Locus 3160

Sequence ID 2L_DroMel_CAF1
Location 9,039,934 – 9,040,073
Length 139
Max. P 0.961226
window5023 window5024 window5025 window5026

overview

Window 3

Location 9,039,934 – 9,040,046
Length 112
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 89.55
Mean single sequence MFE -29.56
Consensus MFE -23.08
Energy contribution -22.20
Covariance contribution -0.88
Combinations/Pair 1.20
Mean z-score -1.65
Structure conservation index 0.78
SVM decision value 0.40
SVM RNA-class probability 0.721029
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9039934 112 + 22407834
ACUAAUGUGGGCAUAAUAGCUUUCGAUUAUCGAGAAGAAGAAGGAAAUGGGGGAAAAGCGGAGAAGGGUGCCGGAAAAGGUGCCUAUGUAGGCACUCUUUAAUGCCUUUAAG
.....((.((((((......(((((.....)))))...........................((((((((((.....((....)).....)))))))))).)))))).)).. ( -28.10)
>DroSec_CAF1 34009 112 + 1
ACUAAUGUGGGCAUAAUAGCUUUCGAUUAUCGAGGAGAAGAAGGAAAUGGGGGAAAAGCGGAGAGGGGUGCCGGAAAAGGUGCCUAUGUAGGCACUCUUUAAUGCCUUUAAG
.....((.((((((....((((((.(((.((...........)).))).))....))))...((((((((((.....((....)).....)))))))))).)))))).)).. ( -27.80)
>DroSim_CAF1 37790 111 + 1
ACUAAUGUGGGCAUAAUAGCUUUCGAUUAUCGAGGAGAAGAAGGAAAUGGGGGAAAAGCGGAGAA-GGUGCCGGAAAAGGUGCCUAUGUAGGCACUCUUUAAUGCCUUUAAG
.....((.((((((......(((((.....))))).(((((.................(((....-....)))......((((((....))))))))))).)))))).)).. ( -25.70)
>DroEre_CAF1 36468 111 + 1
ACUAAUGUGGGCGUAAUAGCUUUCGAUUAUCGGGGGGAAGAAGGAAAAGAGGGCGAGGAGGAGGAGCCUG-CGAAGAAGGUGCCUGUAUAGGCACUCUUUAAUGCCUUUAAG
...................((..((.....))..))............(((((((..((((((..((((.-......))))((((....)))).))))))..)))))))... ( -31.60)
>DroYak_CAF1 35260 112 + 1
ACUAAUGUGGGCAUAAUAGCUUUCGAUUAUCGAGGGGCAGAAAGAAAAGAGGGUAAGGCGGAGGAGCCUGGUGGAAAAGGUGCCUCUAUAGGCACUCUUUAAUGCCUUUAAG
.....((.((((((.....((((((.....)))))).........((((((.((...(..((((.((((........)))).))))..)..)).)))))).)))))).)).. ( -34.60)
>consensus
ACUAAUGUGGGCAUAAUAGCUUUCGAUUAUCGAGGAGAAGAAGGAAAUGGGGGAAAAGCGGAGAAGGGUGCCGGAAAAGGUGCCUAUGUAGGCACUCUUUAAUGCCUUUAAG
.....((.((((((.....(((((..((......))...)))))...............................((((((((((....)))))).)))).)))))).)).. (-23.08 = -22.20 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,039,934 – 9,040,046
Length 112
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 89.55
Mean single sequence MFE -20.94
Consensus MFE -16.84
Energy contribution -17.44
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.14
Structure conservation index 0.80
SVM decision value 1.52
SVM RNA-class probability 0.961226
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9039934 112 - 22407834
CUUAAAGGCAUUAAAGAGUGCCUACAUAGGCACCUUUUCCGGCACCCUUCUCCGCUUUUCCCCCAUUUCCUUCUUCUUCUCGAUAAUCGAAAGCUAUUAUGCCCACAUUAGU
