Locus 7008

Sequence ID 2L_DroMel_CAF1
Location 19,513,427 – 19,513,671
Length 244
Max. P 0.971336
window11175 window11176 window11177 window11178 window11179 window11180 window11181

overview

Window 5

Location 19,513,427 – 19,513,540
Length 113
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 89.17
Mean single sequence MFE -33.09
Consensus MFE -28.13
Energy contribution -27.80
Covariance contribution -0.33
Combinations/Pair 1.12
Mean z-score -2.54
Structure conservation index 0.85
SVM decision value 1.00
SVM RNA-class probability 0.897830
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19513427 113 - 22407834
---ACACACUUACAUACUUGCUACACUGGUAUGUGUGCAAGUAUAUGUGCAAAAGCUUCGCCGCACAGUGGAACUGUCCAAUGGUUCC-CAAAAAACCAAUGUCCUUGUCCAUAAGA
---..........((((((((.((((......)))))))))))).(((((............)))))(((((...(..((.(((((..-.....))))).))..)...))))).... ( -33.20)
>DroSec_CAF1 8676 117 - 1
CGCACACACUUACAUACUUGCUGCACUGGUAUGUGUGCGAGUAUGUGUGCAAAAGCUCCGUCGCACAGUGGAACUCUCCAAUUGUUCUUUAAAAAAGCAAUGUCCUUGUCUAUAUGA
.((...((((.((((((((((.((((......))))))))))))))((((............))))))))((((.........)))).........))................... ( -31.20)
>DroSim_CAF1 8170 117 - 1
CGCACACACUUACAUACUCGCUGCACUAGUAUGUGUGCGAGUAUGUGUGCAAAAGCUCGGUCGCACAGUGGAACUCUCCAAUUGUUCUUUAAAAAAGCAAUGUCCUUGUCCAUAUGA
.(((((((......(((((((.((((......))))))))))))))))))....((......))...(((((........((((((.........)))))).......))))).... ( -34.86)
>consensus
CGCACACACUUACAUACUUGCUGCACUGGUAUGUGUGCGAGUAUGUGUGCAAAAGCUCCGUCGCACAGUGGAACUCUCCAAUUGUUCUUUAAAAAAGCAAUGUCCUUGUCCAUAUGA
......((((.((((((((((.((((......))))))))))))))((((............))))))))((((.........)))).............................. (-28.13 = -27.80 +  -0.33)

alignment

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secondary structure

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Window 6

Location 19,513,463 – 19,513,577
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.71
Mean single sequence MFE -41.47
Consensus MFE -30.33
Energy contribution -30.23
Covariance contribution -0.10
Combinations/Pair 1.20
Mean z-score -3.65
Structure conservation index 0.73
SVM decision value 1.22
SVM RNA-class probability 0.932964
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19513463 114 + 22407834
UGGACAGUUCCACUGUGCGGCGAAGCUUUUGCACAUAUACUUGCACACAUACCAGUGUAGCAAGUAUGUAAGUGUGU------GAGUGCUUUCUCGCAGAGAGAGAAAAUAAAGAAAACG
((((....))))((.(((((.(((((.((..(((((((((((((((((......)))).))))))))....))))).------.)).))))).))))).))................... ( -42.50)
>DroSec_CAF1 8713 118 + 1
UGGAGAGUUCCACUGUGCGACGGAGCUUUUGCACACAUACUCGCACACAUACCAGUGCAGCAAGUAUGUAAGUGUGUGCGUGUGAGUGCUCUCUUGCAGA--GAGAAAAUAAAGAAAACG
..(((((((((..........)))))))))((((.(((((.(((((((.(((..((((.....))))))).))))))).))))).))))((((((...))--)))).............. ( -41.80)
>DroSim_CAF1 8207 118 + 1
UGGAGAGUUCCACUGUGCGACCGAGCUUUUGCACACAUACUCGCACACAUACUAGUGCAGCGAGUAUGUAAGUGUGUGCGUGUAAGUGCUCUCUUACAGA--GAGAAAAUAAAGAAAUCG
(((......)))(((((.((..((((.(((((((((((((((((.(((......)))..))))))))))..((....))))))))).)))))).))))).--.................. ( -40.10)
>consensus
UGGAGAGUUCCACUGUGCGACGGAGCUUUUGCACACAUACUCGCACACAUACCAGUGCAGCAAGUAUGUAAGUGUGUGCGUGUGAGUGCUCUCUUGCAGA__GAGAAAAUAAAGAAAACG
((((....))))(((((.((..((((.(((((((((((((((((.(((......)))..))))))))))..........))))))).)))))).)))))..................... (-30.33 = -30.23 +  -0.10)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,513,463 – 19,513,577
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.71
Mean single sequence MFE -34.30
Consensus MFE -30.93
Energy contribution -30.49
Covariance contribution -0.44
Combinations/Pair 1.17
Mean z-score -2.67
Structure conservation index 0.90
SVM decision value 1.67
SVM RNA-class probability 0.971336
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19513463 114 - 22407834
CGUUUUCUUUAUUUUCUCUCUCUGCGAGAAAGCACUC------ACACACUUACAUACUUGCUACACUGGUAUGUGUGCAAGUAUAUGUGCAAAAGCUUCGCCGCACAGUGGAACUGUCCA
.((((......(((((((.......))))))).....------.(((......((((((((.((((......)))))))))))).(((((............))))))))))))...... ( -30.00)
>DroSec_CAF1 8713 118 - 1
CGUUUUCUUUAUUUUCUC--UCUGCAAGAGAGCACUCACACGCACACACUUACAUACUUGCUGCACUGGUAUGUGUGCGAGUAUGUGUGCAAAAGCUCCGUCGCACAGUGGAACUCUCCA
.((((..........(((--((.....)))))......((((((((((......(((((((.((((......))))))))))))))))))....((......))...)))))))...... ( -35.00)
>DroSim_CAF1 8207 118 - 1
CGAUUUCUUUAUUUUCUC--UCUGUAAGAGAGCACUUACACGCACACACUUACAUACUCGCUGCACUAGUAUGUGUGCGAGUAUGUGUGCAAAAGCUCGGUCGCACAGUGGAACUCUCCA
.((.(((........(((--((.....)))))......((((((((((......(((((((.((((......))))))))))))))))))....((......))...)))))).)).... ( -37.90)
>consensus
CGUUUUCUUUAUUUUCUC__UCUGCAAGAGAGCACUCACACGCACACACUUACAUACUUGCUGCACUGGUAUGUGUGCGAGUAUGUGUGCAAAAGCUCCGUCGCACAGUGGAACUCUCCA
.((((((((................)))))))).............((((.((((((((((.((((......))))))))))))))((((............)))))))).......... (-30.93 = -30.49 +  -0.44)

