Locus 5378

Sequence ID X_DroMel_CAF1
Location 13,980,269 – 13,980,498
Length 229
Max. P 0.938624
window8726 window8727 window8728 window8729 window8730

overview

Window 6

Location 13,980,269 – 13,980,379
Length 110
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 89.01
Mean single sequence MFE -24.88
Consensus MFE -21.34
Energy contribution -21.70
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -1.58
Structure conservation index 0.86
SVM decision value 0.16
SVM RNA-class probability 0.611886
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13980269 110 - 22224390
GCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUGACAUUUAUUGUCAAGCCAAGCCCCAAAAAAAGGCAAACUGAGAGAACGCGAGUUCGAAACCGA-----AACCAAA
...((((...(.........((((.((((((...)))((((((.....)))))))))..(((.........)))...))))..((((....)))))...))))-----....... ( -27.60)
>DroPse_CAF1 118072 92 - 1
GCAUCGAGCGCGCAAAUAAAUUAGCGGCCGCAAAGUGUUGACAUUUAUUGUCAAGCCAAGCCCCAAAAAAA-G-AAACAGA---------------------AACCGAAACGGAA
((..((.((.(((..........)))))))....(..((((((.....))))))..)..))..........-.-.......---------------------..(((...))).. ( -15.50)
>DroSec_CAF1 13334 109 - 1
GCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUGACAUUUAUUGUCAAGCCAAGCCCCAAAAAAA-GCAAACUGAGGGAACGCGAGUUCGAAACCGA-----AACCAAA
...((((((.(((............((((((...)))((((((.....)))))))))...(((((......-......)).)))...))).))))))......-----....... ( -26.80)
>DroSim_CAF1 13413 109 - 1
GCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUGACAUUUAUUGUCAAGCCAAGCCCCAAAAAAA-GCAAACUGAGAGAACGCGAGUUCGAAACCGA-----AACCAAA
...((((((((............))((((((...)))((((((.....)))))))))..))))........-...........((((....))))))......-----....... ( -26.50)
>DroEre_CAF1 7730 108 - 1
GCAUCG-GCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUGACAUUUAUUGUCAAGCCAAGCCCCAAAAAAA-GCAAACUGAGAGAACGCGAGUUCGAAACCGA-----AACCAAA
...(((-(.((((..........))((((((...)))((((((.....)))))))))..............-)).........((((....))))....))))-----....... ( -24.90)
>DroYak_CAF1 14092 109 - 1
GCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUGACAUUUAUUGUCAAGCCAAGCCCCAAAAAAA-GCAAACUGCGAGAACGCGAGUUCGAAACCGA-----AACCAAA
...((((((((............))((((((...)))((((((.....)))))))))..))))........-((.....))))((((....))))........-----....... ( -28.00)
>consensus
GCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUGACAUUUAUUGUCAAGCCAAGCCCCAAAAAAA_GCAAACUGAGAGAACGCGAGUUCGAAACCGA_____AACCAAA
.....((((((............))((((((...)))((((((.....)))))))))..))))....................((((....)))).................... (-21.34 = -21.70 +   0.36)

alignment

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secondary structure

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Window 7

Location 13,980,299 – 13,980,418
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 97.80
Mean single sequence MFE -32.86
Consensus MFE -29.16
Energy contribution -29.52
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -1.72
Structure conservation index 0.89
SVM decision value 1.18
SVM RNA-class probability 0.927457
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13980299 119 - 22224390
CCACCUCCUCCUGGGAAACCGCCACCUCAUGUGGCGAACGCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUGACAUUUAUUGUCAAGCCAAGCCCCAAAAAAAGGCAAACUG
...(((.....((((....((((((.....))))))...((....(((.(((..........)))))).....(..((((((.....))))))..)..)))))).....)))....... ( -34.70)
>DroSec_CAF1 13364 118 - 1
CCAGCUCCUCCUGGGAAACCGCCACCUCAUGUGGCGAACGCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUGACAUUUAUUGUCAAGCCAAGCCCCAAAAAAA-GCAAACUG
...(((.....((((....((((((.....))))))...((....(((.(((..........)))))).....(..((((((.....))))))..)..)))))).....)-))...... ( -35.80)
>DroSim_CAF1 13443 118 - 1
CCAGCUCCUCCUGGGAAACCGCCACCUCAUGUGGCGAACGCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUGACAUUUAUUGUCAAGCCAAGCCCCAAAAAAA-GCAAACUG
...(((.....((((....((((((.....))))))...((....(((.(((..........)))))).....(..((((((.....))))))..)..)))))).....)-))...... ( -35.80)
>DroEre_CAF1 7760 117 - 1
CCACCUCCUCCUGGGAAACAGCCACCUCAUGUGGUGAACGCAUCG-GCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUGACAUUUAUUGUCAAGCCAAGCCCCAAAAAAA-GCAAACUG
...........((((.....(((((.....)))))....((...(-((.(((..........)))))).....(..((((((.....))))))..)..))))))......-........ ( -28.80)
>DroYak_CAF1 14122 118 - 1
CCACCUCCUCCUGGGAAACAGCCACCUCAUGUGGUGAACGCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUGACAUUUAUUGUCAAGCCAAGCCCCAAAAAAA-GCAAACUG
.....(((.....)))....((((((......))))........((((((............))((((((...)))((((((.....)))))))))..))))........-))...... ( -29.20)
>consensus
CCACCUCCUCCUGGGAAACCGCCACCUCAUGUGGCGAACGCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUGACAUUUAUUGUCAAGCCAAGCCCCAAAAAAA_GCAAACUG
...........((((....((((((.....))))))...((....(((.(((..........)))))).....(..((((((.....))))))..)..))))))............... (-29.16 = -29.52 +   0.36)

