Locus 7258

Sequence ID X_DroMel_CAF1
Location 18,101,020 – 18,101,267
Length 247
Max. P 0.791869
window11886 window11887 window11888 window11889 window11890

overview

Window 6

Location 18,101,020 – 18,101,114
Length 94
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.77
Mean single sequence MFE -40.30
Consensus MFE -29.13
Energy contribution -29.72
Covariance contribution 0.59
Combinations/Pair 1.08
Mean z-score -1.78
Structure conservation index 0.72
SVM decision value 0.04
SVM RNA-class probability 0.555797
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18101020 94 + 22224390
----CGACCGGCUGUUAUGCAAAUGCGACCGCC-------------------GU--GGGGAGACGGAGACAUCGCCAUCUUGGCAGGCCGAUGGCUGAUCUC-UCGCCAUCUUGGUCGCC
----((((((((.(((..((....))))).)))-------------------((--((.((((.(....)(((((((((..((....)))))))).))).))-)).))))...))))).. ( -40.10)
>DroSec_CAF1 9648 94 + 1
----CGACCGGCUGUUAUGCAAAUGCGACCGCC-------------------GU--GGGGAGACGGAGACAUCGCCAUCUUGGCAGGCCGAUGGCUGAUCUC-UCGCCAUCUUGGUCGCC
----((((((((.(((..((....))))).)))-------------------((--((.((((.(....)(((((((((..((....)))))))).))).))-)).))))...))))).. ( -40.10)
>DroSim_CAF1 9722 94 + 1
----CGACCGGCUGUUAUGCAAAUGCGACCGCC-------------------GU--GGGGAGACGGAGACAUCGCCAUCUUGGCAGGCCGAUGGCUGAUCUC-UCGCCAUCUUGGUCGCC
----((((((((.(((..((....))))).)))-------------------((--((.((((.(....)(((((((((..((....)))))))).))).))-)).))))...))))).. ( -40.10)
>DroEre_CAF1 7100 94 + 1
----CGACCGGCUGUUAUGCAAAUGCGACCGCC-------------------GU--GGGUAGACGGAGACAUCGCCAUCUUGGCAGGCCGAUGGCUGAUCUC-UCGCCAUCUUGGUCGCC
----(((((((((....(((....)))...(((-------------------(.--.(((.((.(....).)))))....)))).))))((((((.((....-))))))))..))))).. ( -38.30)
>DroYak_CAF1 8777 100 + 1
ACAGCGACCGGCUGUUAUGCAAAUGCGACCGCC-------------------GUGUGGGGAGACGGAGACAUCGCCAUCUUGGCUGGCCGAUGGCUGAUCUC-UCGCCAUCUUGGUCGCC
...((((((((((....(((....)))...(((-------------------(.((((.((...(....).)).))))..)))).))))((((((.((....-))))))))..)))))). ( -44.70)
>DroAna_CAF1 12054 109 + 1
----GGGUGGGCUGUUAUGCAAAUAUAUUCUCCAAAGAGGGGGGGGGGAGGGGA--GGAGAAAAGGAGACAUCGCCAUCUUGGCAGG-AGAUGGCUGAUCUCUUCGCCAUCUUUGG----
----(((((.((......)).....))))).(((((((.((.(((((((.....--........(....)...((((((((.....)-)))))))...))))))).)).)))))))---- ( -38.50)
>consensus
____CGACCGGCUGUUAUGCAAAUGCGACCGCC___________________GU__GGGGAGACGGAGACAUCGCCAUCUUGGCAGGCCGAUGGCUGAUCUC_UCGCCAUCUUGGUCGCC
..........((......))....(((((((((............................((.(....).))(((.....))).))).((((((.((.....))))))))..)))))). (-29.13 = -29.72 +   0.59)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 18,101,020 – 18,101,114
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.77
Mean single sequence MFE -38.12
Consensus MFE -30.15
Energy contribution -30.79
Covariance contribution 0.64
Combinations/Pair 1.15
Mean z-score -2.12
Structure conservation index 0.79
SVM decision value 0.57
SVM RNA-class probability 0.785004
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18101020 94 - 22224390
GGCGACCAAGAUGGCGA-GAGAUCAGCCAUCGGCCUGCCAAGAUGGCGAUGUCUCCGUCUCCCC--AC-------------------GGCGGUCGCAUUUGCAUAACAGCCGGUCG----
..(((((..((((((((-....)).))))))(((..(((.....)))(((((..(((((.....--..-------------------)))))..))))).........))))))))---- ( -39.30)
