Locus 1395

Sequence ID 2L_DroMel_CAF1
Location 3,712,300 – 3,712,456
Length 156
Max. P 0.706803
window2274 window2275 window2276

overview

Window 4

Location 3,712,300 – 3,712,398
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.18
Mean single sequence MFE -30.50
Consensus MFE -15.53
Energy contribution -15.87
Covariance contribution 0.34
Combinations/Pair 1.22
Mean z-score -1.73
Structure conservation index 0.51
SVM decision value 0.31
SVM RNA-class probability 0.684676
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3712300 98 - 22407834
ACACGUGAGAACGCAGAUACAUCCGUGUCUGCACAAGAUCAAAGGACUUCUAGAUCCGGAAACCUGCAUCAAGUGUCCGCGGUGUCAUAAGUCCAUUU----------------------
...(....)...((((((((....))))))))...........((((((..(.(((((((...((......))..)))).))).)...))))))....---------------------- ( -29.90)
>DroSec_CAF1 174651 98 - 1
ACACGUGAGAACGCAGAUACAUCCGUGUCUGCACAGGAUCGCAGGUCUUCUAGAUCCGGAAACUUGCAUCAAGUGUCCGCGGUGUCAUAAGUCCAUUU----------------------
....((((....((((((((....))))))))......)))).((.(((..(.(((((((.(((((...))))).)))).))).)...))).))....---------------------- ( -31.70)
>DroSim_CAF1 183542 98 - 1
ACGCGUGAGAACGCAGAUACAUCCGUGUCUGCACAGGAUCGUAGGUCUUCUAGAUCCGGAAACUUGCAUCAAGUGUCCGCGGUGUCAUAAGUCCAUUU----------------------
.(((........((((((((....))))))))...(((((.(((.....))))))))(((.(((((...))))).)))))).................---------------------- ( -33.10)
>DroEre_CAF1 187820 98 - 1
CAACCUGAUAACGCAGAUACAUCCGUGUCUGCACAGGGUCACAGGUAAUCGAGAUCCGGAAACCUGCCUCAAGUGCCCGCGGUGUCAAAAGCCCAUUU----------------------
.....(((((.(((((((((....))))))((((.(((...(((((..(((.....)))..))))))))...))))..))).)))))...........---------------------- ( -28.90)
>DroYak_CAF1 188212 98 - 1
AAAACUGAGAACGCAGAUACAUCCGUGUUUGCACAGGAUUAAAGGACUUUUGGAUCCGGACACCUGCCCCAAUUGUCCGCGGUGUCAAAAGCCCAUUU----------------------
............((((((((....))))))))...........((.((((((((((((((((..((...))..)))))).))).))))))).))....---------------------- ( -29.50)
>DroAna_CAF1 199115 120 - 1
UACUGUGAUUUCGGUGAUAUAUCCCUGUCUGCACAGCGUUAAAGGUCGUGUUGAUCCGGACACGGAUUCGAAGUGUCCUCUUUGUAAAAAACCUAUUCACAAAGUGUUUACAAAGGCUAG
..(((((....(((.((....)).)))....)))))......(((.((..((((((((....)))).))))..)).)))(((((((((....((........))..)))))))))..... ( -29.90)
>consensus
AAACGUGAGAACGCAGAUACAUCCGUGUCUGCACAGGAUCAAAGGUCUUCUAGAUCCGGAAACCUGCAUCAAGUGUCCGCGGUGUCAAAAGCCCAUUU______________________
.....(((.(.(((((((((....))))))((((.(((((............)))))(....).........))))..))).).)))................................. (-15.53 = -15.87 +   0.34)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,712,318 – 3,712,429
Length 111
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.44
Mean single sequence MFE -33.25
Consensus MFE -19.20
Energy contribution -19.82
Covariance contribution 0.61
Combinations/Pair 1.20
Mean z-score -1.57
Structure conservation index 0.58
SVM decision value 0.37
SVM RNA-class probability 0.706803
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3712318 111 - 22407834
---------UGGAUAUUGCCGAGCCAAUCGCAGCAAAGGAACACGUGAGAACGCAGAUACAUCCGUGUCUGCACAAGAUCAAAGGACUUCUAGAUCCGGAAACCUGCAUCAAGUGUCCGC
---------.(((((((...((.....))((((....(((.(.(....)...((((((((....))))))))....................).)))(....)))))....))))))).. ( -31.70)
>DroSec_CAF1 174669 111 - 1
---------UGGAUAUUGCCGAGCCAAUCGCAGCAAAGGCACACGUGAGAACGCAGAUACAUCCGUGUCUGCACAGGAUCGCAGGUCUUCUAGAUCCGGAAACUUGCAUCAAGUGUCCGC
---------.((((((((((..((........))...)))....(..((...((((((((....))))))))...(((((..((.....)).))))).....))..)....))))))).. ( -38.60)
>DroSim_CAF1 183560 111 - 1
---------UGGAUAUUGCCGAGCCAAUCGCAGCAAAGCAACGCGUGAGAACGCAGAUACAUCCGUGUCUGCACAGGAUCGUAGGUCUUCUAGAUCCGGAAACUUGCAUCAAGUGUCCGC
