Locus 4695

Sequence ID 3L_DroMel_CAF1
Location 13,237,199 – 13,237,329
Length 130
Max. P 0.995611
window7398 window7399 window7400

overview

Window 8

Location 13,237,199 – 13,237,295
Length 96
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 84.28
Mean single sequence MFE -22.43
Consensus MFE -18.65
Energy contribution -18.57
Covariance contribution -0.08
Combinations/Pair 1.13
Mean z-score -2.24
Structure conservation index 0.83
SVM decision value 0.86
SVM RNA-class probability 0.868024
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13237199 96 + 23771897
UGAAAUUGAAAUUUAAUUUGCGAAGCGAGCUGGCAAAAAAAAA------AAAGCGCCAGCUCAUCAACGGCGGCAUUAGUUUGCACAUAUUCAAAUCAGUUU
..(((((((.................((((((((.........------.....))))))))..........(((......)))...........))))))) ( -22.54)
>DroSec_CAF1 30499 84 + 1
UGAAAUUUAAUUUUA-------AAGCGAGCUGGCA-A----AA------AAAGCGCCAGCUCAUCAACGGCGGCAUUAGUUUGCACAUAUUCAAAUCAGUUU
((((...........-------....((((((((.-.----..------.....))))))))..........(((......))).....))))......... ( -20.50)
>DroSim_CAF1 38106 92 + 1
UGAAAUUGAAAUUUAAUUUGCGAAGCGAGCUGGCGAA----AA------AAAGCGCCAGCUCAUCAACGGCGGCAUUAGUUUGCACAUAUUCAAAUCAGUUU
..(((((((.................(((((((((..----..------....)))))))))..........(((......)))...........))))))) ( -26.00)
>DroEre_CAF1 20005 91 + 1
UGAAAUUGAAAUUUAAUUUGCGAAGCGAGCUGGCGAAA-----------AAAGCGCCAGCUCAUCAACAGCGGCAUUAGUUUGCACAUAUUCAAAUCACUUU
.....(((((........(((.....(((((((((...-----------....))))))))).......)))(((......))).....)))))........ ( -25.10)
>DroYak_CAF1 30687 93 + 1
UGAAAUUGAAAUUUAAUUUGCGAAGCGAGCUGGCGAAA---AA------AAAACGCCAGCUCAUCAACAGCGGCAUUAGUUUGCACAUAUUCAAAUCACUUU
.....(((((........(((.....(((((((((...---..------....))))))))).......)))(((......))).....)))))........ ( -24.40)
>DroAna_CAF1 116541 94 + 1
GGA------AAUUUAAUUUGC--AGGGACUUGGCUAACAAAAAAAAACGAAAACGCCAGGUCAUCAUCAGCGGCAUUAGUUUGCACAUAUUCAAAUCAGUUU
.((------(........(((--...((((((((....................)))))))).......)))(((......))).....))).......... ( -16.05)
>consensus
UGAAAUUGAAAUUUAAUUUGCGAAGCGAGCUGGCGAAA___AA______AAAGCGCCAGCUCAUCAACAGCGGCAUUAGUUUGCACAUAUUCAAAUCAGUUU
((((......................((((((((....................))))))))..........(((......))).....))))......... (-18.65 = -18.57 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,237,199 – 13,237,295
Length 96
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 84.28
Mean single sequence MFE -22.25
Consensus MFE -18.40
Energy contribution -19.12
Covariance contribution 0.72
Combinations/Pair 1.10
Mean z-score -1.89
Structure conservation index 0.83
SVM decision value 0.49
SVM RNA-class probability 0.755387
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13237199 96 - 23771897
AAACUGAUUUGAAUAUGUGCAAACUAAUGCCGCCGUUGAUGAGCUGGCGCUUU------UUUUUUUUUGCCAGCUCGCUUCGCAAAUUAAAUUUCAAUUUCA
....(((((((.....(.(((......))))..((..(.((((((((((....------........)))))))))))..)))))))))............. ( -22.30)
>DroSec_CAF1 30499 84 - 1
AAACUGAUUUGAAUAUGUGCAAACUAAUGCCGCCGUUGAUGAGCUGGCGCUUU------UU----U-UGCCAGCUCGCUU-------UAAAAUUAAAUUUCA
.....(((((((......((....(((((....)))))..(((((((((....------..----.-)))))))))))..-------.....)))))))... ( -20.22)
>DroSim_CAF1 38106 92 - 1
AAACUGAUUUGAAUAUGUGCAAACUAAUGCCGCCGUUGAUGAGCUGGCGCUUU------UU----UUCGCCAGCUCGCUUCGCAAAUUAAAUUUCAAUUUCA
....(((((((.....(.(((......))))..((..(.((((((((((....------..----..)))))))))))..)))))))))............. ( -24.70)