>DroSec_CAF1 9648 94 - 1
GGCGACCAAGAUGGCGA-GAGAUCAGCCAUCGGCCUGCCAAGAUGGCGAUGUCUCCGUCUCCCC--AC-------------------GGCGGUCGCAUUUGCAUAACAGCCGGUCG----
..(((((..((((((((-....)).))))))(((..(((.....)))(((((..(((((.....--..-------------------)))))..))))).........))))))))---- ( -39.30)
>DroSim_CAF1 9722 94 - 1
GGCGACCAAGAUGGCGA-GAGAUCAGCCAUCGGCCUGCCAAGAUGGCGAUGUCUCCGUCUCCCC--AC-------------------GGCGGUCGCAUUUGCAUAACAGCCGGUCG----
..(((((..((((((((-....)).))))))(((..(((.....)))(((((..(((((.....--..-------------------)))))..))))).........))))))))---- ( -39.30)
>DroEre_CAF1 7100 94 - 1
GGCGACCAAGAUGGCGA-GAGAUCAGCCAUCGGCCUGCCAAGAUGGCGAUGUCUCCGUCUACCC--AC-------------------GGCGGUCGCAUUUGCAUAACAGCCGGUCG----
..(((((..((((((((-....)).))))))(((..(((.....)))(((((..(((((.....--..-------------------)))))..))))).........))))))))---- ( -39.30)
>DroYak_CAF1 8777 100 - 1
GGCGACCAAGAUGGCGA-GAGAUCAGCCAUCGGCCAGCCAAGAUGGCGAUGUCUCCGUCUCCCCACAC-------------------GGCGGUCGCAUUUGCAUAACAGCCGGUCGCUGU
(((((((..((((((((-....)).))))))(((..(((.....)))(((((..(((((.........-------------------)))))..))))).........)))))))))).. ( -44.50)
>DroAna_CAF1 12054 109 - 1
----CCAAAGAUGGCGAAGAGAUCAGCCAUCU-CCUGCCAAGAUGGCGAUGUCUCCUUUUCUCC--UCCCCUCCCCCCCCCCUCUUUGGAGAAUAUAUUUGCAUAACAGCCCACCC----
----........(((...(((((..(((((((-.......)))))))...)))))...((((((--.....................))))))...............))).....---- ( -27.00)
>consensus
GGCGACCAAGAUGGCGA_GAGAUCAGCCAUCGGCCUGCCAAGAUGGCGAUGUCUCCGUCUCCCC__AC___________________GGCGGUCGCAUUUGCAUAACAGCCGGUCG____
..(((((..((((((..........))))))(((..(((.....)))(((((..(((((............................)))))..))))).........)))))))).... (-30.15 = -30.79 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 18,101,075 – 18,101,168
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 89.62
Mean single sequence MFE -28.07
Consensus MFE -23.96
Energy contribution -23.78
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -1.44
Structure conservation index 0.85
SVM decision value 0.15
SVM RNA-class probability 0.607576
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18101075 93 + 22224390
UGGCAGGCCGAUGGCUGAUCUCUCGCCAUCUUGGUCGCCGUCACUGCAGCACUGCACCACCACCUCCAUCAGCACCGCCACCUUCUGCUCCUG
((((.(((.((((((.((((............))))))))))..((((....))))...............)).).))))............. ( -24.10)
>DroSec_CAF1 9703 90 + 1
UGGCAGGCCGAUGGCUGAUCUCUCGCCAUCUUGGUCGCCGCCACUGCAGCACUGCACCACCUCCUCCA---CCACCGCCACCUUCUGCUGCUG
((((.((((((((((.((....))))))))..))))...))))..((((((.................---..............)))))).. ( -26.48)
>DroSim_CAF1 9777 90 + 1
UGGCAGGCCGAUGGCUGAUCUCUCGCCAUCUUGGUCGCCGCCACUGCAGCACUGCACCACCACCUCCA---GCACCGCCACCUUCUGCUGCUG
((((.((((((((((.((....))))))))..))))...)))).((((....))))..........((---(((..((........))))))) ( -28.30)
>DroEre_CAF1 7155 83 + 1
UGGCAGGCCGAUGGCUGAUCUCUCGCCAUCUUGGUCGCCGCCACUGCUGCACUGCAGCACC---GC-A---GCACCGCCACCA---ACUCCUG
((((.((((((((((.((....))))))))..))))((.((...((((((...))))))..---))-.---))...))))...---....... ( -33.40)
>consensus
UGGCAGGCCGAUGGCUGAUCUCUCGCCAUCUUGGUCGCCGCCACUGCAGCACUGCACCACCACCUCCA___GCACCGCCACCUUCUGCUCCUG