alignment

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secondary structure

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Window 8

Location 19,513,503 – 19,513,614
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.52
Mean single sequence MFE -27.63
Consensus MFE -16.76
Energy contribution -17.43
Covariance contribution 0.67
Combinations/Pair 1.11
Mean z-score -2.16
Structure conservation index 0.61
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19513503 111 + 22407834
UUGCACACAUACCAGUGUAGCAAGUAUGUAAGUGUGU------GAGUGCUUUCUCGCAGAGAGAGAAAAUAAAGAAAACGUAUCGUUAUCGUUAUCGCAAAACCAACACACAUAUA---U
((((((((......)))).))))..(((((.((((((------...(((((((((.....)))))).......((.((((((....)).)))).)))))......)))))).))))---) ( -30.20)
>DroSec_CAF1 8753 114 + 1
UCGCACACAUACCAGUGCAGCAAGUAUGUAAGUGUGUGCGUGUGAGUGCUCUCUUGCAGA--GAGAAAAUAAAGAAAACGUAUCGUUAUCGUUAUCGUAAAAUCAACA----UAUAAAUA
..((((((((....((((.....))))....))))))))((((((.(((((((((...))--)))).......((.((((((....)).)))).)))))...)).)))----)....... ( -28.90)
>DroSim_CAF1 8247 118 + 1
UCGCACACAUACUAGUGCAGCGAGUAUGUAAGUGUGUGCGUGUAAGUGCUCUCUUACAGA--GAGAAAAUAAAGAAAUCGUAUCGUUAUCGUUAUCGUAAAAUCAAAAUAAAUAUAGAUA
.(((((((((....((((.....))))....)))))))))((((....(((((.....))--)))........((...((((.((....)).)).)).....))........)))).... ( -23.80)
>consensus
UCGCACACAUACCAGUGCAGCAAGUAUGUAAGUGUGUGCGUGUGAGUGCUCUCUUGCAGA__GAGAAAAUAAAGAAAACGUAUCGUUAUCGUUAUCGUAAAAUCAACA_A_AUAUA_AUA
.(((((((((....((((.....))))....)))))))))......(((..((((.......)))).......((.((((((....)).)))).)))))..................... (-16.76 = -17.43 +   0.67)

