Locus 5642

Sequence ID 3L_DroMel_CAF1
Location 15,492,507 – 15,492,784
Length 277
Max. P 0.926623
window8916 window8917 window8918 window8919 window8920

overview

Window 6

Location 15,492,507 – 15,492,624
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.15
Mean single sequence MFE -39.81
Consensus MFE -29.75
Energy contribution -31.62
Covariance contribution 1.88
Combinations/Pair 1.06
Mean z-score -1.50
Structure conservation index 0.75
SVM decision value 0.08
SVM RNA-class probability 0.573277
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15492507 117 - 23771897
CUGCGAUGGCGAUGAUUCCUACUACUGCAAUGGGGAUUGUCGUGAGGCCGUGGAGUGUUAUACCAAUGUGGUUACCACA---CCGGUUACCACAUUAAGACCCAUAGGAACCUCUACGGA
......(.((((..(((((((.........)))))))..)))).)..((((((((.(((.....((((((((.(((...---..))).))))))))....((....))))))))))))). ( -44.50)
>DroSec_CAF1 33724 120 - 1
CUGCGAUGGCGAUGACUCCUACUACUGCAAUGGGGAUUGUCGUGAGCCCGUGGAGUGUCAUACCAAUGUGGUUACCACACCAUCGGUUACCACCUUAAGACCCAUAGGAACCUCUACGGA
..((....((((..(..((((.........))))..)..))))..))((((((((.((.........(((((.(((........))).))))).......((....)).)))))))))). ( -36.80)
>DroSim_CAF1 35750 120 - 1
CUGCGAUGGCGAUGAUUCCUACUACUGCAAUGGGGAUUGUCGUGAGCCCGUGGAGUGUCAUACCAAUGUGGUAACCAGACCACCGGUUACCACCUUAAGACCCAUAGGAACCUCUACGGA
..((....((((..(((((((.........)))))))..))))..))((((((((.((.........(((((((((........))))))))).......((....)).)))))))))). ( -43.80)
>DroYak_CAF1 116124 117 - 1
CUGCGAUGGCGAUGAUUCCUACUACUGCAAUGGGGAUUGCCGCGAGGCGGUCGAGUGUUACACCAAUGUGGUUACCACG---CCAGCUACCACUUUACGGCCUACAGUAGCCACUACGAA
((((..(.(((..((((((((.........))))))))..))).).))))(((((((((((......((((...))))(---((..............))).....)))).)))).))). ( -34.14)
>consensus
CUGCGAUGGCGAUGAUUCCUACUACUGCAAUGGGGAUUGUCGUGAGCCCGUGGAGUGUCAUACCAAUGUGGUUACCACA___CCGGUUACCACCUUAAGACCCAUAGGAACCUCUACGGA
......(.(((((((((((((.........))))))))))))).)..((((((((.((.........(((((.(((........))).))))).......((....)).)))))))))). (-29.75 = -31.62 +   1.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,492,545 – 15,492,664
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.35
Mean single sequence MFE -31.91
Consensus MFE -24.39
Energy contribution -24.20
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -1.68
Structure conservation index 0.76
SVM decision value -0.04
SVM RNA-class probability 0.515178
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15492545 119 + 23771897
-UGUGGUAACCACAUUGGUAUAACACUCCACGGCCUCACGACAAUCCCCAUUGCAGUAGUAGGAAUCAUCGCCAUCGCAGUGAACAAACUCACUGCACUCCUGAUUCUCAUUGGUCACCU
-.((((..(((.....)))........))))((((..((..((((....))))..))(((..((((((........(((((((......))))))).....))))))..))))))).... ( -29.52)
>DroSec_CAF1 33764 120 + 1
GUGUGGUAACCACAUUGGUAUGACACUCCACGGGCUCACGACAAUCCCCAUUGCAGUAGUAGGAGUCAUCGCCAUCGCAGUGAACAAACUCACUGCACUCCUGAUUCUCAUUAGUCACCU
((((((...))))))(((((((((..(((....(((.((..((((....))))..))))).)))))))).))))..(((((((......))))))).....(((((......)))))... ( -33.60)
>DroSim_CAF1 35790 120 + 1