((((.((((((((((.((....))))))))..))))((.((....)).))..........................))))............. (-23.96 = -23.78 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 18,101,075 – 18,101,168
Length 93
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 89.62
Mean single sequence MFE -37.25
Consensus MFE -26.98
Energy contribution -27.48
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.72
SVM decision value 0.15
SVM RNA-class probability 0.606990
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18101075 93 - 22224390
CAGGAGCAGAAGGUGGCGGUGCUGAUGGAGGUGGUGGUGCAGUGCUGCAGUGACGGCGACCAAGAUGGCGAGAGAUCAGCCAUCGGCCUGCCA
.............((((((.((((((((.(((.((.((.((.((...)).)))).)).)))....((((....).))).)))))))))))))) ( -37.10)
>DroSec_CAF1 9703 90 - 1
CAGCAGCAGAAGGUGGCGGUGG---UGGAGGAGGUGGUGCAGUGCUGCAGUGGCGGCGACCAAGAUGGCGAGAGAUCAGCCAUCGGCCUGCCA
...........(((((((((.(---(.(..(..(..((.....))..)..)..).)).)))..((((((((....)).)))))).))).))). ( -33.90)
>DroSim_CAF1 9777 90 - 1
CAGCAGCAGAAGGUGGCGGUGC---UGGAGGUGGUGGUGCAGUGCUGCAGUGGCGGCGACCAAGAUGGCGAGAGAUCAGCCAUCGGCCUGCCA
..((((((....(((.((.(((---.....))).)).)))..))))))..((((((.(.((..((((((((....)).))))))))))))))) ( -36.20)
>DroEre_CAF1 7155 83 - 1
CAGGAGU---UGGUGGCGGUGC---U-GC---GGUGCUGCAGUGCAGCAGUGGCGGCGACCAAGAUGGCGAGAGAUCAGCCAUCGGCCUGCCA
.......---((((((((((((---(-((---.(((((((...)))))).).))))).)))..((((((((....)).)))))).))).)))) ( -41.80)
>consensus
CAGCAGCAGAAGGUGGCGGUGC___UGGAGGUGGUGGUGCAGUGCUGCAGUGGCGGCGACCAAGAUGGCGAGAGAUCAGCCAUCGGCCUGCCA
...........(((((((((.............(.....)..((((((....)))))))))..((((((((....)).)))))).))).))). (-26.98 = -27.48 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 18,101,168 – 18,101,267
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -37.10
Consensus MFE -33.94
Energy contribution -33.38
Covariance contribution -0.56
Combinations/Pair 1.12
Mean z-score -1.67
Structure conservation index 0.91
SVM decision value 0.59
SVM RNA-class probability 0.791869
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18101168 99 - 22224390
UCUGCUUCGCUCUCGCUCGCUCUAAUCUGGGGAAUGCCAUCGCAGGAGCCACAGAACAAUGGCUCAGCGGAUCAGGAUCUCCGAAGGGAGGAGCAGGAG
.........(((..((((.((((..((.(((((...((.((((..((((((........)))))).))))....)).)))))))..))))))))..))) ( -38.90)
>DroSec_CAF1 9793 99 - 1
UCUGCUUCGCUCUCGCUCGCUCUAAUCUGGGGAAUGCCAUCGCAGGAGCCACAGAACAAUGGCUCAGCGGAUCAGGAUCUCCGAAGGGAGGAGCAGGAG
.........(((..((((.((((..((.(((((...((.((((..((((((........)))))).))))....)).)))))))..))))))))..))) ( -38.90)
>DroSim_CAF1 9867 99 - 1
UCUGCUUCGCUCUCGCUCGCUCUAAUCUGGGGAAUGCCAUCGCAGGAGCCACAGAACAAUGGCUCAGCGGAUCAGGAUCUCCGAAGGGAGGAGCAGGAG
.........(((..((((.((((..((.(((((...((.((((..((((((........)))))).))))....)).)))))))..))))))))..))) ( -38.90)
>DroYak_CAF1 8950 93 - 1
UCUGCUACGCUCUCGCUCGCUCUAAUCUGGGGAAUGCCAUCGCAGGAGCCACAGAACAAUGGCUCAG--GAU----AUCUUCAAAUGGAGGGGCAGGAG
.........(((..((((.(((((...((((((.(((....))).((((((........))))))..--...----.))))))..)))))))))..))) ( -31.70)
>consensus
UCUGCUUCGCUCUCGCUCGCUCUAAUCUGGGGAAUGCCAUCGCAGGAGCCACAGAACAAUGGCUCAGCGGAUCAGGAUCUCCGAAGGGAGGAGCAGGAG
.........(((..((((.((((....((((((.(((....))).((((((........))))))............))))))...))))))))..))) (-33.94 = -33.38 +  -0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:28 2006