Locus 7916

Sequence ID 3L_DroMel_CAF1
Location 21,055,566 – 21,055,841
Length 275
Max. P 0.769395
window12904 window12905 window12906 window12907 window12908

overview

Window 4

Location 21,055,566 – 21,055,682
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.07
Mean single sequence MFE -40.42
Consensus MFE -34.48
Energy contribution -35.68
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -1.45
Structure conservation index 0.85
SVM decision value 0.52
SVM RNA-class probability 0.769395
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21055566 116 + 23771897
UCAAUGCUGGGCCAUAAAUAUCUCUGCACUUGAGUUGGCCUCCUUGCUA----GUUUUUCCGACUCAUGUGAGCCAUGACGCAGGGAAAAGCCCCACGAAAGUCGCGGGGCGUUGCCAUU
.........(((.((.....(((((((...((((((((....((....)----).....)))))))).((.(....).)))))))))...(((((.((.....)).))))))).)))... ( -40.00)
>DroSec_CAF1 110585 116 + 1
UCAAUGCUGGGCCAUAAAUAUCUCUGCACUUGAGUUGGCCUCCUUGCUG----GUUUUUCCGACUCAUGUGAGCCAUGACGCAGGGAAAAGCCCCACGAAAGUCGGGGGGCGUUGCCAUU
.(((((((.(((((.......(((.......))).)))))(((((((((----(.....)))..(((((.....))))).)))))))....((((((....)).)))))))))))..... ( -43.60)
>DroSim_CAF1 16843 116 + 1
UCAAUGCUGGGCCAUAAAUAUCUCUGCACUUGAGUUGGCCUCCUUGCUG----GUUUUUCCGACUCAUGUGAGCCAUGACGCAGGGAAAAGCCCCACGAAAGUCGGGGGGCGUUGCCAUU
.(((((((.(((((.......(((.......))).)))))(((((((((----(.....)))..(((((.....))))).)))))))....((((((....)).)))))))))))..... ( -43.60)
>DroEre_CAF1 33135 119 + 1
UCAAUGCUGGGCCAUAAAUAUCUCUGCACUUAAGCUGGCCUCCUUGCGAGUGAGUUUUUCCGACUCAUGUGAGCCAUGACGCAGGGAAAAGA-CCACGAAAGUCAGGGGGCGUUGCCAUU
.(((((((.(((((...........((......)))))))((((((((.(((((((.....)))))))(((...)))..)))))))).....-((((....))..)).)))))))..... ( -36.70)
>DroYak_CAF1 4051 115 + 1
UCAAUGCUGGGCCAUAAAUAUCUCUGCACUUGAGUU-GCCUCCUUGCGC----GUUUUUCCGACUCAUGUGAGCCAUGACGCAGGGAAAAGCCCCACGAAAGUCGGGGGGCGUUGCCAUU
.(((((((.(((.........(((.......)))..-)))((((((((.----(((.....)))(((((.....)))))))))))))....((((((....)).)))))))))))..... ( -38.20)
>consensus
UCAAUGCUGGGCCAUAAAUAUCUCUGCACUUGAGUUGGCCUCCUUGCUA____GUUUUUCCGACUCAUGUGAGCCAUGACGCAGGGAAAAGCCCCACGAAAGUCGGGGGGCGUUGCCAUU
