Locus 6609

Sequence ID 3R_DroMel_CAF1
Location 17,386,788 – 17,386,899
Length 111
Max. P 0.822134
window10757 window10758 window10759 window10760

overview

Window 7

Location 17,386,788 – 17,386,879
Length 91
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.33
Mean single sequence MFE -19.56
Consensus MFE -13.55
Energy contribution -13.67
Covariance contribution 0.11
Combinations/Pair 1.11
Mean z-score -1.83
Structure conservation index 0.69
SVM decision value 0.07
SVM RNA-class probability 0.566609
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17386788 91 + 27905053
-----------------------GCG--GC----UGGUGGAAUGAAAACAAAAACAGAAACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCACUAAACGCAAAGGCCCAA
-----------------------(((--..----(((((.((((....))..........(((((((((((.....)))))).))))).........)).)))))..))).......... ( -20.50)
>DroVir_CAF1 47869 92 + 1
------------------C----GCGAACC----UGGUGAAAUGAAAACAAAAACAGA-ACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCACUAAACGCAAA-GCGGAA
------------------(----((....(----((..................))).-.(((((((((((.....)))))).)))))........(((((.......)))))-)))... ( -18.17)
>DroWil_CAF1 47096 116 + 1
GAUGGAGUGUGGAUGGUACGCGAGCAAAGU----UGGUGAAAUGAAAACAAAAACAGAAACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCACUAAACGCAAAAGCGGAA
.....((((..(((....(((.(((...))----).))).....................(((((((((((.....)))))).))))).......)))..))))...(((....)))... ( -26.40)
>DroYak_CAF1 53251 95 + 1
-----------------------GCG--GUUGGUUGGUGGAAUGAAAACAAAAACAGAAACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCACUAAACGCAAAGGCGGAA
-----------------------((.--.((((((((((.((((....))..........(((((((((((.....)))))).))))).........)).)))).))).)))..)).... ( -19.40)
>DroMoj_CAF1 43649 93 + 1
------------------C----GUGGCGC----UGGGGAAAUGAAAACAAAAACAGAAACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCACUAAACGCAAA-GCAAAA
------------------.----...((.(----((..................)))...(((((((((((.....)))))).)))))........(((((.......)))))-)).... ( -16.07)
>DroAna_CAF1 30373 88 + 1
----------------------------GU----UGGCGAAAUGAAAACAAAAACAGAAACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCUCUAAACGCAAAAGCGGAA
----------------------------((----(.(((....((...((((..(((...(((((((((((.....)))))).)))))...)))..)))).))....)))...))).... ( -16.80)
>consensus
_______________________GCG__GC____UGGUGAAAUGAAAACAAAAACAGAAACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCACUAAACGCAAA_GCGGAA
............................................................(((((((((((.....)))))).)))))...(((..(((((.......)))))..))).. (-13.55 = -13.67 +   0.11)

alignment

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secondary structure

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Window 8

Location 17,386,788 – 17,386,879
Length 91
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.33
Mean single sequence MFE -17.05
Consensus MFE -14.09
Energy contribution -14.15
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -1.34
Structure conservation index 0.83
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17386788 91 - 27905053
UUGGGCCUUUGCGUUUAGUGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGUUUCUGUUUUUGUUUUCAUUCCACCA----GC--CGC-----------------------
...(((.............(((((..((....(((((.(((((.......))))))))))....))..))))).............----))--)..----------------------- ( -18.07)
>DroVir_CAF1 47869 92 - 1
UUCCGC-UUUGCGUUUAGUGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGU-UCUGUUUUUGUUUUCAUUUCACCA----GGUUCGC----G------------------
...(((-((((.((..((((((((..((....(((((.(((((.......)))))))))).-..))..))))....))))..))))----))...))----)------------------ ( -16.20)
>DroWil_CAF1 47096 116 - 1
UUCCGCUUUUGCGUUUAGUGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGUUUCUGUUUUUGUUUUCAUUUCACCA----ACUUUGCUCGCGUACCAUCCACACUCCAUC
...(((....(((...((((((((..((....(((((.(((((.......))))))))))....))..))))).............----))).)))..))).................. ( -17.81)
>DroYak_CAF1 53251 95 - 1
UUCCGCCUUUGCGUUUAGUGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGUUUCUGUUUUUGUUUUCAUUCCACCAACCAAC--CGC-----------------------
...(((....)))....(.(((((..((....(((((.(((((.......))))))))))....))..)))))...)...............--...----------------------- ( -15.00)
>DroMoj_CAF1 43649 93 - 1
UUUUGC-UUUGCGUUUAGUGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGUUUCUGUUUUUGUUUUCAUUUCCCCA----GCGCCAC----G------------------
......-...(((((.((((((((..((....(((((.(((((.......))))))))))....))..))))....)))).....)----))))...----.------------------ ( -16.20)
>DroAna_CAF1 30373 88 - 1
UUCCGCUUUUGCGUUUAGAGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGUUUCUGUUUUUGUUUUCAUUUCGCCA----AC----------------------------
..........(((...((((((((..((....(((((.(((((.......))))))))))....))..)))))))).....)))..----..---------------------------- ( -19.00)
>consensus
UUCCGC_UUUGCGUUUAGUGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGUUUCUGUUUUUGUUUUCAUUUCACCA____AC__CGC_______________________
...(((....)))......(((((..((....(((((.(((((.......))))))))))....))..)))))............................................... (-14.09 = -14.15 +   0.06)

