Locus 5440

Sequence ID 3R_DroMel_CAF1
Location 14,353,408 – 14,353,571
Length 163
Max. P 0.994393
window8848 window8849 window8850 window8851 window8852 window8853

overview

Window 8

Location 14,353,408 – 14,353,498
Length 90
Sequences 4
Columns 90
Reading direction forward
Mean pairwise identity 83.83
Mean single sequence MFE -26.55
Consensus MFE -21.07
Energy contribution -21.70
Covariance contribution 0.63
Combinations/Pair 1.07
Mean z-score -2.35
Structure conservation index 0.79
SVM decision value 1.60
SVM RNA-class probability 0.966580
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14353408 90 + 27905053
UUGUUAUAUGCACAAAUGUGUCAAGCAUUACAGCAGCAGUAGCAGAAGCAGGCAUCUGCAUCUGCUGUCAGUGGUGGCAUCUCGUGGAUA
......(((.(((....((((((..((((...(((((((..(((((.(....).)))))..))))))).)))).))))))...))).))) ( -30.60)
>DroSec_CAF1 132187 84 + 1
UUGUUAUAUGCACAAAUGUGUCAAGCAUUACAGCAGCAGCAGCAGCAGC------CUGCAUCUGCUGUCAGUGAUGGCAUCUCGUGGAUA
......(((.(((....((((((..(((((((((((..(((((....).------))))..))))))).)))).))))))...))).))) ( -28.20)
>DroSim_CAF1 127870 89 + 1
UUGUUAUAUGCACAAAUGUGUCAAGCAUUACAGCAGCAGCAGCAGCAUCU-GCAUCUGCAUCUGCUGUCAGUGGUGGCAUCUCGUGGAUA
......(((.(((....((((((..(((((((((((..((((..((....-))..))))..))))))).)))).))))))...))).))) ( -31.30)
>DroYak_CAF1 141176 68 + 1
UUGUUAUAUGCACAAAUGUGUCAAGCAUUACAGCAGCAG-------------------CAUCUGCUGUCAGU---GGCACCUCGUAGAUA
.................((((((....(.(((((((...-------------------...))))))).).)---))))).......... ( -16.10)
>consensus
UUGUUAUAUGCACAAAUGUGUCAAGCAUUACAGCAGCAGCAGCAGCAGC______CUGCAUCUGCUGUCAGUGGUGGCAUCUCGUGGAUA
......(((.(((....((((((..(((((((((((..((((.............))))..))))))).)))).))))))...))).))) (-21.07 = -21.70 +   0.63)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,353,408 – 14,353,498
Length 90
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 83.83
Mean single sequence MFE -22.25
Consensus MFE -16.39
Energy contribution -16.45
Covariance contribution 0.06
Combinations/Pair 1.09
Mean z-score -1.59
Structure conservation index 0.74
SVM decision value 0.19
SVM RNA-class probability 0.624700
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14353408 90 - 27905053
UAUCCACGAGAUGCCACCACUGACAGCAGAUGCAGAUGCCUGCUUCUGCUACUGCUGCUGUAAUGCUUGACACAUUUGUGCAUAUAACAA
(((.((((((.((.((......(((((((..(((((.(....).))))).....)))))))......)).))..)))))).)))...... ( -24.00)
>DroSec_CAF1 132187 84 - 1
UAUCCACGAGAUGCCAUCACUGACAGCAGAUGCAG------GCUGCUGCUGCUGCUGCUGUAAUGCUUGACACAUUUGUGCAUAUAACAA
(((.((((((.((.((......(((((((..((((------.(....)))))..)))))))......)).))..)))))).)))...... ( -23.10)
>DroSim_CAF1 127870 89 - 1
UAUCCACGAGAUGCCACCACUGACAGCAGAUGCAGAUGC-AGAUGCUGCUGCUGCUGCUGUAAUGCUUGACACAUUUGUGCAUAUAACAA
(((.((((((.((.((......(((((((..((((..((-....))..))))..)))))))......)).))..)))))).)))...... ( -24.60)
>DroYak_CAF1 141176 68 - 1
UAUCUACGAGGUGCC---ACUGACAGCAGAUG-------------------CUGCUGCUGUAAUGCUUGACACAUUUGUGCAUAUAACAA
(((.(((((((((.(---(...(((((((...-------------------...)))))))......)).))).)))))).)))...... ( -17.30)
>consensus
UAUCCACGAGAUGCCACCACUGACAGCAGAUGCAG______GCUGCUGCUGCUGCUGCUGUAAUGCUUGACACAUUUGUGCAUAUAACAA
