Locus 8305

Sequence ID X_DroMel_CAF1
Location 20,657,186 – 20,657,376
Length 190
Max. P 0.997313
window13637 window13638 window13639 window13640 window13641

overview

Window 7

Location 20,657,186 – 20,657,305
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.37
Mean single sequence MFE -32.46
Consensus MFE -25.78
Energy contribution -26.09
Covariance contribution 0.31
Combinations/Pair 1.14
Mean z-score -1.46
Structure conservation index 0.79
SVM decision value 0.07
SVM RNA-class probability 0.567833
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20657186 119 - 22224390
GGGGAAGGGUUAAGGGAAAGCCAGGCGUUUUUCCUGAUUACG-GGAAAUACCCUUACCCAUUGAGAGAGAGCUCACAAAUAAUUCAACAAAUCGGAAAGUAUUUUUUCUAAUAUGAGUGG
(..(((((((.(((((...((...))...(((((((....))-)))))..))))))))).(((.(((....))).)))....)))..)..((..(((((....)))))..))........ ( -30.20)
>DroSec_CAF1 53881 113 - 1
GGGGAAGGGUUAAGGGAAAGCCAGGCGUUUUUCCUGAUUGCG-GAAAAUACCCUUUCCCAUCG------AGCUCUCAAAUAAUUCAACAAAUCGGAAAGUAUUUUUUCUAAUAUGAGUGG
((((((((((..(((((((((.....))))))))).......-......))))))))))....------............(((((....((..(((((....)))))..)).))))).. ( -30.56)
>DroEre_CAF1 54631 114 - 1
GGGAAAGGGUUAAGGGAAGGCCAGGCGUUUUUCCUGAUUGCGCGGAAAUACCCUUUCCCAUUGGGC--GGGCUCACCUAUAGUUCAACAAAUGGAGACCAAGU---UUAAAUGUGA-GUG
((((((((((..(((((((((.....)))))))))..............)))))))))).......--..((((((......((.(((....(....)...))---).))..))))-)). ( -33.19)
>DroYak_CAF1 55838 114 - 1
GGGGAAGGGUUAAGGGAAAGCCAGGGGUUUUUCCUGAUUGCG-GCAAAUACCCUUUCCCAUUGAGU--GGCCUCACAAACAAUUCAACAAAUUGAGAGGUAUU---UCCAAAAUUAUUUG
((((((((((..((((((((((...)))))))))).......-......))))))))))...(((.--.(((((.(((.............))).)))))..)---))............ ( -35.88)
>consensus
GGGGAAGGGUUAAGGGAAAGCCAGGCGUUUUUCCUGAUUGCG_GGAAAUACCCUUUCCCAUUGAG___GAGCUCACAAAUAAUUCAACAAAUCGAAAAGUAUU___UCUAAUAUGAGUGG
((((((((((..(((((((((.....)))))))))..............))))))))))...(((......))).............................................. (-25.78 = -26.09 +   0.31)

alignment

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secondary structure

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Window 8

Location 20,657,226 – 20,657,343
Length 117
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 88.56
Mean single sequence MFE -35.13
Consensus MFE -30.37
Energy contribution -30.43
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.90
Structure conservation index 0.86
SVM decision value 1.03
SVM RNA-class probability 0.902966
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20657226 117 + 22224390
AUUUGUGAGCUCUCUCUCAAUGGGUAAGGGUAUUUCC-CGUAAUCAGGAAAAACGCCUGGCUUUCCCUUAACCCUUCCCCGGCCCUUGUGGGCCUGUUUUCCCUGUUCGUUUCAGUCU
......((((...........(((.((((((......-...(..((((.......))))..)........)))))).)))(((((....)))))..........)))).......... ( -33.43)
>DroSec_CAF1 53921 111 + 1
AUUUGAGAGCU------CGAUGGGAAAGGGUAUUUUC-CGCAAUCAGGAAAAACGCCUGGCUUUCCCUUAACCCUUCCCCGGCCCCUGUGGGCCUGUUUUCCCUGUUCAUUUCAGUCU
....((((((.------....(((.((((((.(((((-(.......))))))......((.....))...)))))).)))(((((....))))).)))))).(((.......)))... ( -35.30)
>DroEre_CAF1 54667 116 + 1
AUAGGUGAGCCC--GCCCAAUGGGAAAGGGUAUUUCCGCGCAAUCAGGAAAAACGCCUGGCCUUCCCUUAACCCUUUCCCGGCCCCUUUGGGCCUGUUUUCCCUGUUCAUUUCAGUCU
(((((.(((..(--.......((((((((((.(((((.........))))).......((.....))...))))))))))(((((....))))).)..))))))))............ ( -39.20)
>DroYak_CAF1 55875 115 + 1
GUUUGUGAGGCC--ACUCAAUGGGAAAGGGUAUUUGC-CGCAAUCAGGAAAAACCCCUGGCUUUCCCUUAACCCUUCCCCGGCCCCUGUGGGCCCGUUUUCCCUGUUCAUUUCAGUCU
.....((((...--.))))..(((.((((((......-.....(((((.......)))))..........)))))).)))(((((....)))))........(((.......)))... ( -32.60)
>consensus
AUUUGUGAGCCC___CUCAAUGGGAAAGGGUAUUUCC_CGCAAUCAGGAAAAACGCCUGGCUUUCCCUUAACCCUUCCCCGGCCCCUGUGGGCCUGUUUUCCCUGUUCAUUUCAGUCU
......((((...........(((.((((((........((...((((.......)))))).........)))))).)))(((((....)))))..........)))).......... (-30.37 = -30.43 +   0.06)

