Locus 8116

Sequence ID X_DroMel_CAF1
Location 20,181,534 – 20,181,714
Length 180
Max. P 0.999889
window13327 window13328 window13329 window13330 window13331

overview

Window 7

Location 20,181,534 – 20,181,643
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.46
Mean single sequence MFE -46.42
Consensus MFE -32.80
Energy contribution -34.40
Covariance contribution 1.60
Combinations/Pair 1.06
Mean z-score -2.18
Structure conservation index 0.71
SVM decision value 0.95
SVM RNA-class probability 0.887712
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20181534 109 - 22224390
UGAUCGGCAUGGCAAUCAAAGCCUCGGGGCUGCAGCUGCACUGCAUCCCC-AGGGGCAGAGGCGCCCCCCAA-AGGGGCAAACCAGUGCUGCACUGCGGCGUCUUGAACA---------C
((((..((...)).))))..(((((((((.(((((.....))))).))))-.))))).((((((((((....-.)))))........(((((...)))))))))).....---------. ( -48.30)
>DroSec_CAF1 3161 116 - 1
UGAUCGGCAUGGCAAUCAAAGCCUCGGGCCUGCAGCUGCACUGCAUCCCC-AGGGGCAGAGGCGCCC-CCAA-AGGGGCAAG-CAUUGCUGCACUGAGGCGGCUUGAACAGAUGGUUAAC
((((((...((....((((.(((((((...(((((((((.((((..((..-..))))))....((((-(...-.)))))..)-))..)))))))))))))...)))).))..)))))).. ( -49.00)
>DroSim_CAF1 2607 116 - 1
UGAUCGGCAUGGCAAUCAAAGCCUCGGGCCUGCAGCUGCACUGCAUCCCC-AGGGGCAGAGGCGCCC-CCAA-AGGGGCAAG-CAUUGCUGCACUGAGGCGGCUUGAACAGAUGGUUAAC
((((((...((....((((.(((((((...(((((((((.((((..((..-..))))))....((((-(...-.)))))..)-))..)))))))))))))...)))).))..)))))).. ( -49.00)
>DroEre_CAF1 1566 107 - 1
UGAUCGGCAUGGCAAUCAAAGCCUCGGGCAUGCUGUUGCACUGCAUCCCC-AGGAGCAGAGGCGCCC-CCAA-AGGGGCGAA-CAUUGCUGCAGUGAGGCCGCUGGAGCA---------C
...(((((..(((.......)))...(((..(((((.(((((((.(((..-.)))))))...(((((-(...-.))))))..-...))).)))))...))))))))....---------. ( -45.50)
>DroYak_CAF1 3128 97 - 1
UGAUCGGCAUGGCAAUCAAAGCCCCGGGCCAGCAGCUGCACUGCCUCCCCAAGGAGCAGAGGCGCCC-CCAAAAGGGGCAAA-CAUUGCUGCAGU------------GCA---------C
.....(((..(((.......)))....))).(((((.((.((((.(((....)))))))..))((((-(.....)))))...-....)))))...------------...---------. ( -40.30)
>consensus
UGAUCGGCAUGGCAAUCAAAGCCUCGGGCCUGCAGCUGCACUGCAUCCCC_AGGGGCAGAGGCGCCC_CCAA_AGGGGCAAA_CAUUGCUGCACUGAGGCGGCUUGAACA_________C
((((..((...)).))))..(((((((...((((((.((.((((.(((....)))))))..))((((........))))........))))))))))))).................... (-32.80 = -34.40 +   1.60)

