Locus 7133

Sequence ID 3R_DroMel_CAF1
Location 18,781,283 – 18,781,418
Length 135
Max. P 0.999766
window11537 window11538 window11539 window11540

overview

Window 7

Location 18,781,283 – 18,781,381
Length 98
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 90.95
Mean single sequence MFE -30.90
Consensus MFE -27.37
Energy contribution -27.70
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.58
Structure conservation index 0.89
SVM decision value 3.39
SVM RNA-class probability 0.999136
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18781283 98 + 27905053
C---------CCUUACUUUUUCGCUUGCCAACAGCAUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUU-UUAGCCGGGGCCAAAAGAUGUCGGCGA
.---------...............(((....((((..((((....))))..))))....)))...((((((((.((.((-((.((....)).)))))).)))))))) ( -32.80)
>DroSec_CAF1 6661 98 + 1
C---------CCUUACUUUUUCGCUUGCCAACAGCAUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUU-UUAGCCGGGGCCAAAAGAUGUCGGCGA
.---------...............(((....((((..((((....))))..))))....)))...((((((((.((.((-((.((....)).)))))).)))))))) ( -32.80)
>DroSim_CAF1 8370 98 + 1
C---------CCUUACUUUUUCGCUUGCCAACAGCAUUUCUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUU-UUAGCCGGGGCCAAAAGAUGUCGGCGA
.---------...............(((....((((..(.((....)).)..))))....)))...((((((((.((.((-((.((....)).)))))).)))))))) ( -26.80)
>DroEre_CAF1 6534 101 + 1
C-----GUUUCCGCACUUUUUCGCUUGCCAACAGCAUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUU-UUAGCCGG-GCCAAAAGACGUCGGCGA
.-----......((........)).(((....((((..((((....))))..))))....)))...((((((((.((.((-((.((...-)).)))))).)))))))) ( -30.60)
>DroYak_CAF1 7152 107 + 1
CAUUUGGUUUACGUAGUUUUUCGCUUGCCAACAGCAUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUU-UUAGCCGGGGCCAAAAGAUGUCGGCGA
...(((((...((........))...))))).((((..((((....))))..))))..........((((((((.((.((-((.((....)).)))))).)))))))) ( -35.90)
>DroAna_CAF1 7760 95 + 1
C----------CGUACUUUUUCGCUUGCCAACAGCAUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUUUUUAGCAAGAGC---AAGAUGUCGGCGC
.----------..............(((....((((..((((....))))..))))....)))....(((((((.....((((.((....))---)))).))))))). ( -26.50)
>consensus
C_________CCGUACUUUUUCGCUUGCCAACAGCAUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUU_UUAGCCGGGGCCAAAAGAUGUCGGCGA
.........................(((....((((..((((....))))..))))....)))...((((((((.((.((....((....))...)))).)))))))) (-27.37 = -27.70 +   0.33)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,781,283 – 18,781,381
Length 98
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 90.95
Mean single sequence MFE -37.43
Consensus MFE -33.85
Energy contribution -34.68
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -4.77
Structure conservation index 0.90
SVM decision value 4.03
SVM RNA-class probability 0.999766
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18781283 98 - 27905053
UCGCCGACAUCUUUUGGCCCCGGCUAA-AAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAUGCUGUUGGCAAGCGAAAAAGUAAGG---------G
((((((((.(((((((((....)))))-)).)).))))))))(..(((...(((((..((((....))))..)))))...)))..)............---------. ( -39.60)
>DroSec_CAF1 6661 98 - 1