alignment

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secondary structure

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Window 9

Location 19,513,540 – 19,513,647
Length 107
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 82.44
Mean single sequence MFE -23.66
Consensus MFE -17.21
Energy contribution -17.56
Covariance contribution 0.34
Combinations/Pair 1.16
Mean z-score -2.42
Structure conservation index 0.73
SVM decision value 1.23
SVM RNA-class probability 0.933929
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19513540 107 - 22407834
ACAAUCGUUAUCAAAAAACCAGAUAUGCUUGUAA---UAUAUGUGUGUUGGUUUUGCGAUAACGAUAACGAUACGUUUUCUUUAUUUUCUCUCUCUGCGAGAAAGCACUC---
...(((((((((..(((((((.((((((......---.....)))))))))))))..)))))))))........((((((((................))))))))....--- ( -27.59)
>DroSec_CAF1 8793 106 - 1
GCAAUCGUUAUCAAAAAG-CAGAUAUGGAUAUAUAUUUAUA----UGUUGAUUUUACGAUAACGAUAACGAUACGUUUUCUUUAUUUUCUC--UCUGCAAGAGAGCACUCACA
((.(((((((((..((((-(((((((((((....)))))))----).))).))))..))))))))).....................((((--(.....)))))))....... ( -22.00)
>DroSim_CAF1 8287 110 - 1
GCUAUCGUUAUCAAAAAA-CAGAUAUGCAUAUAUAUCUAUAUUUAUUUUGAUUUUACGAUAACGAUAACGAUACGAUUUCUUUAUUUUCUC--UCUGUAAGAGAGCACUUACA
((((((((((((......-.(((((((....)))))))....(((((.((....)).))))).))))))))))..............((((--(.....)))))))....... ( -21.40)
>consensus
GCAAUCGUUAUCAAAAAA_CAGAUAUGCAUAUAUAU_UAUAU_U_UGUUGAUUUUACGAUAACGAUAACGAUACGUUUUCUUUAUUUUCUC__UCUGCAAGAGAGCACUCACA
...(((((((((..((((...((((((..((((....))))..))))))..))))..)))))))))........((((((((................))))))))....... (-17.21 = -17.56 +   0.34)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,513,577 – 19,513,671
Length 94
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 85.17
Mean single sequence MFE -17.59
Consensus MFE -10.32
Energy contribution -10.76
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -2.79
Structure conservation index 0.59
SVM decision value 0.08
SVM RNA-class probability 0.572921
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19513577 94 + 22407834
UAUCGUUAUCGUUAUCGCAAAACCAACACACAUAUA---UUACAAGCAUAUCUGGUUUUUUGAUAACGAUUGUCACAUAAAGUUAUUGCUCCUUAAC
....(..((((((((((.(((((((...........---.............))))))).))))))))))...).......((((........)))) ( -17.36)
>DroSec_CAF1 8831 92 + 1
UAUCGUUAUCGUUAUCGUAAAAUCAACA----UAUAAAUAUAUAUCCAUAUCUG-CUUUUUGAUAACGAUUGCCACAUAAAGUUUUUGCUCUUUAAC
....((.((((((((((.((((.((..(----(((..((....))..)))).))-.)))))))))))))).))....(((((........))))).. ( -13.50)
>DroSim_CAF1 8325 96 + 1
UAUCGUUAUCGUUAUCGUAAAAUCAAAAUAAAUAUAGAUAUAUAUGCAUAUCUG-UUUUUUGAUAACGAUAGCCACAUAAAGUUAUUGCUCUUUAAC
....(((((((((((((.((((...........((((((((......)))))))-))))))))))))))))))....(((((........))))).. ( -21.90)
>consensus
UAUCGUUAUCGUUAUCGUAAAAUCAACA_A_AUAUA_AUAUAUAUGCAUAUCUG_UUUUUUGAUAACGAUUGCCACAUAAAGUUAUUGCUCUUUAAC
....((.((((((((((.((((.((...........................)).)))).)))))))))).))....(((((........))))).. (-10.32 = -10.76 +   0.45)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,513,577 – 19,513,671
Length 94
Sequences 3
Columns 97
Reading direction reverse
Mean pairwise identity 85.17
Mean single sequence MFE -20.33
Consensus MFE -15.12
Energy contribution -15.13
Covariance contribution 0.01
Combinations/Pair 1.16
Mean z-score -2.37
Structure conservation index 0.74
SVM decision value 0.70
SVM RNA-class probability 0.828135
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19513577 94 - 22407834
GUUAAGGAGCAAUAACUUUAUGUGACAAUCGUUAUCAAAAAACCAGAUAUGCUUGUAA---UAUAUGUGUGUUGGUUUUGCGAUAACGAUAACGAUA
((((.((((......))))...)))).(((((((((..(((((((.((((((......---.....)))))))))))))..)))))))))....... ( -24.60)
>DroSec_CAF1 8831 92 - 1
GUUAAAGAGCAAAAACUUUAUGUGGCAAUCGUUAUCAAAAAG-CAGAUAUGGAUAUAUAUUUAUA----UGUUGAUUUUACGAUAACGAUAACGAUA
((((....((....((.....)).))..((((((((..((((-(((((((((((....)))))))----).))).))))..)))))))))))).... ( -18.50)
>DroSim_CAF1 8325 96 - 1
GUUAAAGAGCAAUAACUUUAUGUGGCUAUCGUUAUCAAAAAA-CAGAUAUGCAUAUAUAUCUAUAUUUAUUUUGAUUUUACGAUAACGAUAACGAUA
..(((((........)))))(((.(.((((((((((..((((-((((.(((.(((((....))))).))))))).))))..)))))))))).).))) ( -17.90)
>consensus
GUUAAAGAGCAAUAACUUUAUGUGGCAAUCGUUAUCAAAAAA_CAGAUAUGCAUAUAUAU_UAUAU_U_UGUUGAUUUUACGAUAACGAUAACGAUA
((((.((((......))))...)))).(((((((((..((((...((((((..((((....))))..))))))..))))..)))))))))....... (-15.12 = -15.13 +   0.01)

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 12:25:10 2006