alignment

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secondary structure

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Window 8

Location 20,181,565 – 20,181,683
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.09
Mean single sequence MFE -56.38
Consensus MFE -50.92
Energy contribution -50.24
Covariance contribution -0.68
Combinations/Pair 1.11
Mean z-score -2.98
Structure conservation index 0.90
SVM decision value 4.40
SVM RNA-class probability 0.999889
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20181565 118 + 22224390
UGCCCCU-UUGGGGGGCGCCUCUGCCCCU-GGGGAUGCAGUGCAGCUGCAGCCCCGAGGCUUUGAUUGCCAUGCCGAUCAAUCAAGGCAGUGGCAAUCAGUGAUUGAGCCGAUGGUUUGG
.(((((.-....)))))(((((.......-((((.(((((.....))))).))))))))).((((((((((((((..........)))).))))))))))...(..((((...))))..) ( -57.91)
>DroSec_CAF1 3200 117 + 1
UGCCCCU-UUGG-GGGCGCCUCUGCCCCU-GGGGAUGCAGUGCAGCUGCAGGCCCGAGGCUUUGAUUGCCAUGCCGAUCAAUCAAGGCGGUGGCAAUCAGUGAUUGAGCCGAUGGUUUGG
.(((((.-...)-))))(((((.((.(((-.(((.(((((.....)))))..))).)))..((((((((((((((..........))).))))))))))).......)).)).))).... ( -55.50)
>DroSim_CAF1 2646 117 + 1
UGCCCCU-UUGG-GGGCGCCUCUGCCCCU-GGGGAUGCAGUGCAGCUGCAGGCCCGAGGCUUUGAUUGCCAUGCCGAUCAAUCAAGGCAGUGGCAAUCAGUGAUUGAGCCGAUGGUUUGG
.(((((.-...)-))))(((((.((.(((-.(((.(((((.....)))))..))).)))..((((((((((((((..........)))).)))))))))).......)).)).))).... ( -55.90)
>DroEre_CAF1 1596 117 + 1
CGCCCCU-UUGG-GGGCGCCUCUGCUCCU-GGGGAUGCAGUGCAACAGCAUGCCCGAGGCUUUGAUUGCCAUGCCGAUCAAUCAAGGCAGUGGCAAUCAGUGAUUGAGCCGACGGUUUGG
.(((((.-...)-))))(((((.((((((-.(((((((.(.....).)))).))).))...((((((((((((((..........)))).)))))))))).....)))).)).))).... ( -53.40)
>DroYak_CAF1 3146 119 + 1
UGCCCCUUUUGG-GGGCGCCUCUGCUCCUUGGGGAGGCAGUGCAGCUGCUGGCCCGGGGCUUUGAUUGCCAUGCCGAUCAAUCAAGGCAGUGGCAAUCAGUGAUUGAGCCGAUGGUUUGG
.(((((.....)-))))(((((.((((((((((..(((((.....)))))..))))))...((((((((((((((..........)))).)))))))))).....)))).)).))).... ( -59.20)
>consensus
UGCCCCU_UUGG_GGGCGCCUCUGCCCCU_GGGGAUGCAGUGCAGCUGCAGGCCCGAGGCUUUGAUUGCCAUGCCGAUCAAUCAAGGCAGUGGCAAUCAGUGAUUGAGCCGAUGGUUUGG
.((((........))))(((((..(((....))).(((((.....))))).....))))).((((((((((((((..........)))).))))))))))...(..((((...))))..) (-50.92 = -50.24 +  -0.68)

