Locus 5233

Sequence ID 2R_DroMel_CAF1
Location 17,042,604 – 17,042,749
Length 145
Max. P 0.726002
window8358 window8359 window8360

overview

Window 8

Location 17,042,604 – 17,042,709
Length 105
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.50
Mean single sequence MFE -31.32
Consensus MFE -13.17
Energy contribution -13.40
Covariance contribution 0.23
Combinations/Pair 1.22
Mean z-score -2.20
Structure conservation index 0.42
SVM decision value 0.41
SVM RNA-class probability 0.726002
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17042604 105 + 20766785
UUAGCAUGCGAUUUUGCUCGG----UUCGUG------AUUUCACAAAGCGGUGCGAAUCGA---CGGCCACAAGGGCUCACCUUUGUACGCCAAA--CAUGAAUAAUGCUCAUGAAUCGA
..(((((.((((((.(((((.----((.(((------....))).)).))).)))))))).---.(((.(((((((....)))))))..)))...--........))))).......... ( -31.00)
>DroSec_CAF1 135906 107 + 1
UUAGCAUUCGAUU-UGUUCGG----UUCGUG------AUUUCACACAGCGGUGCGAAUCGACGACGGCCACAAGGGCUCACCUUUGUACGCCAAA--CAUGAAUAAUGCUCAUGAAUCGA
.......((((((-(((.(.(----((.(((------......)))))).).)))))))))(((.(((.(((((((....)))))))..)))...--(((((.......)))))..))). ( -34.70)
>DroSim_CAF1 144153 107 + 1
CUAGCAUUCGAUU-UGUUCGG----UUCGUG------AUUUCACAAAGCGGUGCGAAUCGACGACGGCCACAAGGGCUCACCUUUGUACGCCAAA--CAUGAAUAAUGCUCAUGAAUCGA
.......((((((-((((((.----((.(((------....))).)).))).)))))))))(((.(((.(((((((....)))))))..)))...--(((((.......)))))..))). ( -35.20)
>DroEre_CAF1 140100 107 + 1
CAAGCAUUCAAUU----UCGG----CUCGUGAUUGUGAUUUCACAAUGCGGCGCGAAUCGA---CGGCCACAAGGGCUCACCUUUGUACGCCGAA--CAUGAAUAAUGCUCAUGAAUCGA
............(----((((----(.(((.((((((....))))))))))).))))((((---((((.(((((((....)))))))..))))..--(((((.......)))))..)))) ( -36.40)
>DroYak_CAF1 149597 101 + 1
UUGGCCAGCGAUU----UCGG----UUCGUG------AUUUCACAAUGCGGCGCGAAUCGA---CGGCCACAAGGGCUCACCUUUGUGCGCCAAA--CAUGAAUAAUGCUCAUGAAUCGA
........(((((----((((----((((((------.(..(.....)..)))))))))))---.(((((((((((....)))))))).)))...--(((((.......)))))))))). ( -36.30)
>DroAna_CAF1 155494 106 + 1
AAAAAAAUAAAUA----CUGAACCAAUCAUG----ACAUUUCACAAGUUUGCGCAAAUUUU---UGGGAACAAUAGCCCACCAUUGUACGCCAAAAAGAUCAAUAAUAA---UGUCACAA
.............----............((----(((((........(((......((((---((((.(((((........))))).).)))))))...)))....))---)))))... ( -14.30)
>consensus
UUAGCAUUCGAUU____UCGG____UUCGUG______AUUUCACAAAGCGGCGCGAAUCGA___CGGCCACAAGGGCUCACCUUUGUACGCCAAA__CAUGAAUAAUGCUCAUGAAUCGA
...((...(((......)))........(((..........)))...))........((((....(((.(((((((....)))))))..))).....(((((.......)))))..)))) (-13.17 = -13.40 +   0.23)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,042,604 – 17,042,709
Length 105
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.50
Mean single sequence MFE -31.15
Consensus MFE -18.12
Energy contribution -17.98
Covariance contribution -0.13
Combinations/Pair 1.30
Mean z-score -1.59
Structure conservation index 0.58
SVM decision value 0.31
SVM RNA-class probability 0.684046
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17042604 105 - 20766785
UCGAUUCAUGAGCAUUAUUCAUG--UUUGGCGUACAAAGGUGAGCCCUUGUGGCCG---UCGAUUCGCACCGCUUUGUGAAAU------CACGAA----CCGAGCAAAAUCGCAUGCUAA
(((((.((((((.....))))))--...(((.(((((.((....)).)))))))))---))))...(((.((.((((((....------))))))----.)).((......)).)))... ( -30.40)
>DroSec_CAF1 135906 107 - 1
UCGAUUCAUGAGCAUUAUUCAUG--UUUGGCGUACAAAGGUGAGCCCUUGUGGCCGUCGUCGAUUCGCACCGCUGUGUGAAAU------CACGAA----CCGAACA-AAUCGAAUGCUAA
..........((((((.....((--((((((.(((((.((....)).)))))))).((((.(((((((((....))))).)))------))))).----..)))))-.....)))))).. ( -33.70)
>DroSim_CAF1 144153 107 - 1