>DroEre_CAF1 20005 91 - 1
AAAGUGAUUUGAAUAUGUGCAAACUAAUGCCGCUGUUGAUGAGCUGGCGCUUU-----------UUUCGCCAGCUCGCUUCGCAAAUUAAAUUUCAAUUUCA
....(((((((((((((.(((......))))).))))...(((((((((....-----------...)))))))))......)))))))............. ( -24.80)
>DroYak_CAF1 30687 93 - 1
AAAGUGAUUUGAAUAUGUGCAAACUAAUGCCGCUGUUGAUGAGCUGGCGUUUU------UU---UUUCGCCAGCUCGCUUCGCAAAUUAAAUUUCAAUUUCA
....(((((((((((((.(((......))))).))))...(((((((((....------..---...)))))))))......)))))))............. ( -25.30)
>DroAna_CAF1 116541 94 - 1
AAACUGAUUUGAAUAUGUGCAAACUAAUGCCGCUGAUGAUGACCUGGCGUUUUCGUUUUUUUUUGUUAGCCAAGUCCCU--GCAAAUUAAAUU------UCC
.....((((((.....(.(((......))))(((((..(......((((....)))).....)..)))))))))))...--............------... ( -16.20)
>consensus
AAACUGAUUUGAAUAUGUGCAAACUAAUGCCGCCGUUGAUGAGCUGGCGCUUU______UU___UUUCGCCAGCUCGCUUCGCAAAUUAAAUUUCAAUUUCA
....(((((((.....(.(((......)))).........(((((((((..................)))))))))......)))))))............. (-18.40 = -19.12 +   0.72)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,237,225 – 13,237,329
Length 104
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 85.61
Mean single sequence MFE -29.92
Consensus MFE -27.56
Energy contribution -26.93
Covariance contribution -0.63
Combinations/Pair 1.24
Mean z-score -3.07
Structure conservation index 0.92
SVM decision value 2.60
SVM RNA-class probability 0.995611
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13237225 104 + 23771897
GAGCUGGCAAAAAAAAA------AAAGCGCCAGCUCAUCAACGGCGGCAUUAGUUUGCACAUAUUCAAAUCAGUUUUUUAUUUGCCGAACAAAGGCUGCUAAAGAAACGG
((((((((.........------.....))))))))......((((((....(((((((.(((...............))).)).)))))....)))))).......... ( -29.20)
>DroSec_CAF1 30518 99 + 1
GAGCUGGCA-A----AA------AAAGCGCCAGCUCAUCAACGGCGGCAUUAGUUUGCACAUAUUCAAAUCAGUUUUUUAUUUGCCGAACAAAGGCUGCGAAAGAAACGG
((((((((.-.----..------.....)))))))).......(((((....(((((((.(((...............))).)).)))))....)))))........... ( -28.76)
>DroSim_CAF1 38132 100 + 1
GAGCUGGCGAA----AA------AAAGCGCCAGCUCAUCAACGGCGGCAUUAGUUUGCACAUAUUCAAAUCAGUUUUUUAUUUGCCGAACAAAGGCUGCGAAAGAAACGG
(((((((((..----..------....))))))))).......(((((....(((((((.(((...............))).)).)))))....)))))........... ( -31.76)
>DroEre_CAF1 20031 99 + 1
GAGCUGGCGAAA-----------AAAGCGCCAGCUCAUCAACAGCGGCAUUAGUUUGCACAUAUUCAAAUCACUUUUUUAUUUGCCGAACAAAGGCUGCGAAAGAAACGG
(((((((((...-----------....))))))))).......(((((....(((((((.(((...............))).)).)))))....)))))........... ( -31.66)
>DroYak_CAF1 30713 101 + 1
GAGCUGGCGAAA---AA------AAAACGCCAGCUCAUCAACAGCGGCAUUAGUUUGCACAUAUUCAAAUCACUUUUUUAUUUGCCGAACAAAGGCUGCGAAAGAAACGG
(((((((((...---..------....))))))))).......(((((....(((((((.(((...............))).)).)))))....)))))........... ( -30.96)
>DroAna_CAF1 116559 100 + 1
GACUUGGCUAACAAAAAAAAACGAAAACGCCAGGUCAUCAUCAGCGGCAUUAGUUUGCACAUAUUCAAAUCAGUUUUUUAUUUGUUCAGAAGAGGCCGCG----------
((((((((....................)))))))).......(((((.....((((.(((.((..(((.....)))..)).))).))))....))))).---------- ( -27.15)
>consensus
GAGCUGGCGAAA___AA______AAAGCGCCAGCUCAUCAACAGCGGCAUUAGUUUGCACAUAUUCAAAUCAGUUUUUUAUUUGCCGAACAAAGGCUGCGAAAGAAACGG
((((((((....................)))))))).......(((((.((.(((((((.(((...............))).)).))))).)).)))))........... (-27.56 = -26.93 +  -0.63)

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 11:31:00 2006