alignment

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secondary structure

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Window 9

Location 20,181,565 – 20,181,683
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.09
Mean single sequence MFE -54.24
Consensus MFE -46.38
Energy contribution -47.22
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -4.51
Structure conservation index 0.86
SVM decision value 3.52
SVM RNA-class probability 0.999332
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20181565 118 - 22224390
CCAAACCAUCGGCUCAAUCACUGAUUGCCACUGCCUUGAUUGAUCGGCAUGGCAAUCAAAGCCUCGGGGCUGCAGCUGCACUGCAUCCCC-AGGGGCAGAGGCGCCCCCCAA-AGGGGCA
..........(.(((......(((((((((.((((..........)))))))))))))..(((((((((.(((((.....))))).))))-.))))).))).)(((((....-.))))). ( -60.20)
>DroSec_CAF1 3200 117 - 1
CCAAACCAUCGGCUCAAUCACUGAUUGCCACCGCCUUGAUUGAUCGGCAUGGCAAUCAAAGCCUCGGGCCUGCAGCUGCACUGCAUCCCC-AGGGGCAGAGGCGCCC-CCAA-AGGGGCA
..........(.(((......(((((((((..(((..........))).)))))))))..((((((((..(((((.....)))))..)))-.))))).))).)((((-(...-.))))). ( -54.50)
>DroSim_CAF1 2646 117 - 1
CCAAACCAUCGGCUCAAUCACUGAUUGCCACUGCCUUGAUUGAUCGGCAUGGCAAUCAAAGCCUCGGGCCUGCAGCUGCACUGCAUCCCC-AGGGGCAGAGGCGCCC-CCAA-AGGGGCA
..........(.(((......(((((((((.((((..........)))))))))))))..((((((((..(((((.....)))))..)))-.))))).))).)((((-(...-.))))). ( -56.40)
>DroEre_CAF1 1596 117 - 1
CCAAACCGUCGGCUCAAUCACUGAUUGCCACUGCCUUGAUUGAUCGGCAUGGCAAUCAAAGCCUCGGGCAUGCUGUUGCACUGCAUCCCC-AGGAGCAGAGGCGCCC-CCAA-AGGGGCG
.......(((.((((......(((((((((.((((..........)))))))))))))....((.(((.((((.(.....).))))))).-))))))...)))((((-(...-.))))). ( -50.30)
>DroYak_CAF1 3146 119 - 1
CCAAACCAUCGGCUCAAUCACUGAUUGCCACUGCCUUGAUUGAUCGGCAUGGCAAUCAAAGCCCCGGGCCAGCAGCUGCACUGCCUCCCCAAGGAGCAGAGGCGCCC-CCAAAAGGGGCA
.....((...((((.......(((((((((.((((..........))))))))))))).))))..))(((.((....)).((((.(((....))))))).)))((((-(.....))))). ( -49.80)
>consensus
CCAAACCAUCGGCUCAAUCACUGAUUGCCACUGCCUUGAUUGAUCGGCAUGGCAAUCAAAGCCUCGGGCCUGCAGCUGCACUGCAUCCCC_AGGGGCAGAGGCGCCC_CCAA_AGGGGCA
..........(.(((......(((((((((.((((..........)))))))))))))..((((((((..(((((.....)))))..)))..))))).))).)((((........)))). (-46.38 = -47.22 +   0.84)

