Locus 3417

Sequence ID	2L_DroMel_CAF1
Location	9,885,637 – 9,885,797
Length	160
Max. P	0.647271

overview

Window 8

Location	9,885,637 – 9,885,729
Length	92
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	84.89
Mean single sequence MFE	-12.59
Consensus MFE	-9.44
Energy contribution	-9.68
Covariance contribution	0.24
Combinations/Pair	1.06
Mean z-score	-1.61
Structure conservation index	0.75
SVM decision value	0.11
SVM RNA-class probability	0.586030
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9885637 92 - 22407834
CAAGGUAAACAGAACGAGCAAAAAUUGUUGCUCUCUCUUCCCAAGCGCUUUUCCAACUUUCCGCUUUCCU-CCCG-AAAUUUUGCCCACAAAAA
...((((((.(((..((((((......))))))..)))....(((((..............)))))....-....-....))))))........ ( -16.04)
>DroSec_CAF1 93536 90 - 1
CAAGGUAAACAGAACGAGCAAAAAUUGUUGCUCUCUC--CCCAAGCGCUUUUCCACUUUUCCGCUUUCCC-CUC-CCCGAUUUCCCCACAAAAA
..(((..........((((((......))))))....--...(((((..............)))))...)-)).-................... ( -11.44)
>DroSim_CAF1 100388 91 - 1
CAAGGUAAACAGAACGAGCAAAAAUUGUUGCUCUCUC--CCCAAGCGCUUUUCCACUUUUCCGCUUUCCC-CCCGCCCAAUUUCCCCACAAAAA
...(((.........((((((......))))))....--...(((((..............)))))....-...)))................. ( -12.54)
>DroEre_CAF1 98454 81 - 1
CAAGGUAAACAGAACGAGCAA-AAUUGUUGCUCUCUU--CCCCAGCGCUUUUCCACUUUUCUGCUU--------UCCCCAUUUCCCAACA--AA
...((.((((((((.((((((-.....))))))....--....((.(......).)).))))).))--------).))............--.. ( -11.30)
>DroYak_CAF1 99552 90 - 1
CAAGGUAAACAGAACGAGCCA-AAUUGUUGCUCUCUC--CCCAAGCGCUUUUCCACUUUUCCGCUUCUCCGCUAUCCCCAUUUACCCACAA-AA
...((((((......((((..-.......))))....--...(((((..............)))))..............)))))).....-.. ( -11.64)
>consensus
CAAGGUAAACAGAACGAGCAAAAAUUGUUGCUCUCUC__CCCAAGCGCUUUUCCACUUUUCCGCUUUCCC_CCCGCCCAAUUUCCCCACAAAAA
...((.....(((..((((((......)))))))))....))(((((..............)))))............................ ( -9.44 =  -9.68 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	9,885,689 – 9,885,797
Length	108
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	77.61
Mean single sequence MFE	-17.73
Consensus MFE	-11.67
Energy contribution	-12.28
Covariance contribution	0.61
Combinations/Pair	1.16
Mean z-score	-1.29
Structure conservation index	0.66
SVM decision value	0.24
SVM RNA-class probability	0.647271
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9885689 108 - 22407834
AUACAAGCGACAAGUAGAAGCAAGUCGCAUUAAAUCAU--AG----CCAA--UUAAAAAUAUUUGCUUAAACGAACCAAGGUAAACAGAACGAGCAAAAAUUGUUGCUCUCUCUUC
.(((..(((((..((....))..)))))..........--((----(.((--(.......))).))).............)))...(((..((((((......))))))..))).. ( -19.00)
>DroGri_CAF1 106379 105 - 1
AUGCGAUCAAUAAAUUUAAACAAUUUGCUUGCGUGCGUGCAUCCAAUCAACGUUUA-AGUCUUUACUUAACAAUUUCAAGGUAAACAACAACUGCA--AAUUACUGUU--------
.((((........((((((((...(((.(((.(((....))).))).))).)))))-))).(((((((..........))))))).......))))--..........-------- ( -14.20)
>DroSec_CAF1 93588 106 - 1
AUACAAGCGACAAGUAGAAGAAAGUCGCAUUAAAUCGU--AG----CCAA--UUAAAAAUGUUUGCUUAAACGAACCAAGGUAAACAGAACGAGCAAAAAUUGUUGCUCUCUC--C
......(((((............)))))..........--..----....--.......(((((((((..........)))))))))....((((((......))))))....--. ( -21.30)
>DroSim_CAF1 100441 106 - 1
AUACAAGCGACAAGUAGAAGAAAGUCGCAUUAAAUCAU--AG----CCAA--UUAAAAAUGUUUGCUUAAACGAACCAAGGUAAACAGAACGAGCAAAAAUUGUUGCUCUCUC--C
......(((((............)))))..........--..----....--.......(((((((((..........)))))))))....((((((......))))))....--. ( -21.30)
>DroEre_CAF1 98498 102 - 1
UUACAAACGACA---AAUAGAAAGUCGCAUUAAAUCAU--AG----CCAA--UUAAAAAUGUUUGCUUAAACGAACCAAGGUAAACAGAACGAGCAA-AAUUGUUGCUCUCUU--C
.......((((.---........))))...........--..----....--.......(((((((((..........)))))))))....((((((-.....))))))....--. ( -17.00)
>DroYak_CAF1 99605 102 - 1
-UCCAAACGACA--UAACAGAAAGUCGCAUUAAAUCAU--AG----CCAA--UUAAAAAUGUUUGCUUAAACGAACCAAGGUAAACAGAACGAGCCA-AAUUGUUGCUCUCUC--C
-......((((.--.........))))...........--..----....--.......(((((((((..........)))))))))....((((..-.......))))....--. ( -13.60)
>consensus
AUACAAGCGACAAGUAGAAGAAAGUCGCAUUAAAUCAU__AG____CCAA__UUAAAAAUGUUUGCUUAAACGAACCAAGGUAAACAGAACGAGCAA_AAUUGUUGCUCUCUC__C
.......((((............))))................................(((((((((..........)))))))))....((((((......))))))....... (-11.67 = -12.28 +   0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:59 2006