GUCUGGUUACCACAUUGGUAUGACACUCCACGGGCUCACGACAAUCCCCAUUGCAGUAGUAGGAAUCAUCGCCAUCGCAGUGAACAAACUCACUGCACUCCUGAUUCUCAUUAGUCACCU
....(((((((.....)))).(((.......(((............))).......((((..((((((........(((((((......))))))).....))))))..)))))))))). ( -29.32)
>DroYak_CAF1 116162 119 + 1
-CGUGGUAACCACAUUGGUGUAACACUCGACCGCCUCGCGGCAAUCCCCAUUGCAGUAGUAGGAAUCAUCGCCAUCGCAGUGAACGAAUUCACUGCACUCCUGGUUCUCGUUGGUCACCU
-.(((...(((.....)))....)))..(((((((....)))...........(((.(((.((........))...((((((((....))))))))))).))).........)))).... ( -35.20)
>consensus
_UGUGGUAACCACAUUGGUAUAACACUCCACGGCCUCACGACAAUCCCCAUUGCAGUAGUAGGAAUCAUCGCCAUCGCAGUGAACAAACUCACUGCACUCCUGAUUCUCAUUAGUCACCU
....(((.(((.....)))....................(((...........(((.(((.((........))...(((((((......)))))))))).)))..........)))))). (-24.39 = -24.20 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,492,545 – 15,492,664
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.35
Mean single sequence MFE -41.86
Consensus MFE -37.06
Energy contribution -37.94
Covariance contribution 0.87
Combinations/Pair 1.10
Mean z-score -1.98
Structure conservation index 0.89
SVM decision value 1.18
SVM RNA-class probability 0.926623
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15492545 119 - 23771897
AGGUGACCAAUGAGAAUCAGGAGUGCAGUGAGUUUGUUCACUGCGAUGGCGAUGAUUCCUACUACUGCAAUGGGGAUUGUCGUGAGGCCGUGGAGUGUUAUACCAAUGUGGUUACCACA-
.((((((((((((.(.((.((..(((((((((....))))))))).(.((((..(((((((.........)))))))..)))).)..))...)).).)))).......))))))))...- ( -42.11)
>DroSec_CAF1 33764 120 - 1
AGGUGACUAAUGAGAAUCAGGAGUGCAGUGAGUUUGUUCACUGCGAUGGCGAUGACUCCUACUACUGCAAUGGGGAUUGUCGUGAGCCCGUGGAGUGUCAUACCAAUGUGGUUACCACAC
.((((((((((((.(.((.((.((((((((((....))))))))..(.((((..(..((((.........))))..)..)))).)))))...)).).)))).......)))))))).... ( -40.01)
>DroSim_CAF1 35790 120 - 1
AGGUGACUAAUGAGAAUCAGGAGUGCAGUGAGUUUGUUCACUGCGAUGGCGAUGAUUCCUACUACUGCAAUGGGGAUUGUCGUGAGCCCGUGGAGUGUCAUACCAAUGUGGUAACCAGAC
.(((......(((.(.((.((.((((((((((....))))))))..(.((((..(((((((.........)))))))..)))).)))))...)).).)))((((.....))))))).... ( -39.80)
>DroYak_CAF1 116162 119 - 1
AGGUGACCAACGAGAACCAGGAGUGCAGUGAAUUCGUUCACUGCGAUGGCGAUGAUUCCUACUACUGCAAUGGGGAUUGCCGCGAGGCGGUCGAGUGUUACACCAAUGUGGUUACCACG-
.(((((((..........((((((((((((((....))))))))(....)....))))))......(((.(((.(((((((....)))))))..(.....).))).))))))))))...- ( -45.50)
>consensus
AGGUGACCAAUGAGAAUCAGGAGUGCAGUGAGUUUGUUCACUGCGAUGGCGAUGAUUCCUACUACUGCAAUGGGGAUUGUCGUGAGCCCGUGGAGUGUCAUACCAAUGUGGUUACCACA_
.((((((((((((.(.((.((..(((((((((....))))))))).(.(((((((((((((.........))))))))))))).)..))...)).).)))).......)))))))).... (-37.06 = -37.94 +   0.87)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,492,584 – 15,492,704
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.56
Mean single sequence MFE -25.98
Consensus MFE -18.41
Energy contribution -17.59
Covariance contribution -0.81
Combinations/Pair 1.20
Mean z-score -2.03
Structure conservation index 0.71
SVM decision value 1.06
SVM RNA-class probability 0.908924
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15492584 120 + 23771897