alignment

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secondary structure

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Window 9

Location 20,657,226 – 20,657,343
Length 117
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 88.56
Mean single sequence MFE -41.20
Consensus MFE -38.95
Energy contribution -38.89
Covariance contribution -0.06
Combinations/Pair 1.07
Mean z-score -2.78
Structure conservation index 0.95
SVM decision value 2.84
SVM RNA-class probability 0.997313
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20657226 117 - 22224390
AGACUGAAACGAACAGGGAAAACAGGCCCACAAGGGCCGGGGAAGGGUUAAGGGAAAGCCAGGCGUUUUUCCUGAUUACG-GGAAAUACCCUUACCCAUUGAGAGAGAGCUCACAAAU
...(((.......)))........(((((....)))))(((.((((((...((.....)).......(((((((....))-))))).)))))).))).(((.(((....))).))).. ( -38.00)
>DroSec_CAF1 53921 111 - 1
AGACUGAAAUGAACAGGGAAAACAGGCCCACAGGGGCCGGGGAAGGGUUAAGGGAAAGCCAGGCGUUUUUCCUGAUUGCG-GAAAAUACCCUUUCCCAUCG------AGCUCUCAAAU
...............((((.....(((((....)))))((((((((((..(((((((((.....))))))))).......-......))))))))))....------...)))).... ( -40.76)
>DroEre_CAF1 54667 116 - 1
AGACUGAAAUGAACAGGGAAAACAGGCCCAAAGGGGCCGGGAAAGGGUUAAGGGAAGGCCAGGCGUUUUUCCUGAUUGCGCGGAAAUACCCUUUCCCAUUGGGC--GGGCUCACCUAU
..............(((.......(((((....)))))((((((((((..(((((((((.....)))))))))..............))))))))))..((((.--...))))))).. ( -42.49)
>DroYak_CAF1 55875 115 - 1
AGACUGAAAUGAACAGGGAAAACGGGCCCACAGGGGCCGGGGAAGGGUUAAGGGAAAGCCAGGGGUUUUUCCUGAUUGCG-GCAAAUACCCUUUCCCAUUGAGU--GGCCUCACAAAC
...(((.......)))((...((.(((((....)))))((((((((((..((((((((((...)))))))))).......-......)))))))))).....))--..))........ ( -43.56)
>consensus
AGACUGAAAUGAACAGGGAAAACAGGCCCACAGGGGCCGGGGAAGGGUUAAGGGAAAGCCAGGCGUUUUUCCUGAUUGCG_GGAAAUACCCUUUCCCAUUGAG___GAGCUCACAAAU
...............(((......(((((....)))))((((((((((..(((((((((.....)))))))))..............))))))))))............)))...... (-38.95 = -38.89 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,657,265 – 20,657,376
Length 111
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 95.05
Mean single sequence MFE -28.21
Consensus MFE -26.75
Energy contribution -27.00
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.95
SVM decision value 1.14
SVM RNA-class probability 0.921334
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20657265 111 + 22224390
UAAUCAGGAAAAACGCCUGGCUUUCCCUUAACCCUUCCCCGGCCCUUGUGGGCCUGUUUUCCCUGUUCGUUUCAGUCUCGGCGUGUUUAACCCUUUUGCCGGGCCACUUUU
....((((.(((((....((.((......)).))......(((((....))))).))))).)))).........(.(((((((.............))))))).)...... ( -29.92)
>DroSec_CAF1 53954 111 + 1
CAAUCAGGAAAAACGCCUGGCUUUCCCUUAACCCUUCCCCGGCCCCUGUGGGCCUGUUUUCCCUGUUCAUUUCAGUCUCGACGUGUUUAACCCUUUUGCCGGGCCACUUUU
..............(((((((...................(((((....))))).(((....(((.......)))....)))...............)))))))....... ( -26.60)
>DroEre_CAF1 54705 111 + 1
CAAUCAGGAAAAACGCCUGGCCUUCCCUUAACCCUUUCCCGGCCCCUUUGGGCCUGUUUUCCCUGUUCAUUUCAGUCUCGGCGUGUUUAACCCUUUUGCCGGGCCGCUUUU
....((((.(((((....((.....)).............(((((....))))).))))).)))).........(.(((((((.............))))))).)...... ( -28.62)
>DroYak_CAF1 55912 110 + 1
CAAUCAGGAAAAACCCCUGGCUUUCCCUUAACCCUUCCCCGGCCCCUGUGGGCCCGUUUUCCCUGUUCAUUUCAGUCUCGGCGUGUUUAACCCUUUUGCCGGGCCACU-UU
....((((.(((((....((.((......)).))......(((((....))))).))))).)))).........(.(((((((.............))))))).)...-.. ( -27.72)
>consensus
CAAUCAGGAAAAACGCCUGGCUUUCCCUUAACCCUUCCCCGGCCCCUGUGGGCCUGUUUUCCCUGUUCAUUUCAGUCUCGGCGUGUUUAACCCUUUUGCCGGGCCACUUUU
....((((.(((((....((.....)).............(((((....))))).))))).)))).........(.(((((((.............))))))).)...... (-26.75 = -27.00 +   0.25)

