Locus 2293

Sequence ID	2L_DroMel_CAF1
Location	6,186,336 – 6,186,450
Length	114
Max. P	0.988778

overview

Window 1

Location	6,186,336 – 6,186,450
Length	114
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	90.48
Mean single sequence MFE	-31.25
Consensus MFE	-27.68
Energy contribution	-27.75
Covariance contribution	0.07
Combinations/Pair	1.19
Mean z-score	-2.47
Structure conservation index	0.89
SVM decision value	2.13
SVM RNA-class probability	0.988778
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6186336 114 + 22407834
CGCAGGCAGCC-UUUCCCUUCGCACGCUCCACUGCCUCGCUGUGAUUUCCUCGGCUCAGCAAAGCGUGAAACAUUUUUUCGCAACCUUGCGACCUCACACGCCCCCUGCGCCCCU
((((((..((.-..........((((((....(((...((((.(.....).))))...))).))))))..........(((((....)))))........))..))))))..... ( -33.20)
>DroSec_CAF1 22594 114 + 1
CGCAGGCAGCC-UUUCCCUUCGCACGCUCCACUGCCUCGCUGUGAUUUCCUCGGCUCAGCAAAGCGUGAAACAUUUUUUCGCAACCUUGCGACCUCACACGCCCCCUGCGCCCCU
((((((..((.-..........((((((....(((...((((.(.....).))))...))).))))))..........(((((....)))))........))..))))))..... ( -33.20)
>DroSim_CAF1 32052 114 + 1
CGCAGGCAGCC-UUUCCCUUCGCACGCUCCACUGCCUCGCUGUGAUUUCCUCGGCUCAGCAAAGCGUGAAACAUUUUUUCGCAACCUUGCGACCUCACACGCCCCCUGCGCCCCU
((((((..((.-..........((((((....(((...((((.(.....).))))...))).))))))..........(((((....)))))........))..))))))..... ( -33.20)
>DroEre_CAF1 22398 110 + 1
CGCAGGCUGCC-UUUCCCCGCGCACGCUCCACUGCCUCGCUGUGAUUUCCUCAGCUCAGCAAAGCGUGAAACAUUUUUUCGCAACCUUGCGACCUCACACGCCCCU-GCGCC---
((((((..((.-..........((((((....(((...((((.(.....).))))...))).))))))..........(((((....)))))........)).)))-)))..--- ( -32.70)
>DroWil_CAF1 890 108 + 1
CACUU---GCCUUUGCCCUUCUUACGCUCCAGUGCUUUGCUGUGAUUUCCUCAGCUUACCAAAGCGUGAAACAUUUUUUCGCAACCUUGCGACCUCACACGAA---UGCACGCC-
.....---.......................((((((((.(((((.....(((((((....)))).))).........(((((....)))))..)))))))))---.))))...- ( -24.00)
>DroYak_CAF1 33597 113 + 1
CGCAGGCAGCC-UUUCCCUUCGCACGCUCCACUGCCUCGCUGUGAUUUCCUCAGCUCAGCAAAGCGUGAAACAUUUUUUCGCAACCUUGCGACCUCACACGCCCCUUGCGCCCC-
((((((..((.-..........((((((....(((...((((.(.....).))))...))).))))))..........(((((....)))))........))..))))))....- ( -31.20)
>consensus
CGCAGGCAGCC_UUUCCCUUCGCACGCUCCACUGCCUCGCUGUGAUUUCCUCAGCUCAGCAAAGCGUGAAACAUUUUUUCGCAACCUUGCGACCUCACACGCCCCCUGCGCCCC_
((((((..((............((((((...(((....((((.(.....).)))).)))...))))))..........(((((....)))))........))..))))))..... (-27.68 = -27.75 +   0.07)

alignment

secondary structure

dotplot

Window 2

Location	6,186,336 – 6,186,450
Length	114
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	90.48
Mean single sequence MFE	-42.74
Consensus MFE	-32.74
Energy contribution	-33.57
Covariance contribution	0.82
Combinations/Pair	1.12
Mean z-score	-2.72
Structure conservation index	0.77
SVM decision value	-0.00
SVM RNA-class probability	0.532945
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6186336 114 - 22407834
AGGGGCGCAGGGGGCGUGUGAGGUCGCAAGGUUGCGAAAAAAUGUUUCACGCUUUGCUGAGCCGAGGAAAUCACAGCGAGGCAGUGGAGCGUGCGAAGGGAAA-GGCUGCCUGCG
.....((((((.(((........(((((....)))))....((((((((((((((((((....((.....)).))))))))).)))))))))...........-.))).)))))) ( -45.70)
>DroSec_CAF1 22594 114 - 1
AGGGGCGCAGGGGGCGUGUGAGGUCGCAAGGUUGCGAAAAAAUGUUUCACGCUUUGCUGAGCCGAGGAAAUCACAGCGAGGCAGUGGAGCGUGCGAAGGGAAA-GGCUGCCUGCG
.....((((((.(((........(((((....)))))....((((((((((((((((((....((.....)).))))))))).)))))))))...........-.))).)))))) ( -45.70)
>DroSim_CAF1 32052 114 - 1
AGGGGCGCAGGGGGCGUGUGAGGUCGCAAGGUUGCGAAAAAAUGUUUCACGCUUUGCUGAGCCGAGGAAAUCACAGCGAGGCAGUGGAGCGUGCGAAGGGAAA-GGCUGCCUGCG
.....((((((.(((........(((((....)))))....((((((((((((((((((....((.....)).))))))))).)))))))))...........-.))).)))))) ( -45.70)
>DroEre_CAF1 22398 110 - 1
---GGCGC-AGGGGCGUGUGAGGUCGCAAGGUUGCGAAAAAAUGUUUCACGCUUUGCUGAGCUGAGGAAAUCACAGCGAGGCAGUGGAGCGUGCGCGGGGAAA-GGCAGCCUGCG
---..(((-(((.((.((((....))))...(((((.....((((((((((((((((((...(((.....)))))))))))).))))))))).))))).....-.))..)))))) ( -46.20)
>DroWil_CAF1 890 108 - 1
-GGCGUGCA---UUCGUGUGAGGUCGCAAGGUUGCGAAAAAAUGUUUCACGCUUUGGUAAGCUGAGGAAAUCACAGCAAAGCACUGGAGCGUAAGAAGGGCAAAGGC---AAGUG
-.((.(((.---(((..(((((((((((....))))).......))))))((((..((..((((..(....).)))).....))..))))....)))..)))...))---..... ( -29.71)
>DroYak_CAF1 33597 113 - 1
-GGGGCGCAAGGGGCGUGUGAGGUCGCAAGGUUGCGAAAAAAUGUUUCACGCUUUGCUGAGCUGAGGAAAUCACAGCGAGGCAGUGGAGCGUGCGAAGGGAAA-GGCUGCCUGCG
-.((((((..(..((((......(((((....)))))....))))..)((((((..(((.((((..(....).))))....)))..))))))...........-.)).))))... ( -43.40)
>consensus
_GGGGCGCAGGGGGCGUGUGAGGUCGCAAGGUUGCGAAAAAAUGUUUCACGCUUUGCUGAGCCGAGGAAAUCACAGCGAGGCAGUGGAGCGUGCGAAGGGAAA_GGCUGCCUGCG
.....((((.(.(((........(((((....)))))....((((((((((((((((((....((.....)).))))))))).))))))))).............))).).)))) (-32.74 = -33.57 +   0.82)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:16 2006