Locus 4314

Sequence ID 3R_DroMel_CAF1
Location 11,437,127 – 11,437,306
Length 179
Max. P 0.997228
window7036 window7037 window7038 window7039

overview

Window 6

Location 11,437,127 – 11,437,226
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.62
Mean single sequence MFE -28.40
Consensus MFE -22.28
Energy contribution -22.40
Covariance contribution 0.12
Combinations/Pair 1.23
Mean z-score -1.50
Structure conservation index 0.78
SVM decision value 0.09
SVM RNA-class probability 0.578663
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11437127 99 + 27905053
G-------A--------------CGGAGCACAUAGGCGGAAAUAGCCGGAGCUUCGGGGUGCAGGGUGUGGCAAGAAGCACGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAA
.-------.--------------((((((((...(((.......)))...(((((..(.(((.....))).)..)))))..))))...(((((((.......))))))).....)))).. ( -30.70)
>DroSec_CAF1 177213 92 + 1
G-------A--------------CGGAGCGCAUAGGCGGAAAUAGCCGAAGCUUCAG-------GGUGUGGCACGAAGCACGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAA
.-------.--------------.(((((.....(((.......)))...))))).(-------(((((.(((((.....)))))...(((((((.......)))))))..))))))... ( -29.80)
>DroSim_CAF1 171410 99 + 1
G-------G--------------CGGAGCACAUAGGCGGAAAUAGCCGAAGCUUCAGCGUGCUGGGUGUGGCAAGAAGCACGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAA
.-------(--------------((((((.....(((.......)))...))))).(((((((...((...))...)))))))))...(((((((.......)))))))........... ( -30.90)
>DroEre_CAF1 166786 100 + 1
U-------A-------------CCGGGGGAUAUGGGCGGAAAUAGCUUAGGCUUCAGGACGCAGGGUGUGGCAAGAAGCACGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAA
.-------.-------------((.((((...(((((.......)))))..)))).))..(((.(.(((........)))).)))...(((((((.......)))))))........... ( -25.00)
>DroYak_CAF1 169662 120 + 1
GGGAGGGGAGCGGAGGUGAGGGGCAGGGUAUAUAGGCGGAAAUGGCCGAAGCUUGAGGGUGCAGGGUGUGGCAAGAAGCACGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAA
..........((((..((((..(((.(.......(((.......)))...((((...(.(((.....))).)...)))).).))).....(((((.......)))))))))...)))).. ( -25.60)
>consensus
G_______A______________CGGAGCACAUAGGCGGAAAUAGCCGAAGCUUCAGGGUGCAGGGUGUGGCAAGAAGCACGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAA
.......................((((((((...(((.......)))...(((((....(((........))).)))))..))))...(((((((.......))))))).....)))).. (-22.28 = -22.40 +   0.12)