.(((((((.(((((.......(((.......))).)))))(((((((......(((.....)))(((((.....))))).)))))))....((((((....)).)))))))))))..... (-34.48 = -35.68 +   1.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,055,566 – 21,055,682
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.07
Mean single sequence MFE -37.57
Consensus MFE -33.50
Energy contribution -33.58
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.15
Structure conservation index 0.89
SVM decision value -0.02
SVM RNA-class probability 0.521222
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21055566 116 - 23771897
AAUGGCAACGCCCCGCGACUUUCGUGGGGCUUUUCCCUGCGUCAUGGCUCACAUGAGUCGGAAAAAC----UAGCAAGGAGGCCAACUCAAGUGCAGAGAUAUUUAUGGCCCAGCAUUGA
...(((...((((((((.....))))))))((((((..((.(((((.....))))))).)))))).(----(.(((..(((.....)))...)))))...........)))......... ( -40.90)
>DroSec_CAF1 110585 116 - 1
AAUGGCAACGCCCCCCGACUUUCGUGGGGCUUUUCCCUGCGUCAUGGCUCACAUGAGUCGGAAAAAC----CAGCAAGGAGGCCAACUCAAGUGCAGAGAUAUUUAUGGCCCAGCAUUGA
..((((...(((((.((.....)).)))))..((((.(((.....(((((....)))))((.....)----).))).)))))))).....(((((..................))))).. ( -37.77)
>DroSim_CAF1 16843 116 - 1
AAUGGCAACGCCCCCCGACUUUCGUGGGGCUUUUCCCUGCGUCAUGGCUCACAUGAGUCGGAAAAAC----CAGCAAGGAGGCCAACUCAAGUGCAGAGAUAUUUAUGGCCCAGCAUUGA
..((((...(((((.((.....)).)))))..((((.(((.....(((((....)))))((.....)----).))).)))))))).....(((((..................))))).. ( -37.77)
>DroEre_CAF1 33135 119 - 1
AAUGGCAACGCCCCCUGACUUUCGUGG-UCUUUUCCCUGCGUCAUGGCUCACAUGAGUCGGAAAAACUCACUCGCAAGGAGGCCAGCUUAAGUGCAGAGAUAUUUAUGGCCCAGCAUUGA
...(((...(((.(((.......((((-..((((((..((.(((((.....))))))).))))))..)))).....))).)))..((......)).............)))......... ( -30.30)
>DroYak_CAF1 4051 115 - 1
AAUGGCAACGCCCCCCGACUUUCGUGGGGCUUUUCCCUGCGUCAUGGCUCACAUGAGUCGGAAAAAC----GCGCAAGGAGGC-AACUCAAGUGCAGAGAUAUUUAUGGCCCAGCAUUGA
...(((...(((((.((.....)).))))).((((...((((..((((((....)))))).....))----))(((..(((..-..)))...))).))))........)))......... ( -41.10)
>consensus
AAUGGCAACGCCCCCCGACUUUCGUGGGGCUUUUCCCUGCGUCAUGGCUCACAUGAGUCGGAAAAAC____CAGCAAGGAGGCCAACUCAAGUGCAGAGAUAUUUAUGGCCCAGCAUUGA
...(((...(((((.((.....)).)))))((((((..((.(((((.....))))))).))))))........(((..(((.....)))...))).............)))......... (-33.50 = -33.58 +   0.08)