alignment

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secondary structure

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Window 1

Location 20,657,265 – 20,657,376
Length 111
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 95.05
Mean single sequence MFE -35.96
Consensus MFE -34.61
Energy contribution -34.68
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.52
Structure conservation index 0.96
SVM decision value 2.14
SVM RNA-class probability 0.988830
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20657265 111 - 22224390
AAAAGUGGCCCGGCAAAAGGGUUAAACACGCCGAGACUGAAACGAACAGGGAAAACAGGCCCACAAGGGCCGGGGAAGGGUUAAGGGAAAGCCAGGCGUUUUUCCUGAUUA
....(((((((.......))))....))).................((((((((((.(((((....)))))...(...((((.......))))...))))))))))).... ( -35.70)
>DroSec_CAF1 53954 111 - 1
AAAAGUGGCCCGGCAAAAGGGUUAAACACGUCGAGACUGAAAUGAACAGGGAAAACAGGCCCACAGGGGCCGGGGAAGGGUUAAGGGAAAGCCAGGCGUUUUUCCUGAUUG
.....((((((.......))))))..((..(((....)))..))..((((((((((.(((((....)))))...(...((((.......))))...))))))))))).... ( -36.60)
>DroEre_CAF1 54705 111 - 1
AAAAGCGGCCCGGCAAAAGGGUUAAACACGCCGAGACUGAAAUGAACAGGGAAAACAGGCCCAAAGGGGCCGGGAAAGGGUUAAGGGAAGGCCAGGCGUUUUUCCUGAUUG
.....((((.((((...............)))).).))).......((((((((((.(((((....))))).......((((.......))))....)))))))))).... ( -35.56)
>DroYak_CAF1 55912 110 - 1
AA-AGUGGCCCGGCAAAAGGGUUAAACACGCCGAGACUGAAAUGAACAGGGAAAACGGGCCCACAGGGGCCGGGGAAGGGUUAAGGGAAAGCCAGGGGUUUUUCCUGAUUG
..-..(((((((((...............)))....(((.......)))......(.(((((....))))).)....))))))((((((((((...))))))))))..... ( -35.96)
>consensus
AAAAGUGGCCCGGCAAAAGGGUUAAACACGCCGAGACUGAAAUGAACAGGGAAAACAGGCCCACAGGGGCCGGGGAAGGGUUAAGGGAAAGCCAGGCGUUUUUCCUGAUUG
.....((((((.......))))))......................((((((((((.(((((....))))).......((((.......))))....)))))))))).... (-34.61 = -34.68 +   0.06)

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 13:00:40 2006