Locus 1641

Sequence ID 3R_DroMel_CAF1
Location 4,777,137 – 4,777,281
Length 144
Max. P 0.999345
window2699 window2700 window2701

overview

Window 9

Location 4,777,137 – 4,777,243
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.34
Mean single sequence MFE -28.52
Consensus MFE -9.72
Energy contribution -10.68
Covariance contribution 0.96
Combinations/Pair 1.21
Mean z-score -2.67
Structure conservation index 0.34
SVM decision value 1.91
SVM RNA-class probability 0.982294
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4777137 106 - 27905053
CAGGAUAAUGUCCGAGUAUCGUUCAGAACC--CGGAGAUUUU----CCAG--UCUAUAUAUUA-AU-AUAUAUAUAGAGAAACACU----UAAUAGGUCACGCAGUGACAUACACACACU
..(((.(((.((((.((.((.....)))).--)))).))).)----))..--(((((((((..-..-..)))))))))........----......(((((...)))))........... ( -27.10)
>DroSec_CAF1 12655 107 - 1
CAGGAUAAUGUCCGAGUAUCGUUCAGAACU--CGGAGAUUUU----CCAG--UCUAUAUAUUU-GUGGUAUAUAUAGAGAAACACU----UAAUAAGUCACGCAGUGACAUACACACACU
..(((.(((.(((((((.((.....)))))--)))).))).)----))..--(((((((((..-.....)))))))))........----......(((((...)))))........... ( -31.60)
>DroEre_CAF1 12780 107 - 1
CAGGAUUAUGUCUGAGUAUCGUUCAGAACU--CGGGGAUUUU----CCAG--CCUAUAUAUUA-GUGGUAUAUAUAGAGAAACUAU----AAGUCGGCCACGCAGUGACAUACAUACACC
..(((..((.(((((((.((.....)))))--)))).))..)----))..--......((((.-(((((...(((((.....))))----).....)))))..))))............. ( -26.10)
>DroYak_CAF1 12952 107 - 1
CAGGAUAAUGUCCGAGUAUCGUUCAGAACU--CGGAGAUUUU----CCAG--UCUAUAUAUUA-GUGGUAUAUAUAGAGCAAUACU----UAAUGGGCCACGCAGUGACAUACACACACC
..(((.(((.(((((((.((.....)))))--)))).))).)----))..--...........-(((((...(((.(((.....))----).))).)))))...(((.....)))..... ( -30.50)
>DroAna_CAF1 12660 111 - 1
CAGGCUAAU--------AUCGUUUAUAUCUAUCCGAUAUUUGGUUAUUAGCCCCUAUAUAUCAUGUGGGAUAUAUAGAAUA-UAUUUUUUGAAAAGGUCACGCAGUGGCAUACACACACC
..(((((((--------((((...(((((.....))))).))).)))))))).(((((((((......)))))))))....-..............(((((...)))))........... ( -27.30)
>consensus
CAGGAUAAUGUCCGAGUAUCGUUCAGAACU__CGGAGAUUUU____CCAG__UCUAUAUAUUA_GUGGUAUAUAUAGAGAAACACU____UAAUAGGUCACGCAGUGACAUACACACACC
..((..(((.((((....((.....)).....)))).)))......)).....((((((((........))))))))...................(((((...)))))........... ( -9.72 = -10.68 +   0.96)