---------.(((((((...((.((..((((.((........))))))....((((((((....))))))))...)).))((((((.((((......))))))))))....))))))).. ( -36.70)
>DroEre_CAF1 187838 111 - 1
---------UGGAUAUUGCAGAUCCAAACACAGGCAAUAACAACCUGAUAACGCAGAUACAUCCGUGUCUGCACAGGGUCACAGGUAAUCGAGAUCCGGAAACCUGCCUCAAGUGCCCGC
---------.((.((((...(((((.....((((.........)))).....((((((((....))))))))...))))).(((((..(((.....)))..))))).....)))).)).. ( -34.50)
>DroYak_CAF1 188230 111 - 1
---------UGGACAUUGAAGAGACAAUCGCAGGAAAGGAAAAACUGAGAACGCAGAUACAUCCGUGUUUGCACAGGAUUAAAGGACUUUUGGAUCCGGACACCUGCCCCAAUUGUCCGC
---------.((((((((..((.....))(((((..................((((((((....))))))))...(((((.(((....))).))))).....)))))..))).))))).. ( -31.70)
>DroAna_CAF1 199155 120 - 1
AAAACAUUACUGAUAUUGUCGAAAAAAGAAGAAAAAAAGAUACUGUGAUUUCGGUGAUAUAUCCCUGUCUGCACAGCGUUAAAGGUCGUGUUGAUCCGGACACGGAUUCGAAGUGUCCUC
...........((((((.(((((...............((..(((((....(((.((....)).)))....)))))..)).....(((((((......))))))).)))))))))))... ( -26.30)
>consensus
_________UGGAUAUUGCCGAGCCAAUCGCAGCAAAGGAAAACGUGAGAACGCAGAUACAUCCGUGUCUGCACAGGAUCAAAGGUCUUCUAGAUCCGGAAACCUGCAUCAAGUGUCCGC
..........(((((((...................................((((((((....))))))))...(((((............)))))..............))))))).. (-19.20 = -19.82 +   0.61)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,712,358 – 3,712,456
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 69.54
Mean single sequence MFE -25.86
Consensus MFE -9.82
Energy contribution -10.18
Covariance contribution 0.36
Combinations/Pair 1.12
Mean z-score -1.75
Structure conservation index 0.38
SVM decision value 0.03
SVM RNA-class probability 0.546764
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3712358 98 - 22407834
---CUUU---------AUUUCAGAUACUCCACCAGCGGU----------UGGAUAUUGCCGAGCCAAUCGCAGCAAAGGAACACGUGAGAACGCAGAUACAUCCGUGUCUGCACAAGAUC
---....---------.(((((.....(((....(((((----------(((...........))))))))......))).....)))))..((((((((....))))))))........ ( -27.50)
>DroSec_CAF1 174709 98 - 1
---CUUU---------AUUUUAGAUACUGCACCAGCGGU----------UGGAUAUUGCCGAGCCAAUCGCAGCAAAGGCACACGUGAGAACGCAGAUACAUCCGUGUCUGCACAGGAUC
---....---------......(((.((((((..(((((----------(((...........)))))))).((....))....))).....((((((((....)))))))).))).))) ( -30.40)
>DroSim_CAF1 183600 98 - 1
---CUUU---------AUUUUAGAUACUCCACCAGCGGU----------UGGAUAUUGCCGAGCCAAUCGCAGCAAAGCAACGCGUGAGAACGCAGAUACAUCCGUGUCUGCACAGGAUC
---....---------...........(((....(((((----------(((...........))))))))......((...((((....))))((((((....))))))))...))).. ( -28.50)
>DroEre_CAF1 187878 101 - 1
AACAAAU---------CUUUCAGAUAAACCGCCAACAAC----------UGGAUAUUGCAGAUCCAAACACAGGCAAUAACAACCUGAUAACGCAGAUACAUCCGUGUCUGCACAGGGUC
.....((---------(.....))).....(((......----------(((((.......)))))......)))........((((.....((((((((....)))))))).))))... ( -24.80)
>DroYak_CAF1 188270 101 - 1
AACAACU---------AUUUCAGAUACUCCACCCGCGAU----------UGGACAUUGAAGAGACAAUCGCAGGAAAGGAAAAACUGAGAACGCAGAUACAUCCGUGUUUGCACAGGAUU
.......---------.((((((....(((.((.(((((----------((.............))))))).))...)))....))))))..((((((((....))))))))........ ( -29.82)
>DroAna_CAF1 199195 116 - 1
---ACUAAACAAUACAUUUUUAGAUACUCA-GAAGAAAUCAAAACAUUACUGAUAUUGUCGAAAAAAGAAGAAAAAAAGAUACUGUGAUUUCGGUGAUAUAUCCCUGUCUGCACAGCGUU
---.............(((((.((((.(((-(.................))))...)))).)))))............((..(((((....(((.((....)).)))....)))))..)) ( -14.13)
>consensus
___AUUU_________AUUUCAGAUACUCCACCAGCGAU__________UGGAUAUUGCCGAGCCAAUCGCAGCAAAGGAAAACGUGAGAACGCAGAUACAUCCGUGUCUGCACAGGAUC
............................................................................................((((((((....))))))))........ ( -9.82 = -10.18 +   0.36)

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 10:01:35 2006