(((.(((.(((((.........(((((((..((((..........)))).....)))))))...........)))))))).)))...... (-16.39 = -16.45 +   0.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,353,432 – 14,353,538
Length 106
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 92.72
Mean single sequence MFE -39.97
Consensus MFE -38.79
Energy contribution -38.57
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -4.42
Structure conservation index 0.97
SVM decision value 2.13
SVM RNA-class probability 0.988604
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14353432 106 + 27905053
GCAUUACAGCAGCAGUAGCAGAAGCAGGCAUCUGCAUCUGCUGUCAGUGGUGGCAUCUCGUGGAUAUAUAUCUCGAGGAUAUAUAUCUCGGGGAUAUAUAUCUUUU
.((((((.(((((((..(((((.(....).)))))..)))))))..)))))).........(((((((((((((..((((....))))..)))))))))))))... ( -42.10)
>DroSec_CAF1 132211 99 + 1
GCAUUACAGCAGCAGCAGCAGCAGC------CUGCAUCUGCUGUCAGUGAUGGCAUCUCGUGGAUAUAUAUCUCGAGGAUAUAUAUCUCGGGGAUAUAUAUCUU-U
.((((((.(((((((..((((....------))))..)))))))..)))))).........(((((((((((((..((((....))))..))))))))))))).-. ( -39.30)
>DroSim_CAF1 127894 104 + 1
GCAUUACAGCAGCAGCAGCAGCAUCU-GCAUCUGCAUCUGCUGUCAGUGGUGGCAUCUCGUGGAUAUAUAUCUCGAGGAUAUAUAUCUCGGGGAUAUAUAUCUU-U
.(((((((((((..((((..((....-))..))))..))))))).))))............(((((((((((((..((((....))))..))))))))))))).-. ( -38.50)
>consensus
GCAUUACAGCAGCAGCAGCAGCAGC__GCAUCUGCAUCUGCUGUCAGUGGUGGCAUCUCGUGGAUAUAUAUCUCGAGGAUAUAUAUCUCGGGGAUAUAUAUCUU_U
.((((((.(((((((..((((..........))))..)))))))..)))))).........(((((((((((((..((((....))))..)))))))))))))... (-38.79 = -38.57 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,353,432 – 14,353,538
Length 106
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 92.72
Mean single sequence MFE -32.67
Consensus MFE -29.33
Energy contribution -29.33
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.44
Structure conservation index 0.90
SVM decision value 1.80
SVM RNA-class probability 0.977956
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14353432 106 - 27905053
AAAAGAUAUAUAUCCCCGAGAUAUAUAUCCUCGAGAUAUAUAUCCACGAGAUGCCACCACUGACAGCAGAUGCAGAUGCCUGCUUCUGCUACUGCUGCUGUAAUGC
....((((((((((..((((.........)))).))))))))))..................(((((((..(((((.(....).))))).....)))))))..... ( -32.80)
>DroSec_CAF1 132211 99 - 1
A-AAGAUAUAUAUCCCCGAGAUAUAUAUCCUCGAGAUAUAUAUCCACGAGAUGCCAUCACUGACAGCAGAUGCAG------GCUGCUGCUGCUGCUGCUGUAAUGC
.-..((((((((((..((((.........)))).))))))))))..........(((.((.(.((((((..((((------....))))..))))))).)).))). ( -31.80)
>DroSim_CAF1 127894 104 - 1
A-AAGAUAUAUAUCCCCGAGAUAUAUAUCCUCGAGAUAUAUAUCCACGAGAUGCCACCACUGACAGCAGAUGCAGAUGC-AGAUGCUGCUGCUGCUGCUGUAAUGC
.-..((((((((((..((((.........)))).))))))))))..................(((((((..((((..((-....))..))))..)))))))..... ( -33.40)
>consensus
A_AAGAUAUAUAUCCCCGAGAUAUAUAUCCUCGAGAUAUAUAUCCACGAGAUGCCACCACUGACAGCAGAUGCAGAUGC__GCUGCUGCUGCUGCUGCUGUAAUGC
....((((((((((..((((.........)))).))))))))))..................(((((((..((((..........)))).....)))))))..... (-29.33 = -29.33 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,353,468 – 14,353,571
Length 103
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 83.41
Mean single sequence MFE -31.82
Consensus MFE -22.35
Energy contribution -24.10
Covariance contribution 1.75
