Locus 732

Sequence ID 3R_DroMel_CAF1
Location 2,609,322 – 2,609,582
Length 260
Max. P 0.954972
window1154 window1155 window1156 window1157 window1158

overview

Window 4

Location 2,609,322 – 2,609,439
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.33
Mean single sequence MFE -35.33
Consensus MFE -28.35
Energy contribution -27.97
Covariance contribution -0.38
Combinations/Pair 1.19
Mean z-score -1.37
Structure conservation index 0.80
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2609322 117 + 27905053
UAUAAAGUAUACUAAAGCUUCACGGAAACCUCACAACUAAGCUUCACCUGUCUGUCAACUUGGAGUCUUACAUUUCGGGUGGGUAAAUGGGGAAGUUUAGG-GUU-UGGUG-GGCGGAUG
......((.(((((((.(.....(....).......(((((((((.(((((.(..(.(((((((((.....))))))))).)..).)))))))))))))))-.))-)))))-.))..... ( -34.80)
>DroSim_CAF1 73398 119 + 1
UAUAAAGUAUACUAAAGCGGCACGGAAACCUCACAACUAAGCUUCACCUGUCUGUCAACUUGGAGUCUUACAUUUCGGGUGGGGAAAUGGGGAAGUUUUGG-GUUUUGGUGGGGCGGAUG
................((..(((.((((((.((.....(((((((.(((((.(.((.(((((((((.....))))))))).)).).)))))))))))))))-))))).)))..))..... ( -35.00)
>DroEre_CAF1 78054 119 + 1
UAUAAAGUAUACGAAAGCGACAUGGAAACCUCACAACUAAGCUUCACCUGUCUGUCAACUUGGAGUCUUACAUUUUGGUUGGGGGAAUGGGAGAGUUUUGG-GUUUUGGUGGGGCGAAUG
................((..(((.((((((.((.....((((((..((..(((.((((((..((........))..)))))).)))..))..)))))))))-))))).)))..))..... ( -34.10)
>DroYak_CAF1 76568 109 + 1
-----------CGAAAGCGACACGGAAACCUCGCAACUAAGCUCCACCUGUCUGUCAACUUGGAGUCUUACAUUUUGGGUGGGGAAACGGGGGAGUUUUGGUGUUUUGGUGAAGCGAAUG
-----------.....((..(((.(((((...((....(((((((.(((((.(.((.(((..((((.....))))..))).)).).))))))))))))..))))))).)))..))..... ( -37.40)
>consensus
UAUAAAGUAUACGAAAGCGACACGGAAACCUCACAACUAAGCUUCACCUGUCUGUCAACUUGGAGUCUUACAUUUCGGGUGGGGAAAUGGGGAAGUUUUGG_GUUUUGGUGGGGCGAAUG
................((..(((.(((((.(((.....(((((((.(((((.(.((.(((((((((.....))))))))).)).).))))))))))))))).))))).)))..))..... (-28.35 = -27.97 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,609,402 – 2,609,502
Length 100
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.66
Mean single sequence MFE -22.08
Consensus MFE -18.05
Energy contribution -18.42
Covariance contribution 0.38
Combinations/Pair 1.10
Mean z-score -1.61
Structure conservation index 0.82
SVM decision value 0.32
SVM RNA-class probability 0.687469
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2609402 100 - 27905053
GACUGCAUCUGAG----CAGAUGCCUGGCAUAUCUUUUAU-------------GGAGAGCCCGCUCCCCAGACCAUUACUCAUCCGCC-CACCA-AAC-CCUAAACUUCCCCAUUUACCC
....((((((...----.))))))..(((..........(-------------((.(((....))).)))((.......))....)))-.....-...-..................... ( -18.00)
>DroSim_CAF1 73478 115 - 1
GACUGCAUCGGAG----CAGAUGCCUGGCAUAUCUUUUAUCUGUCUGGAAACUGGAGAGCCCGCUCCCCAGACCAUCACUCAUCCGCCCCACCAAAAC-CCAAAACUUCCCCAUUUCCCC
.........((.(----(.((((((.((((.((.....)).)))).))...((((.(((....))).)))).........)))).)).))........-..................... ( -23.70)
>DroEre_CAF1 78134 114 - 1
UACUGCAUCUGAG----CAGAUGCCUGGCAUAUCUUUUAUCUGUCUGGAAACUGGAGAGCCCGCUC-CCAGACCAUCACUCAUUCGCCCCACCAAAAC-CCAAAACUCUCCCAUUCCCCC