alignment

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secondary structure

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Window 8

Location 13,980,339 – 13,980,458
Length 119
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 83.51
Mean single sequence MFE -44.72
Consensus MFE -31.28
Energy contribution -32.72
Covariance contribution 1.44
Combinations/Pair 1.03
Mean z-score -1.92
Structure conservation index 0.70
SVM decision value 0.49
SVM RNA-class probability 0.754818
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13980339 119 + 22224390
CAACACUUGGUGGCCGCUAAUUUAUUUGCGCGCCCGAUGCGUUCGCCACAUGAGGUGGCGGUUUCCCAGGAGGAGGUGGGUCACCGAUUGCAUCGGACCAUCGGUCCAUCGAAUCGCUC
......((((((((((((((.....))).))..((((((((.(((((((.....)))))(((..((((........))))..))))).))))))))......)).)))))))....... ( -46.90)
>DroSec_CAF1 13403 98 + 1
CAACACUUGGUGGCCGCUAAUUUAUUUGCGCGCCCGAUGCGUUCGCCACAUGAGGUGGCGGUUUCCCAGGAGGAGCUGGGCCACCGAUCGCAUCGGG---------------------C
...(((...)))((.((..........))))((((((((((.(((((((.....)))))(((..(((((......)))))..))))).)))))))))---------------------) ( -47.10)
>DroSim_CAF1 13482 98 + 1
CAACACUUGGUGGCCGCUAAUUUAUUUGCGCGCCCGAUGCGUUCGCCACAUGAGGUGGCGGUUUCCCAGGAGGAGCUGGGCCACCGAUCGCAUCGGG---------------------C
...(((...)))((.((..........))))((((((((((.(((((((.....)))))(((..(((((......)))))..))))).)))))))))---------------------) ( -47.10)
>DroEre_CAF1 7799 117 + 1
CAACACUUGGUGGCCGCUAAUUUAUUUGCGCGC-CGAUGCGUUCACCACAUGAGGUGGCUGUUUCCCAGGAGGAGGUGGGUCACCGAUGGCAUCAGACCAUCGGUCCUCCGAAUCAA-C
.....(((((.((((((..........))).))-)((.(((..((((......))))..))).))))))).(((((......(((((((((....).))))))))))))).......-. ( -44.90)
>DroYak_CAF1 14161 111 + 1
CAACACUUGGUGGCCGCUAAUUUAUUUGCGCGCCCGAUGCGUUCACCACAUGAGGUGGCUGUUUCCCAGGAGGAGGUGGGUCACCAAUUGCAUCGGAUCAUCAGACCAUCG--------
......(((((((((((..........))).))((((((((.(((.....)))((((((..(((((.....)))))..).)))))...))))))))..)))))).......-------- ( -37.60)
>consensus
CAACACUUGGUGGCCGCUAAUUUAUUUGCGCGCCCGAUGCGUUCGCCACAUGAGGUGGCGGUUUCCCAGGAGGAGGUGGGUCACCGAUCGCAUCGGA_CAUC_G_CC__CG_______C
...(((...)))(((((..........))).))((((((((.(((((((.....)))))(((..((((........))))..))))).))))))))....................... (-31.28 = -32.72 +   1.44)