alignment

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secondary structure

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Window 6

Location 21,055,606 – 21,055,721
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.75
Mean single sequence MFE -37.10
Consensus MFE -30.76
Energy contribution -31.00
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.47
Structure conservation index 0.83
SVM decision value 0.46
SVM RNA-class probability 0.746934
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21055606 115 - 23771897
CCCAUCGUCCACACCAG-ACACGCCCCCUCGGCGCGAAUCAAUGGCAACGCCCCGCGACUUUCGUGGGGCUUUUCCCUGCGUCAUGGCUCACAUGAGUCGGAAAAAC----UAGCAAGGA
.((.(((((.......)-)).((((.....)))).)).......((...((((((((.....))))))))((((((..((.(((((.....))))))).))))))..----..))..)). ( -40.50)
>DroSec_CAF1 110625 114 - 1
CCCAUCGUCCACACCAG-ACACGCC-CCUCGGCGCGAAUCAAUGGCAACGCCCCCCGACUUUCGUGGGGCUUUUCCCUGCGUCAUGGCUCACAUGAGUCGGAAAAAC----CAGCAAGGA
.((((.(((.......)-)).((((-....)))).......))))....(((((.((.....)).)))))...(((.(((.....(((((....)))))((.....)----).))).))) ( -37.00)
>DroSim_CAF1 16883 114 - 1
CCCAUCGUCCACACCAG-GCACGCC-CCUCGGCGCGAAUCAAUGGCAACGCCCCCCGACUUUCGUGGGGCUUUUCCCUGCGUCAUGGCUCACAUGAGUCGGAAAAAC----CAGCAAGGA
.............((..-((.((((-....))))........(((....(((((.((.....)).)))))((((((..((.(((((.....))))))).)))))).)----))))..)). ( -37.20)
>DroEre_CAF1 33175 119 - 1
CCCAUCGUCCACACCAGGCCACGCCCCCCAUGCGCGAAUCAAUGGCAACGCCCCCUGACUUUCGUGG-UCUUUUCCCUGCGUCAUGGCUCACAUGAGUCGGAAAAACUCACUCGCAAGGA
...............(((((((((.......))..((((((..(((...)))...)))..)))))))-)))..(((.((((...((((((....))))))((.....))...)))).))) ( -29.30)
>DroYak_CAF1 4090 116 - 1
CCCAUCGUCCACACCAAGACACGCCCCCUAUGCGCGAAUCAAUGGCAACGCCCCCCGACUUUCGUGGGGCUUUUCCCUGCGUCAUGGCUCACAUGAGUCGGAAAAAC----GCGCAAGGA
......(((........)))......(((.((((((.......(....)(((((.((.....)).)))))((((((..((.(((((.....))))))).)))))).)----)))))))). ( -41.50)
>consensus
CCCAUCGUCCACACCAG_ACACGCCCCCUCGGCGCGAAUCAAUGGCAACGCCCCCCGACUUUCGUGGGGCUUUUCCCUGCGUCAUGGCUCACAUGAGUCGGAAAAAC____CAGCAAGGA
.......(((.........(.(((.......))).)........((...(((((.((.....)).)))))((((((..((.(((((.....))))))).))))))........))..))) (-30.76 = -31.00 +   0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,055,682 – 21,055,801
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.73
Mean single sequence MFE -31.12
Consensus MFE -26.75
Energy contribution -26.79
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.40
Structure conservation index 0.86
SVM decision value 0.49
SVM RNA-class probability 0.757664
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21055682 119 - 23771897
UUAAUUAAACUCAUCACAAACACUUUUACGAGUGCCAAAGGAGGCGUUUGUAUUAUGAGCGCCGUGGAUUGCUCAUACGCCCCAUCGUCCACACCAG-ACACGCCCCCUCGGCGCGAAUC
..........((((.((((((((((....))))(((......)))))))))...))))((((((.((...((......))......(((.......)-))......)).))))))..... ( -31.80)
>DroSec_CAF1 110701 118 - 1
UUAAUUAAACUCAUCACAAACACUUUUACGAGUGCCAAAGGAGGCGUUUGUAUUAUGAGCGCCGUGGAUUACUCAUACGCCCCAUCGUCCACACCAG-ACACGCC-CCUCGGCGCGAAUC
..........((((.((((((((((....))))(((......)))))))))...))))(((((((((((.................))))))....(-(......-..)))))))..... ( -29.83)
>DroSim_CAF1 16959 118 - 1