....((((((...----.))))))..(((..........(((....)))..((((.(((....)))-))))..............)))..........-..................... ( -22.50)
>DroYak_CAF1 76637 119 - 1
UACUGCAUCUGAGAAGCCAGAUGCCUGGCAUGUCUUUUAUCCGUCUGAAAACUGGAGAGCUUGCUC-CCAGACCAUCACUCAUUCGCUUCACCAAAACACCAAAACUCCCCCGUUUCCCC
....((...((((..(((((....)))))......................((((.(((....)))-)))).......))))...))................................. ( -24.10)
>consensus
GACUGCAUCUGAG____CAGAUGCCUGGCAUAUCUUUUAUCUGUCUGGAAACUGGAGAGCCCGCUC_CCAGACCAUCACUCAUCCGCCCCACCAAAAC_CCAAAACUCCCCCAUUUCCCC
....(((((((......)))))))..((((((.....)))...........((((.(((....))).))))..............)))................................ (-18.05 = -18.42 +   0.38)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,609,439 – 2,609,542
Length 103
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.17
Mean single sequence MFE -37.40
Consensus MFE -27.85
Energy contribution -29.10
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.38
Structure conservation index 0.74
SVM decision value 1.45
SVM RNA-class probability 0.954972
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2609439 103 + 27905053
AGUAAUGGUCUGGGGAGCGGGCUCUCC-------------AUAAAAGAUAUGCCAGGCAUCUG----CUCAGAUGCAGUCGCCAGCAGAUGCAUCUGCGAAAUGGAAAUGGAAACGGAAU
..........(((((((....))))))-------------)...........((((((..(((----(......))))..))).(((((....)))))....)))...((....)).... ( -34.40)
>DroSim_CAF1 73517 116 + 1
AGUGAUGGUCUGGGGAGCGGGCUCUCCAGUUUCCAGACAGAUAAAAGAUAUGCCAGGCAUCUG----CUCCGAUGCAGUCGCCAGCAGAUGCAUCUGCGAAAUGGAAAUGGAAACGGAAU
.((..(((.((((((((....))))))))...))).))..............((((((..(((----(......))))..))).(((((....)))))....)))...((....)).... ( -42.20)
>DroEre_CAF1 78173 109 + 1
AGUGAUGGUCUGG-GAGCGGGCUCUCCAGUUUCCAGACAGAUAAAAGAUAUGCCAGGCAUCUG----CUCAGAUGCAGUAGCCAGCAGAUGCAUCUGCGAAAUGGAAAUGGAA------A
.......((((((-((((.((....)).))))))))))..............((((((..(((----(......))))..))).(((((....)))))....)))........------. ( -38.10)
>DroYak_CAF1 76677 113 + 1
AGUGAUGGUCUGG-GAGCAAGCUCUCCAGUUUUCAGACGGAUAAAAGACAUGCCAGGCAUCUGGCUUCUCAGAUGCAGUAGCCAGCAGAUGCAUCUGCGAAAUGGAUAAGGAA------U
.......(((((.-.(((..........)))..)))))..........((((((((....)))))(((.((((((((...(....)...)))))))).)))))).........------. ( -34.90)
>consensus
AGUGAUGGUCUGG_GAGCGGGCUCUCCAGUUUCCAGACAGAUAAAAGAUAUGCCAGGCAUCUG____CUCAGAUGCAGUAGCCAGCAGAUGCAUCUGCGAAAUGGAAAUGGAA______U
.....((((((((((((....))))))))...........................(((((((......)))))))....))))(((((....)))))...................... (-27.85 = -29.10 +   1.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,609,439 – 2,609,542
Length 103
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.17
Mean single sequence MFE -32.90
Consensus MFE -24.38
Energy contribution -25.62
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 0.74
SVM decision value 1.41
SVM RNA-class probability 0.951271
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2609439 103 - 27905053
AUUCCGUUUCCAUUUCCAUUUCGCAGAUGCAUCUGCUGGCGACUGCAUCUGAG----CAGAUGCCUGGCAUAUCUUUUAU-------------GGAGAGCCCGCUCCCCAGACCAUUACU
...............(((....(((((....))))).((((.((((......)----))).)))))))...........(-------------((.(((....))).))).......... ( -26.60)