Combinations/Pair 1.12
Mean z-score -3.24
Structure conservation index 0.70
SVM decision value 2.48
SVM RNA-class probability 0.994393
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14353468 103 + 27905053
UCUGCUGUCAGUGGUGGCAUCUCGUGGAUAUAUAUCUCGAGGAUAUAUAUCUCGGGGAUAUAUAUCUUUUUCGGGUGCACACACAAAUGUACAUCGCCUGCAG
....((((..(((((((((((.((.(((((((((((((..((((....))))..)))))))))))))....)))))))(((......))).))))))..)))) ( -38.30)
>DroSec_CAF1 132241 102 + 1
UCUGCUGUCAGUGAUGGCAUCUCGUGGAUAUAUAUCUCGAGGAUAUAUAUCUCGGGGAUAUAUAUCUU-UUCGGGUGCACACACAAAUGUACAACCCCUUUAG
..........(((.(((((((.((.(((((((((((((..((((....))))..))))))))))))).-..))))))).)))))................... ( -32.50)
>DroSim_CAF1 127929 102 + 1
UCUGCUGUCAGUGGUGGCAUCUCGUGGAUAUAUAUCUCGAGGAUAUAUAUCUCGGGGAUAUAUAUCUU-UUCGGGUGCACACACAAAUGUACAACCCCUUCAG
.....(((((.((((((((((.((.(((((((((((((..((((....))))..))))))))))))).-..))))))).))).))..)).))).......... ( -33.90)
>DroYak_CAF1 141217 81 + 1
UCUGCUGUCAGU---GGCACCUCGUAGAUAUAUA---------------UCUCGGGGAUAUGUAUCUU-UU-GGGUCCAUAC--AAAAAUACAUCCCCUUCAG
.....(((..((---((.((((...(((((((((---------------((.....))))))))))).-..-))))))))))--).................. ( -22.60)
>consensus
UCUGCUGUCAGUGGUGGCAUCUCGUGGAUAUAUAUCUCGAGGAUAUAUAUCUCGGGGAUAUAUAUCUU_UUCGGGUGCACACACAAAUGUACAACCCCUUCAG
..........(((...((((((...(((((((((((((..((((....))))..))))))))))))).....)))))).)))..................... (-22.35 = -24.10 +   1.75)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,353,468 – 14,353,571
Length 103
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 83.41
Mean single sequence MFE -27.00
Consensus MFE -17.98
Energy contribution -20.10
Covariance contribution 2.12
Combinations/Pair 1.04
Mean z-score -2.24
Structure conservation index 0.67
SVM decision value 0.97
SVM RNA-class probability 0.891832
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14353468 103 - 27905053
CUGCAGGCGAUGUACAUUUGUGUGUGCACCCGAAAAAGAUAUAUAUCCCCGAGAUAUAUAUCCUCGAGAUAUAUAUCCACGAGAUGCCACCACUGACAGCAGA
((((.((.(.(((((((....))))))))))......((((((((((..((((.........)))).)))))))))).....................)))). ( -30.00)
>DroSec_CAF1 132241 102 - 1
CUAAAGGGGUUGUACAUUUGUGUGUGCACCCGAA-AAGAUAUAUAUCCCCGAGAUAUAUAUCCUCGAGAUAUAUAUCCACGAGAUGCCAUCACUGACAGCAGA
......((((.((((((....))))))))))((.-..((((((((((.....))))))))))((((.(((....)))..))))......)).(((....))). ( -29.20)
>DroSim_CAF1 127929 102 - 1
CUGAAGGGGUUGUACAUUUGUGUGUGCACCCGAA-AAGAUAUAUAUCCCCGAGAUAUAUAUCCUCGAGAUAUAUAUCCACGAGAUGCCACCACUGACAGCAGA
(((.((((((.((((((....))))))))))...-..((((((((((..((((.........)))).))))))))))...............))..))).... ( -29.70)
>DroYak_CAF1 141217 81 - 1
CUGAAGGGGAUGUAUUUUU--GUAUGGACCC-AA-AAGAUACAUAUCCCCGAGA---------------UAUAUAUCUACGAGGUGCC---ACUGACAGCAGA
(((..((((((((((((((--...((....)-))-))))))))..))))).(((---------------(....))))..........---........))). ( -19.10)
>consensus
CUGAAGGGGAUGUACAUUUGUGUGUGCACCCGAA_AAGAUAUAUAUCCCCGAGAUAUAUAUCCUCGAGAUAUAUAUCCACGAGAUGCCACCACUGACAGCAGA
......(((.(((((((....))))))))))......((((((((((..((((.........)))).))))))))))...............(((....))). (-17.98 = -20.10 +   2.12)

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 11:54:45 2006