Locus 6111

Sequence ID	2R_DroMel_CAF1
Location	19,231,825 – 19,231,946
Length	121
Max. P	0.943500

overview

Window 4

Location	19,231,825 – 19,231,915
Length	90
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	77.52
Mean single sequence MFE	-30.87
Consensus MFE	-22.82
Energy contribution	-22.77
Covariance contribution	-0.05
Combinations/Pair	1.18
Mean z-score	-1.79
Structure conservation index	0.74
SVM decision value	1.34
SVM RNA-class probability	0.943500
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19231825 90 + 20766785
CCC----------------GAAUAUCAGAACAAACAGAUGUGCGCCAUUCGCACGCUGGCAGUAGUCCAAAAAGGCUUUCGCCUC-GUUCCGAGUGGCAAAGGGGCG
(((----------------(.(((((..........))))).)((((((((.(((..(((...((((......))))...))).)-))..))))))))...)))... ( -31.40)
>DroVir_CAF1 23791 94 + 1
-----------AUGAGCAACAAUAUUAA-AUAAACAGAUGUGCGCCAUUCGGAUUCUGGCAACAGUCCAAA-AGGCUUUUGCCUCUAGGGUGAGUGACAGAAUCACG
-----------.................-.......(((.(((((((((((((..(((....))))))...-((((....))))...))))).))).))..)))... ( -24.00)
>DroSec_CAF1 22952 90 + 1
GCC----------------GAAUAUCAGAACAAACAGAUGUGCGCCAUUCGCACGCUGGCAGGAGUCCAAAAAGGCUUUCGCCUC-GGGCCGAGUGGCAAAGGGGCA
(((----------------(.(((((..........))))).)(((((((((.((..(((..(((((......)))))..))).)-).).)))))))).....))). ( -35.10)
>DroSim_CAF1 21455 90 + 1
GUC----------------GAAUAUCAGAACAAACAGAUGUGCGCCAUUCGCACGCUGGCAGGAGUCCAAAAAGGCUUUCGCCUC-GGGCCGAGUGGCAAAGGGGCA
(((----------------(.(((((..........))))).)(((((((((.((..(((..(((((......)))))..))).)-).).)))))))).....))). ( -32.40)
>DroEre_CAF1 22566 86 + 1
-CC----------------AAAUAUCAGAGCAAACAGAUGUGCGCCAUUCGCACGCUGGCAGGAGUCCAAAAAGGCUUUCGCCUC-GGGCCGAGUGGCAAAGGC---
-((----------------..........(((........)))(((((((((.((..(((..(((((......)))))..))).)-).).))))))))...)).--- ( -30.90)
>DroAna_CAF1 21261 102 + 1
GUCACCGUGGCAUGAG-AGCAAUAUCAAAAUAAACAGAUGUGCGCCAUUCGCACUCUGGCAGGAGUCCAAAAAGGCUUUCGCCUU-UGGCCGAGUGGUAAGCGU---
.........((.....-.(((.((((..........)))))))((((((((..(...(((..(((((......)))))..)))..-.)..))))))))..))..--- ( -31.40)
>consensus
GCC________________GAAUAUCAGAACAAACAGAUGUGCGCCAUUCGCACGCUGGCAGGAGUCCAAAAAGGCUUUCGCCUC_GGGCCGAGUGGCAAAGGGGC_
.....................(((((..........)))))..((((((((......(((.((((((......)))))).))).......))))))))......... (-22.82 = -22.77 +  -0.05)

alignment

secondary structure

dotplot

Window 5

Location	19,231,848 – 19,231,946
Length	98
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	75.91
Mean single sequence MFE	-27.80
Consensus MFE	-19.82
Energy contribution	-20.02
Covariance contribution	0.19
Combinations/Pair	1.06
Mean z-score	-1.17
Structure conservation index	0.71
SVM decision value	0.57
SVM RNA-class probability	0.786062
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19231848 98 - 20766785
CCAGUCAAUCACUCAAUCAGCU-CAAUCA--------AGUCGCCCCUUUGCCACUCGGAAC-GAGGCGAAAGCCUUUUUGGACUACUGCCAGCGUGCGAAUGGCGCAC
...................((.-.....(--------((......))).((((.(((..((-(((((....))))..((((.(....)))))))).))).)))))).. ( -24.60)
>DroVir_CAF1 23818 86 - 1
---GUCAGUCA----------GUAUGUCA--------UGUCGUGAUUCUGUCACUCACCCUAGAGGCAAAAGCCU-UUUGGACUGUUGCCAGAAUCCGAAUGGCGCAC
---........----------((.(((((--------(.(((.(((((((.((..((.((.((((((....))))-)).))..)).)).)))))))))))))))).)) ( -29.20)
>DroSec_CAF1 22975 106 - 1
CCAGUCAAUCACUCAAUCAGCC-CAAUCAGCUCAAUCAGCUGCCCCUUUGCCACUCGGCCC-GAGGCGAAAGCCUUUUUGGACUCCUGCCAGCGUGCGAAUGGCGCAC
...................(((-((..(((((.....)))))....((((((.((.(((((-(((((....)))))...))......))))).).)))))))).)).. ( -30.00)
>DroSim_CAF1 21478 106 - 1
CCAGUCAAUCACUCAAUCAGCC-CAAUCAGCUCAAUCAGCUGCCCCUUUGCCACUCGGCCC-GAGGCGAAAGCCUUUUUGGACUCCUGCCAGCGUGCGAAUGGCGCAC
...................(((-((..(((((.....)))))....((((((.((.(((((-(((((....)))))...))......))))).).)))))))).)).. ( -30.00)
>DroEre_CAF1 22588 86 - 1
CCAGUCAAUCACUCAAUCAGCC---------------------GCCUUUGCCACUCGGCCC-GAGGCGAAAGCCUUUUUGGACUCCUGCCAGCGUGCGAAUGGCGCAC
...................((.---------------------(((((((((.((.(((((-(((((....)))))...))......))))).).))))).))))).. ( -27.80)
>DroYak_CAF1 22553 86 - 1
CCAGUCAAUCACUCAAUCAGCC---------------------GCCUUUGCCACUCGGAAC-GAGGCGAAAGCCUUUUUGGACUCCUGCCAGCGUGCGAAUGGCGCAC
...................((.---------------------((((((((.((.(.....-(((((....)))))..(((.(....))))).))))))).))))).. ( -25.20)
>consensus
CCAGUCAAUCACUCAAUCAGCC_CAAUCA________AG__GCCCCUUUGCCACUCGGCCC_GAGGCGAAAGCCUUUUUGGACUCCUGCCAGCGUGCGAAUGGCGCAC
.................................................((((.(((.....(((((....))))).((((.(....)))))....))).)))).... (-19.82 = -20.02 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:01 2006