>DroSim_CAF1 73517 116 - 1
AUUCCGUUUCCAUUUCCAUUUCGCAGAUGCAUCUGCUGGCGACUGCAUCGGAG----CAGAUGCCUGGCAUAUCUUUUAUCUGUCUGGAAACUGGAGAGCCCGCUCCCCAGACCAUCACU
............((((((....(((((((.((.((((((((.((((......)----))).)))).)))).))....))))))).))))))((((.(((....))).))))......... ( -37.10)
>DroEre_CAF1 78173 109 - 1
U------UUCCAUUUCCAUUUCGCAGAUGCAUCUGCUGGCUACUGCAUCUGAG----CAGAUGCCUGGCAUAUCUUUUAUCUGUCUGGAAACUGGAGAGCCCGCUC-CCAGACCAUCACU
.------.....((((((....(((((((.((.(((((((..((((......)----)))..))).)))).))....))))))).))))))((((.(((....)))-))))......... ( -35.20)
>DroYak_CAF1 76677 113 - 1
A------UUCCUUAUCCAUUUCGCAGAUGCAUCUGCUGGCUACUGCAUCUGAGAAGCCAGAUGCCUGGCAUGUCUUUUAUCCGUCUGAAAACUGGAGAGCUUGCUC-CCAGACCAUCACU
.------(((.........(((.((((((((...(....)...)))))))).)))(((((....))))).................)))..((((.(((....)))-))))......... ( -32.70)
>consensus
A______UUCCAUUUCCAUUUCGCAGAUGCAUCUGCUGGCGACUGCAUCUGAG____CAGAUGCCUGGCAUAUCUUUUAUCUGUCUGGAAACUGGAGAGCCCGCUC_CCAGACCAUCACU
......................(((((....)))))..((((..(((((((......))))))).))))......................((((.(((....))).))))......... (-24.38 = -25.62 +   1.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,609,466 – 2,609,582
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.88
Mean single sequence MFE -37.12
Consensus MFE -30.55
Energy contribution -30.67
Covariance contribution 0.13
Combinations/Pair 1.07
Mean z-score -2.07
Structure conservation index 0.82
SVM decision value 0.99
SVM RNA-class probability 0.895151
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2609466 116 + 27905053
AUAAAAGAUAUGCCAGGCAUCUG----CUCAGAUGCAGUCGCCAGCAGAUGCAUCUGCGAAAUGGAAAUGGAAACGGAAUCGGAACCUUGAUCUUCAGGGCGCGGGGAAAGUCUUUCUCU
...((((((...((..(((((((----((..(((...)))...)))))))))..(((((.....((..((....))...))....(((((.....))))))))))))...)))))).... ( -38.10)
>DroSim_CAF1 73557 116 + 1
AUAAAAGAUAUGCCAGGCAUCUG----CUCCGAUGCAGUCGCCAGCAGAUGCAUCUGCGAAAUGGAAAUGGAAACGGAAUCGGAACCUUGAUCUUCAGGGUGCGGGGAAAGUCUUUCUCU
...((((((...((..(((((((----((.((((...))))..)))))))))..((((......((..((....))...))...((((((.....))))))))))))...)))))).... ( -38.90)
>DroEre_CAF1 78212 110 + 1
AUAAAAGAUAUGCCAGGCAUCUG----CUCAGAUGCAGUAGCCAGCAGAUGCAUCUGCGAAAUGGAAAUGGAA------ACGGAACCUUGAUCUUCAGGGUGCGGGGAAAGUCUUUCUCU
...((((((...((..(((((((----((.....((....)).)))))))))..((((..........((...------.))..((((((.....))))))))))))...)))))).... ( -35.90)
>DroYak_CAF1 76716 114 + 1
AUAAAAGACAUGCCAGGCAUCUGGCUUCUCAGAUGCAGUAGCCAGCAGAUGCAUCUGCGAAAUGGAUAAGGAA------UGGGAACCUUGAUCUUCAGGGUGUGGGGAAAGUCUUUCUCU
...((((((...((..((((((((....)))))))).....((((((((....)))))...............------.....((((((.....)))))).)))))...)))))).... ( -35.60)
>consensus
AUAAAAGAUAUGCCAGGCAUCUG____CUCAGAUGCAGUAGCCAGCAGAUGCAUCUGCGAAAUGGAAAUGGAA______UCGGAACCUUGAUCUUCAGGGUGCGGGGAAAGUCUUUCUCU
...((((((...((..(((((((......))))))).....((.(((((....)))))........................(.((((((.....)))))).)))))...)))))).... (-30.55 = -30.67 +   0.13)

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 09:50:32 2006