alignment

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secondary structure

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Window 9

Location 17,386,799 – 17,386,899
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.67
Mean single sequence MFE -20.90
Consensus MFE -12.90
Energy contribution -13.02
Covariance contribution 0.11
Combinations/Pair 1.11
Mean z-score -1.96
Structure conservation index 0.62
SVM decision value 0.68
SVM RNA-class probability 0.822134
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17386799 100 + 27905053
AAUGAAAACAAAAACAGAAACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCACUAAACGCAAAGGCCCAAA-C---GGGA--AUGGU----CCGC-----UAGAG-----
....................(((((((((((.....)))))).)))))........(((((.......)))))((.(((..-.---....--.))).----))..-----.....----- ( -18.20)
>DroVir_CAF1 47883 106 + 1
AAUGAAAACAAAAACAGA-ACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCACUAAACGCAAA-GCGGAAA-UGCCGGAC--AUGGC----CAGGCAAAUCUGGC-----
..............((((-.(((((((((((.....)))))).)))))........(((((.((...(((...-)))....-.((((...--.))))----.)))))))))))..----- ( -25.50)
>DroGri_CAF1 41172 103 + 1
AAUGAAAACAAAAACAGAAACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCACUAAACGCAAA-GCGGAAG-UGCUAUCCAACUGCC----CAG------CAGGC-----
....................(((((((((((.....)))))).)))))...(((.((..(((((...(((...-)))..))-))).)).)))((((.----..)------)))..----- ( -22.80)
>DroWil_CAF1 47132 109 + 1
AAUGAAAACAAAAACAGAAACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCACUAAACGCAAAAGCGGAAA-C---GGAA--ACAUUAAAACGGC-----CAGAACCAGC
((((................(((((((((((.....)))))).)))))........(((((.......)))))..((....-)---)...--.)))).....((.-----.....))... ( -18.90)
>DroMoj_CAF1 43663 108 + 1
AAUGAAAACAAAAACAGAAACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCACUAAACGCAAA-GCAAAAUGGGCCGAAC--CUGGC----CAGACGAAACGGUC-----
....................(((((((((((.....)))))).))))).((((...(((((.......)))))-....))))(((((...--.))))----).(((......)))----- ( -23.40)
>DroAna_CAF1 30381 100 + 1
AAUGAAAACAAAAACAGAAACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCUCUAAACGCAAAAGCGGAAA-U---GAAA--AUGGU----CUAA-----GCGGG-----
....................(((((((((((.....)))))).))))).........(((((.....(((....)))((.(-(---....--))..)----)..)-----)))).----- ( -16.60)
>consensus
AAUGAAAACAAAAACAGAAACGUGCUAAUUGCAAAUUAAUUAUGCACGAUAUUGAAUUUGCACUAAACGCAAA_GCGGAAA_U___GGAA__AUGGC____CAGA_____CAGGC_____
....................(((((((((((.....)))))).)))))...(((..(((((.......)))))..))).......................................... (-12.90 = -13.02 +   0.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,386,799 – 17,386,899
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.67
Mean single sequence MFE -21.70
Consensus MFE -13.96
Energy contribution -14.02
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -1.44
Structure conservation index 0.64
SVM decision value 0.14
SVM RNA-class probability 0.603917
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17386799 100 - 27905053
-----CUCUA-----GCGG----ACCAU--UCCC---G-UUUGGGCCUUUGCGUUUAGUGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGUUUCUGUUUUUGUUUUCAUU
-----(((.(-----((((----.....--..))---)-)).)))............(.(((((..((....(((((.(((((.......))))))))))....))..)))))...)... ( -20.40)
>DroVir_CAF1 47883 106 - 1
-----GCCAGAUUUGCCUG----GCCAU--GUCCGGCA-UUUCCGC-UUUGCGUUUAGUGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGU-UCUGUUUUUGUUUUCAUU
-----(((((......)))----)).((--((..(((.-.....))-)..))))...(.(((((..((....(((((.(((((.......)))))))))).-..))..)))))...)... ( -24.80)
>DroGri_CAF1 41172 103 - 1
-----GCCUG------CUG----GGCAGUUGGAUAGCA-CUUCCGC-UUUGCGUUUAGUGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGUUUCUGUUUUUGUUUUCAUU
-----(((..------...----))).(((((((.(((-((..(((-...)))...)))))..)))))))..(((((.(((((.......)))))))))).................... ( -25.50)
>DroWil_CAF1 47132 109 - 1
GCUGGUUCUG-----GCCGUUUUAAUGU--UUCC---G-UUUCCGCUUUUGCGUUUAGUGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGUUUCUGUUUUUGUUUUCAUU
((((((....-----)))..........--....---.-....(((....)))...)))(((((..((....(((((.(((((.......))))))))))....))..)))))....... ( -19.20)
>DroMoj_CAF1 43663 108 - 1
-----GACCGUUUCGUCUG----GCCAG--GUUCGGCCCAUUUUGC-UUUGCGUUUAGUGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGUUUCUGUUUUUGUUUUCAUU
-----(((......))).(----(((..--....))))((((..((-.....))..))))((((..((....(((((.(((((.......))))))))))....))..))))........ ( -21.70)
>DroAna_CAF1 30381 100 - 1
-----CCCGC-----UUAG----ACCAU--UUUC---A-UUUCCGCUUUUGCGUUUAGAGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGUUUCUGUUUUUGUUUUCAUU
-----.....-----....----.....--....---.-....(((....)))...((((((((..((....(((((.(((((.......))))))))))....))..)))))))).... ( -18.60)
>consensus
_____GCCUG_____GCUG____ACCAU__GUCC___A_UUUCCGC_UUUGCGUUUAGUGCAAAUUCAAUAUCGUGCAUAAUUAAUUUGCAAUUAGCACGUUUCUGUUUUUGUUUUCAUU
...........................................(((....)))......(((((..((....(((((.(((((.......))))))))))....))..)))))....... (-13.96 = -14.02 +   0.06)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:47 2006