Locus 9035

Sequence ID 3R_DroMel_CAF1
Location 24,182,873 – 24,183,075
Length 202
Max. P 0.978164
window14471 window14472 window14473

overview

Window 1

Location 24,182,873 – 24,182,979
Length 106
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 81.03
Mean single sequence MFE -19.02
Consensus MFE -15.10
Energy contribution -15.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.79
SVM decision value 0.70
SVM RNA-class probability 0.826627
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24182873 106 + 27905053
UCGCCCCUGGUCCACCGA----------AAAAUGUGUAUGCAAAAAUGCAAUAAGCGAGCACAGCUUAAAUAAAAUGCAUUUCAAUGAUUGCAUUUUGGAUUAAAGCAACAAACAU
..((...((((((.....----------......(((((......))))).(((((.......)))))...((((((((..........))))))))))))))..))......... ( -21.90)
>DroPse_CAF1 5254 101 + 1
UCGGA----------CAA--AAGGUUUCCAAAUUUGUAUGCAAAAAUGCAAUAAGCGAGUGCAGCUUAAAUAAAAUGCAUUUCAAUGAUUGCAUUUUGGAUUAAAACAACAAC---
.....----------...--......(((((.((((....))))((((((((....(((((((............))))))).....))))))))))))).............--- ( -19.60)
>DroSec_CAF1 5888 105 + 1
UCGACCCUGUCC-CCCGA----------AAAAUGUGUAUGCAAAAAUGCAAUAAGCGAGCACAGCUUAAAUAAAAUGCAUUUCAAUGAUUGCAUUUUGGAUUAAAGCAACAAACAU
............-.....----------....(((((.(((.............))).)))))((((...(((((((((..........))))))))).....))))......... ( -19.02)
>DroEre_CAF1 8794 92 + 1
--------------CCAA----------AAAAUGUGUAUGCAAAAAUGCAAUAAGCGAGCGCAGCUUAAAUAAAAUGCAUUUCAAUGAUUGCAUUUUGGAUUAAACCAACAAACAU
--------------....----------.....((((.((((....)))).(((((.......)))))..(((((((((..........)))))))))..............)))) ( -16.00)
>DroYak_CAF1 6587 105 + 1
UCGUUAGGGGC-CACCAA----------AAAAUGUAUAUGCAAAAAUGCAAUAAGCGAGCGCAGCUUAAAUAAAAUGCAUUUCAAUGAUUGCAUUUUGGAUUAAACCAACAAACAU
..(((.((...-..((((----------(((((((((.((((....)))).(((((.......)))))......))))))))..(((....))))))))......)))))...... ( -19.50)
>DroAna_CAF1 4507 104 + 1
------------CACCACACAAGCCUUUCAAAUUUGUAUGCAAAAAUGCAAUAAGCGAGUGCAGCUUAAAUAAAAUGCAUUUCAAUGAUUGCAUUUUGGAUUAAAACAACAAAAAU
------------..((......((....((....))...)).((((((((((....(((((((............))))))).....))))))))))))................. ( -18.10)
>consensus
UCG__________ACCAA__________AAAAUGUGUAUGCAAAAAUGCAAUAAGCGAGCGCAGCUUAAAUAAAAUGCAUUUCAAUGAUUGCAUUUUGGAUUAAAACAACAAACAU
......................................((((....)))).(((((.......)))))..(((((((((..........))))))))).................. (-15.10 = -15.10 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 24,182,979 – 24,183,075
Length 96
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 78.49
Mean single sequence MFE -19.47
Consensus MFE -10.66
Energy contribution -11.62
Covariance contribution 0.96
Combinations/Pair 1.12
Mean z-score -2.50
Structure conservation index 0.55
SVM decision value 1.81
SVM RNA-class probability 0.978164
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24182979 96 + 27905053
-UCGACAGGGCAC-AACAAUAACAUCGAGAACAGUCGACAAUUCUUUGUGCAAAACC--------UGCAUACAUACUC-GUACUAUAUACAGUACCCCAUGCCCAUU
-......(((((.-............(((.......((....))..((((((.....--------))))))....)))-(((((......)))))....)))))... ( -20.60)
>DroSec_CAF1 5993 96 + 1
-UCGACAGGGCAC-AACAAUAACAUCGAGAACAGUCGACAGUUCUUUGUGCAAAACC--------UGCAUACAUACCC-GUACUAUACACAGUAUCCCAUGCCCAUU
-......(((((.-............((((((........))))))((((((.....--------)))))).......-(((((......)))))....)))))... ( -20.90)
>DroSim_CAF1 5019 96 + 1
-UCGACAGGGCAC-AACAAUAACAUCGAGAACAGUCGACAGUUCUUUGUGCAAAACC--------UGCAUACAUACCC-GUACUAUACACAGUAUCCCAUGCCCAUU
-......(((((.-............((((((........))))))((((((.....--------)))))).......-(((((......)))))....)))))... ( -20.90)
>DroEre_CAF1 8886 93 + 1
UUCGACUGGGCAC-AACAAUAACAUCCACAGCAGUCGACAUCUCUUUGUGCAAUACCUAC--UCGUACAUACAUACCC-GCACUGUAUA----------UACCCAUU
......(((((((-((........((.((....)).)).......)))))).........--..(((.(((((.....-....))))).----------)))))).. ( -13.06)
>DroYak_CAF1 6692 100 + 1
UUCGACUGGGCACCAACAAUAACAGCCAGAGACAUCGACAUCUCUUUGUGCAAAUCGUACAAACAUACAUACAUACCCCUUACCAUAUAGAG-------UGCCCAUU
......((((((((.............(((((........)))))((((((.....))))))...........................).)-------)))))).. ( -21.90)
>consensus
_UCGACAGGGCAC_AACAAUAACAUCGAGAACAGUCGACAGUUCUUUGUGCAAAACC________UGCAUACAUACCC_GUACUAUAUACAGUA_CCCAUGCCCAUU
.......(((((..............((((((........))))))((((((.............))))))............................)))))... (-10.66 = -11.62 +   0.96)

