Locus 7174

Sequence ID 3R_DroMel_CAF1
Location 18,910,319 – 18,910,418
Length 99
Max. P 0.819467
window11601 window11602

overview

Window 1

Location 18,910,319 – 18,910,418
Length 99
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 77.19
Mean single sequence MFE -32.88
Consensus MFE -18.67
Energy contribution -20.28
Covariance contribution 1.61
Combinations/Pair 1.14
Mean z-score -1.59
Structure conservation index 0.57
SVM decision value 0.11
SVM RNA-class probability 0.586059
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18910319 99 + 27905053
UUGCCAC-----CACUGCAGC----CAGCUGCAUUGUUCCGACCAGCUGCCACGCCCCUUGGG---CU-------GGUGGCCGCCCCCCUUUUUCGCCGCAUUGUGGCAAUCUGUCAA
(((((((-----((.(((((.----...))))).)).........((..(((.((((...)))---))-------))..))......................)))))))........ ( -34.90)
>DroSec_CAF1 20564 101 + 1
UUGCCAC-----CACUGCAGC----CAGCUGCAUUGUUCCGACCAGCUGCCACGCCCCUUUAGACCCU-------GGUGGCCGCCCCCCUU-UUCGCCGCAUUGUGGCAAUCUGUCAA
(((((((-----...(((.((----((((((............))))))....(((((..........-------)).)))..........-...)).)))..)))))))........ ( -28.70)
>DroSim_CAF1 21097 101 + 1
UUGCCAC-----CACUGCAGC----CAGCUGCAUUGUUCCGACCAGCUGCCACGCCCCUUUAGACCCC-------GGUGGCCGCCCCCCUU-UUCGCCGCAUUGUGGCAAUCUGUCAA
(((((((-----...(((.((----((((((............))))))....(((((..........-------)).)))..........-...)).)))..)))))))........ ( -28.10)
>DroEre_CAF1 20318 100 + 1
UUGCCAC-----CACUGCAGC----CAGCUGCAUUGUUUCGACCAGCUGCCACGCCCCUUUGGCCGCUCU---UU----GCGCC-CCCGUU-UUCGCCGCAUUGUGGCAAUCUGUCAA
(((((((-----((.(((((.----...))))).))........(((.((((........)))).)))..---.(----(((..-..((..-..)).))))..)))))))........ ( -29.30)
>DroYak_CAF1 22265 111 + 1
UUGCCACCA-ACCACUGCAGC----CAGCUGCAUUGUUCCGACCAGCUGCCACGCCCCUUUGGGCGCUCCGGUUCGGAGGCCGC-CCCCUU-UUCGCCGCAUUGUGGCAAUCUGUCAA
(((((((..-..((.(((((.----...))))).))((((((...((((...(((((....)))))...))))))))))((.((-......-...)).))...)))))))........ ( -39.30)
>DroPer_CAF1 24128 97 + 1
UUGCCGCUGUAACGUUGCGACGUUGCAGCUGCACCAUUGUG--------ACACGCCCCGU--GCCACU-------GCUCCUCGCCUCCG----UCGUCGCAGUGUGGCAAUCUGUCAA
(((((((((((((((....)))))))))).....(((((((--------(((((...((.--((....-------))....))....))----).))))))))).)))))........ ( -37.00)
>consensus
UUGCCAC_____CACUGCAGC____CAGCUGCAUUGUUCCGACCAGCUGCCACGCCCCUUUGGACCCU_______GGUGGCCGCCCCCCUU_UUCGCCGCAUUGUGGCAAUCUGUCAA
(((((((.....((.((((((......)))))).)).........((.(((((.......................))))).))...................)))))))........ (-18.67 = -20.28 +   1.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 18,910,319 – 18,910,418
Length 99
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 77.19
Mean single sequence MFE -39.95
Consensus MFE -24.08
Energy contribution -24.33
Covariance contribution 0.25
Combinations/Pair 1.24
Mean z-score -1.73
Structure conservation index 0.60
SVM decision value 0.68
SVM RNA-class probability 0.819467
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18910319 99 - 27905053
UUGACAGAUUGCCACAAUGCGGCGAAAAAGGGGGGCGGCCACC-------AG---CCCAAGGGGCGUGGCAGCUGGUCGGAACAAUGCAGCUG----GCUGCAGUG-----GUGGCAA
........(((((((..((((((..............(((((.-------.(---(((...)))))))))(((((............))))).----))))))...-----))))))) ( -41.60)
>DroSec_CAF1 20564 101 - 1
UUGACAGAUUGCCACAAUGCGGCGAA-AAGGGGGGCGGCCACC-------AGGGUCUAAAGGGGCGUGGCAGCUGGUCGGAACAAUGCAGCUG----GCUGCAGUG-----GUGGCAA
........(((((((..((((((...-..........(((((.-------...((((....)))))))))(((((............))))).----))))))...-----))))))) ( -37.60)
>DroSim_CAF1 21097 101 - 1
UUGACAGAUUGCCACAAUGCGGCGAA-AAGGGGGGCGGCCACC-------GGGGUCUAAAGGGGCGUGGCAGCUGGUCGGAACAAUGCAGCUG----GCUGCAGUG-----GUGGCAA
........(((((((..((((((...-..........(((((.-------...((((....)))))))))(((((............))))).----))))))...-----))))))) ( -37.60)
>DroEre_CAF1 20318 100 - 1
UUGACAGAUUGCCACAAUGCGGCGAA-AACGGG-GGCGC----AA---AGAGCGGCCAAAGGGGCGUGGCAGCUGGUCGAAACAAUGCAGCUG----GCUGCAGUG-----GUGGCAA
........(((((((..((((((...-.....(-(.(((----..---...))).))............((((((............))))))----))))))...-----))))))) ( -39.30)
>DroYak_CAF1 22265 111 - 1
UUGACAGAUUGCCACAAUGCGGCGAA-AAGGGG-GCGGCCUCCGAACCGGAGCGCCCAAAGGGGCGUGGCAGCUGGUCGGAACAAUGCAGCUG----GCUGCAGUGGU-UGGUGGCAA
........(((((((...(((((...-......-...)))(((((.((((.((((((....)))))).....))))))))).((.(((((...----.))))).))))-..))))))) ( -47.90)
>DroPer_CAF1 24128 97 - 1
UUGACAGAUUGCCACACUGCGACGA----CGGAGGCGAGGAGC-------AGUGGC--ACGGGGCGUGU--------CACAAUGGUGCAGCUGCAACGUCGCAACGUUACAGCGGCAA
........(((((.((((((..(..----((....)).)..))-------.(((((--(((...)))))--------)))...))))..((((.(((((....))))).))))))))) ( -35.70)
>consensus
UUGACAGAUUGCCACAAUGCGGCGAA_AAGGGGGGCGGCCACC_______AGCGGCCAAAGGGGCGUGGCAGCUGGUCGGAACAAUGCAGCUG____GCUGCAGUG_____GUGGCAA
........(((((((..(((.(((.....((.......))...............((....)).))).)))...........((.((((((......)))))).)).....))))))) (-24.08 = -24.33 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:12 2006