......(((((.((((.((((((....))))))))))................((((((.............................))))))....)))))......... ( -19.85)
>DroSec_CAF1 34009 112 - 1
CUUAAAGGCAUUAAAGAGUGCCUACAUAGGCACCUUUUCCGGCACCCCUCUCCGCUUUUCCCCCAUUUCCUUCUUCUCCUCGAUAAUCGAAAGCUAUUAUGCCCACAUUAGU
......(((((.((((.((((((....))))))))))................((((((.............................))))))....)))))......... ( -19.85)
>DroSim_CAF1 37790 111 - 1
CUUAAAGGCAUUAAAGAGUGCCUACAUAGGCACCUUUUCCGGCACC-UUCUCCGCUUUUCCCCCAUUUCCUUCUUCUCCUCGAUAAUCGAAAGCUAUUAUGCCCACAUUAGU
......(((((.((((.((((((....))))))))))..(((....-....))).........................(((.....)))........)))))......... ( -19.90)
>DroEre_CAF1 36468 111 - 1
CUUAAAGGCAUUAAAGAGUGCCUAUACAGGCACCUUCUUCG-CAGGCUCCUCCUCCUCGCCCUCUUUUCCUUCUUCCCCCCGAUAAUCGAAAGCUAUUACGCCCACAUUAGU
......(((....(((.((((((....)))))))))....(-(.(((...........)))...................((.....))...))......)))......... ( -20.30)
>DroYak_CAF1 35260 112 - 1
CUUAAAGGCAUUAAAGAGUGCCUAUAGAGGCACCUUUUCCACCAGGCUCCUCCGCCUUACCCUCUUUUCUUUCUGCCCCUCGAUAAUCGAAAGCUAUUAUGCCCACAUUAGU
......((((..(((((((((((....))))))..........((((......))))..........))))).))))..(((.....)))..((......)).......... ( -24.80)
>consensus
CUUAAAGGCAUUAAAGAGUGCCUACAUAGGCACCUUUUCCGGCACCCUUCUCCGCUUUUCCCCCAUUUCCUUCUUCUCCUCGAUAAUCGAAAGCUAUUAUGCCCACAUUAGU
......(((((.((((.((((((....))))))))))..........................................(((.....)))........)))))......... (-16.84 = -17.44 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,039,974 – 9,040,073
Length 99
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 84.12
Mean single sequence MFE -25.16
Consensus MFE -14.62
Energy contribution -14.66
Covariance contribution 0.04
Combinations/Pair 1.17
Mean z-score -2.44
Structure conservation index 0.58
SVM decision value 0.45
SVM RNA-class probability 0.741042
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9039974 99 + 22407834
AAGGAAAUGGGGGAAAAGCGGAGAAGGGUGCCGGAAAAGGUGCCUAUGUAGGCACUCUUUAAUGCCUUUAAGGGAUAACAGAAAAAU------AUCUAUUCAAAA
...(((.......(((.(((..((((((((((.....((....)).....))))))))))..))).)))...(((((.........)------)))).))).... ( -23.20)
>DroSec_CAF1 34049 99 + 1
AAGGAAAUGGGGGAAAAGCGGAGAGGGGUGCCGGAAAAGGUGCCUAUGUAGGCACUCUUUAAUGCCUUUAAGGGAUAACAGAAAAAU------AUCUAUUCAAAA
...(((.((((((...(..(((((((((..((......))..))).((....))))))))..).))))))..(((((.........)------)))).))).... ( -23.30)
>DroSim_CAF1 37830 98 + 1
AAGGAAAUGGGGGAAAAGCGGAGAA-GGUGCCGGAAAAGGUGCCUAUGUAGGCACUCUUUAAUGCCUUUAAGGGAUAACAGAAAAAU------AUCUAUUCAAAA
...(((.((((((.....(((....-....)))..((((((((((....)))))).))))....))))))..(((((.........)------)))).))).... ( -21.90)
>DroEre_CAF1 36508 104 + 1
