Locus 4164

Sequence ID 2L_DroMel_CAF1
Location 11,963,930 – 11,964,107
Length 177
Max. P 0.998931
window6572 window6573 window6574 window6575 window6576

overview

Window 2

Location 11,963,930 – 11,964,038
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.47
Mean single sequence MFE -31.98
Consensus MFE -19.14
Energy contribution -19.14
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.60
SVM decision value 1.13
SVM RNA-class probability 0.919946
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11963930 108 + 22407834
A--------UCCCGCUUUUGGGCCAUUCUGAACUUCAUUAGCGACUGCGAAUCAACAA--AGCUGAUGAGCAGCUUAGGGCCAACAGA--GCGACUUGUGGCGAGGAAACAGAAAUGGUA
.--------(((((((....((((...(((....((((((((...((........)).--.)))))))).))).....)))).((((.--.....)))))))).)))..((....))... ( -30.70)
>DroSec_CAF1 183369 100 + 1
A--------UCCCGCUUUUGGGCCAUUCUGAACUUCAUUAGCGACUGCGAAUCAACAA--AGCUGAUGAGCAGCUUAGGGCCAACAGA--GCGCCUAGUGGUGAGGAA-CA-------UA
.--------(((((((.((((((..(((((...(((((((((...((........)).--.)))))))))..((.....))...))))--).)))))).)))).))).-..-------.. ( -32.10)
>DroSim_CAF1 149755 86 + 1
A--------UCCCGCUUUUGGGCCAUUCUGAACUUCAUUAGCGACUGCGAAUCAACAA--AGCUGAUGAGCAGCUUAGGGCCAACAGA----------------GGAA-AA-------UA
.--------..((.((.((((.(((..(((....((((((((...((........)).--.)))))))).)))..).)).)))).)).----------------))..-..-------.. ( -24.80)
>DroEre_CAF1 158237 84 + 1
A--------UCCCGCUUGUGGGCCAUUCUGAACUUCAUUAGCGACUGCGAAUCAACAA--AGCUGAUGAGCAGCUUAGGGCCCACAGA--GCGCCU------------------------
.--------...((((((((((((...(((....((((((((...((........)).--.)))))))).))).....)))))))).)--)))...------------------------ ( -33.60)
>DroYak_CAF1 154440 120 + 1
AUCGCAUCAUCCAGCUUUUGGGCCAUUCUGAACUUCAUUAGCGGCUGCGAAUCAACAAAUAGCUGAUGAGCAGCUUAGGGCCCACAGAGAGCGCCUUGAGGUGAUGAAAUACAAAUGGUA
(((((.(((....(((((((((((...((((......)))).((((((..((((.(.....).))))..))))))...))))))...)))))....))).)))))............... ( -38.70)
>consensus
A________UCCCGCUUUUGGGCCAUUCUGAACUUCAUUAGCGACUGCGAAUCAACAA__AGCUGAUGAGCAGCUUAGGGCCAACAGA__GCGCCU_G_GG_GAGGAA_CA_______UA
....................((((...(((....((((((((...((........))....)))))))).))).....))))...................................... (-19.14 = -19.14 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,963,930 – 11,964,038
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.47
Mean single sequence MFE -30.14
Consensus MFE -21.94
Energy contribution -22.38
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.50
Structure conservation index 0.73
SVM decision value 0.34
SVM RNA-class probability 0.693886
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11963930 108 - 22407834
UACCAUUUCUGUUUCCUCGCCACAAGUCGC--UCUGUUGGCCCUAAGCUGCUCAUCAGCU--UUGUUGAUUCGCAGUCGCUAAUGAAGUUCAGAAUGGCCCAAAAGCGGGA--------U
......((((((((....((((......((--(..((((((.....(((((..((((((.--..))))))..))))).))))))..)))......))))....))))))))--------. ( -31.20)
>DroSec_CAF1 183369 100 - 1
