Locus 7257

Sequence ID X_DroMel_CAF1
Location 18,100,210 – 18,100,346
Length 136
Max. P 0.973322
window11882 window11883 window11884 window11885

overview

Window 2

Location 18,100,210 – 18,100,311
Length 101
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 72.03
Mean single sequence MFE -33.25
Consensus MFE -19.08
Energy contribution -21.00
Covariance contribution 1.92
Combinations/Pair 1.32
Mean z-score -1.95
Structure conservation index 0.57
SVM decision value 1.59
SVM RNA-class probability 0.966010
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18100210 101 + 22224390
UGUGUAUUUAAUUUAUGUGCUCGACGUGACACUUGCCAAGGGCCCCUGGCAUUGG--CGAUGGUGGUUCUUGGC--UGGU------AUGAGUAUGCAUAUUAUAGCAU---------AUA
((((((((((..((((((.....)))))).(((.(((((((((((((.((....)--).).)).))))))))))--.)))------.))))))))))...........---------... ( -34.60)
>DroSec_CAF1 8867 101 + 1
UGUGUAUUUAAUUUAUGUGCUCGACGUGACACUUGCCAAGGGCCCCUGGCAUUGG--CGAUGGUGGUUCUUGGC--UGGU------AUGGGUAUGCAUAUUAUAGCAU---------AUA
((((((((((..((((((.....)))))).(((.(((((((((((((.((....)--).).)).))))))))))--.)))------.))))))))))...........---------... ( -33.70)
>DroSim_CAF1 8923 101 + 1
UGUGUAUUUAAUUUAUGUGCUCGACGUGACACUUGCCAAGGGCCCCUGGCAUUGG--CGAUGGUGGUUCUUGGC--UGGU------AUGGGUAUGCAUAUUAUAGCAU---------AUA
((((((((((..((((((.....)))))).(((.(((((((((((((.((....)--).).)).))))))))))--.)))------.))))))))))...........---------... ( -33.70)
>DroEre_CAF1 6361 76 + 1
UAUGUUACUAAUUUAUGUGCCUGGCGUGACACUUGCCAGGGGCUCCUGGCACUGG--CGAUGGUGGUUCCUGGA--UGGU----------------------------------------
......((((......((.(((((((.......))))))).))(((.((((((..--....))))...)).)))--))))---------------------------------------- ( -23.80)
>DroYak_CAF1 8007 116 + 1
UGUGUAUUUAAUUUAUGUGCUUGACGUGACACUUGCCAAGGGCCUCCGGCAUUGG--CGAUGGUGGUUCUGGGC--UGGUAAUGGUAUGGGUAUAUAUAUUAUAGCAUAUGGUAUAUAUA
(((((((.....(((((((((.........(((.(((.((((((.(((((....)--)..))).)))))).)))--.))).((((((((......))))))))))))))))).))))))) ( -34.00)
>DroAna_CAF1 11145 108 + 1
UGUGUAUUUAAUUUAUGUGGUUGACGUGACACUUGCCGGGGGCCUCCGGGGGUGGACCGACCG----ACUUGGCCCUGGC------AUUGGUCCAAAAA-GGCGGCAAGUGGCA-AGGUA
..(((.......((((((.....))))))(((((((((((((((..(((.((....))..)))----....))))))(((------....)))......-..))))))))))))-..... ( -39.70)
>consensus
UGUGUAUUUAAUUUAUGUGCUCGACGUGACACUUGCCAAGGGCCCCUGGCAUUGG__CGAUGGUGGUUCUUGGC__UGGU______AUGGGUAUGCAUAUUAUAGCAU_________AUA
((((((((((..((((((.....))))))((...((((((((((...(.(((((...))))).)))))))))))..)).........))))))))))....................... (-19.08 = -21.00 +   1.92)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,100,210 – 18,100,311
Length 101
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 72.03
Mean single sequence MFE -23.35
Consensus MFE -12.15
Energy contribution -12.40
Covariance contribution 0.25
Combinations/Pair 1.27
Mean z-score -2.13
Structure conservation index 0.52
SVM decision value 1.71
SVM RNA-class probability 0.973322
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18100210 101 - 22224390
UAU---------AUGCUAUAAUAUGCAUACUCAU------ACCA--GCCAAGAACCACCAUCG--CCAAUGCCAGGGGCCCUUGGCAAGUGUCACGUCGAGCACAUAAAUUAAAUACACA
..(---------((((........))))).....------....--((((((..((.((...(--(....))..))))..))))))..((((........))))................ ( -23.10)
>DroSec_CAF1 8867 101 - 1
UAU---------AUGCUAUAAUAUGCAUACCCAU------ACCA--GCCAAGAACCACCAUCG--CCAAUGCCAGGGGCCCUUGGCAAGUGUCACGUCGAGCACAUAAAUUAAAUACACA
..(---------((((........))))).....------....--((((((..((.((...(--(....))..))))..))))))..((((........))))................ ( -23.10)
>DroSim_CAF1 8923 101 - 1
UAU---------AUGCUAUAAUAUGCAUACCCAU------ACCA--GCCAAGAACCACCAUCG--CCAAUGCCAGGGGCCCUUGGCAAGUGUCACGUCGAGCACAUAAAUUAAAUACACA
..(---------((((........))))).....------....--((((((..((.((...(--(....))..))))..))))))..((((........))))................ ( -23.10)
>DroEre_CAF1 6361 76 - 1
----------------------------------------ACCA--UCCAGGAACCACCAUCG--CCAGUGCCAGGAGCCCCUGGCAAGUGUCACGCCAGGCACAUAAAUUAGUAACAUA
----------------------------------------.((.--....))...........--....(((((((....))))))).(((((......)))))................ ( -19.80)
>DroYak_CAF1 8007 116 - 1
UAUAUAUACCAUAUGCUAUAAUAUAUAUACCCAUACCAUUACCA--GCCCAGAACCACCAUCG--CCAAUGCCGGAGGCCCUUGGCAAGUGUCACGUCAAGCACAUAAAUUAAAUACACA
((((((((..(((...)))..))))))))...............--(((.((..((.((...(--(....)).)).))..)).)))..((((........))))................ ( -16.30)
>DroAna_CAF1 11145 108 - 1
UACCU-UGCCACUUGCCGCC-UUUUUGGACCAAU------GCCAGGGCCAAGU----CGGUCGGUCCACCCCCGGAGGCCCCCGGCAAGUGUCACGUCAACCACAUAAAUUAAAUACACA
.....-((.(((((((((..-....(((......------.)))(((((...(----(((..((....)).)))).))))).))))))))).)).......................... ( -34.70)
>consensus
UAU_________AUGCUAUAAUAUGCAUACCCAU______ACCA__GCCAAGAACCACCAUCG__CCAAUGCCAGGGGCCCUUGGCAAGUGUCACGUCAAGCACAUAAAUUAAAUACACA
.....................................................................(((((((....))))))).((((........))))................ (-12.15 = -12.40 +   0.25)