UCGCCGACAUCUUUUGGCCCCGGCUAA-AAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAUGCUGUUGGCAAGCGAAAAAGUAAGG---------G
((((((((.(((((((((....)))))-)).)).))))))))(..(((...(((((..((((....))))..)))))...)))..)............---------. ( -39.60)
>DroSim_CAF1 8370 98 - 1
UCGCCGACAUCUUUUGGCCCCGGCUAA-AAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGAGAAAUGCUGUUGGCAAGCGAAAAAGUAAGG---------G
((((((((.(((((((((....)))))-)).)).))))))))(..(((...(((((..(.((....)).)..)))))...)))..)............---------. ( -35.70)
>DroEre_CAF1 6534 101 - 1
UCGCCGACGUCUUUUGGC-CCGGCUAA-AAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAUGCUGUUGGCAAGCGAAAAAGUGCGGAAAC-----G
((((((((.(((((((((-...)))))-)).)).))))))))(..(((...(((((..((((....))))..)))))...)))..).........((....)-----) ( -39.00)
>DroYak_CAF1 7152 107 - 1
UCGCCGACAUCUUUUGGCCCCGGCUAA-AAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAUGCUGUUGGCAAGCGAAAAACUACGUAAACCAAAUG
((((((((.(((((((((....)))))-)).)).))))))))(..(((...(((((..((((....))))..)))))...)))..)...................... ( -39.60)
>DroAna_CAF1 7760 95 - 1
GCGCCGACAUCUU---GCUCUUGCUAAAAAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAUGCUGUUGGCAAGCGAAAAAGUACG----------G
((((((((..(((---((((((((..(........)..))))))..))))).((((..((((....))))..))))))))))..))...........----------. ( -31.10)
>consensus
UCGCCGACAUCUUUUGGCCCCGGCUAA_AAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAUGCUGUUGGCAAGCGAAAAAGUAAGG_________G
((((((((.((..(((((....)))))....)).))))))))(..(((...(((((..((((....))))..)))))...)))..)...................... (-33.85 = -34.68 +   0.83)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,781,307 – 18,781,418
Length 111
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 95.28
Mean single sequence MFE -32.05
Consensus MFE -27.47
Energy contribution -27.52
Covariance contribution 0.06
Combinations/Pair 1.07
Mean z-score -2.76
Structure conservation index 0.86
SVM decision value 2.19
SVM RNA-class probability 0.989891
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18781307 111 + 27905053
GCAUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUU-UUAGCCGGGGCCAAAAGAUGUCGGCGAUUGAUUCAAUUUGUUGCC-ACUCUGUUUACAAAGCGUU
(((..((((....))))..))).....((.(..((((((((.((.((-((.((....)).)))))).))))))))..)......(((((.((.-.....))..)))))))... ( -34.60)
>DroSec_CAF1 6685 111 + 1
GCAUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUU-UUAGCCGGGGCCAAAAGAUGUCGGCGAUUGAUUCAAUUUGUUGCC-ACUCUGUUUACAAAGCGUU
(((..((((....))))..))).....((.(..((((((((.((.((-((.((....)).)))))).))))))))..)......(((((.((.-.....))..)))))))... ( -34.60)
>DroSim_CAF1 8394 111 + 1
GCAUUUCUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUU-UUAGCCGGGGCCAAAAGAUGUCGGCGAUUGAUUCAAUUUGUUGCC-ACUCUGUUUACAAAGCGUU
((.........((((....(((.....)))(..((((((((.((.((-((.((....)).)))))).))))))))..)..))))(((((.((.-.....))..)))))))... ( -28.80)
>DroEre_CAF1 6562 110 + 1
GCAUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUU-UUAGCCGG-GCCAAAAGACGUCGGCGAUUGAUUCAAUUUGUUGCC-ACUCUGUUUACAAAGCGUU
(((..((((....))))..))).....((.(..((((((((.((.((-((.((...-)).)))))).))))))))..)......(((((.((.-.....))..)))))))... ( -31.60)
>DroYak_CAF1 7185 111 + 1
GCAUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUU-UUAGCCGGGGCCAAAAGAUGUCGGCGAUUGAUUCAAUUUGUUGCC-ACUCUGUUUACAAAGCGUU
