Locus 3943

Sequence ID 2R_DroMel_CAF1
Location 13,018,486 – 13,018,775
Length 289
Max. P 0.962812
window6366 window6367 window6368 window6369

overview

Window 6

Location 13,018,486 – 13,018,599
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.72
Mean single sequence MFE -30.03
Consensus MFE -20.97
Energy contribution -20.37
Covariance contribution -0.61
Combinations/Pair 1.24
Mean z-score -2.31
Structure conservation index 0.70
SVM decision value 0.01
SVM RNA-class probability 0.539351
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13018486 113 + 20766785
--AAAACAAGGAAAGGCAAAAGAUUCUGGC--G---AAACGAGUGAUGCAUUCCCAUCAUUAUUUCCGAAUCAGAGUCGCAGUCAUUAAGUCUGCUCGAUGUUUUUGCAUCGAUUCUUCG
--......(((((........(((((((.(--(---.....(((((((......))))))).....))...)))))))((((.(.....).))))(((((((....)))))))))))).. ( -32.10)
>DroSec_CAF1 32144 113 + 1
--AAAACAAGGAAAGGCAUAAGAUUCUGGU--G---AAACGAGUAAUGCAUUCCCAUCAUUAUUUCCGAAUCAGAGUCGCAGUCAUUAAGUCUACUCGAUGUUUUUGCAUCGAUUCUUCA
--......(((((.(((....(((((((((--.---....((((((((.((....))))))))))....)))))))))...)))...........(((((((....)))))))))))).. ( -28.10)
>DroSim_CAF1 28502 115 + 1
AUAAAACAAGGAAAGGCAUAAGAUUCUGGU--G---AAACGAGUAAUGCAUUCCCAUCAUUAUUUCCGAAUCAGAGUCGCAGUCAUUAAGUCUGCUCGAUGUUUUUGCAUCGAUUCUUCA
........(((((........(((((((((--.---....((((((((.((....))))))))))....)))))))))((((.(.....).))))(((((((....)))))))))))).. ( -31.00)
>DroEre_CAF1 28007 112 + 1
---AAUCAAGGAAAGGAAAGAGAUUCUGGG--G---AAACGAGUGAUGCAUUCCCAUCAUUAUUUCCGAAUCAGAGUCGCAGUCAUUAAGUCUGCUCGGUGUUUUUGCAUCGAUUCUUCA
---.......(((.(((....(((((((((--(---(((..(((((((......))))))).)))))...))))))))((((.(.....).))))(((((((....))))))))))))). ( -35.20)
>DroYak_CAF1 28839 111 + 1
---AAACAAGGAAAGGAAAAAGAUUCUGGC--G---AAACGAGUGAUGCAUUCCCAUCAUUAUUUCCGAAUCAGAGUUGCAGUCAUUAAGUCUGCUCGGUGUUUUUGCAUCGAUUCUUC-
---..........(((((...(((((((.(--(---.....(((((((......))))))).....))...)))))))((((.(.....).))))(((((((....)))))))))))).- ( -28.70)
>DroPer_CAF1 27087 106 + 1
--AAGA-----------CCCAGACUCUGGCCCGAACUAAUGAAUAAUGCAUUCCCAUCAUUAUAUCUGAAUCAAAGUCUCGGCCAUUAAGUCUGUUCGGUGCUUUUGCAUCAAUUUUUU-
--..((-----------..((((((.(((((.(((((..(((((((((.((....)))))))).......))).))).)))))))...)))))).))(((((....)))))........- ( -25.11)
>consensus
__AAAACAAGGAAAGGCAAAAGAUUCUGGC__G___AAACGAGUAAUGCAUUCCCAUCAUUAUUUCCGAAUCAGAGUCGCAGUCAUUAAGUCUGCUCGAUGUUUUUGCAUCGAUUCUUCA
.....................(((((.((...........((((((((.((....)))))))))))))))))((((((((((.(.....).))))..(((((....)))))))))))... (-20.97 = -20.37 +  -0.61)