alignment

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secondary structure

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Window 9

Location 13,980,339 – 13,980,458
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 83.51
Mean single sequence MFE -43.58
Consensus MFE -32.60
Energy contribution -32.80
Covariance contribution 0.20
Combinations/Pair 1.08
Mean z-score -2.26
Structure conservation index 0.75
SVM decision value 1.27
SVM RNA-class probability 0.938624
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13980339 119 - 22224390
GAGCGAUUCGAUGGACCGAUGGUCCGAUGCAAUCGGUGACCCACCUCCUCCUGGGAAACCGCCACCUCAUGUGGCGAACGCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUG
.(((.(((.(.(((.((....(((((((((..(((((..((((........))))..)))(((((.....)))))))..)))))))))((............))))))).).)))))). ( -44.10)
>DroSec_CAF1 13403 98 - 1
G---------------------CCCGAUGCGAUCGGUGGCCCAGCUCCUCCUGGGAAACCGCCACCUCAUGUGGCGAACGCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUG
(---------------------(((((((((.(((((..(((((......)))))..)))(((((.....))))))).)))))))))).(((..........))).............. ( -48.60)
>DroSim_CAF1 13482 98 - 1
G---------------------CCCGAUGCGAUCGGUGGCCCAGCUCCUCCUGGGAAACCGCCACCUCAUGUGGCGAACGCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUG
(---------------------(((((((((.(((((..(((((......)))))..)))(((((.....))))))).)))))))))).(((..........))).............. ( -48.60)
>DroEre_CAF1 7799 117 - 1
G-UUGAUUCGGAGGACCGAUGGUCUGAUGCCAUCGGUGACCCACCUCCUCCUGGGAAACAGCCACCUCAUGUGGUGAACGCAUCG-GCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUG
(-(((.(((((((((..((((((.....))))))((((...))))))))))...))).))))((((......))))(((((...(-((.(((..........)))))).....))))). ( -42.10)
>DroYak_CAF1 14161 111 - 1
--------CGAUGGUCUGAUGAUCCGAUGCAAUUGGUGACCCACCUCCUCCUGGGAAACAGCCACCUCAUGUGGUGAACGCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUG
--------...((((.........((((((.....((..((((........))))..)).(((((.....)))))....))))))(((.(((..........))))))))))....... ( -34.50)
>consensus
G_______CG__GG_C_GAUG_UCCGAUGCAAUCGGUGACCCACCUCCUCCUGGGAAACCGCCACCUCAUGUGGCGAACGCAUCGGGCGCGCAAAUAAAUUAGCGGCCACCAAGUGUUG
........................((((((....(((..((((........))))..)))(((((.....)))))....))))))(((.(((..........))))))........... (-32.60 = -32.80 +   0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,980,379 – 13,980,498
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 70.60
Mean single sequence MFE -31.23
Consensus MFE -16.18
Energy contribution -16.02
Covariance contribution -0.16
Combinations/Pair 1.20
Mean z-score -1.89
Structure conservation index 0.52
SVM decision value 1.09
SVM RNA-class probability 0.912858
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13980379 119 - 22224390
UAUUUUUCCAGUAGUAUUACCAUCAAUGCCAUUCCAAAUCGAGCGAUUCGAUGGACCGAUGGUCCGAUGCAAUCGGUGACCCACCUCCUCCUGGGAAACCGCCACCUCAUGUGGCGAAC
...((((((((..(((((((((((....(((((...((((....)))).)))))...))))))..)))))....((((...)))).....)))))))).((((((.....))))))... ( -40.00)
>DroSec_CAF1 13443 98 - 1
UAUUUUUCCAGUAGCAUUACCAUCAAUGCCAUUCCAAAUCG---------------------CCCGAUGCGAUCGGUGGCCCAGCUCCUCCUGGGAAACCGCCACCUCAUGUGGCGAAC
.............(((((......)))))........((((---------------------(.....))))).(((..(((((......)))))..)))(((((.....))))).... ( -29.90)
>DroSim_CAF1 13522 98 - 1
UAUUUUUCCAGUAGCAUUACCAUCAAUGCCAUUCCAAAUCG---------------------CCCGAUGCGAUCGGUGGCCCAGCUCCUCCUGGGAAACCGCCACCUCAUGUGGCGAAC
.............(((((......)))))........((((---------------------(.....))))).(((..(((((......)))))..)))(((((.....))))).... ( -29.90)
>DroEre_CAF1 7838 109 - 1
AAUCUUCUGAAGACGUUCAGCUUC---------CUAAGUCG-UUGAUUCGGAGGACCGAUGGUCUGAUGCCAUCGGUGACCCACCUCCUCCUGGGAAACAGCCACCUCAUGUGGUGAAC
...((((((((.....(((((..(---------....)..)-))))))))))))(((((((((.....)))))))))..((((........)))).....(((((.....))))).... ( -35.70)
>DroYak_CAF1 14201 102 - 1
AAUGUCUCAAAGACCUUUAUUAUC---------UCAAGUC--------CGAUGGUCUGAUGAUCCGAUGCAAUUGGUGACCCACCUCCUCCUGGGAAACAGCCACCUCAUGUGGUGAAC
..((..(((.(((((.........---------.......--------....)))))..)))..))..((....((((...))))(((.....)))....))((((......))))... ( -20.65)
>consensus
UAUUUUUCCAGUAGCAUUACCAUCAAUGCCAUUCCAAAUCG_______CG__GG_C_GAUG_UCCGAUGCAAUCGGUGACCCACCUCCUCCUGGGAAACCGCCACCUCAUGUGGCGAAC
...............................................................(((((...)))))...((((........))))....((((((.....))))))... (-16.18 = -16.02 +  -0.16)

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 11:46:33 2006