Locus 1029

Sequence ID 2L_DroMel_CAF1
Location 2,913,987 – 2,914,211
Length 224
Max. P 0.647238
window1654 window1655 window1656

overview

Window 4

Location 2,913,987 – 2,914,100
Length 113
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 84.69
Mean single sequence MFE -28.15
Consensus MFE -23.29
Energy contribution -23.35
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.53
Structure conservation index 0.83
SVM decision value 0.21
SVM RNA-class probability 0.633209
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2913987 113 - 22407834
ACGCGGCGUAUGAGCAAUUUGCUCGCUCUCAAAGCGAAAAUGCGAGCACAUUUCGAAAUGCCAAGCGGAGCAUAUGCUGAAAUCUCUCCUCCAACGCGACACACCCCCCUCCC
.(((((((((((.((....(((((((..((.....))....)))))))((((....))))....))....))))))).((....))........))))............... ( -28.00)
>DroSec_CAF1 32491 96 - 1
ACGCGGCGUAUGAGCAAUUUGCUCGCUCUCAAAGCGAAAAUGCGAGCACAUUUCGAAAUGCCAAGAGGAGCAUAUGCUGAAAUCUCUGCCGCAU-----------------CC
..(((((((((..(.(((.(((((((..((.....))....))))))).))).)...))))..((((((((....)))....))))))))))..-----------------.. ( -32.50)
>DroSim_CAF1 33105 96 - 1
ACGCGGCGUAUGAGCAAUUUGCCCGCUCUCAAAGCGAAAAUGCGAGCACAUUUCGGAAUGCCAAGCGGAGCAUAUGCUGAAAUCUCUGCCCCAU-----------------CC
..((((.(..(.((((...((((((((..((...(((((.((....))..)))))...))...))))).)))..)))).)...).)))).....-----------------.. ( -25.20)
>DroYak_CAF1 33447 92 - 1
ACGCGGCGUAUGAGCAAUUUGCUCGCUCUCAAAGCGAAAAUGUGAGCACAUUUCGAAAUGCCAAGCGGAGCAUAUGCUGAAAUCUGA----AAU-----------------CU
...((((((((((((.....))))(((((.....(((((.(((....))))))))....((...)))))))))))))))........----...-----------------.. ( -26.90)
>consensus
ACGCGGCGUAUGAGCAAUUUGCUCGCUCUCAAAGCGAAAAUGCGAGCACAUUUCGAAAUGCCAAGCGGAGCAUAUGCUGAAAUCUCUGCCCCAU_________________CC
...(((((((((..(....(((((((..((.....))....)))))))((((....)))).......)..))))))))).................................. (-23.29 = -23.35 +   0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,914,100 – 2,914,211
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.89
Mean single sequence MFE -37.76
Consensus MFE -27.63
Energy contribution -27.51
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.71
Structure conservation index 0.73
SVM decision value 0.20
SVM RNA-class probability 0.629315
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2914100 111 + 22407834
UGGGCGCCAGAUGCGGGCGCCAAAGGACGACGACGAGGACGACGACGGUGAAGAAA-----GAACGUC----AGCUCAUAAUUACGGUUAUAUGAGCCGUGAUUAUUCGCUUUUGCCCCU
..((((((.......))))))..(((.((....)).((.(((.((((.........-----...))))----(((..((((((((((((.....))))))))))))..))).)))))))) ( -37.40)
>DroSec_CAF1 32587 112 + 1
UGGGCGCCAGAUGCGGGCGCCAAAGGACGACGACG---ACGACGACGGUGAAGAAA-----GCACGUCAGUCAGCUCAUAAUUAUGGUUAUAUGAGCCGUGAUUAUUCGACUUUGCCCCU
..((((((.......))))))...((.(((.(.((---(.(((((((((.......-----)).)))).))).....((((((((((((.....))))))))))))))).).)))))... ( -38.00)
>DroSim_CAF1 33201 112 + 1
UGGGCGCCAGAUGCGGGUGCCAAAGGACGACGACG---ACGACGACGGUGAAGAAA-----GCACGUCAGUCAGCUCAUAAUUAUGGUUAUAUGAGCCGUGAUUAUUCGCUUUUGCCCCU
..((((((.......))))))...((.(((.....---..(((((((((.......-----)).)))).)))(((..((((((((((((.....))))))))))))..))).)))))... ( -36.60)
