Locus 802

Sequence ID 2L_DroMel_CAF1
Location 2,283,507 – 2,283,602
Length 95
Max. P 0.893665
window1313 window1314

overview

Window 3

Location 2,283,507 – 2,283,602
Length 95
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 84.04
Mean single sequence MFE -27.52
Consensus MFE -21.43
Energy contribution -23.63
Covariance contribution 2.19
Combinations/Pair 1.08
Mean z-score -2.92
Structure conservation index 0.78
SVM decision value 0.98
SVM RNA-class probability 0.893665
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2283507 95 + 22407834
UAGUGCGAAAA--------AAAAUUGCGUACAUAAAAAUGGGUUACCAGUGCAAGGCUGCCCAAGGCAUAUUACGUAUACGUA--CGUAUACGUAAUGCAGUUGC
..(((((....--------.......))))).......(((((..((.......))..)))))..((((..(((((((((...--.)))))))))))))...... ( -29.30)
>DroSec_CAF1 19725 94 + 1
UAGUGCGAAAA---------AAAUUGCGUACAUAAAAAUGGGUUACCAGUGCAAGGCUGCCCAAGGCACAUUACGUAUACGUA--CGUAUACGUAAUGCAGUUGC
..(((((....---------......))))).......(((((..((.......))..))))).(((.((((((((((((...--.))))))))))))..))).. ( -30.40)
>DroSim_CAF1 19813 95 + 1
UAGUGCGAAAA--------AAAAUUGCGUACAUAAAAAUGGGUUACCAGUGCAAGGCUGCCCAAGGCACAUUACGUAUACGUA--CGUAUACGUAAUGCAGUUGC
..(((((....--------.......))))).......(((((..((.......))..))))).(((.((((((((((((...--.))))))))))))..))).. ( -30.30)
>DroEre_CAF1 19777 95 + 1
UAGUGCGAAAA--------AACGUUGCGUACAUAAAAAUGGGUUACCAGUGCAAGGCUGCCCAAGGCAUAUUACGUAUACGUA--CGUAUACGUAAUGCAGUUGC
..(((((....--------.......))))).......(((((..((.......))..)))))..((((..(((((((((...--.)))))))))))))...... ( -29.30)
>DroYak_CAF1 20074 103 + 1
UAGUGCGAAAAAAACGUAAAACGUUGCGUACAUAAAAAUGGGUUACCAGUGCAAGGCUGCCCAAGGCAUAUUACGUAUACGUA--CGUAUACGUAAUGCAGUUGC
..(((((.....((((.....)))).))))).......(((((..((.......))..)))))..((((..(((((((((...--.)))))))))))))...... ( -33.90)
>DroAna_CAF1 19414 79 + 1
UAGUGCGAAAAA-------AAAGUUGCGUACAUAAAAAUGGGUUACCAGAGCAAGGGUA------------------UACAUUUUCG-AUUUAAAUUGCGGUUUC
..(((((.((..-------....)).)))))...((((((...((((........))))------------------..))))))..-................. ( -11.90)
>consensus
UAGUGCGAAAA________AAAAUUGCGUACAUAAAAAUGGGUUACCAGUGCAAGGCUGCCCAAGGCAUAUUACGUAUACGUA__CGUAUACGUAAUGCAGUUGC
..(((((...................))))).......(((((..((.......))..))))).....(((((((((((((....)))))))))))))....... (-21.43 = -23.63 +   2.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,283,507 – 2,283,602
Length 95
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 84.04
Mean single sequence MFE -24.42
Consensus MFE -17.45
Energy contribution -19.82
Covariance contribution 2.36
Combinations/Pair 1.05
Mean z-score -2.65
Structure conservation index 0.71
SVM decision value 0.46
SVM RNA-class probability 0.743759
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2283507 95 - 22407834
GCAACUGCAUUACGUAUACG--UACGUAUACGUAAUAUGCCUUGGGCAGCCUUGCACUGGUAACCCAUUUUUAUGUACGCAAUUUU--------UUUUCGCACUA
((....(((((((((((((.--...)))))))))..))))..((((..(((.......)))..))))...........))......--------........... ( -25.50)
>DroSec_CAF1 19725 94 - 1
GCAACUGCAUUACGUAUACG--UACGUAUACGUAAUGUGCCUUGGGCAGCCUUGCACUGGUAACCCAUUUUUAUGUACGCAAUUU---------UUUUCGCACUA
((....(((((((((((((.--...)))))))))))))....((((..(((.......)))..))))...........)).....---------........... ( -28.90)
>DroSim_CAF1 19813 95 - 1
GCAACUGCAUUACGUAUACG--UACGUAUACGUAAUGUGCCUUGGGCAGCCUUGCACUGGUAACCCAUUUUUAUGUACGCAAUUUU--------UUUUCGCACUA
((....(((((((((((((.--...)))))))))))))....((((..(((.......)))..))))...........))......--------........... ( -28.90)
>DroEre_CAF1 19777 95 - 1
GCAACUGCAUUACGUAUACG--UACGUAUACGUAAUAUGCCUUGGGCAGCCUUGCACUGGUAACCCAUUUUUAUGUACGCAACGUU--------UUUUCGCACUA
((...((((((((((((((.--...)))))))))))......((((..(((.......)))..))))...........)))..(..--------....))).... ( -25.80)
>DroYak_CAF1 20074 103 - 1
GCAACUGCAUUACGUAUACG--UACGUAUACGUAAUAUGCCUUGGGCAGCCUUGCACUGGUAACCCAUUUUUAUGUACGCAACGUUUUACGUUUUUUUCGCACUA
((....(((((((((((((.--...)))))))))))......((((..(((.......)))..))))...........))((((.....))))......)).... ( -28.60)
>DroAna_CAF1 19414 79 - 1
GAAACCGCAAUUUAAAU-CGAAAAUGUA------------------UACCCUUGCUCUGGUAACCCAUUUUUAUGUACGCAACUUU-------UUUUUCGCACUA
......((.........-.(((((((..------------------((((........))))...))))))).((....)).....-------......)).... (  -8.80)
>consensus
GCAACUGCAUUACGUAUACG__UACGUAUACGUAAUAUGCCUUGGGCAGCCUUGCACUGGUAACCCAUUUUUAUGUACGCAACUUU________UUUUCGCACUA
.....(((((((((((((((....))))))))))))......((((..(((.......)))..))))...........)))........................ (-17.45 = -19.82 +   2.36)

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 09:46:02 2006