UUAAUUAAACUCAUCACAAACACUUUUACGAGUGCCAAAGGAGGCGUUGGUAUUAUGAGCGCCGUGGAUUACUCAUACGCCCCAUCGUCCACACCAG-GCACGCC-CCUCGGCGCGAAUC
.............((.(..............(((((...((.((((((.((...)).))))))((((((.................)))))).)).)-))))(((-....)))).))... ( -31.43)
>DroEre_CAF1 33254 119 - 1
UUAAUUAAACUCAUCACAAACACUU-UGCGAGUGCCAAAGGAGGCGUUCGUAUUAUGAGCGCCGUGGAUUACUCAUACGCCCCAUCGUCCACACCAGGCCACGCCCCCCAUGCGCGAAUC
.......................((-((((.(((.....((.(((((((((...)))))))))((((((.................)))))).)).(((...)))...))).)))))).. ( -31.83)
>DroYak_CAF1 4166 120 - 1
UUAAUUAAACGCAUCACAAACACUUUUACGAGUGCCAAAGGAGGCGUUCGUAUUAUGAGCGCCGUGGAUUACUCAUACGCCCCAUCGUCCACACCAAGACACGCCCCCUAUGCGCGAAUC
.........(((........(((((....))))).((.(((.(((((((((...)))))))))((((((.................))))))..............))).)).))).... ( -30.73)
>consensus
UUAAUUAAACUCAUCACAAACACUUUUACGAGUGCCAAAGGAGGCGUUCGUAUUAUGAGCGCCGUGGAUUACUCAUACGCCCCAUCGUCCACACCAG_ACACGCCCCCUCGGCGCGAAUC
....................(((((....))))).....((.(((((((((...)))))))))((((((.................)))))).))....(.(((.......))).).... (-26.75 = -26.79 +   0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,055,721 – 21,055,841
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.33
Mean single sequence MFE -31.09
Consensus MFE -28.88
Energy contribution -28.76
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -1.11
Structure conservation index 0.93
SVM decision value 0.14
SVM RNA-class probability 0.601885
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21055721 120 - 23771897
UCUGCUGGGCGAAAUGCAAAUGCAAAUCCCUCGCAGAUCUUUAAUUAAACUCAUCACAAACACUUUUACGAGUGCCAAAGGAGGCGUUUGUAUUAUGAGCGCCGUGGAUUGCUCAUACGC
(((((.(((.((..(((....)))..))))).)))))..................((((((((((....))))(((......)))))))))..((((((((........))))))))... ( -35.10)
>DroSec_CAF1 110739 114 - 1
UCUGCUGGGCGAAAUG------CAAAUCCCUCGCAGAUCUUUAAUUAAACUCAUCACAAACACUUUUACGAGUGCCAAAGGAGGCGUUUGUAUUAUGAGCGCCGUGGAUUACUCAUACGC
(((((.(((.((....------....))))).)))))................................((((((((.....((((((..(...)..)))))).)))..)))))...... ( -28.80)
>DroSim_CAF1 16997 114 - 1
UCUGCUGGGCGAAAUG------CAAAUCCCUCGCAGAUCUUUAAUUAAACUCAUCACAAACACUUUUACGAGUGCCAAAGGAGGCGUUGGUAUUAUGAGCGCCGUGGAUUACUCAUACGC
(((((.(((.((....------....))))).)))))................................((((((((.....((((((.((...)).)))))).)))..)))))...... ( -28.10)
>DroEre_CAF1 33294 113 - 1
UCUGCCUGGCGGAAUG------CAAAUCCCUCGCAGAUCUUUAAUUAAACUCAUCACAAACACUU-UGCGAGUGCCAAAGGAGGCGUUCGUAUUAUGAGCGCCGUGGAUUACUCAUACGC
((..(.(((((((...------....)))((((((((..........................))-)))))).)))).....(((((((((...))))))))))..))............ ( -31.97)
>DroYak_CAF1 4206 114 - 1
UCUGCUGGGCGGAAUG------CAAAUCCCUCGCAGGUCUUUAAUUAAACGCAUCACAAACACUUUUACGAGUGCCAAAGGAGGCGUUCGUAUUAUGAGCGCCGUGGAUUACUCAUACGC
(((((.(((.(((...------....)))))))))))................................((((((((.....(((((((((...))))))))).)))..)))))...... ( -31.50)
>consensus
UCUGCUGGGCGAAAUG______CAAAUCCCUCGCAGAUCUUUAAUUAAACUCAUCACAAACACUUUUACGAGUGCCAAAGGAGGCGUUCGUAUUAUGAGCGCCGUGGAUUACUCAUACGC
(((((.(((.((..(((....)))..))))).)))))................................((((.(((.....(((((((((...))))))))).)))...))))...... (-28.88 = -28.76 +  -0.12)

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 13:00:46 2006