>DroEre_CAF1 33433 99 + 1
UGGGCGCGAGAUGCGGGCGAAAAAGGACGCCG------------ACGGUGAAGAAG-----GCACGUC----GGCUCAUAAUUAUGGUUAUAUGAGCCGUGAUUAUUCGCUUUUGCCCCU
.(((.((((((.((((.........((.((((------------(((((.......-----)).))))----)))))((((((((((((.....))))))))))))))))))))))))). ( -42.50)
>DroYak_CAF1 33539 107 + 1
UGGGCGCGAGAUGCGGGCGAAAAAGGACGACGACG---------ACGAUGAAGAAGAAAGCGCACGUC----AGCUCAUAAUUAUGGUUAUAUGAGCCGUGAUUAUUCGCUUUUGCCCCU
.(((.((((((.((((((......(.....)...(---------(((.((............))))))----.))))((((((((((((.....))))))))))))..))))))))))). ( -34.30)
>consensus
UGGGCGCCAGAUGCGGGCGCCAAAGGACGACGACG___ACGACGACGGUGAAGAAA_____GCACGUC____AGCUCAUAAUUAUGGUUAUAUGAGCCGUGAUUAUUCGCUUUUGCCCCU
.(((.((.(((.((((((.......((((...................................)))).....))))((((((((((((.....))))))))))))..)).)))))))). (-27.63 = -27.51 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,914,100 – 2,914,211
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.89
Mean single sequence MFE -34.74
Consensus MFE -22.53
Energy contribution -22.77
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.13
Structure conservation index 0.65
SVM decision value 0.24
SVM RNA-class probability 0.647238
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2914100 111 - 22407834
AGGGGCAAAAGCGAAUAAUCACGGCUCAUAUAACCGUAAUUAUGAGCU----GACGUUC-----UUUCUUCACCGUCGUCGUCCUCGUCGUCGUCCUUUGGCGCCCGCAUCUGGCGCCCA
((((((......((((.....(((((((((..........))))))))----)..))))-----..........(.((.((....)).)).))))))).((((((.......)))))).. ( -34.90)
>DroSec_CAF1 32587 112 - 1
AGGGGCAAAGUCGAAUAAUCACGGCUCAUAUAACCAUAAUUAUGAGCUGACUGACGUGC-----UUUCUUCACCGUCGUCGU---CGUCGUCGUCCUUUGGCGCCCGCAUCUGGCGCCCA
((((((...(.(((........((((((((..........))))))))(((.((((((.-----......)).))))))).)---)).)...)))))).((((((.......)))))).. ( -38.20)
>DroSim_CAF1 33201 112 - 1
AGGGGCAAAAGCGAAUAAUCACGGCUCAUAUAACCAUAAUUAUGAGCUGACUGACGUGC-----UUUCUUCACCGUCGUCGU---CGUCGUCGUCCUUUGGCACCCGCAUCUGGCGCCCA
.(((((....(((........(((((((((..........)))))))))......((((-----(.....(..((.((....---)).))..)......))))).))).....)).))). ( -33.70)
>DroEre_CAF1 33433 99 - 1
AGGGGCAAAAGCGAAUAAUCACGGCUCAUAUAACCAUAAUUAUGAGCC----GACGUGC-----CUUCUUCACCGU------------CGGCGUCCUUUUUCGCCCGCAUCUCGCGCCCA
..((((....((((.......(((((((((..........))))))))----)......-----..........((------------.((((........)))).))...)))))))). ( -34.80)
>DroYak_CAF1 33539 107 - 1
AGGGGCAAAAGCGAAUAAUCACGGCUCAUAUAACCAUAAUUAUGAGCU----GACGUGCGCUUUCUUCUUCAUCGU---------CGUCGUCGUCCUUUUUCGCCCGCAUCUCGCGCCCA
..((((....(((((.((..((((((((((..........))))))))----((((.((((.............).---------)))))))))..)).)))))..((.....)))))). ( -32.12)
>consensus
AGGGGCAAAAGCGAAUAAUCACGGCUCAUAUAACCAUAAUUAUGAGCU____GACGUGC_____UUUCUUCACCGUCGUCGU___CGUCGUCGUCCUUUGGCGCCCGCAUCUGGCGCCCA
..((((....(((.........((((((((..........))))))))....((((...................................))))......)))..((.....)))))). (-22.53 = -22.77 +   0.24)

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 09:51:31 2006