Locus 9539

Sequence ID 3R_DroMel_CAF1
Location 25,200,323 – 25,200,445
Length 122
Max. P 0.955298
window15258 window15259 window15260

overview

Window 8

Location 25,200,323 – 25,200,423
Length 100
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 81.23
Mean single sequence MFE -24.90
Consensus MFE -18.08
Energy contribution -17.58
Covariance contribution -0.50
Combinations/Pair 1.25
Mean z-score -1.23
Structure conservation index 0.73
SVM decision value 0.02
SVM RNA-class probability 0.542772
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25200323 100 + 27905053
----AGAGC----GGGAGAUUUGCGAUAAAAAAUGAUUGCACAUGCGAGCGUUUU-GGCUCGAAAUUGCAGCAUUUGCGGCAUGGA-AAUAUAUUUAGAUGUAUAUAUGC-
----...((----((.....))))......(((((.(((((....(((((.....-.)))))....))))))))))...(((((..-.((((((....)))))).)))))- ( -24.00)
>DroPse_CAF1 62897 94 + 1
----AGAGC----GAGAGAUUUGCGAUAAAAAAUGAUUGCACAUGUGAGCGUUCCGGGCUCAAAAUUGCAGCAUUUGCGGCAUGGA-AA-AUAUUUCAC-------AGGCC
----...((----(((...)))))......(((((.(((((....(((((.......)))))....))))))))))..(((.((((-(.-....))).)-------).))) ( -23.40)
>DroWil_CAF1 141676 93 + 1
----AGACA----GAGAGAUUUGCGAUAAAAAAUGAUUGCACAUGUGAGUGUU-U-GGCUGAAAAUUGCAACAUUUGCGGCAUGAA-AAUAUAUUUCAC-------GAGGC
----.....----..(((((.((((((........))))))(((((((((((.-.-.((........)).))))))...)))))..-.....)))))..-------..... ( -17.30)
>DroMoj_CAF1 76062 96 + 1
GGCGGGGCA----GCGAGAUUUGCGAUAAAAAAUGAUUGCACAUGCGAGUGUUUU-GCCUCGAAAUUGCAACAUUUGCGGCAUGAA-AAUGC--CGCAC-------AAGCC
((((((((.----((((...)))).....(((((..((((....))))..)))))-)))))..............((((((((...-.))))--)))).-------..))) ( -35.60)
>DroAna_CAF1 56511 98 + 1
----AGAGCGACCGGGAGAUUUGCGAUAAAAAAUGAUUGCACAUGCGAGCGUUUU-GGCUCGAAAUUGCAGCAUUUGCGGCAUGGAAAAUAUAUUUCGC-------AGGC-
----...((((..........((((((........))))))(((((((((.....-.)))).....(((((...))))))))))...........))))-------....- ( -25.70)
>DroPer_CAF1 63825 94 + 1
----AGAGC----GAGAGAUUUGCGAUAAAAAAUGAUUGCACAUGUGAGCGUUCCGGGCUCAAAAUUGCAGCAUUUGCGGCAUGGA-AA-AUAUUUCAC-------AGGCC
----...((----(((...)))))......(((((.(((((....(((((.......)))))....))))))))))..(((.((((-(.-....))).)-------).))) ( -23.40)
>consensus
____AGAGC____GAGAGAUUUGCGAUAAAAAAUGAUUGCACAUGCGAGCGUUUU_GGCUCAAAAUUGCAGCAUUUGCGGCAUGGA_AAUAUAUUUCAC_______AGGCC
.............((((....((((((........))))))(((((((((.......)))).....(((((...)))))))))).........)))).............. (-18.08 = -17.58 +  -0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 25,200,352 – 25,200,445
Length 93
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 74.74
Mean single sequence MFE -22.02
Consensus MFE -13.61
Energy contribution -13.42
Covariance contribution -0.19
Combinations/Pair 1.14
Mean z-score -1.91
Structure conservation index 0.62
SVM decision value 1.45
SVM RNA-class probability 0.955298
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25200352 93 + 27905053
UGCACAUGCGAGCGUUUU-GGCUCGAAAUUGCAGCAUUUGCGGCAUGGA-AAUAUAUUUAGAUGUAUAUAUGC---AAGGAGAUCUACUAUAGAUAAA
(((((((((((((.....-.)))).....(((((...))))))))))..-.((((((......)))))).)))---).....(((((...)))))... ( -22.50)
>DroPse_CAF1 62926 82 + 1
UGCACAUGUGAGCGUUCCGGGCUCAAAAUUGCAGCAUUUGCGGCAUGGA-AA-AUAUUUCAC-------AGGCCA-AAGGAAACU------CAACAAA
((((....(((((.......)))))....))))((....))(((.((((-(.-....))).)-------).))).-.((....))------....... ( -21.50)
