Locus 2876

Sequence ID 3R_DroMel_CAF1
Location 7,700,706 – 7,700,892
Length 186
Max. P 0.739826
window4642 window4643 window4644

overview

Window 2

Location 7,700,706 – 7,700,815
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 88.40
Mean single sequence MFE -28.44
Consensus MFE -24.25
Energy contribution -23.83
Covariance contribution -0.41
Combinations/Pair 1.17
Mean z-score -1.66
Structure conservation index 0.85
SVM decision value 0.22
SVM RNA-class probability 0.638332
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7700706 109 + 27905053
UAUUUGUAU-------CCCUAUCUGUACGUG--AAUCC--AAAUGCUGUUGUGGCGUGUGAUAACCAUCACAUUCCGCACACAUGAAAGACUGAUAGCACCACUUAGUGGCACUUUAGGA
.........-------.((((...((.....--.....--...(((((((((((.(((((((....))))))).)))).(....).......)))))))((((...)))).))..)))). ( -26.40)
>DroSec_CAF1 50403 109 + 1
UAUUUGUAU-------CCCUAUCUGCACGUG--AAUCC--AAAUGCUGUUGUGGCGUGUGAUAACCAUCACAUUCCGCACACAUGAAAGAAUGAUAGCACCACUUAGUGGCACUUUAGGA
.........-------.((((..(((.....--.....--...(((((((((((.(((((((....))))))).)))))..(((......))))))))).(((...))))))...)))). ( -28.80)
>DroSim_CAF1 50571 109 + 1
UAUUUGUAU-------CCCUAUCUGCACGUG--AAUCC--AAAUGCUGUUGUGGCGUGUGAUAACCAUCACAUUCCGCACACAUGAAAGAAUGAUAGCACCACUUAGUGGCACUUUAGGA
.........-------.((((..(((.....--.....--...(((((((((((.(((((((....))))))).)))))..(((......))))))))).(((...))))))...)))). ( -28.80)
>DroEre_CAF1 50974 109 + 1
UAUUUGUAU-------CCCUAUCUGUACGUG--AAUCC--AAACGCUGUUGUGGCGUGUGAUAACCAUCACAUUCCGCACACAUGAAAGAAUGAUAGCACCACUUAGUGGCACUUUAGGA
.........-------.((((...((.....--.....--....((((((((((.(((((((....))))))).)))))..(((......)))))))).((((...)))).))..)))). ( -27.90)
>DroYak_CAF1 52161 116 + 1
UAUUUGUAUCCCCUAUCCCUAUCUGUAUGUG--AAUCC--AAAUGCUGUUGUGGCGUGUGAUAACCAUCACAUUCCGCACACAUGAAAGAAUGAUAGCACCACUUAGUGGCACUUUAGGA
...........((((...(((((.((((.((--....)--).))))((((((((.(((((((....))))))).))))).))).........)))))..((((...)))).....)))). ( -28.70)
>DroAna_CAF1 52482 113 + 1
UCCUUAUCC-------GCAUUUCUGUUCAUGUCCCUCCACACACGCUGUGGUGGGUUGUGAUAAGCAUUACAUUCCACAAAUAUAAAAGAAUGAUAGCACCACUUAGUGGCACUUAAGGA
((((((.((-------((........(((((.(((.(((((.....))))).))).)))))...((....(((((.............)))))...))........))))....)))))) ( -30.02)
>consensus
UAUUUGUAU_______CCCUAUCUGUACGUG__AAUCC__AAAUGCUGUUGUGGCGUGUGAUAACCAUCACAUUCCGCACACAUGAAAGAAUGAUAGCACCACUUAGUGGCACUUUAGGA
.................((((..(((..................(((((.((((.(((((((....))))))).))))...(((......))))))))..(((...))))))...)))). (-24.25 = -23.83 +  -0.41)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,700,735 – 7,700,855
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.22
Mean single sequence MFE -32.65
Consensus MFE -28.56
Energy contribution -28.83
Covariance contribution 0.28
Combinations/Pair 1.04
Mean z-score -1.53
Structure conservation index 0.87
SVM decision value 0.45
SVM RNA-class probability 0.739826
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7700735 120 - 27905053
UGAGCGAAACGUAAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUAAAGUGCCACUAAGUGGUGCUAUCAGUCUUUCAUGUGUGCGGAAUGUGAUGGUUAUCACACGCCACAACAGCAUUU
...((((((.....((((((((.......)))))))).........((..((((...))))..)).......)))).((((.(((...((((((....)))))))))))))...)).... ( -35.10)
>DroSec_CAF1 50432 120 - 1
UGAGCGAAACGUAAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUAAAGUGCCACUAAGUGGUGCUAUCAUUCUUUCAUGUGUGCGGAAUGUGAUGGUUAUCACACGCCACAACAGCAUUU
...((((((.....((((((((.......)))))))).........((..((((...))))..)).......)))).((((.(((...((((((....)))))))))))))...)).... ( -35.10)
>DroSim_CAF1 50600 120 - 1
UGAGCGAAACGUAAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUAAAGUGCCACUAAGUGGUGCUAUCAUUCUUUCAUGUGUGCGGAAUGUGAUGGUUAUCACACGCCACAACAGCAUUU
...((((((.....((((((((.......)))))))).........((..((((...))))..)).......)))).((((.(((...((((((....)))))))))))))...)).... ( -35.10)