AAGGAAAAGAGGGCGAGGAGGAGGAGCCUG-CGAAGAAGGUGCCUGUAUAGGCACUCUUUAAUGCCUUUAAGGGGUAACAGAAGUAUACUCGUAUCUAAUCAAGC
..(((...(((((((..((((((..((((.-......))))((((....)))).))))))..)))))))...(((((((....)).)))))...)))........ ( -30.60)
>DroYak_CAF1 35300 99 + 1
AAAGAAAAGAGGGUAAGGCGGAGGAGCCUGGUGGAAAAGGUGCCUCUAUAGGCACUCUUUAAUGCCUUUAAGGGGUAACCGAAAUAU------AUAUAUUAAAGA
........(((((((((((......))))......((((((((((....)))))).))))..)))))))..((.....)).......------............ ( -26.80)
>consensus
AAGGAAAUGGGGGAAAAGCGGAGAAGGGUGCCGGAAAAGGUGCCUAUGUAGGCACUCUUUAAUGCCUUUAAGGGAUAACAGAAAAAU______AUCUAUUCAAAA
........(((((.....(((.........)))..((((((((((....)))))).))))....))))).................................... (-14.62 = -14.66 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,039,974 – 9,040,073
Length 99
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 84.12
Mean single sequence MFE -20.44
Consensus MFE -13.12
Energy contribution -13.76
Covariance contribution 0.64
Combinations/Pair 1.06
Mean z-score -2.93
Structure conservation index 0.64
SVM decision value 1.49
SVM RNA-class probability 0.958081
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9039974 99 - 22407834
UUUUGAAUAGAU------AUUUUUCUGUUAUCCCUUAAAGGCAUUAAAGAGUGCCUACAUAGGCACCUUUUCCGGCACCCUUCUCCGCUUUUCCCCCAUUUCCUU
.....((((((.------.....)))))).......((((((...((((.((((((....))))))))))...((.........))))))))............. ( -19.80)
>DroSec_CAF1 34049 99 - 1
UUUUGAAUAGAU------AUUUUUCUGUUAUCCCUUAAAGGCAUUAAAGAGUGCCUACAUAGGCACCUUUUCCGGCACCCCUCUCCGCUUUUCCCCCAUUUCCUU
.....((((((.------.....)))))).......((((((...((((.((((((....))))))))))...((....)).....))))))............. ( -20.30)
>DroSim_CAF1 37830 98 - 1
UUUUGAAUAGAU------AUUUUUCUGUUAUCCCUUAAAGGCAUUAAAGAGUGCCUACAUAGGCACCUUUUCCGGCACC-UUCUCCGCUUUUCCCCCAUUUCCUU
.....((((((.------.....)))))).......((((((...((((.((((((....))))))))))...((....-....))))))))............. ( -20.60)
>DroEre_CAF1 36508 104 - 1
GCUUGAUUAGAUACGAGUAUACUUCUGUUACCCCUUAAAGGCAUUAAAGAGUGCCUAUACAGGCACCUUCUUCG-CAGGCUCCUCCUCCUCGCCCUCUUUUCCUU
(((((....((((.(((....))).)))).........(((((((....)))))))...))))).........(-((((........))).))............ ( -20.60)
>DroYak_CAF1 35300 99 - 1
UCUUUAAUAUAU------AUAUUUCGGUUACCCCUUAAAGGCAUUAAAGAGUGCCUAUAGAGGCACCUUUUCCACCAGGCUCCUCCGCCUUACCCUCUUUUCUUU
............------.......(((...........((....((((.((((((....))))))))))....))((((......)))).)))........... ( -20.90)
>consensus
UUUUGAAUAGAU______AUUUUUCUGUUAUCCCUUAAAGGCAUUAAAGAGUGCCUACAUAGGCACCUUUUCCGGCACCCUUCUCCGCUUUUCCCCCAUUUCCUU
.....((((((............))))))..........((....((((.((((((....)))))))))).))................................ (-13.12 = -13.76 +   0.64)

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 10:45:50 2006