alignment

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secondary structure

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Window 7

Location 11,437,146 – 11,437,266
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.67
Mean single sequence MFE -34.12
Consensus MFE -29.36
Energy contribution -30.04
Covariance contribution 0.68
Combinations/Pair 1.06
Mean z-score -1.83
Structure conservation index 0.86
SVM decision value 1.73
SVM RNA-class probability 0.974213
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11437146 120 + 27905053
AAUAGCCGGAGCUUCGGGGUGCAGGGUGUGGCAAGAAGCACGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAACGCAAACACAAACGCAAUUAAGCGCGGCGUCAGUGUAAUG
....(((...(((((..(.(((.....))).)..)))))..((((..((.((((((....(((((..((((.....))))))))).....)))))).))..)))))))............ ( -35.60)
>DroSec_CAF1 177232 113 + 1
AAUAGCCGAAGCUUCAG-------GGUGUGGCACGAAGCACGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAACGCAAACACAAACGCAAUUAAGCGCGGCGUCAGUGUAAUG
....((((..(((((((-------(.(((.(((((.....)))))...(((((((.......)))))))..))))))))).)).........(((......)))))))............ ( -32.90)
>DroSim_CAF1 171429 120 + 1
AAUAGCCGAAGCUUCAGCGUGCUGGGUGUGGCAAGAAGCACGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAACCCAAACACAAACGCAAUUAAGCGCGGCGUCAGUGUAAUG
....((((..((((..((((..(((((....((((..((....))...(((((((.......))))))).....)))).))))).......))))....)))).))))............ ( -32.20)
>DroEre_CAF1 166806 120 + 1
AAUAGCUUAGGCUUCAGGACGCAGGGUGUGGCAAGAAGCACGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAACGCAAACACAAACGCAAUUAAGCGCGGCGUCAGUGUAAUG
......(((.(((....(((((...((((........))))((((..((.((((((....(((((..((((.....))))))))).....)))))).))..)))).)))))))).))).. ( -33.30)
>DroYak_CAF1 169702 120 + 1
AAUGGCCGAAGCUUGAGGGUGCAGGGUGUGGCAAGAAGCACGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAACGCAAACACAAACGCAAUUAAGCGCGGCGUCAGUGUAAUG
....((((..((((((...(((.(..((((((((.....((((........)))).....))))((.((((.....)))).))...))))..)))).)))))).))))............ ( -36.60)
>consensus
AAUAGCCGAAGCUUCAGGGUGCAGGGUGUGGCAAGAAGCACGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAACGCAAACACAAACGCAAUUAAGCGCGGCGUCAGUGUAAUG
....((((.(.(((........))).).))))..((.((.(((((..((.((((((....(((((..((((.....))))))))).....)))))).))..))))))).))......... (-29.36 = -30.04 +   0.68)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,437,146 – 11,437,266
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.67
Mean single sequence MFE -33.66
Consensus MFE -29.46
Energy contribution -29.86
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.88
SVM decision value 2.82
SVM RNA-class probability 0.997228
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11437146 120 - 27905053
CAUUACACUGACGCCGCGCUUAAUUGCGUUUGUGUUUGCGUUCAAAUGUUGAAUGCGCAAUUUUAACGCAUUUUUGCACGUGCUUCUUGCCACACCCUGCACCCCGAAGCUCCGGCUAUU
............((((.((..((.((((((...(((((((((((.....)))))))).)))...)))))).))..))..(.(((((.(((........)))....))))).))))).... ( -34.90)
>DroSec_CAF1 177232 113 - 1
CAUUACACUGACGCCGCGCUUAAUUGCGUUUGUGUUUGCGUUCAAAUGUUGAAUGCGCAAUUUUAACGCAUUUUUGCACGUGCUUCGUGCCACACC-------CUGAAGCUUCGGCUAUU
.....(((.((.((((.((..((.((((((...(((((((((((.....)))))))).)))...)))))).))..)).)).)).))))).......-------....(((....)))... ( -35.30)
>DroSim_CAF1 171429 120 - 1
CAUUACACUGACGCCGCGCUUAAUUGCGUUUGUGUUUGGGUUCAAAUGUUGAAUGCGCAAUUUUAACGCAUUUUUGCACGUGCUUCUUGCCACACCCAGCACGCUGAAGCUUCGGCUAUU
............((.((((......))))..(((((.((((.....(((.(((((((.........)))))))..))).((((.....).))))))))))))))...(((....)))... ( -33.30)
>DroEre_CAF1 166806 120 - 1
CAUUACACUGACGCCGCGCUUAAUUGCGUUUGUGUUUGCGUUCAAAUGUUGAAUGCGCAAUUUUAACGCAUUUUUGCACGUGCUUCUUGCCACACCCUGCGUCCUGAAGCCUAAGCUAUU
.........(((((.(.((..((.((((((...(((((((((((.....)))))))).)))...)))))).))..)).)((((.....).))).....)))))....(((....)))... ( -32.80)
>DroYak_CAF1 169702 120 - 1
CAUUACACUGACGCCGCGCUUAAUUGCGUUUGUGUUUGCGUUCAAAUGUUGAAUGCGCAAUUUUAACGCAUUUUUGCACGUGCUUCUUGCCACACCCUGCACCCUCAAGCUUCGGCCAUU
.........((.((((.((..((.((((((...(((((((((((.....)))))))).)))...)))))).))..)).)).)).)).(((........))).......((....)).... ( -32.00)
>consensus
CAUUACACUGACGCCGCGCUUAAUUGCGUUUGUGUUUGCGUUCAAAUGUUGAAUGCGCAAUUUUAACGCAUUUUUGCACGUGCUUCUUGCCACACCCUGCACCCUGAAGCUUCGGCUAUU
.........((.((((.((..((.((((((...(((((((((((.....)))))))).)))...)))))).))..)).)).)).)).....................(((....)))... (-29.46 = -29.86 +   0.40)

alignment

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secondary structure

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Window 9

Location 11,437,186 – 11,437,306
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.07
Mean single sequence MFE -35.10
Consensus MFE -27.18
Energy contribution -30.18
Covariance contribution 3.00
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 0.77
SVM decision value 0.87
SVM RNA-class probability 0.870154
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11437186 120 + 27905053
CGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAACGCAAACACAAACGCAAUUAAGCGCGGCGUCAGUGUAAUGAAAGUGUCUGGCGGAGGGGAGCCACCCAAGUCCAAGGGUA
(((((..((.((((((....(((((..((((.....))))))))).....)))))).))..))))).((((((....((....))..))))))..((....))((((........)))). ( -37.00)
>DroSec_CAF1 177265 120 + 1
CGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAACGCAAACACAAACGCAAUUAAGCGCGGCGUCAGUGUAAUGAAAGUGUCUGGCGGAGGGGAGCCACCCAAGUCCAGGGGUA
(((((..((.((((((....(((((..((((.....))))))))).....)))))).))..))))).((((((....((....))..))))))..((....))((((........)))). ( -36.90)
>DroSim_CAF1 171469 120 + 1
CGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAACCCAAACACAAACGCAAUUAAGCGCGGCGUCAGUGUAAUGAAAGUGUCUGGCGGAGGGGAGCCACCCAAGUCCAGGGGUA
.((.....(((((((.......)))))))..))......((((..((((..((((...........))))..))))...........(((((...(((......)))..).)))))))). ( -33.00)
>DroEre_CAF1 166846 118 + 1
CGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAACGCAAACACAAACGCAAUUAAGCGCGGCGUCAGUGUAAUGAAAGUGUCUGGCGGGGGC--GCCACCCAAGGCCGGGCGAA
(((((..((.((((((....(((((..((((.....))))))))).....)))))).))..)))))...(((......)))...((((((((.(((..--....)))...)))))))).. ( -39.30)
>DroYak_CAF1 169742 98 + 1
CGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAACGCAAACACAAACGCAAUUAAGCGCGGCGUCAGUGUAAUGAAAGUGUCUGGCGGAGGG----------------------
(((((..((.((((((....(((((..((((.....))))))))).....)))))).))..))))).((((((....((....))..)))))).....---------------------- ( -29.30)
>consensus
CGUGCAAAAAUGCGUUAAAAUUGCGCAUUCAACAUUUGAACGCAAACACAAACGCAAUUAAGCGCGGCGUCAGUGUAAUGAAAGUGUCUGGCGGAGGGGAGCCACCCAAGUCCAGGGGUA
(((((..((.((((((....(((((..((((.....))))))))).....)))))).))..))))).((((((....((....))..))))))..(((......)))............. (-27.18 = -30.18 +   3.00)

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 11:25:47 2006