Locus 3002

Sequence ID	2R_DroMel_CAF1
Location	10,356,170 – 10,356,269
Length	99
Max. P	0.701789

overview

Window 6

Location	10,356,170 – 10,356,269
Length	99
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	80.86
Mean single sequence MFE	-23.92
Consensus MFE	-16.95
Energy contribution	-17.90
Covariance contribution	0.95
Combinations/Pair	1.16
Mean z-score	-1.52
Structure conservation index	0.71
SVM decision value	0.35
SVM RNA-class probability	0.701789
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10356170 99 + 20766785
GGGGGAGUGAGCAUAAAUUUGCGUGGCC-CAACUCCACCGGAAUUC-GCUUUUCUUUUUUUUUCUUUUUUUUGCGUUUGCAAAUCCGUGCGAAUUUUCCUA-
(((..(((..((((..((((((((((..-.....)))).......(-((.......................)))...))))))..))))..)))..))).- ( -25.60)
>DroSec_CAF1 75038 87 + 1
GGGGGAGUGAGCAUAAAUUUGCGUGGCC-CAACUCCGCCGGAAUUC-GCUUUCCAUU------------UUUGCGUUUGCAAAUCCGUGCGAAUUUUCCUA-
(((..(((..((((..(((((((.(((.-.......)))((((...-...))))...------------........)))))))..))))..)))..))).- ( -29.20)
>DroSim_CAF1 71047 87 + 1
UGGGGGGUGAGCAUAAAUUUGCGUGGCC-CAACUCCGCCGGAAUUC-GCUUUCCAUU------------UUUGCGUUUGCAAAUCCGUGCGAAUUUUCCUA-
.((..(((..((((..(((((((.(((.-.......)))((((...-...))))...------------........)))))))..))))..)))..))..- ( -28.00)
>DroEre_CAF1 70812 86 + 1
-GGGGAGUGAGCAUAAAUUUGCGUAGCC-CAACUCCUCAGGAUUUC-GCUUUUCUUU------------UUCACGUUUGCAAAUCCGUGCGAAUUUUUCUG-
-(((((((..(((......)))......-..))))))).((((((.-((........------------.........))))))))...............- ( -19.63)
>DroYak_CAF1 72049 87 + 1
-GGGGAGUGAGCAUAAAUUUGCGUAGCC-CAACUCCUCCGGAAUUCCUUUUUUCUUU------------UUUACGCUUGCAAAUCCGUGCGAAUUUUUCUA-
-(..((((..((((..(((((((.(((.-..........((((........))))..------------.....))))))))))..))))..))))..)..- ( -20.47)
>DroPer_CAF1 80740 86 + 1
UGGGGAGUGAGCAUAAAUUUCCAUGGCUUCAGCUCCGGCGGAAUUU-CUCCUCCUUA------------UUUUCG---GCAAAUCCGUGCUAAAUUUUGUAU
(((((((.(((...((((((((..(((....)))...).)))))))-))))))))))------------.....(---(((......))))........... ( -20.60)
>consensus
_GGGGAGUGAGCAUAAAUUUGCGUGGCC_CAACUCCGCCGGAAUUC_GCUUUCCUUU____________UUUGCGUUUGCAAAUCCGUGCGAAUUUUCCUA_
.(((((((..((((..((((((((((........)))).((((.......))))........................))))))..))))..)))))))... (-16.95 = -17.90 +   0.95)

alignment

secondary structure

dotplot

Window 7

Location	10,356,170 – 10,356,269
Length	99
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	80.86
Mean single sequence MFE	-21.75
Consensus MFE	-13.76
Energy contribution	-13.98
Covariance contribution	0.22
Combinations/Pair	1.06
Mean z-score	-1.51
Structure conservation index	0.63
SVM decision value	0.01
SVM RNA-class probability	0.540796
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10356170 99 - 20766785
-UAGGAAAAUUCGCACGGAUUUGCAAACGCAAAAAAAAGAAAAAAAAAGAAAAGC-GAAUUCCGGUGGAGUUG-GGCCACGCAAAUUUAUGCUCACUCCCCC
-..(((..((((((.....(((((....)))))....................))-)))))))((.(((((.(-(((.............))))))))))). ( -23.23)
>DroSec_CAF1 75038 87 - 1
-UAGGAAAAUUCGCACGGAUUUGCAAACGCAAA------------AAUGGAAAGC-GAAUUCCGGCGGAGUUG-GGCCACGCAAAUUUAUGCUCACUCCCCC
-..(((..((((((.((..(((((....)))))------------..))....))-)))))))((.(((((.(-(((.............))))))))))). ( -28.12)
>DroSim_CAF1 71047 87 - 1
-UAGGAAAAUUCGCACGGAUUUGCAAACGCAAA------------AAUGGAAAGC-GAAUUCCGGCGGAGUUG-GGCCACGCAAAUUUAUGCUCACCCCCCA
-..(((..((((((.((..(((((....)))))------------..))....))-)))))))((.((.(.((-(((.............))))).))))). ( -24.52)
>DroEre_CAF1 70812 86 - 1
-CAGAAAAAUUCGCACGGAUUUGCAAACGUGAA------------AAAGAAAAGC-GAAAUCCUGAGGAGUUG-GGCUACGCAAAUUUAUGCUCACUCCCC-
-............((.((((((((.....(...------------.)......))-.)))))))).(((((.(-(((.............)))))))))..- ( -18.12)
>DroYak_CAF1 72049 87 - 1
-UAGAAAAAUUCGCACGGAUUUGCAAGCGUAAA------------AAAGAAAAAAGGAAUUCCGGAGGAGUUG-GGCUACGCAAAUUUAUGCUCACUCCCC-
-...........(((..(((((((.(((.(((.------------..........((....)).......)))-.)))..)))))))..))).........- ( -18.57)
>DroPer_CAF1 80740 86 - 1
AUACAAAAUUUAGCACGGAUUUGC---CGAAAA------------UAAGGAGGAG-AAAUUCCGCCGGAGCUGAAGCCAUGGAAAUUUAUGCUCACUCCCCA
...............(((.....)---))....------------...(((((((-........(((..((....))..))).........))).))))... ( -17.93)
>consensus
_UAGAAAAAUUCGCACGGAUUUGCAAACGCAAA____________AAAGAAAAGC_GAAUUCCGGCGGAGUUG_GGCCACGCAAAUUUAUGCUCACUCCCC_
............(((..(((((((.................................((((((...))))))..(....))))))))..))).......... (-13.76 = -13.98 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:59 2006