Locus 899

Sequence ID 3L_DroMel_CAF1
Location 2,725,762 – 2,725,897
Length 135
Max. P 0.999907
window1381 window1382 window1383

overview

Window 1

Location 2,725,762 – 2,725,857
Length 95
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 77.47
Mean single sequence MFE -15.34
Consensus MFE -8.22
Energy contribution -7.38
Covariance contribution -0.84
Combinations/Pair 1.48
Mean z-score -1.82
Structure conservation index 0.54
SVM decision value 0.20
SVM RNA-class probability 0.628678
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2725762 95 - 23771897
GAUGCAAAUGGAAAAAGUGUGUACACAACACGAAUUAUGCAAUGGUAUAUUUG-CCCAAAAA-UUAA-----AAAAAAAAAGUUUAAAUUGAAAAGUUUACA
...(((((((......((((.......))))......(((....)))))))))-).......-....-----............((((((....)))))).. ( -12.40)
>DroSim_CAF1 84106 101 - 1
GAUGCAAAUGGAAAAAGUGUGUACACAACACGAAUUAUGCAAUGGCAUAUUUG-CCCAAAAAUUCAAAAAAAAAAAAAAAAGUUUAAAUUGAAAAGUUUACA
...(((((((......((((.......))))......(((....)))))))))-).............................((((((....)))))).. ( -14.40)
>DroEre_CAF1 94206 91 - 1
GAUGCAAAUGGAAAAAUUGUGUACACAACACGAAUUAUGCAAUGGCAUAUUUG-CCCAAAAA-UUCA-----A--A--AAAGUUUAAAUUGAAAAGUUUGCA
..(((((((.....((((((((.....))))(((((.......((((....))-))....))-))).-----.--.--........)))).....))))))) ( -17.60)
>DroYak_CAF1 87615 93 - 1
GAUGCAAAUGGAAAAAGUGUGUACACAACACGAAUUAUGCAAUGGCAUAUUUG-CCCAAAAA-UUCA-----A--AAAAAAGUUUAAAUUGAAAAGUUUGCA
..(((((((.......((((.......))))(((((.......((((....))-))....))-))).-----.--....................))))))) ( -17.20)
>DroAna_CAF1 84300 91 - 1
CUCGCAAAUCGCAAAUAAAAGUCAACAAUGCUGGU-CUUCAGCGAGAUAUUUAGUUGGAAAA-CUCG---------ACAAACUUUAAAUUAAAAAGUUUUCU
...((.....))........(((.....(((((..-...)))))........((((....))-)).)---------))(((((((.......)))))))... ( -15.10)
>consensus
GAUGCAAAUGGAAAAAGUGUGUACACAACACGAAUUAUGCAAUGGCAUAUUUG_CCCAAAAA_UUCA_____A__AAAAAAGUUUAAAUUGAAAAGUUUACA
........(((......(((((.....)))))((.(((((....))))).))...)))..........................((((((....)))))).. ( -8.22 =  -7.38 +  -0.84)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,725,792 – 2,725,897
Length 105
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 93.90
Mean single sequence MFE -15.53
Consensus MFE -14.30
Energy contribution -14.50
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.19
Structure conservation index 0.92
SVM decision value 0.38
SVM RNA-class probability 0.714082
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2725792 105 + 23771897
----UUAA-UUUUUGGGCAAAUAUACCAUUGCAUAAUUCGUGUUGUGUACACACUUUUUCCAUUUGCAUCGUCUCAUUUUAACUUUUCCCUUUGAUUCGCCCCGCCUUUU
----....-.....((((...........((((((((....)))))))).....................(..(((................)))..)))))........ ( -13.69)
>DroSec_CAF1 85923 109 + 1
UUUUUUGA-UUUUUGGGCAAAUAUGCCAUUGCAUAAUUCGUGUUGUGUACACACUUUUUCCAUUUGCAUCGUCUCAUUUUAACUUUUCCCUUUGAUUCGCCCCGCCUUUU
........-.....((((...(((((....)))))....((((.....))))..............................................))))........ ( -15.60)
>DroSim_CAF1 84137 110 + 1
