Locus 517

Sequence ID 2R_DroMel_CAF1
Location 2,796,287 – 2,796,487
Length 200
Max. P 0.887025
window976 window977 window978 window979 window980

overview

Window 6

Location 2,796,287 – 2,796,387
Length 100
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 82.76
Mean single sequence MFE -34.34
Consensus MFE -20.13
Energy contribution -20.65
Covariance contribution 0.52
Combinations/Pair 1.08
Mean z-score -2.52
Structure conservation index 0.59
SVM decision value 0.94
SVM RNA-class probability 0.887025
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2796287 100 + 20766785
---CUCAGACUCAGACCUGGACUCGCG--UCAU-GACUCAACUGCAGGCGGCCUAAGUCCGACCGGUCCGAUCCGAUCCGGUCUGAGAU-CACGUACACAUAUAC--UC
---....((((((((((.((((.((.(--((..-((((...(((....)))....)))).)))))))))(((...))).)))))))).)-)..............--.. ( -31.60)
>DroSec_CAF1 3241 98 + 1
-----CAGACUCAGACCUGGACUCGCG--UCAU-GACUCAACUGCAGGCGGCCUAAGUCCGACCGGUCCGAUGCGAUCCGGUCUGAGAU-CACGUACACAUAUAC--UC
-----..((((((((((.(((.(((((--((..-((((........((((((....).))).)))))).)))))))))))))))))).)-)..............--.. ( -37.20)
>DroSim_CAF1 3315 98 + 1
-----CAGACUCAGACCUGGACUCGCG--UCAU-GACUCAACUGCAGGCGGGCUAAGUCCGACCGGUCCGAUGCGAUCCGGUCUGAGAU-CACGUACACAUAUAC--UC
-----..((((((((((.(((.(((((--((..-((((........(((((((...))))).)))))).)))))))))))))))))).)-)..............--.. ( -40.50)
>DroEre_CAF1 3226 100 + 1
--UAUCAGACUCAGACCUGGACUCGCGACUCAUGGACUCAUGGACUCAUGACUCAAGAGCGACCGGUCCG-----AUCCGGUCUGAGAU-CACGUACACAUACAAAUG-
--.....((((((((((((((((.(((.(((...((.(((((....))))).))..))))).).))))))-----....)))))))).)-).................- ( -34.40)
>DroYak_CAF1 3292 101 + 1
UGUCUCAGAUUCAGACCUGGACUCGCG--UCAU-GACUCAACUGCAGGCGGCUUAAGACCGACCGGUCCG-----AUCCGGUCUGAGAUACAUAUACACAUAUACAUUU
(((((((((.......(((((.(((((--((.(-(.(......)))))))......((((....))))))-----)))))))))))))))................... ( -28.01)
>consensus
____UCAGACUCAGACCUGGACUCGCG__UCAU_GACUCAACUGCAGGCGGCCUAAGUCCGACCGGUCCGAU_CGAUCCGGUCUGAGAU_CACGUACACAUAUAC__UC
.........((((((((((((((.(((.......((((...(((....)))....)))))).).)))))).........))))))))...................... (-20.13 = -20.65 +   0.52)

alignment

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secondary structure

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Window 7

Location 2,796,287 – 2,796,387
Length 100
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 82.76
Mean single sequence MFE -38.14
Consensus MFE -20.86
Energy contribution -21.46
Covariance contribution 0.60
Combinations/Pair 1.11
Mean z-score -2.02
Structure conservation index 0.55
SVM decision value -0.05
SVM RNA-class probability 0.510044
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2796287 100 - 20766785
GA--GUAUAUGUGUACGUG-AUCUCAGACCGGAUCGGAUCGGACCGGUCGGACUUAGGCCGCCUGCAGUUGAGUC-AUGA--CGCGAGUCCAGGUCUGAGUCUGAG---
..--((((....))))...-..(((((((....(((((((((((((((((((((((.((.....))...))))))-.)))--).)).)))).))))))))))))))--- ( -39.70)
>DroSec_CAF1 3241 98 - 1
GA--GUAUAUGUGUACGUG-AUCUCAGACCGGAUCGCAUCGGACCGGUCGGACUUAGGCCGCCUGCAGUUGAGUC-AUGA--CGCGAGUCCAGGUCUGAGUCUG-----
((--(..((((....))))-..))).((((((.(((...))).))))))((((((((((((....).........-..((--(....)))..))))))))))).----- ( -38.40)
>DroSim_CAF1 3315 98 - 1
GA--GUAUAUGUGUACGUG-AUCUCAGACCGGAUCGCAUCGGACCGGUCGGACUUAGCCCGCCUGCAGUUGAGUC-AUGA--CGCGAGUCCAGGUCUGAGUCUG-----
..--((((....))))..(-(.((((((((.(((...)))((((((((((((((((((..(....).))))))))-.)))--).)).)))).))))))))))..----- ( -39.40)
>DroEre_CAF1 3226 100 - 1
-CAUUUGUAUGUGUACGUG-AUCUCAGACCGGAU-----CGGACCGGUCGCUCUUGAGUCAUGAGUCCAUGAGUCCAUGAGUCGCGAGUCCAGGUCUGAGUCUGAUA--
-......((((....))))-...(((((((((((-----(((((..((.((((..((.(((((....))))).))...)))).))..)))).)))))).))))))..-- ( -38.50)
>DroYak_CAF1 3292 101 - 1
AAAUGUAUAUGUGUAUAUGUAUCUCAGACCGGAU-----CGGACCGGUCGGUCUUAAGCCGCCUGCAGUUGAGUC-AUGA--CGCGAGUCCAGGUCUGAAUCUGAGACA
..(((((((....))))))).(((((((.(((((-----((((((((((((.(((((((.....))..))))).)-.)))--).)).)))).))))))..))))))).. ( -34.70)
>consensus
GA__GUAUAUGUGUACGUG_AUCUCAGACCGGAUCG_AUCGGACCGGUCGGACUUAGGCCGCCUGCAGUUGAGUC_AUGA__CGCGAGUCCAGGUCUGAGUCUGA____
......................(((((((((........)((((((.((((((((((.(.(....).))))))))..)))....)).)))).))))))))......... (-20.86 = -21.46 +   0.60)