ACAAUCCCCAUUGCAGUAGUAGGAAUCAUCGCCAUCGCAGUGAACAAACUCACUGCACUCCUGAUUCUCAUUGGUCACCUUAUUGAUGAUCACACCUUUGCAUUCCUCGAGAAAAACCGC
...........(((((..((.(..((((((......(((((((......))))))).....(((((......))))).......))))))..)))..))))).................. ( -27.20)
>DroSec_CAF1 33804 120 + 1
ACAAUCCCCAUUGCAGUAGUAGGAGUCAUCGCCAUCGCAGUGAACAAACUCACUGCACUCCUGAUUCUCAUUAGUCACCUUAUUGAUGAUCACACCCUUGCAUUCCUCGAGAAAAACCGC
...........(((((..((.(..((((((......(((((((......))))))).....(((((......))))).......))))))..)))..))))).................. ( -26.80)
>DroSim_CAF1 35830 120 + 1
ACAAUCCCCAUUGCAGUAGUAGGAAUCAUCGCCAUCGCAGUGAACAAACUCACUGCACUCCUGAUUCUCAUUAGUCACCUUANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
...........((.(.((((..((((((........(((((((......))))))).....))))))..)))).)))........................................... ( -18.62)
>DroYak_CAF1 116201 120 + 1
GCAAUCCCCAUUGCAGUAGUAGGAAUCAUCGCCAUCGCAGUGAACGAAUUCACUGCACUCCUGGUUCUCGUUGGUCACCUUAUUGAUGAUCACACCUUUGCAUUCCUCGAGGAAAACCGC
((.........(((((..((.(..((((((......((((((((....))))))))......(((((.....))..))).....))))))..)))..)))))((((....))))....)) ( -31.30)
>consensus
ACAAUCCCCAUUGCAGUAGUAGGAAUCAUCGCCAUCGCAGUGAACAAACUCACUGCACUCCUGAUUCUCAUUAGUCACCUUAUUGAUGAUCACACCUUUGCAUUCCUCGAGAAAAACCGC
...........((.(.((((..((((((........(((((((......))))))).....))))))..)))).)))........................................... (-18.41 = -17.59 +  -0.81)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,492,664 – 15,492,784
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.30
Mean single sequence MFE -41.03
Consensus MFE -38.51
Energy contribution -38.30
Covariance contribution -0.21
Combinations/Pair 1.11
Mean z-score -2.02
Structure conservation index 0.94
SVM decision value 0.87
SVM RNA-class probability 0.871560
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15492664 120 - 23771897
UGCAGAAAGCCUAUUGAAUGUGGCAAUUGUUGAUAGUCUUGGCCUGCCUGUUACCUGGCUACCUCUGGGUGCAGGUGCAGGCGGUUUUUCUCGAGGAAUGCAAAGGUGUGAUCAUCAAUA
........(((..........)))...(((((((.(((...((((((((((.(((((.(.(((....))))))))))))))).((.((((....)))).))..))))..))).))))))) ( -40.20)
>DroSec_CAF1 33884 118 - 1
U--UGAAAGCCUAUUGAAUGUGGCAAUUGUUGAUAGUCUUGGCCUGCCUGUUACCUGGCUACCUAUGGUUGCAGGUGCAGGCGGUUUUUCUCGAGGAAUGCAAGGGUGUGAUCAUCAAUA
.--.....(((..........)))...(((((((.(((...((((((((((.(((((.(.(((...))).)))))))))))).((.((((....)))).))..))))..))).))))))) ( -38.90)
>DroYak_CAF1 116281 118 - 1
U--UGAAAGCCUAUUGAAUGUGGCAAUUGUUGUUAGUCUUGGCCUGCCUGCUACCUGGUUGCCUCCGGGUGCAGGUGCAGGCGGUUUUCCUCGAGGAAUGCAAAGGUGUGAUCAUCAAUA
.--........((((((..((.(((....((((...(((((((((((((((.((((((......))))))))))..))))))((....)).)))))...))))...))).))..)))))) ( -44.00)
>consensus
U__UGAAAGCCUAUUGAAUGUGGCAAUUGUUGAUAGUCUUGGCCUGCCUGUUACCUGGCUACCUCUGGGUGCAGGUGCAGGCGGUUUUUCUCGAGGAAUGCAAAGGUGUGAUCAUCAAUA
........(((..........)))...(((((((.(((...((((((((((.(((((..((((....))))))))))))))).((.((((....)))).))..))))..))).))))))) (-38.51 = -38.30 +  -0.21)

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 11:55:27 2006