UUUUUUGAAUUUUUGGGCAAAUAUGCCAUUGCAUAAUUCGUGUUGUGUACACACUUUUUCCAUUUGCAUCGUCUCAUUUUAACUUUUCCCUUUGAUUCGCCCCGCCUUUU
......(((((...(((.((((((((....)))))....((((.....))))...............................))).)))...)))))............ ( -16.40)
>DroEre_CAF1 94232 105 + 1
----UGAA-UUUUUGGGCAAAUAUGCCAUUGCAUAAUUCGUGUUGUGUACACAAUUUUUCCAUUUGCAUCGUCUCAUUUUAACUUUCUCCUUUGAUUCGCCCCGCCUUUU
----.(((-((...((((((((((((....)))))....((((.....))))..........)))))...((.........)).....))...)))))............ ( -15.90)
>DroYak_CAF1 87643 105 + 1
----UGAA-UUUUUGGGCAAAUAUGCCAUUGCAUAAUUCGUGUUGUGUACACACUUUUUCCAUUUGCAUCGUCUCAUUUUAACUUUUUCCUUUGACUCGCCCCGCCAUUU
----....-.....((((...(((((....)))))....((((.....))))..................(((....................)))..))))........ ( -16.05)
>consensus
____UUAA_UUUUUGGGCAAAUAUGCCAUUGCAUAAUUCGUGUUGUGUACACACUUUUUCCAUUUGCAUCGUCUCAUUUUAACUUUUCCCUUUGAUUCGCCCCGCCUUUU
..............((((...(((((....)))))....((((.....))))..............................................))))........ (-14.30 = -14.50 +   0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,725,792 – 2,725,897
Length 105
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 93.90
Mean single sequence MFE -20.62
Consensus MFE -20.62
Energy contribution -20.30
Covariance contribution -0.32
Combinations/Pair 1.08
Mean z-score -2.20
Structure conservation index 1.00
SVM decision value 4.49
SVM RNA-class probability 0.999907
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2725792 105 - 23771897
AAAAGGCGGGGCGAAUCAAAGGGAAAAGUUAAAAUGAGACGAUGCAAAUGGAAAAAGUGUGUACACAACACGAAUUAUGCAAUGGUAUAUUUGCCCAAAAA-UUAA----
........((((((((...........(((.......))).((((...((.(.((..(((((.....)))))..)).).))...)))))))))))).....-....---- ( -18.80)
>DroSec_CAF1 85923 109 - 1
AAAAGGCGGGGCGAAUCAAAGGGAAAAGUUAAAAUGAGACGAUGCAAAUGGAAAAAGUGUGUACACAACACGAAUUAUGCAAUGGCAUAUUUGCCCAAAAA-UCAAAAAA
........((((((((...........(((.......))).((((...((.(.((..(((((.....)))))..)).).))...)))))))))))).....-........ ( -20.80)
>DroSim_CAF1 84137 110 - 1
AAAAGGCGGGGCGAAUCAAAGGGAAAAGUUAAAAUGAGACGAUGCAAAUGGAAAAAGUGUGUACACAACACGAAUUAUGCAAUGGCAUAUUUGCCCAAAAAUUCAAAAAA
........((((((((...........(((.......))).((((...((.(.((..(((((.....)))))..)).).))...)))))))))))).............. ( -20.80)
>DroEre_CAF1 94232 105 - 1
AAAAGGCGGGGCGAAUCAAAGGAGAAAGUUAAAAUGAGACGAUGCAAAUGGAAAAAUUGUGUACACAACACGAAUUAUGCAAUGGCAUAUUUGCCCAAAAA-UUCA----
........((((((((...........(((.......))).((((...((.(.((.((((((.....)))))).)).).))...)))))))))))).....-....---- ( -21.90)
>DroYak_CAF1 87643 105 - 1
AAAUGGCGGGGCGAGUCAAAGGAAAAAGUUAAAAUGAGACGAUGCAAAUGGAAAAAGUGUGUACACAACACGAAUUAUGCAAUGGCAUAUUUGCCCAAAAA-UUCA----
........((((((((...........(((.......))).((((...((.(.((..(((((.....)))))..)).).))...)))))))))))).....-....---- ( -20.80)
>consensus
AAAAGGCGGGGCGAAUCAAAGGGAAAAGUUAAAAUGAGACGAUGCAAAUGGAAAAAGUGUGUACACAACACGAAUUAUGCAAUGGCAUAUUUGCCCAAAAA_UUAA____
........((((((((...........(((.......))).((((...((.(.((..(((((.....)))))..)).).))...)))))))))))).............. (-20.62 = -20.30 +  -0.32)

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 09:53:55 2006