alignment

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secondary structure

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dotplot

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Window 3

Location 24,182,979 – 24,183,075
Length 96
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 78.49
Mean single sequence MFE -28.52
Consensus MFE -15.54
Energy contribution -15.26
Covariance contribution -0.28
Combinations/Pair 1.33
Mean z-score -1.90
Structure conservation index 0.54
SVM decision value 0.33
SVM RNA-class probability 0.689624
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24182979 96 - 27905053
AAUGGGCAUGGGGUACUGUAUAUAGUAC-GAGUAUGUAUGCA--------GGUUUUGCACAAAGAAUUGUCGACUGUUCUCGAUGUUAUUGUU-GUGCCCUGUCGA-
....((((.((....(((((((((....-.....))))))))--------).....((((((.....((((((......))))))......))-))))))))))..- ( -27.30)
>DroSec_CAF1 5993 96 - 1
AAUGGGCAUGGGAUACUGUGUAUAGUAC-GGGUAUGUAUGCA--------GGUUUUGCACAAAGAACUGUCGACUGUUCUCGAUGUUAUUGUU-GUGCCCUGUCGA-
....((((.((....(((((((((....-.....))))))))--------).....((((((..(((.(((((......))))))))....))-))))))))))..- ( -27.80)
>DroSim_CAF1 5019 96 - 1
AAUGGGCAUGGGAUACUGUGUAUAGUAC-GGGUAUGUAUGCA--------GGUUUUGCACAAAGAACUGUCGACUGUUCUCGAUGUUAUUGUU-GUGCCCUGUCGA-
....((((.((....(((((((((....-.....))))))))--------).....((((((..(((.(((((......))))))))....))-))))))))))..- ( -27.80)
>DroEre_CAF1 8886 93 - 1
AAUGGGUA----------UAUACAGUGC-GGGUAUGUAUGUACGA--GUAGGUAUUGCACAAAGAGAUGUCGACUGCUGUGGAUGUUAUUGUU-GUGCCCAGUCGAA
..((((((----------((.(((((((-((.(((.(((......--))).))))))))).....((((((.((....)).))))))..))))-)))))))...... ( -29.10)
>DroYak_CAF1 6692 100 - 1
AAUGGGCA-------CUCUAUAUGGUAAGGGGUAUGUAUGUAUGUUUGUACGAUUUGCACAAAGAGAUGUCGAUGUCUCUGGCUGUUAUUGUUGGUGCCCAGUCGAA
..((((((-------((....(..((((.(((((.((.(((((....))))))).)))....((((((......))))))..)).))))..).))))))))...... ( -30.60)
>consensus
AAUGGGCAUGGG_UACUGUAUAUAGUAC_GGGUAUGUAUGCA________GGUUUUGCACAAAGAAAUGUCGACUGUUCUCGAUGUUAUUGUU_GUGCCCUGUCGA_
...((((((........(((((((.(((...))))))))))...............(((...(((((........)))))...)))........))))))....... (-15.54 = -15.26 +  -0.28)

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 13:25:14 2006