>DroYak_CAF1 61474 91 + 1
UGCACAUGCGAGCGUUUU-GGCUCGAAAUUGCAGCAUUUGCGGCAUGGA-AAUAUAUUUAGAUGU--AUAUGG---ACGGAGAUCUAGUAUAGAUAAA
....(((((((((.....-.)))).....(((((...))))))))))..-......((((..(((--((.(((---(......)))))))))..)))) ( -20.20)
>DroMoj_CAF1 76095 81 + 1
UGCACAUGCGAGUGUUUU-GCCUCGAAAUUGCAACAUUUGCGGCAUGAA-AAUGC--CGCAC-------AAGCCAAAAGAAAACC------CAACACA
((((....((((.(....-.)))))....)))).....((((((((...-.))))--)))).-------................------....... ( -24.30)
>DroAna_CAF1 56544 82 + 1
UGCACAUGCGAGCGUUUU-GGCUCGAAAUUGCAGCAUUUGCGGCAUGGAAAAUAUAUUUCGC-------AGGC---CAGAAGAACU-----CAACAAA
((((....(((((.....-.)))))....))))((....))(((.((((((.....)))).)-------).))---).........-----....... ( -22.10)
>DroPer_CAF1 63854 82 + 1
UGCACAUGUGAGCGUUCCGGGCUCAAAAUUGCAGCAUUUGCGGCAUGGA-AA-AUAUUUCAC-------AGGCCA-AAGGAAACU------CAACAAA
((((....(((((.......)))))....))))((....))(((.((((-(.-....))).)-------).))).-.((....))------....... ( -21.50)
>consensus
UGCACAUGCGAGCGUUUU_GGCUCGAAAUUGCAGCAUUUGCGGCAUGGA_AAUAUAUUUCAC_______AGGC___AAGGAAACC______CAACAAA
....(((((((((.......)))).....(((((...))))))))))................................................... (-13.61 = -13.42 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 25,200,352 – 25,200,445
Length 93
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 74.74
Mean single sequence MFE -20.10
Consensus MFE -10.90
Energy contribution -10.65
Covariance contribution -0.25
Combinations/Pair 1.17
Mean z-score -1.64
Structure conservation index 0.54
SVM decision value 0.28
SVM RNA-class probability 0.667874
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25200352 93 - 27905053
UUUAUCUAUAGUAGAUCUCCUU---GCAUAUAUACAUCUAAAUAUAUU-UCCAUGCCGCAAAUGCUGCAAUUUCGAGCC-AAAACGCUCGCAUGUGCA
...(((((...))))).....(---((((((.................-....(((.((....)).)))....(((((.-.....))))).))))))) ( -18.80)
>DroPse_CAF1 62926 82 - 1
UUUGUUG------AGUUUCCUU-UGGCCU-------GUGAAAUAU-UU-UCCAUGCCGCAAAUGCUGCAAUUUUGAGCCCGGAACGCUCACAUGUGCA
..(((.(------(((((((..-.(((.(-------(.(((....-.)-)))).)))(((.....)))............)))).)))))))...... ( -19.50)
>DroYak_CAF1 61474 91 - 1
UUUAUCUAUACUAGAUCUCCGU---CCAUAU--ACAUCUAAAUAUAUU-UCCAUGCCGCAAAUGCUGCAAUUUCGAGCC-AAAACGCUCGCAUGUGCA
...(((((...)))))....(.---.(((..--...............-....(((.((....)).)))....(((((.-.....))))).)))..). ( -15.10)
>DroMoj_CAF1 76095 81 - 1
UGUGUUG------GGUUUUCUUUUGGCUU-------GUGCG--GCAUU-UUCAUGCCGCAAAUGUUGCAAUUUCGAGGC-AAAACACUCGCAUGUGCA
.(((((.------.(((((......((..-------.((((--((((.-...))))))))......))......)))))-..)))))..((....)). ( -25.70)
>DroAna_CAF1 56544 82 - 1
UUUGUUG-----AGUUCUUCUG---GCCU-------GCGAAAUAUAUUUUCCAUGCCGCAAAUGCUGCAAUUUCGAGCC-AAAACGCUCGCAUGUGCA
.......-----(((..((.((---((.(-------(.((((.....)))))).)))).))..)))(((....(((((.-.....)))))....))). ( -22.00)
>DroPer_CAF1 63854 82 - 1
UUUGUUG------AGUUUCCUU-UGGCCU-------GUGAAAUAU-UU-UCCAUGCCGCAAAUGCUGCAAUUUUGAGCCCGGAACGCUCACAUGUGCA
..(((.(------(((((((..-.(((.(-------(.(((....-.)-)))).)))(((.....)))............)))).)))))))...... ( -19.50)
>consensus
UUUGUUG______GGUCUCCUU___GCCU_______GCGAAAUAUAUU_UCCAUGCCGCAAAUGCUGCAAUUUCGAGCC_AAAACGCUCGCAUGUGCA
.........................((..........................(((.((....)).)))....(((((.......))))).....)). (-10.90 = -10.65 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:36:45 2006