((.....)))).)).)))))..................(((((((.(((((........))))).)))))))... ( -39.10)
>consensus
GGUCUGACAAUGCGCACUCAAGCGAGAAAGCACAUAUGGGGCAAGGGUACCAAGCUCGCAUCACCCUAUUACUUAAGCUUCACUGACCCAUAGGCCAAAUCAAAGGCCUUUGGGUCAUUC
..........(((...(((....)))...)))....((((((.(((((..............))))).........)))))).(((((((.(((((........))))).)))))))... (-35.76 = -35.60 +  -0.16)

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 13:54:38 2006