Locus 7468

Sequence ID X_DroMel_CAF1
Location 18,648,667 – 18,648,819
Length 152
Max. P 0.742969
window12246 window12247 window12248

overview

Window 6

Location 18,648,667 – 18,648,782
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.99
Mean single sequence MFE -38.63
Consensus MFE -29.86
Energy contribution -30.82
Covariance contribution 0.96
Combinations/Pair 1.10
Mean z-score -1.51
Structure conservation index 0.77
SVM decision value 0.09
SVM RNA-class probability 0.578947
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18648667 115 - 22224390
UUGGGGUC-----GGCCUUCGUGAGCCAAGCUGACGUAAGGCCGAAAGCGUUGAUCGACUUGGGCAGGCUUCACUGUAGAUCGAAUCAACAAACAUUUUUACAGACUUUCCUGGCCAACG
((((..((-----(((((((((.(((...))).))).))))))))....(((((((((.((..((((......)))).))))).))))))...........(((......))).)))).. ( -41.10)
>DroSec_CAF1 7573 119 - 1
UUGGGGUCGUUUUGGCCUUCGUGAGCCAAGCUGACGUAAGGCCGAAAGCGUUGAUCGACUUGGGCAGGCUCCACUGUAGAUCGAAUCAACAAACAUUUUUACAGACUUU-CUGGCCAACG
....((((((((((((((((((.(((...))).))).)))))).)))))(((((((((.((..((((......)))).))))).))))))...................-..)))).... ( -42.20)
>DroSim_CAF1 7623 119 - 1
UUGGGGUCGUUUUGGCCUUCGUGAGCCAAGCUGACGUAAGGCCGAAAGCGCUGAUCGACUUGGGCAGGCUCCACUGUAGAUCGAAUCAACAAACAUUUUUACAGACUUU-CUGGCCAACG
.(((((((((((((((((((((.(((...))).))).)))))).)))))(((.(......).))).)))))))(((((((.................))))))).....-.......... ( -40.93)
>DroEre_CAF1 7010 114 - 1
UUGGGGUC-----GGCCAUCGUGAGUCAAGCUGACGUAAGGCCAAAAGCGUCGAUCGACUCGGCCAGGCUCCACUGUAGAUCGAGUCAACAAACAUUUUUACACACUUU-CUGGCCAACU
...(((((-----((((..(((.((.....)).)))...))))......(.....))))))(((((((......((((((....((......))...)))))).....)-)))))).... ( -34.30)
>DroYak_CAF1 7116 114 - 1
GUGAUGUC-----CGCCUUCGUGAGUGAAGCUGACGUAAGGCAAAAGGCGCCGAUCGACUUGGGCAGGCUCCACUGUAGAUCGAGUCAACAAACAUUUUUACAGACUUU-CUGGCCAACU
........-----.((((((((.((.....)).))).)))))....(((.......(((((((((((......))))...)))))))..............(((.....-)))))).... ( -34.60)
>consensus
UUGGGGUC_____GGCCUUCGUGAGCCAAGCUGACGUAAGGCCGAAAGCGUUGAUCGACUUGGGCAGGCUCCACUGUAGAUCGAAUCAACAAACAUUUUUACAGACUUU_CUGGCCAACG
....((((.....(((((((((.(((...))).))).))))))......(((((((((.((..((((......)))).))))).))))))......................)))).... (-29.86 = -30.82 +   0.96)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,648,707 – 18,648,819
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.38
Mean single sequence MFE -42.14
Consensus MFE -32.78
Energy contribution -31.54
Covariance contribution -1.24
Combinations/Pair 1.21
Mean z-score -1.61
Structure conservation index 0.78
SVM decision value 0.21
SVM RNA-class probability 0.635444
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18648707 112 + 22224390
UCUACAGUGAAGCCUGCCCAAGUCGAUCAACGCUUUCGGCCUUACGUCAGCUUGGCUCACGAAGGCC-----GACCCCAAAAGU---AAUGGGAGACAGCUGGUUCAGCUGGGCGAAGCU
..........(((.(((((..(((...........((((((((.(((.(((...))).)))))))))-----)).((((.....---..)))).)))(((((...))))))))))..))) ( -42.80)
>DroSec_CAF1 7612 117 + 1
UCUACAGUGGAGCCUGCCCAAGUCGAUCAACGCUUUCGGCCUUACGUCAGCUUGGCUCACGAAGGCCAAAACGACCCCAAAAGU---AAUGGGAGACAGCUGGUUCAGCUGGGCGAAGCU
..........(((.(((((..(((......((.(((.((((((.(((.(((...))).))))))))).)))))..((((.....---..)))).)))(((((...))))))))))..))) ( -41.00)
>DroSim_CAF1 7662 117 + 1