UCGAUUCAUGAGCAUUAUUCAUG--UUUGGCGUACAAAGGUGAGCCCUUGUGGCCGUCGUCGAUUCGCACCGCUUUGUGAAAU------CACGAA----CCGAACA-AAUCGAAUGCUAG
..........((((((.....((--((((((.(((((.((....)).)))))))).((((.((((((((......)))).)))------))))).----..)))))-.....)))))).. ( -31.10)
>DroEre_CAF1 140100 107 - 1
UCGAUUCAUGAGCAUUAUUCAUG--UUCGGCGUACAAAGGUGAGCCCUUGUGGCCG---UCGAUUCGCGCCGCAUUGUGAAAUCACAAUCACGAG----CCGA----AAUUGAAUGCUUG
.........((((((...(((..--((((((.....((((.....))))(((((((---......)).)))))((((((....)))))).....)----))))----)..))))))))). ( -35.10)
>DroYak_CAF1 149597 101 - 1
UCGAUUCAUGAGCAUUAUUCAUG--UUUGGCGCACAAAGGUGAGCCCUUGUGGCCG---UCGAUUCGCGCCGCAUUGUGAAAU------CACGAA----CCGA----AAUCGCUGGCCAA
(((((.((((((.....))))))--...(((.(((((.((....)).)))))))))---))))...(.(((((.(((((....------))))).----..(.----...))).)))).. ( -31.70)
>DroAna_CAF1 155494 106 - 1
UUGUGACA---UUAUUAUUGAUCUUUUUGGCGUACAAUGGUGGGCUAUUGUUCCCA---AAAAUUUGCGCAAACUUGUGAAAUGU----CAUGAUUGGUUCAG----UAUUUAUUUUUUU
(..(((((---((..........(((((((.(.(((((((....))))))).))))---))))....((((....)))).)))))----))..).........----............. ( -24.90)
>consensus
UCGAUUCAUGAGCAUUAUUCAUG__UUUGGCGUACAAAGGUGAGCCCUUGUGGCCG___UCGAUUCGCACCGCUUUGUGAAAU______CACGAA____CCGA____AAUCGAAUGCUAA
((((..((((((.....))))))....((((.(((((.((....)).)))))))))...))))((((((......))))))....................................... (-18.12 = -17.98 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,042,634 – 17,042,749
Length 115
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 92.23
Mean single sequence MFE -38.24
Consensus MFE -28.50
Energy contribution -27.78
Covariance contribution -0.72
Combinations/Pair 1.12
Mean z-score -1.80
Structure conservation index 0.75
SVM decision value 0.12
SVM RNA-class probability 0.592212
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17042634 115 - 20766785
AAAGCCUUUGAAACAGAGGGCAGAACUGAACGAUUAUCGAUCGAUUCAUGAGCAUUAUUCAUGUUUGGCGUACAAAGGUGAGCCCUUGUGGCCG---UCGAUUCGCACCGCUUUGUGA
...((((((......)))))).........((.....))((((((.((((((.....))))))...(((.(((((.((....)).)))))))))---)))))(((((......))))) ( -31.60)
>DroSec_CAF1 135935 116 - 1
AAAGCCUUUGAAACAGAGGGCAGAACUG--CGAUUAUCGAUCGAUUCAUGAGCAUUAUUCAUGUUUGGCGUACAAAGGUGAGCCCUUGUGGCCGUCGUCGAUUCGCACCGCUGUGUGA
....((((((...))))))((((...((--(((..(((((.((((.((((((.....))))))...(((.(((((.((....)).))))))))))))))))))))))...)))).... ( -40.80)
>DroSim_CAF1 144182 116 - 1
AAAGCCUUUGAAACAGAGGGCAGAACUG--CGAUUAUCGAUCGAUUCAUGAGCAUUAUUCAUGUUUGGCGUACAAAGGUGAGCCCUUGUGGCCGUCGUCGAUUCGCACCGCUUUGUGA
...((((((......))))))((...((--(((..(((((.((((.((((((.....))))))...(((.(((((.((....)).))))))))))))))))))))))...))...... ( -38.30)
>DroEre_CAF1 140132 112 - 1
AACACCUUUGAAACAGAGGGCA-AACUG--CGAUUAGCGAUCGAUUCAUGAGCAUUAUUCAUGUUCGGCGUACAAAGGUGAGCCCUUGUGGCCG---UCGAUUCGCGCCGCAUUGUGA
....((((((...))))))(((-(..((--((....(((((((((....((((((.....))))))(((.(((((.((....)).)))))))))---)))).))))..)))))))).. ( -40.10)
>DroYak_CAF1 149623 112 - 1
AACACCUUUGAAACGGAGGGCA-CUCUG--CGAUUAGUGAUCGAUUCAUGAGCAUUAUUCAUGUUUGGCGCACAAAGGUGAGCCCUUGUGGCCG---UCGAUUCGCGCCGCAUUGUGA
....((((((...)))))).((-(..((--((....(((((((((.((((((.....))))))...(((.(((((.((....)).)))))))))---)))).))))..))))..))). ( -40.40)
>consensus
AAAGCCUUUGAAACAGAGGGCAGAACUG__CGAUUAUCGAUCGAUUCAUGAGCAUUAUUCAUGUUUGGCGUACAAAGGUGAGCCCUUGUGGCCG___UCGAUUCGCACCGCUUUGUGA
....((((((...))))))...................((((((..((((((.....))))))..((((.(((((.((....)).)))))))))...))))))((((......)))). (-28.50 = -27.78 +  -0.72)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:46 2006