Locus 3775

Sequence ID 2R_DroMel_CAF1
Location 12,485,094 – 12,485,225
Length 131
Max. P 0.628048
window6114 window6115 window6116

overview

Window 4

Location 12,485,094 – 12,485,205
Length 111
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 88.51
Mean single sequence MFE -19.77
Consensus MFE -13.98
Energy contribution -14.22
Covariance contribution 0.25
Combinations/Pair 1.19
Mean z-score -1.63
Structure conservation index 0.71
SVM decision value 0.09
SVM RNA-class probability 0.577871
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12485094 111 + 20766785
AUUAAUCUCCUUGUAAUUUAUCCCUUAGGAGUCC-UUUUACAAACCCCAAACCAAUCAUUGCUGCAUUGUUAUGCAUACAUGUGACUUUUCCCUGUCGAUACAGCAUAGUAA
..........((((((....(((....)))....-..))))))................((((((((....)))).......((((........))))....))))...... ( -16.00)
>DroSec_CAF1 19773 111 + 1
AUUAAUCUCCUUGUAAUUUAUCCCUUGGGAGUCC-UUUUACAAACCCCAAACCAAUCUUUGCUGCAUUGUUAUGCAUACAUGUGACUUUUCCCUGUCGAUGCAGCGUAGUAA
..........((((((....(((....)))....-..)))))).............((.(((((((((..((((....)))).(((........)))))))))))).))... ( -24.30)
>DroEre_CAF1 14741 110 + 1
AUUAAUCUGCUUGUAAUUUACCCCUAAAAACUCCUUUUUGCAAACCCCAAACCAAUCAGUGCUGCAUUGUUGUGCAUACAUGUGACUU--CCCUGUCGAUACAGCACAGUAA
.......(((((((((.....................))))))...............(((((((((....)))).......((((..--....))))....))))).))). ( -16.80)
>DroYak_CAF1 15088 111 + 1
AUUAAUCUCCUUGUAAUUUAUCCUUAAGCACUCCCUUUUGCAAGCCCCAAACCAAUCUAUGCUGCAUUGUUAUGCAUUCAUGUGACUUU-UCCUGUCGCUACAGCAUAGUAA
.........(((((((.....................)))))))............(((((((((((....))))......(((((...-....)))))...)))))))... ( -22.00)
>consensus
AUUAAUCUCCUUGUAAUUUAUCCCUAAGGACUCC_UUUUACAAACCCCAAACCAAUCAUUGCUGCAUUGUUAUGCAUACAUGUGACUUU_CCCUGUCGAUACAGCAUAGUAA
..........((((((.....................)))))).............(((((((((((....)))).......((((........))))....)))))))... (-13.98 = -14.22 +   0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,485,128 – 12,485,225
Length 97
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 89.76
Mean single sequence MFE -15.31
Consensus MFE -12.12
Energy contribution -12.62
Covariance contribution 0.50
Combinations/Pair 1.20
Mean z-score -1.56
Structure conservation index 0.79
SVM decision value 0.19
SVM RNA-class probability 0.628048
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12485128 97 + 20766785
-UUUUACAAACCCCAAACCAAUCAUUGCUGCAUUGUUAUGCAUACAUGUGACUUUUCCCUGUCGAUACAGCAUAGUAAUUCAUUUCACUUUCCCAGUU
-...........................((.((((((((((.......((((........)))).....)))))))))).))................ ( -10.50)
>DroSec_CAF1 19807 97 + 1
-UUUUACAAACCCCAAACCAAUCUUUGCUGCAUUGUUAUGCAUACAUGUGACUUUUCCCUGUCGAUGCAGCGUAGUAAUUCAUUUCACUUUCCCAGUU
-.....................((.(((((((((..((((....)))).(((........)))))))))))).))....................... ( -16.60)
>DroEre_CAF1 14775 96 + 1
UUUUUGCAAACCCCAAACCAAUCAGUGCUGCAUUGUUGUGCAUACAUGUGACUU--CCCUGUCGAUACAGCACAGUAAUUCAUUUCACUUUCCCAUUU
.......................((((.((.((((((((((.......((((..--....)))).....)))))))))).))...))))......... ( -15.30)
>DroYak_CAF1 15122 97 + 1
CUUUUGCAAGCCCCAAACCAAUCUAUGCUGCAUUGUUAUGCAUUCAUGUGACUUU-UCCUGUCGCUACAGCAUAGUAAUUCAUUUCACUUUCAUACUU
....((.(((............(((((((((((....))))......(((((...-....)))))...)))))))............))).))..... ( -18.85)
>consensus
_UUUUACAAACCCCAAACCAAUCAUUGCUGCAUUGUUAUGCAUACAUGUGACUUU_CCCUGUCGAUACAGCAUAGUAAUUCAUUUCACUUUCCCAGUU
......................(((((((((((....)))).......((((........))))....)))))))....................... (-12.12 = -12.62 +   0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,485,128 – 12,485,225
Length 97
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 89.76
Mean single sequence MFE -20.92
Consensus MFE -16.79
Energy contribution -17.85
Covariance contribution 1.06
Combinations/Pair 1.11
Mean z-score -1.40
Structure conservation index 0.80
SVM decision value -0.02
SVM RNA-class probability 0.521387
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12485128 97 - 20766785
AACUGGGAAAGUGAAAUGAAUUACUAUGCUGUAUCGACAGGGAAAAGUCACAUGUAUGCAUAACAAUGCAGCAAUGAUUGGUUUGGGGUUUGUAAAA-
...((.(((..(.((((.(((((...((((((((.(((........)))..(((....)))....)))))))).))))).)))).)..))).))...- ( -19.80)
>DroSec_CAF1 19807 97 - 1
AACUGGGAAAGUGAAAUGAAUUACUACGCUGCAUCGACAGGGAAAAGUCACAUGUAUGCAUAACAAUGCAGCAAAGAUUGGUUUGGGGUUUGUAAAA-
...((.(((..(.((((.((((.....(((((((.(((........)))..(((....)))....)))))))...)))).)))).)..))).))...- ( -18.80)
>DroEre_CAF1 14775 96 - 1
AAAUGGGAAAGUGAAAUGAAUUACUGUGCUGUAUCGACAGGG--AAGUCACAUGUAUGCACAACAAUGCAGCACUGAUUGGUUUGGGGUUUGCAAAAA
...((.(((..(.((((.(((((..(((((((((.(((....--..)))...(((....)))...)))))))))))))).)))).)..))).)).... ( -24.20)
>DroYak_CAF1 15122 97 - 1
AAGUAUGAAAGUGAAAUGAAUUACUAUGCUGUAGCGACAGGA-AAAGUCACAUGAAUGCAUAACAAUGCAGCAUAGAUUGGUUUGGGGCUUGCAAAAG
.....((.((((.((((.(((..(((((((((((.(((....-...))).)(((....))).....))))))))))))).))))...)))).)).... ( -20.90)
>consensus
AACUGGGAAAGUGAAAUGAAUUACUAUGCUGUAUCGACAGGG_AAAGUCACAUGUAUGCAUAACAAUGCAGCAAAGAUUGGUUUGGGGUUUGCAAAA_
...((.(((..(.((((.((((...((((((((..(((........)))..(((....))).....)))))))).)))).)))).)..))).)).... (-16.79 = -17.85 +   1.06)

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 11:03:51 2006