alignment

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secondary structure

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Window 0

Location 20,181,603 – 20,181,714
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.50
Mean single sequence MFE -46.32
Consensus MFE -43.40
Energy contribution -43.12
Covariance contribution -0.28
Combinations/Pair 1.10
Mean z-score -2.39
Structure conservation index 0.94
SVM decision value 4.19
SVM RNA-class probability 0.999830
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20181603 111 + 22224390
UGCAGCUGCAGCCCCGAGGCUUUGAUUGCCAUGCCGAUCAAUCAAGGCAGUGGCAAUCAGUGAUUGAGCCGAUGGUUUGGACAACUGGGCCGCGGGCGUAAUUCAAUCCAG---------
(((....)))(((((..((((((((((((((((((..........)))).)))))))))......)))))...((((..(....)..))))).))))..............--------- ( -43.60)
>DroSec_CAF1 3237 111 + 1
UGCAGCUGCAGGCCCGAGGCUUUGAUUGCCAUGCCGAUCAAUCAAGGCGGUGGCAAUCAGUGAUUGAGCCGAUGGUUUGGACAACUGGGCCGCGGGCGUAAUUCAAUCCAG---------
(((....))).(((((.((((((((((((((((((..........))).)))))))))))((.(..((((...))))..).))....)))).)))))..............--------- ( -45.20)
>DroSim_CAF1 2683 111 + 1
UGCAGCUGCAGGCCCGAGGCUUUGAUUGCCAUGCCGAUCAAUCAAGGCAGUGGCAAUCAGUGAUUGAGCCGAUGGUUUGGACAACCGGGCCGCGGGCGUAAUUCAAUCCAG---------
(((....))).(((((.((((((((((((((((((..........)))).)))))))))......)))))...(((((((....))))))).)))))..............--------- ( -47.30)
>DroEre_CAF1 1633 120 + 1
UGCAACAGCAUGCCCGAGGCUUUGAUUGCCAUGCCGAUCAAUCAAGGCAGUGGCAAUCAGUGAUUGAGCCGACGGUUUGGACAACUGGGCCGCGGGCGUAAUUCAAUCCGGCUCCAGCUC
.((....))(((((((.((((((((((((((((((..........)))).)))))))))......)))))..(((((..(....)..))))))))))))..........(((....))). ( -49.30)
>DroYak_CAF1 3185 111 + 1
UGCAGCUGCUGGCCCGGGGCUUUGAUUGCCAUGCCGAUCAAUCAAGGCAGUGGCAAUCAGUGAUUGAGCCGAUGGUUUGGACAACUGCGCCGCGGGCGUAAUUUAAUCCGG---------
.((....))..(((((.(((..(((((((((((((..........)))).)))))))))((..(((..((((....)))).)))..))))).)))))..............--------- ( -46.20)
>consensus
UGCAGCUGCAGGCCCGAGGCUUUGAUUGCCAUGCCGAUCAAUCAAGGCAGUGGCAAUCAGUGAUUGAGCCGAUGGUUUGGACAACUGGGCCGCGGGCGUAAUUCAAUCCAG_________
.((....))..(((((.((((((((((((((((((..........)))).)))))))))......)))))..((((..((....))..)))))))))....................... (-43.40 = -43.12 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,181,603 – 20,181,714
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.50
Mean single sequence MFE -40.55
Consensus MFE -37.22
Energy contribution -37.62
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.92
SVM decision value 2.93
SVM RNA-class probability 0.997761
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20181603 111 - 22224390
---------CUGGAUUGAAUUACGCCCGCGGCCCAGUUGUCCAAACCAUCGGCUCAAUCACUGAUUGCCACUGCCUUGAUUGAUCGGCAUGGCAAUCAAAGCCUCGGGGCUGCAGCUGCA
---------..............((..(((((((.(((.....)))....((((.......(((((((((.((((..........))))))))))))).))))...))))))).)).... ( -39.10)
>DroSec_CAF1 3237 111 - 1
---------CUGGAUUGAAUUACGCCCGCGGCCCAGUUGUCCAAACCAUCGGCUCAAUCACUGAUUGCCACCGCCUUGAUUGAUCGGCAUGGCAAUCAAAGCCUCGGGCCUGCAGCUGCA
---------..............(((((.(((...((((.((........))..))))...(((((((((..(((..........))).)))))))))..))).)))))..((....)). ( -37.00)
>DroSim_CAF1 2683 111 - 1
---------CUGGAUUGAAUUACGCCCGCGGCCCGGUUGUCCAAACCAUCGGCUCAAUCACUGAUUGCCACUGCCUUGAUUGAUCGGCAUGGCAAUCAAAGCCUCGGGCCUGCAGCUGCA
---------..............(((((.(((..(((((.((........))..)))))..(((((((((.((((..........)))))))))))))..))).)))))..((....)). ( -42.50)
>DroEre_CAF1 1633 120 - 1
GAGCUGGAGCCGGAUUGAAUUACGCCCGCGGCCCAGUUGUCCAAACCGUCGGCUCAAUCACUGAUUGCCACUGCCUUGAUUGAUCGGCAUGGCAAUCAAAGCCUCGGGCAUGCUGUUGCA
..(((.(((.(.((((((.....(((.((((..............)))).)))))))))..(((((((((.((((..........)))))))))))))..).))).))).(((....))) ( -44.44)
>DroYak_CAF1 3185 111 - 1
---------CCGGAUUAAAUUACGCCCGCGGCGCAGUUGUCCAAACCAUCGGCUCAAUCACUGAUUGCCACUGCCUUGAUUGAUCGGCAUGGCAAUCAAAGCCCCGGGCCAGCAGCUGCA
---------..............(((((.((((..((((.((........))..))))..)(((((((((.((((..........)))))))))))))..))).)))))..((....)). ( -39.70)
>consensus
_________CUGGAUUGAAUUACGCCCGCGGCCCAGUUGUCCAAACCAUCGGCUCAAUCACUGAUUGCCACUGCCUUGAUUGAUCGGCAUGGCAAUCAAAGCCUCGGGCCUGCAGCUGCA
.......................(((((.(((...((((.((........))..))))...(((((((((.((((..........)))))))))))))..))).)))))..((....)). (-37.22 = -37.62 +   0.40)

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 12:55:58 2006