>DroEre_CAF1 51003 108 - 1
------------AAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUAAAGUGCCACUAAGUGGUGCUAUCAUUCUUUCAUGUGUGCGGAAUGUGAUGGUUAUCACACGCCACAACAGCGUUU
------------..((((((((.......)))))))).........((..((((...))))..))............((((.(((...((((((....)))))))))))))......... ( -30.80)
>DroYak_CAF1 52197 120 - 1
UGAGCGAAACGUAAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUAAAGUGCCACUAAGUGGUGCUAUCAUUCUUUCAUGUGUGCGGAAUGUGAUGGUUAUCACACGCCACAACAGCAUUU
...((((((.....((((((((.......)))))))).........((..((((...))))..)).......)))).((((.(((...((((((....)))))))))))))...)).... ( -35.10)
>DroAna_CAF1 52515 120 - 1
UAAACGAACCGUAAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUUAAGUGCCACUAAGUGGUGCUAUCAUUCUUUUAUAUUUGUGGAAUGUAAUGCUUAUCACAACCCACCACAGCGUGU
...(((....((((((((((((.......)))))))).........((..((((...))))..)).........))))..((((((...((..((.....))..))...))))))))).. ( -24.70)
>consensus
UGAGCGAAACGUAAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUAAAGUGCCACUAAGUGGUGCUAUCAUUCUUUCAUGUGUGCGGAAUGUGAUGGUUAUCACACGCCACAACAGCAUUU
..............((((((((.......)))))))).........((..((((...))))..))...........((((.((.((..((((((....))))))..)).))...)))).. (-28.56 = -28.83 +   0.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,700,775 – 7,700,892
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.40
Mean single sequence MFE -30.46
Consensus MFE -20.54
Energy contribution -22.93
Covariance contribution 2.39
Combinations/Pair 1.04
Mean z-score -1.93
Structure conservation index 0.67
SVM decision value 0.04
SVM RNA-class probability 0.554732
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7700775 117 - 27905053
GAAGUUCAGGUUUACUCCAACUU-UU--UUUCGAGCAUCCUGAGCGAAACGUAAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUAAAGUGCCACUAAGUGGUGCUAUCAGUCUUUCAUGU
...(((((((....(((.((...-..--.)).)))...)))))))((((.....((((((((.......)))))))).........((..((((...))))..)).......)))).... ( -31.40)
>DroSec_CAF1 50472 119 - 1
GAAGUUCAGGUUUACUCCAACUU-UUUUUUUGGAGCAUCCUGAGCGAAACGUAAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUAAAGUGCCACUAAGUGGUGCUAUCAUUCUUUCAUGU
...(((((((....((((((...-.....))))))...)))))))((((.....((((((((.......)))))))).........((..((((...))))..)).......)))).... ( -37.70)
>DroSim_CAF1 50640 119 - 1
GAACUUCAGGUUUACUCCAACUU-UUUUUUUGGAGCAUCCUGAGCGAAACGUAAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUAAAGUGCCACUAAGUGGUGCUAUCAUUCUUUCAUGU
(((..(((((....((((((...-.....))))))...)))))(((((((((((((....)..))))).).)))))).........((..((((...))))..))........))).... ( -33.50)
>DroEre_CAF1 51043 96 - 1
GAACUUUAGGUUUACUCCAACUC-GG---UUG--------------------AAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUAAAGUGCCACUAAGUGGUGCUAUCAUUCUUUCAUGU
((((((((((.......((((..-.)---)))--------------------..((((((((.......))))))))....))))))))(((((...)))))....))............ ( -23.50)
>DroYak_CAF1 52237 116 - 1
GAACUUCAGGCUUACUCCAACUC-GG---CUGGAGCAUCCUGAGCGAAACGUAAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUAAAGUGCCACUAAGUGGUGCUAUCAUUCUUUCAUGU
(((..(((((....(((((....-..---.)))))...)))))(((((((((((((....)..))))).).)))))).........((..((((...))))..))........))).... ( -31.90)
>DroAna_CAF1 52555 113 - 1
------CCUGGGU-CCUCAACUGACUCUAUUGGAGUUUCCUAAACGAACCGUAAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUUAAGUGCCACUAAGUGGUGCUAUCAUUCUUUUAUAU
------...((.(-(.......(((((.....)))))........)).))....((((((((.......)))))))).........((..((((...))))..))............... ( -24.76)
>consensus
GAACUUCAGGUUUACUCCAACUU_UU__UUUGGAGCAUCCUGAGCGAAACGUAAGCGGAAGUCCUUACAGCUUUUGCAUAUCCUAAAGUGCCACUAAGUGGUGCUAUCAUUCUUUCAUGU
.....(((((....((((((.........))))))...)))))...........((((((((.......)))))))).........((..((((...))))..))............... (-20.54 = -22.93 +   2.39)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:51 2006