alignment

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secondary structure

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Window 8

Location 2,796,321 – 2,796,414
Length 93
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 80.79
Mean single sequence MFE -29.92
Consensus MFE -19.52
Energy contribution -20.20
Covariance contribution 0.68
Combinations/Pair 1.17
Mean z-score -1.63
Structure conservation index 0.65
SVM decision value 0.03
SVM RNA-class probability 0.546465
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2796321 93 - 20766785
CAGCAUGCGAGUGAAUACACAACGUACGA--GUAUAUGUGUACGUG-AUCUCAGACCGGAUCGGAUCGGACCGGUCGGACUUAGGCCGCCUGCAGU
..(((.(((.(((....))).(((((((.--.......))))))).-...((.((((((.(((...))).)))))).)).......))).)))... ( -29.90)
>DroSec_CAF1 3273 93 - 1
CAGCAUGCGAGUGAAUAUACAACGUACGA--GUAUAUGUGUACGUG-AUCUCAGACCGGAUCGCAUCGGACCGGUCGGACUUAGGCCGCCUGCAGU
..(((.(((.((.........(((((((.--.......))))))).-...((.((((((.(((...))).)))))).)).....))))).)))... ( -29.80)
>DroSim_CAF1 3347 93 - 1
CAGCAUGCGAGUGAAUAUACAACGUACGA--GUAUAUGUGUACGUG-AUCUCAGACCGGAUCGCAUCGGACCGGUCGGACUUAGCCCGCCUGCAGU
..(((.(((.((.........(((((((.--.......))))))).-...((.((((((.(((...))).)))))).))....)).))).)))... ( -29.90)
>DroEre_CAF1 3264 82 - 1
CAGCAUGCGAGUGAAUACAC--------CAUUUGUAUGUGUACGUG-AUCUCAGACCGGAU-----CGGACCGGUCGCUCUUGAGUCAUGAGUCCA
..(((((((((((.......--------)))))))))))...((((-(.((((((((((..-----....)))))).....)))))))))...... ( -30.80)
>DroYak_CAF1 3329 90 - 1
CAGCAUGCGAGUGAAUAUAA-AUGUAUAAAUGUAUAUGUGUAUAUGUAUCUCAGACCGGAU-----CGGACCGGUCGGUCUUAAGCCGCCUGCAGU
..(((.(((((...(((((.-(((((((....))))))).)))))....))).((((((..-----....))))))(((.....))))).)))... ( -29.20)
>consensus
CAGCAUGCGAGUGAAUAUACAACGUACGA__GUAUAUGUGUACGUG_AUCUCAGACCGGAUCG_AUCGGACCGGUCGGACUUAGGCCGCCUGCAGU
..(((.(((.(((.((((((...........))))))...)))..........((((((.((......))))))))..........))).)))... (-19.52 = -20.20 +   0.68)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,796,387 – 2,796,487
Length 100
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 88.66
Mean single sequence MFE -20.60
Consensus MFE -16.42
Energy contribution -17.10
Covariance contribution 0.68
Combinations/Pair 1.07
Mean z-score -1.81
Structure conservation index 0.80
SVM decision value 0.79
SVM RNA-class probability 0.850324
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2796387 100 + 20766785
GUACGUUGUGUAUUCACUCGCAUGCUGCAGAAGCAACCUUUACCUUUCCUUUCCAUUCGCUACCUC------CGUUGCCGCUGCUCUGGAUGCUUUCACUUUCCAU
.......(((....)))..((((.(.((((..(((((.............................------.)))))..))))...).))))............. ( -17.91)
>DroSec_CAF1 3339 100 + 1
GUACGUUGUAUAUUCACUCGCAUGCUGCAGAGGCAACCUUUACCUUUCCUUUCCAUUCGCUACCUC------CGUUGCCGCUGCUCUGGAUGCUUUCACUUUCCAU
...................((((.(.((((.((((((.............................------.)))))).))))...).))))............. ( -20.61)
>DroSim_CAF1 3413 100 + 1