UA-------UG-UUCCUCACCACUAGGCGC--UCUGUUGGCCCUAAGCUGCUCAUCAGCU--UUGUUGAUUCGCAGUCGCUAAUGAAGUUCAGAAUGGCCCAAAAGCGGGA--------U
..-------..-.......(((.(..(.((--(..((((((.....(((((..((((((.--..))))))..))))).))))))..))).)..).)))(((......))).--------. ( -26.40)
>DroSim_CAF1 149755 86 - 1
UA-------UU-UUCC----------------UCUGUUGGCCCUAAGCUGCUCAUCAGCU--UUGUUGAUUCGCAGUCGCUAAUGAAGUUCAGAAUGGCCCAAAAGCGGGA--------U
..-------..-((((----------------.((.((((......(((((..((((((.--..))))))..))))).((((.((.....))...)))))))).)).))))--------. ( -23.30)
>DroEre_CAF1 158237 84 - 1
------------------------AGGCGC--UCUGUGGGCCCUAAGCUGCUCAUCAGCU--UUGUUGAUUCGCAGUCGCUAAUGAAGUUCAGAAUGGCCCACAAGCGGGA--------U
------------------------...(((--(.((((((((....(((((..((((((.--..))))))..))))).(((.....))).......))))))))))))...--------. ( -32.70)
>DroYak_CAF1 154440 120 - 1
UACCAUUUGUAUUUCAUCACCUCAAGGCGCUCUCUGUGGGCCCUAAGCUGCUCAUCAGCUAUUUGUUGAUUCGCAGCCGCUAAUGAAGUUCAGAAUGGCCCAAAAGCUGGAUGAUGCGAU
......(((((..(((((.((....)).(((.....((((((....(((((..((((((.....))))))..))))).(((.....))).......))))))..)))..)))))))))). ( -37.10)
>consensus
UA_______UG_UUCCUC_CC_C_AGGCGC__UCUGUUGGCCCUAAGCUGCUCAUCAGCU__UUGUUGAUUCGCAGUCGCUAAUGAAGUUCAGAAUGGCCCAAAAGCGGGA________U
................................((((((((((....(((((..((((((.....))))))..))))).(((.....))).......))))....)))))).......... (-21.94 = -22.38 +   0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,963,962 – 11,964,067
Length 105
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 74.85
Mean single sequence MFE -28.43
Consensus MFE -17.15
Energy contribution -19.40
Covariance contribution 2.25
Combinations/Pair 1.07
Mean z-score -1.94
Structure conservation index 0.60
SVM decision value 1.19
SVM RNA-class probability 0.927865
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11963962 105 + 22407834
GCGACUGCGAAUCAACAA--AGCUGAUGAGCAGCUUAGGGCCAACAGA--GCGACUUGUGGCGAGGAAACAGAAAUGGUAUAUGGCACAAUAC--CAUACCA---UAUACCAUU
.((.(..(((.((..(.(--(((((.....)))))).).(((....).--)))).)))..))).(....)...((((((((((((........--....)))---))))))))) ( -31.70)
>DroSec_CAF1 183401 86 + 1
GCGACUGCGAAUCAACAA--AGCUGAUGAGCAGCUUAGGGCCAACAGA--GCGCCUAGUGGUGAGGAA-CA-------UAUA-------------UAUACCA---UAUACCAUU
..(.((((..((((....--...))))..))))).(((((((....).--)).))))((((((.((..-..-------....-------------....)).---..)))))). ( -18.60)
>DroYak_CAF1 154480 111 + 1
GCGGCUGCGAAUCAACAAAUAGCUGAUGAGCAGCUUAGGGCCCACAGAGAGCGCCUUGAGGUGAUGAAAUACAAAUGGUAUAUGGUGUG---CCAUAUACUAUACUAAACCAUU
...(((((..((((.(.....).))))..)))))(((((((.(.......).)))))))(((..((.....)).(((((((((((....---))))))))))).....)))... ( -35.00)
>consensus
GCGACUGCGAAUCAACAA__AGCUGAUGAGCAGCUUAGGGCCAACAGA__GCGCCUUGUGGUGAGGAAACA_AAAUGGUAUAUGG_______C__UAUACCA___UAUACCAUU
..(.((((..((((.(.....).))))..)))))...((((((..((.......))..)))).............((((((((((.......)))))))))).......))... (-17.15 = -19.40 +   2.25)