(((..((((....))))..))).....((.(..((((((((.((.((-((.((....)).)))))).))))))))..)......(((((.((.-.....))..)))))))... ( -34.60)
>DroAna_CAF1 7783 110 + 1
GCAUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUUUUUAGCAAGAGC---AAGAUGUCGGCGCUUGAUUCAAUUUGUUCCAAACUCUGUUUGCAAAGUGUU
(((..((((....))))..))).....((((((.(((((((.....((((.((....))---)))).)))))))...)).....(((((..((.....))...))))))))). ( -28.10)
>consensus
GCAUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUU_UUAGCCGGGGCCAAAAGAUGUCGGCGAUUGAUUCAAUUUGUUGCC_ACUCUGUUUACAAAGCGUU
(((..((((....))))..))).....((.(..((((((((.((.((....((....))...)))).))))))))..)......(((((..............)))))))... (-27.47 = -27.52 +   0.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,781,307 – 18,781,418
Length 111
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 95.28
Mean single sequence MFE -37.40
Consensus MFE -31.12
Energy contribution -31.82
Covariance contribution 0.70
Combinations/Pair 1.03
Mean z-score -4.45
Structure conservation index 0.83
SVM decision value 3.29
SVM RNA-class probability 0.998931
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18781307 111 - 27905053
AACGCUUUGUAAACAGAGU-GGCAACAAAUUGAAUCAAUCGCCGACAUCUUUUGGCCCCGGCUAA-AAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAUGC
..(((((((....))))))-)........(((...(..((((((((.(((((((((....)))))-)).)).))))))))..)..)))...(((..((((....))))..))) ( -40.50)
>DroSec_CAF1 6685 111 - 1
AACGCUUUGUAAACAGAGU-GGCAACAAAUUGAAUCAAUCGCCGACAUCUUUUGGCCCCGGCUAA-AAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAUGC
..(((((((....))))))-)........(((...(..((((((((.(((((((((....)))))-)).)).))))))))..)..)))...(((..((((....))))..))) ( -40.50)
>DroSim_CAF1 8394 111 - 1
AACGCUUUGUAAACAGAGU-GGCAACAAAUUGAAUCAAUCGCCGACAUCUUUUGGCCCCGGCUAA-AAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGAGAAAUGC
..(((((((....))))))-)........((((.....((((((((.(((((((((....)))))-)).)).))))))))...(((.....)))....))))........... ( -37.10)
>DroEre_CAF1 6562 110 - 1
AACGCUUUGUAAACAGAGU-GGCAACAAAUUGAAUCAAUCGCCGACGUCUUUUGGC-CCGGCUAA-AAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAUGC
..(((((((....))))))-)........(((...(..((((((((.(((((((((-...)))))-)).)).))))))))..)..)))...(((..((((....))))..))) ( -37.50)
>DroYak_CAF1 7185 111 - 1
AACGCUUUGUAAACAGAGU-GGCAACAAAUUGAAUCAAUCGCCGACAUCUUUUGGCCCCGGCUAA-AAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAUGC
..(((((((....))))))-)........(((...(..((((((((.(((((((((....)))))-)).)).))))))))..)..)))...(((..((((....))))..))) ( -40.50)
>DroAna_CAF1 7783 110 - 1
AACACUUUGCAAACAGAGUUUGGAACAAAUUGAAUCAAGCGCCGACAUCUU---GCUCUUGCUAAAAAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAUGC
...((((.(((..(...((((((..(.....)..))))))((((((.((..---((....)).......)).))))))..)..))))))).(((..((((....))))..))) ( -28.30)
>consensus
AACGCUUUGUAAACAGAGU_GGCAACAAAUUGAAUCAAUCGCCGACAUCUUUUGGCCCCGGCUAA_AAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAUGC
...((((((....))))))..........(((......((((((((.((..(((((....)))))....)).)))))))).....)))...(((..((((....))))..))) (-31.12 = -31.82 +   0.70)

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 12:38:14 2006