GUACGUUGUAUAUUCACUCGCAUGCUGCAGAGGCAACCUUUACCUUUCCUUUCCAUUCGCUACCUC------CGUCGCCGCUGCUCUGGAUGCUUUCACUUUCCAU
...................((((.(.((((.(((.((.............................------.)).))).))))...).))))............. ( -16.51)
>DroEre_CAF1 3326 93 + 1
-------GUGUAUUCACUCGCAUGCUGCAGCGGCAACCUUUACCUUUCCUUUCCAUUUGCUAUCUC------CGCUGCCGCUGCUCUGGAUGCUUUCACUUUCCAG
-------(((....)))..((((.(.(((((((((...............................------...)))))))))...).))))............. ( -24.08)
>DroYak_CAF1 3393 105 + 1
AUACAU-UUAUAUUCACUCGCAUGCUGCAGAGGCAACCUUUGCCUUUCCUUUCUAUUUGCUAUCUCCAGUGCCGCUGCUGCUGCUCUGGAUGCUUUCACUUUCCAU
......-............(((....(((((((...))))))).....................(((((.((.((....)).)).))))))))............. ( -23.90)
>consensus
GUACGUUGUAUAUUCACUCGCAUGCUGCAGAGGCAACCUUUACCUUUCCUUUCCAUUCGCUACCUC______CGUUGCCGCUGCUCUGGAUGCUUUCACUUUCCAU
...................((((.(.((((.((((((....................................)))))).))))...).))))............. (-16.42 = -17.10 +   0.68)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,796,387 – 2,796,487
Length 100
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 88.66
Mean single sequence MFE -26.09
Consensus MFE -18.82
Energy contribution -18.50
Covariance contribution -0.32
Combinations/Pair 1.19
Mean z-score -1.99
Structure conservation index 0.72
SVM decision value 0.40
SVM RNA-class probability 0.719820
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2796387 100 - 20766785
AUGGAAAGUGAAAGCAUCCAGAGCAGCGGCAACG------GAGGUAGCGAAUGGAAAGGAAAGGUAAAGGUUGCUUCUGCAGCAUGCGAGUGAAUACACAACGUAC
.((((..((....)).))))..(((...((..((------((((((((.....................))))))))))..)).)))..(((....)))....... ( -24.60)
>DroSec_CAF1 3339 100 - 1
AUGGAAAGUGAAAGCAUCCAGAGCAGCGGCAACG------GAGGUAGCGAAUGGAAAGGAAAGGUAAAGGUUGCCUCUGCAGCAUGCGAGUGAAUAUACAACGUAC
.((((..((....)).))))..(((...((..((------((((((((.....................))))))))))..)).)))................... ( -25.60)
>DroSim_CAF1 3413 100 - 1
AUGGAAAGUGAAAGCAUCCAGAGCAGCGGCGACG------GAGGUAGCGAAUGGAAAGGAAAGGUAAAGGUUGCCUCUGCAGCAUGCGAGUGAAUAUACAACGUAC
.((((..((....)).))))..(((...((..((------((((((((.....................))))))))))..)).)))................... ( -27.10)
>DroEre_CAF1 3326 93 - 1
CUGGAAAGUGAAAGCAUCCAGAGCAGCGGCAGCG------GAGAUAGCAAAUGGAAAGGAAAGGUAAAGGUUGCCGCUGCAGCAUGCGAGUGAAUACAC-------
(((((..((....)).))))).(((((((((((.------...((......(....)......))....)))))))))))...................------- ( -29.60)
>DroYak_CAF1 3393 105 - 1
AUGGAAAGUGAAAGCAUCCAGAGCAGCAGCAGCGGCACUGGAGAUAGCAAAUAGAAAGGAAAGGCAAAGGUUGCCUCUGCAGCAUGCGAGUGAAUAUAA-AUGUAU
.((((..((....)).))))..(((((.((((.((((((.......((...............))...)).)))).)))).)).)))............-...... ( -23.56)
>consensus
AUGGAAAGUGAAAGCAUCCAGAGCAGCGGCAACG______GAGGUAGCGAAUGGAAAGGAAAGGUAAAGGUUGCCUCUGCAGCAUGCGAGUGAAUAUACAACGUAC
.((((..((....)).))))..((((.((((((....................................)))))).)))).......................... (-18.82 = -18.50 +  -0.32)

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 09:40:45 2006