alignment

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secondary structure

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Window 5

Location 11,963,962 – 11,964,067
Length 105
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 74.85
Mean single sequence MFE -31.43
Consensus MFE -18.22
Energy contribution -19.00
Covariance contribution 0.78
Combinations/Pair 1.11
Mean z-score -2.92
Structure conservation index 0.58
SVM decision value 3.29
SVM RNA-class probability 0.998931
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11963962 105 - 22407834
AAUGGUAUA---UGGUAUG--GUAUUGUGCCAUAUACCAUUUCUGUUUCCUCGCCACAAGUCGC--UCUGUUGGCCCUAAGCUGCUCAUCAGCU--UUGUUGAUUCGCAGUCGC
(((((((((---((((((.--.....)))))))))))))))...........((((..((....--.))..)))).....(((((..((((((.--..))))))..)))))... ( -36.00)
>DroSec_CAF1 183401 86 - 1
AAUGGUAUA---UGGUAUA-------------UAUA-------UG-UUCCUCACCACUAGGCGC--UCUGUUGGCCCUAAGCUGCUCAUCAGCU--UUGUUGAUUCGCAGUCGC
..((((...---.((.(((-------------....-------))-).))..)))).((((.((--(.....))))))).(((((..((((((.--..))))))..)))))... ( -21.60)
>DroYak_CAF1 154480 111 - 1
AAUGGUUUAGUAUAGUAUAUGG---CACACCAUAUACCAUUUGUAUUUCAUCACCUCAAGGCGCUCUCUGUGGGCCCUAAGCUGCUCAUCAGCUAUUUGUUGAUUCGCAGCCGC
..((((..((((((((((((((---....))))))))....))))))..)))).....(((.((((.....)))))))..(((((..((((((.....))))))..)))))... ( -36.70)
>consensus
AAUGGUAUA___UGGUAUA__G_______CCAUAUACCAUUU_UGUUUCCUCACCACAAGGCGC__UCUGUUGGCCCUAAGCUGCUCAUCAGCU__UUGUUGAUUCGCAGUCGC
...((.........(((((((((.....)))))))))................(((..((.......))..))).))...(((((..((((((.....))))))..)))))... (-18.22 = -19.00 +   0.78)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,964,000 – 11,964,107
Length 107
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 76.20
Mean single sequence MFE -25.33
Consensus MFE -13.81
Energy contribution -16.73
Covariance contribution 2.92
Combinations/Pair 1.07
Mean z-score -1.96
Structure conservation index 0.55
SVM decision value 0.04
SVM RNA-class probability 0.553681
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11964000 107 + 22407834
CCAACAGA--GCGACUUGUGGCGAGGAAACAGAAAUGGUAUAUGGCACAAUAC--CAUACCA---UAUACCAUUAUAGUCGAAAACAAAGACAUUUCAUAGUUACGUGUUGGCU
((((((..--(..(((.((((...(....)...((((((((((((........--....)))---)))))))))...(((.........)))...)))))))..).)))))).. ( -30.70)
>DroSec_CAF1 183439 88 + 1
CCAACAGA--GCGCCUAGUGGUGAGGAA-CA-------UAUA-------------UAUACCA---UAUACCAUUAUAGUCGAAAACAAAGACAUUUCAUAGUUACGUGUUGGCU
((((((.(--((...((((((((.((..-..-------....-------------....)).---..))))))))..(((.........)))........)))...)))))).. ( -17.10)
>DroYak_CAF1 154520 111 + 1
CCCACAGAGAGCGCCUUGAGGUGAUGAAAUACAAAUGGUAUAUGGUGUG---CCAUAUACUAUACUAAACCAUUAUGGUCGAAAACAAAGACAUUUCAUAGUUACGUGUUGGCU
((.(((...((((((....))).(((((((....(((((((((((....---)))))))))))..............(((.........)))))))))).)))...))).)).. ( -28.20)
>consensus
CCAACAGA__GCGCCUUGUGGUGAGGAAACA_AAAUGGUAUAUGG_______C__UAUACCA___UAUACCAUUAUAGUCGAAAACAAAGACAUUUCAUAGUUACGUGUUGGCU
((((((.....((((....))))..((((......((((((((((.......))))))))))...............(((.........))).)))).........)))))).. (-13.81 = -16.73 +   2.92)

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 11:11:16 2006