alignment

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secondary structure

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Window 7

Location 13,018,599 – 13,018,710
Length 111
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 81.08
Mean single sequence MFE -30.00
Consensus MFE -15.60
Energy contribution -17.78
Covariance contribution 2.18
Combinations/Pair 1.12
Mean z-score -2.18
Structure conservation index 0.52
SVM decision value 0.42
SVM RNA-class probability 0.729182
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13018599 111 - 20766785
GAAUAUAAAGCCAGUUUGUUCGCUAUCGGGAACAGGAAUGGGAACAAUGCUGGUGGGUAAUCGAUGAGAAGAGAGCUCUCA--GCGAAGACUAGAGAGUGAAGACUCUGGACC
.........((((((((((((.(((((........).)))))))))).)))))).(((..(((.(((((.......)))))--.)))...((((((........))))))))) ( -32.80)
>DroSec_CAF1 32257 105 - 1
GAAAAUAAAGCCAGUUUGUUGGCCAUCAG------GAACGGGAACAAUGCUGGUGGGUAAUCGAUGAGAAGAGAGCUCUCA--GCGAAGACUGGAGAGUGAAGACUCCGGACC
..........(((((((.(((.(((((((------.(..(....)..).))))))).)))(((.(((((.......)))))--.)))))))))).((((....))))...... ( -32.10)
>DroSim_CAF1 28617 105 - 1
GAAAAUAAAGCCAGUUUGUUGGCCAUCAG------GAACGGGAACAAUGCUGGUGGGUAAUCGAUGAGAAGAGAGCUCUCA--GCGAAGACUGGAGAGUGAAGACUCUGGACC
..........(((((((.(((.(((((((------.(..(....)..).))))))).)))(((.(((((.......)))))--.))))))))))(((((....)))))..... ( -33.80)
>DroEre_CAF1 28119 92 - 1
-UAUAUAAAGCCAGUU----CGGCAUCGG------GAACGGGAACAACGCUGGUGGGUAAUCGAUGAGAAGAGAGCUCACU--GCGAAGACUGG------AAGAC--UGGACC
-.........((((((----((((.(((.------...)))......(((.(((((((..((........))..)))))))--)))..).))).------..)))--)))... ( -26.80)
>DroYak_CAF1 28950 96 - 1
-AAAAUAAAGCCAGUUUGUUUGGCAUCGG------GAAUGGGAACACUGCUGGUGGGUAAUCGAUGAGAAGAGAGCUCAGAGAGUGAAGACUCU------GAACC--UGGA--
-........(((((.....))))).((((------(..((((..(.((.((.((.(.....).)).)).)).)..)))).(((((....)))))------...))--))).-- ( -24.50)
>consensus
GAAAAUAAAGCCAGUUUGUUCGCCAUCGG______GAACGGGAACAAUGCUGGUGGGUAAUCGAUGAGAAGAGAGCUCUCA__GCGAAGACUGGAGAGUGAAGACUCUGGACC
.........((((((((((((....((........))....)))))).))))))((((..((........))..))))............((((((........))))))... (-15.60 = -17.78 +   2.18)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,018,670 – 13,018,775
Length 105
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 75.24
Mean single sequence MFE -10.20
Consensus MFE -8.12
Energy contribution -9.12
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.80
SVM decision value 1.54
SVM RNA-class probability 0.962812
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13018670 105 + 20766785
CAUUCCUGUUCCCGAUAGCGAACAAACUGGCUUUAUAUUCCUUAUUU-UUUUUUUUUUUUGUUUUUAUCAAUUUCCCUGUGCUUAUCCCAGUCGCCAUCACCAUUA
.............(((.((((.......(((................-................................)))........)))).)))....... (  -8.87)
>DroSec_CAF1 32328 100 + 1
CGUUC------CUGAUGGCCAACAAACUGGCUUUAUUUUCCUCCUUUUUUCUUUUUUUUUGUUUUUAUCAAUUUCCCUCUGCUUAUCCCAGUCGCCAUCACCAUUA
.....------.(((((((......(((((.........................................................))))).)))))))...... ( -11.12)
>DroEre_CAF1 28182 79 + 1
CGUUC------CCGAUGCCG----AACUGGCUUUAUAUA-----------------UAUUUUUUUUAUCAAUUUCCCUCUGCUUAUCCCAGUCGCCAUCACCAUUA
.....------..((((.((----(.((((.........-----------------...............................))))))).))))....... ( -10.60)
>consensus
CGUUC______CCGAUGGCGAACAAACUGGCUUUAUAUUCCU__UUU_UU_UUUUUUUUUGUUUUUAUCAAUUUCCCUCUGCUUAUCCCAGUCGCCAUCACCAUUA
.............(((((((.....(((((.........................................................))))))))))))....... ( -8.12 =  -9.12 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,018,670 – 13,018,775
Length 105
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 75.24
Mean single sequence MFE -14.50
Consensus MFE -11.06
Energy contribution -10.95
Covariance contribution -0.11
Combinations/Pair 1.15
Mean z-score -1.42
Structure conservation index 0.76
SVM decision value 0.92
SVM RNA-class probability 0.882671
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13018670 105 - 20766785
UAAUGGUGAUGGCGACUGGGAUAAGCACAGGGAAAUUGAUAAAAACAAAAAAAAAAAA-AAAUAAGGAAUAUAAAGCCAGUUUGUUCGCUAUCGGGAACAGGAAUG
.......((((((((.....((((((.(((.....)))....................-......((.........)).))))))))))))))(....)....... ( -15.20)
>DroSec_CAF1 32328 100 - 1
UAAUGGUGAUGGCGACUGGGAUAAGCAGAGGGAAAUUGAUAAAAACAAAAAAAAAGAAAAAAGGAGGAAAAUAAAGCCAGUUUGUUGGCCAUCAG------GAACG
......((((((((((((((.....).........(((.......)))............................)))))).....))))))).------..... ( -14.50)
>DroEre_CAF1 28182 79 - 1
UAAUGGUGAUGGCGACUGGGAUAAGCAGAGGGAAAUUGAUAAAAAAAAUA-----------------UAUAUAAAGCCAGUU----CGGCAUCGG------GAACG
.......((((.(((((((...............................-----------------.........)))).)----)).))))(.------...). ( -13.80)
>consensus
UAAUGGUGAUGGCGACUGGGAUAAGCAGAGGGAAAUUGAUAAAAACAAAAAAAAA_AA_AAA__AGGAAUAUAAAGCCAGUUUGUUCGCCAUCGG______GAACG
......(((((((((((((.........................................................)))))).....)))))))............ (-11.06 = -10.95 +  -0.11)

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 11:07:57 2006