Locus 4690

Sequence ID	2L_DroMel_CAF1
Location	13,484,201 – 13,484,305
Length	104
Max. P	0.954076

overview

Window 3

Location	13,484,201 – 13,484,305
Length	104
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	80.20
Mean single sequence MFE	-32.37
Consensus MFE	-18.77
Energy contribution	-20.38
Covariance contribution	1.61
Combinations/Pair	1.16
Mean z-score	-2.99
Structure conservation index	0.58
SVM decision value	1.44
SVM RNA-class probability	0.954076
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13484201 104 + 22407834
AAAUUCAAACGAAAAUGAAAUCUCCUACGAAUACAAAGCCGCGUGACGUGAACGCUACGUAGCAAAAGG-CCAG-GCGUUGCGUUACGUCGCGCUACGUAACGACA-
........(((.........((......))..........(((((((((((.(((.((((.((.....)-)...-)))).))))))))))))))..))).......- ( -30.90)
>DroVir_CAF1 133678 100 + 1
AAAUACAAACGAAAAUGAAAUCACCGACGAAUACGUUGCUGCGUGACGUGAACGCAACGUAACAACACAGUAAC-GC-----GUUACGUUACGCUACGUAACGGUU-
.................................((((((.(((((((((((.(((...((.((......)).))-))-----))))))))))))...))))))...- ( -28.00)
>DroPse_CAF1 125808 105 + 1
AGAUUCAAACGAAAAUGAAAUCGCCGACGAACACAAUGCUGCGUGACGUGAACGCUACGUAGCAGCACG-GCAGAGCACGGCGUUACGUUACGCCGCGUAACGAUA-
...((((........))))(((((((..(....)..(((((((((.((....)).)))))))))...))-))...((.((((((......)))))).))...))).- ( -36.60)
>DroMoj_CAF1 112434 104 + 1
AAAUACAAACGAAAAUGAAAUCACCAACGAAUACGUUGCUGCGUAACGUUAAUGCAACGUAGCGACGCAGCAAC-AC--GGAGUUACGCUACGCUACGUAACGGACC
.......................((.........((((((((((.(((((.....)))))....))))))))))-..--...((((((........))))))))... ( -30.30)
>DroAna_CAF1 146866 104 + 1
AAAUUCAAACGAAAAUGAAAUCGCCAACGAAUACAAUGCUGCGUGACGUGAACGCUACGUAGCAGAAGG-CCAG-GCGUUUCGUUACGCUCCGCUACGUAACGAUA-
...((((........))))((((...(((.......(((((((((.((....)).)))))))))...((-(..(-((((......)))))..))).)))..)))).- ( -31.80)
>DroPer_CAF1 100376 105 + 1
AGAUUCAAACGAAAAUGAAAUCGCCGACGAACACAAUGCUGCGUGACGUGAACGCUACGUAGCAGCACG-GCAGAGCACGGCGUUACGUUACGCCGCGUAACGAUA-
...((((........))))(((((((..(....)..(((((((((.((....)).)))))))))...))-))...((.((((((......)))))).))...))).- ( -36.60)
>consensus
AAAUUCAAACGAAAAUGAAAUCGCCGACGAAUACAAUGCUGCGUGACGUGAACGCUACGUAGCAACACG_CCAG_GC__GGCGUUACGUUACGCUACGUAACGAUA_
...................(((..............((((((((..((....))..))))))))..................((((((........))))))))).. (-18.77 = -20.38 +   1.61)

alignment

secondary structure

dotplot

Window 4

Location	13,484,201 – 13,484,305
Length	104
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	80.20
Mean single sequence MFE	-32.72
Consensus MFE	-17.66
Energy contribution	-17.88
Covariance contribution	0.23
Combinations/Pair	1.19
Mean z-score	-1.91
Structure conservation index	0.54
SVM decision value	-0.01
SVM RNA-class probability	0.527304
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13484201 104 - 22407834
-UGUCGUUACGUAGCGCGACGUAACGCAACGC-CUGG-CCUUUUGCUACGUAGCGUUCACGUCACGCGGCUUUGUAUUCGUAGGAGAUUUCAUUUUCGUUUGAAUUU
-.........((.(((.((((((((((.(((.-.(((-(.....))))))).))))).))))).))).)).....(((((.(.((((......)))).).))))).. ( -31.50)
>DroVir_CAF1 133678 100 - 1
-AACCGUUACGUAGCGUAACGUAAC-----GC-GUUACUGUGUUGUUACGUUGCGUUCACGUCACGCAGCAACGUAUUCGUCGGUGAUUUCAUUUUCGUUUGUAUUU
-...(((.(((((((((((((((((-----((-(......)).)))))))))))))).)))).)))((.(.(((....))).).))..................... ( -29.30)
>DroPse_CAF1 125808 105 - 1
-UAUCGUUACGCGGCGUAACGUAACGCCGUGCUCUGC-CGUGCUGCUACGUAGCGUUCACGUCACGCAGCAUUGUGUUCGUCGGCGAUUUCAUUUUCGUUUGAAUCU
-.((((((.((((((((......))))))))....((-.(((((((...((..((....))..))))))))).)).......))))))((((........))))... ( -34.40)
>DroMoj_CAF1 112434 104 - 1
GGUCCGUUACGUAGCGUAGCGUAACUCC--GU-GUUGCUGCGUCGCUACGUUGCAUUAACGUUACGCAGCAACGUAUUCGUUGGUGAUUUCAUUUUCGUUUGUAUUU
((...(((((((......))))))).))--..-((((((((((....((((((...)))))).))))))))))((((.((..((((....))))..))...)))).. ( -35.20)
>DroAna_CAF1 146866 104 - 1
-UAUCGUUACGUAGCGGAGCGUAACGAAACGC-CUGG-CCUUCUGCUACGUAGCGUUCACGUCACGCAGCAUUGUAUUCGUUGGCGAUUUCAUUUUCGUUUGAAUUU
-...((((((((((((((((((......))))-....-...))))))))))))))....(((((((.(........).)).)))))..((((........))))... ( -31.51)
>DroPer_CAF1 100376 105 - 1
-UAUCGUUACGCGGCGUAACGUAACGCCGUGCUCUGC-CGUGCUGCUACGUAGCGUUCACGUCACGCAGCAUUGUGUUCGUCGGCGAUUUCAUUUUCGUUUGAAUCU
-.((((((.((((((((......))))))))....((-.(((((((...((..((....))..))))))))).)).......))))))((((........))))... ( -34.40)
>consensus
_UAUCGUUACGUAGCGUAACGUAACGCC__GC_CUGG_CGUGCUGCUACGUAGCGUUCACGUCACGCAGCAUUGUAUUCGUCGGCGAUUUCAUUUUCGUUUGAAUUU
.....(((((((......)))))))...................(((.(((.(((....))).))).))).....(((((..(((((........)))))))))).. (-17.66 = -17.88 +   0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:41 2006