alignment

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secondary structure

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Window 0

Location 4,777,173 – 4,777,281
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.12
Mean single sequence MFE -23.56
Consensus MFE -7.18
Energy contribution -7.90
Covariance contribution 0.72
Combinations/Pair 1.15
Mean z-score -3.41
Structure conservation index 0.30
SVM decision value 3.53
SVM RNA-class probability 0.999345
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4777173 108 + 27905053
UCUCUAUAUAUAU-AU-UAAUAUAUAGA--CUGG----AAAAUCUCCG--GGUUCUGAACGAUACUCGGACAUUAUCCUGGCCCAGCACUGACACACACACAC--AUAUAUAUAUAUAGA
..(((((((((((-((-...........--(.((----(.(((.((((--(((((.....)).))))))).))).))).)((...))................--..))))))))))))) ( -25.60)
>DroSec_CAF1 12691 101 + 1
UCUCUAUAUAUACCAC-AAAUAUAUAGA--CUGG----AAAAUCUCCG--AGUUCUGAACGAUACUCGGACAUUAUCCUGGUCCAGCACUGACACACACACAC--AC--------ACAGA
..(((((((((.....-..)))))))))--(.((----(.(((.((((--(((((.....)).))))))).))).))).)(((.......)))..........--..--------..... ( -23.40)
>DroEre_CAF1 12816 103 + 1
UCUCUAUAUAUACCAC-UAAUAUAUAGG--CUGG----AAAAUCCCCG--AGUUCUGAACGAUACUCAGACAUAAUCCUGGCCCAGCACUGACUCACACACACGCAC--------ACAGA
...((((((((.....-..))))))))(--((((----.....((..(--(..(((((.......))))).....))..)).)))))....................--------..... ( -17.70)
>DroYak_CAF1 12988 98 + 1
GCUCUAUAUAUACCAC-UAAUAUAUAGA--CUGG----AAAAUCUCCG--AGUUCUGAACGAUACUCGGACAUUAUCCUG-CCCAGCACUGACUCACACAC----AC--------ACAGA
(((((((((((.....-..)))))))))--..((----(.(((.((((--(((((.....)).))))))).))).)))..-....)).(((..........----..--------.))). ( -24.02)
>DroAna_CAF1 12699 100 + 1
AUUCUAUAUAUCCCACAUGAUAUAUAGGGGCUAAUAACCAAAUAUCGGAUAGAUAUAAACGAU--------AUUAGCCUGGUCCAGCACUGGCACACACGC----AC--------CCAGA
...(((((((((......)))))))))(((..........(((((((..((....))..))))--------))).((.(((((((....))).)).)).))----.)--------))... ( -27.10)
>consensus
UCUCUAUAUAUACCAC_UAAUAUAUAGA__CUGG____AAAAUCUCCG__AGUUCUGAACGAUACUCGGACAUUAUCCUGGCCCAGCACUGACACACACACAC__AC________ACAGA
..(((((((((........)))))))))..(((....................(((((.......))))).......(((...)))..............................))). ( -7.18 =  -7.90 +   0.72)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,777,173 – 4,777,281
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.12
Mean single sequence MFE -30.98
Consensus MFE -10.14
Energy contribution -10.78
Covariance contribution 0.64
Combinations/Pair 1.19
Mean z-score -2.49
Structure conservation index 0.33
SVM decision value 1.89
SVM RNA-class probability 0.981567
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4777173 108 - 27905053
UCUAUAUAUAUAUAU--GUGUGUGUGUGUCAGUGCUGGGCCAGGAUAAUGUCCGAGUAUCGUUCAGAACC--CGGAGAUUUU----CCAG--UCUAUAUAUUA-AU-AUAUAUAUAGAGA
(((((((((((((..--(((((((((.(((.......)))))(((.(((.((((.((.((.....)))).--)))).))).)----))..--..)))))))..-))-))))))))))).. ( -32.90)
>DroSec_CAF1 12691 101 - 1
UCUGU--------GU--GUGUGUGUGUGUCAGUGCUGGACCAGGAUAAUGUCCGAGUAUCGUUCAGAACU--CGGAGAUUUU----CCAG--UCUAUAUAUUU-GUGGUAUAUAUAGAGA
(((((--------((--(((.(..(......)..)(((((..(((.(((.(((((((.((.....)))))--)))).))).)----)).)--)))).......-....)))))))))).. ( -32.10)
>DroEre_CAF1 12816 103 - 1
UCUGU--------GUGCGUGUGUGUGAGUCAGUGCUGGGCCAGGAUUAUGUCUGAGUAUCGUUCAGAACU--CGGGGAUUUU----CCAG--CCUAUAUAUUA-GUGGUAUAUAUAGAGA
(((((--------(((..(..(..(......)..)(((((..(((..((.(((((((.((.....)))))--)))).))..)----)).)--)))).......-...)..)))))))).. ( -28.70)
>DroYak_CAF1 12988 98 - 1
UCUGU--------GU----GUGUGUGAGUCAGUGCUGGG-CAGGAUAAUGUCCGAGUAUCGUUCAGAACU--CGGAGAUUUU----CCAG--UCUAUAUAUUA-GUGGUAUAUAUAGAGC
(((((--------((----(((..(......)..)((((-(.(((.(((.(((((((.((.....)))))--)))).))).)----)).)--)))).......-.....))))))))).. ( -31.60)
>DroAna_CAF1 12699 100 - 1
UCUGG--------GU----GCGUGUGUGCCAGUGCUGGACCAGGCUAAU--------AUCGUUUAUAUCUAUCCGAUAUUUGGUUAUUAGCCCCUAUAUAUCAUGUGGGAUAUAUAGAAU
....(--------((----.((.(..(....)..))).))).(((((((--------((((...(((((.....))))).))).)))))))).(((((((((......)))))))))... ( -29.60)
>consensus
UCUGU________GU__GUGUGUGUGUGUCAGUGCUGGGCCAGGAUAAUGUCCGAGUAUCGUUCAGAACU__CGGAGAUUUU____CCAG__UCUAUAUAUUA_GUGGUAUAUAUAGAGA
..................................((((........(((.((((....((.....)).....)))).)))......))))...((((((((........))))))))... (-10.14 = -10.78 +   0.64)

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 10:15:33 2006