alignment

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secondary structure

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Window 4

Location 18,100,250 – 18,100,346
Length 96
Sequences 3
Columns 96
Reading direction forward
Mean pairwise identity 93.59
Mean single sequence MFE -28.47
Consensus MFE -27.23
Energy contribution -27.23
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.96
SVM decision value 0.19
SVM RNA-class probability 0.628241
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18100250 96 + 22224390
GGCCCCUGGCAUUGGCGAUGGUGGUUCUUGGCUGGUAUGAGUAUGCAUAUUAUAGCAUAUAGCAUAUCGGCAUUGGCUGGUUAGUGUGGUAAGUGU
.(((((((((...(.((((((....))...(((((((((.((((((........))))))..))))))))))))).)..))))).).)))...... ( -29.80)
>DroSec_CAF1 8907 89 + 1
GGCCCCUGGCAUUGGCGAUGGUGGUUCUUGGCUGGUAUGGGUAUGCAUAUUAUAGCAUAUAGCAUAUCGGCAUUGGCUGGUAAGUGUGG-------
(((((((.((....)).).)).))))....(((((((((.((((((........))))))..)))))))))....(((....)))....------- ( -27.80)
>DroSim_CAF1 8963 89 + 1
GGCCCCUGGCAUUGGCGAUGGUGGUUCUUGGCUGGUAUGGGUAUGCAUAUUAUAGCAUAUAGCAUAUCGGCAUUGGCUGGUAAGUGUGG-------
(((((((.((....)).).)).))))....(((((((((.((((((........))))))..)))))))))....(((....)))....------- ( -27.80)
>consensus
GGCCCCUGGCAUUGGCGAUGGUGGUUCUUGGCUGGUAUGGGUAUGCAUAUUAUAGCAUAUAGCAUAUCGGCAUUGGCUGGUAAGUGUGG_______
(((((((.((....)).).)).........(((((((((.((((((........))))))..)))))))))...)))).................. (-27.23 = -27.23 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,100,250 – 18,100,346
Length 96
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 93.59
Mean single sequence MFE -14.70
Consensus MFE -14.70
Energy contribution -14.70
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.23
Structure conservation index 1.00
SVM decision value 0.01
SVM RNA-class probability 0.538604
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18100250 96 - 22224390
ACACUUACCACACUAACCAGCCAAUGCCGAUAUGCUAUAUGCUAUAAUAUGCAUACUCAUACCAGCCAAGAACCACCAUCGCCAAUGCCAGGGGCC
...................(((...((.(.((((...(((((........)))))..)))).).)).........((...((....))..))))). ( -14.70)
>DroSec_CAF1 8907 89 - 1
-------CCACACUUACCAGCCAAUGCCGAUAUGCUAUAUGCUAUAAUAUGCAUACCCAUACCAGCCAAGAACCACCAUCGCCAAUGCCAGGGGCC
-------............(((...((.(.((((...(((((........)))))..)))).).)).........((...((....))..))))). ( -14.70)
>DroSim_CAF1 8963 89 - 1
-------CCACACUUACCAGCCAAUGCCGAUAUGCUAUAUGCUAUAAUAUGCAUACCCAUACCAGCCAAGAACCACCAUCGCCAAUGCCAGGGGCC
-------............(((...((.(.((((...(((((........)))))..)))).).)).........((...((....))..))))). ( -14.70)
>consensus
_______CCACACUUACCAGCCAAUGCCGAUAUGCUAUAUGCUAUAAUAUGCAUACCCAUACCAGCCAAGAACCACCAUCGCCAAUGCCAGGGGCC
...................(((...((.(.((((...(((((........)))))..)))).).)).........((...((....))..))))). (-14.70 = -14.70 +   0.00)

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 12:34:24 2006