UCUACAGUGGAGCCUGCCCAAGUCGAUCAGCGCUUUCGGCCUUACGUCAGCUUGGCUCACGAAGGCCAAAACGACCCCAAAAGU---AAUGGGAGACAGCUGGUUCAGCUGGGCGAAGCU
..........(((.((((((.((.(((((((......((((((.(((.(((...))).)))))))))........((((.....---..)))).....)))))))..))))))))..))) ( -42.80)
>DroEre_CAF1 7049 112 + 1
UCUACAGUGGAGCCUGGCCGAGUCGAUCGACGCUUUUGGCCUUACGUCAGCUUGACUCACGAUGGCC-----GACCCCAAAAUG---AAUGGCAGACAGCUGGCUCGGUUGGGCGAAGCA
......((...(((..((((((((...........((((((...(((.((.....)).)))..))))-----))..........---...(((.....)))))))))))..)))...)). ( -41.50)
>DroYak_CAF1 7155 115 + 1
UCUACAGUGGAGCCUGCCCAAGUCGAUCGGCGCCUUUUGCCUUACGUCAGCUUCACUCACGAAGGCG-----GACAUCACAAUCUGUAGUGGGUGACAGCUGGUUCAGUUGGGCAAAGCA
...........((.(((((((.(.((.(((((.....))))......(((((((((((((....(((-----((........))))).)))))))).)))))).))).)))))))..)). ( -42.60)
>consensus
UCUACAGUGGAGCCUGCCCAAGUCGAUCAACGCUUUCGGCCUUACGUCAGCUUGGCUCACGAAGGCC_____GACCCCAAAAGU___AAUGGGAGACAGCUGGUUCAGCUGGGCGAAGCU
......((...(((..((((.((......))......((((((.(((.((.....)).)))))))))......................))))...((((((...)))))))))...)). (-32.78 = -31.54 +  -1.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,648,707 – 18,648,819
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.38
Mean single sequence MFE -43.34
Consensus MFE -33.56
Energy contribution -34.36
Covariance contribution 0.80
Combinations/Pair 1.12
Mean z-score -1.76
Structure conservation index 0.77
SVM decision value 0.45
SVM RNA-class probability 0.742969
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18648707 112 - 22224390
AGCUUCGCCCAGCUGAACCAGCUGUCUCCCAUU---ACUUUUGGGGUC-----GGCCUUCGUGAGCCAAGCUGACGUAAGGCCGAAAGCGUUGAUCGACUUGGGCAGGCUUCACUGUAGA
(((((.(((((((((...)))))((((((((..---.....)))))((-----(((((((((.(((...))).))).))))))))...........)))..))))))))).......... ( -47.70)
>DroSec_CAF1 7612 117 - 1
AGCUUCGCCCAGCUGAACCAGCUGUCUCCCAUU---ACUUUUGGGGUCGUUUUGGCCUUCGUGAGCCAAGCUGACGUAAGGCCGAAAGCGUUGAUCGACUUGGGCAGGCUCCACUGUAGA
(((((.(((((((((...)))))((((((((..---.....))))).(((((((((((((((.(((...))).))).)))))).))))))......)))..))))))))).......... ( -48.70)
>DroSim_CAF1 7662 117 - 1
AGCUUCGCCCAGCUGAACCAGCUGUCUCCCAUU---ACUUUUGGGGUCGUUUUGGCCUUCGUGAGCCAAGCUGACGUAAGGCCGAAAGCGCUGAUCGACUUGGGCAGGCUCCACUGUAGA
(((((.(((((((((...)))))(((.((((..---.....))))(.(((((((((((((((.(((...))).))).)))))).))))))).....)))..))))))))).......... ( -48.50)
>DroEre_CAF1 7049 112 - 1
UGCUUCGCCCAACCGAGCCAGCUGUCUGCCAUU---CAUUUUGGGGUC-----GGCCAUCGUGAGUCAAGCUGACGUAAGGCCAAAAGCGUCGAUCGACUCGGCCAGGCUCCACUGUAGA
..............(((((.........(((..---.....)))((((-----((((..(((.((.....)).)))...))))....(.(((....))).))))).)))))......... ( -35.10)
>DroYak_CAF1 7155 115 - 1
UGCUUUGCCCAACUGAACCAGCUGUCACCCACUACAGAUUGUGAUGUC-----CGCCUUCGUGAGUGAAGCUGACGUAAGGCAAAAGGCGCCGAUCGACUUGGGCAGGCUCCACUGUAGA
.((((.((((((......(((((.((((.(((....((..(((.....-----)))..))))).))))))))).((...(((.......)))...))..))))))))))........... ( -36.70)
>consensus
AGCUUCGCCCAGCUGAACCAGCUGUCUCCCAUU___ACUUUUGGGGUC_____GGCCUUCGUGAGCCAAGCUGACGUAAGGCCGAAAGCGUUGAUCGACUUGGGCAGGCUCCACUGUAGA
.((((.((((((.(((....(((...(((((..........))))).......(((((((((.(((...))).))).))))))...))).....)))..))))))))))........... (-33.56 = -34.36 +   0.80)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:39 2006