Locus 6789

Sequence ID 3L_DroMel_CAF1
Location 18,235,716 – 18,235,853
Length 137
Max. P 0.997276
window11028 window11029 window11030 window11031

overview

Window 8

Location 18,235,716 – 18,235,817
Length 101
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 74.61
Mean single sequence MFE -26.70
Consensus MFE -9.71
Energy contribution -11.77
Covariance contribution 2.06
Combinations/Pair 1.06
Mean z-score -3.32
Structure conservation index 0.36
SVM decision value 2.67
SVM RNA-class probability 0.996198
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18235716 101 + 23771897
AUUGCAUUGGUUUUAAAAAUGUUGAACGUGGAGGGGGUUAAUUCCACUCCACAACUGUGCAAAUAUUUGCGAAAACAUUUUCGCAUUUGUAAUGCACAAAA
...(((((.........))))).....((((((.(((.....))).))))))...((((((.(((..(((((((....)))))))..)))..))))))... ( -32.40)
>DroSec_CAF1 18333 100 + 1
AUUCCAUGGGUUUUAAAAAUGUUGUGUGUGGAGAGGGUUAAUUCCACUCCACAACUGUGCAAAUAUUUGCGAAAACAUUUUCGCAUUUGUAAUGCACAAA-
..........................(((((((.(((.....))).)))))))..((((((.(((..(((((((....)))))))..)))..))))))..- ( -31.60)
>DroSim_CAF1 24356 99 + 1
AUUGCAUUGGUUUUAAAAAUGUUGUGUGUGGAGGGGGUUAAUUCCACUCCACAACUGUGCAAAUAUUUGCGGAAACAUUUUCGCAUUUGUAAUGCACAA--
((.(((((.........))))).)).(((((((.(((.....))).)))))))..((((((.(((..(((((((....)))))))..)))..)))))).-- ( -32.60)
>DroEre_CAF1 18461 94 + 1
AUAUU-CUGGCUUUAAAAAUGUUGAGCGUGGAGAGAGUUAAUAC-----CACAACUGUGCAAAUAUUUGCGAAAACAUUUUCGCAUUUGUAAUGCACAAA-
.....-...((((..........))))((((............)-----)))...((((((.(((..(((((((....)))))))..)))..))))))..- ( -23.80)
>DroYak_CAF1 25127 95 + 1
AUAGUAUUGGCUUUAAAAAUGUUUUGCGUGGAGGGAGUUAAUCC-----CACAACUGUGCAAAUAUUUGCGAAAACAUUUUCGCAUUUGUAAUGCACAAA-
...((((((.......((((((((.(((..(.((((.....)))-----)....)..)))))))))))((((((....)))))).....)))))).....- ( -25.70)
>DroAna_CAF1 23165 80 + 1
ACAAUCCACAUUUGGGAUCAGUUUUUUGUGGCA-UUUUUAAGCC-----ACCAACUGUGCAAAUAUUUCAG-CAUUUUUUUCACAAU--------------
...((((.(....)))))(((((....(((((.-.......)))-----)).)))))(((..........)-)).............-------------- ( -14.10)
>consensus
AUAGCAUUGGUUUUAAAAAUGUUGUGCGUGGAGGGGGUUAAUUC_____CACAACUGUGCAAAUAUUUGCGAAAACAUUUUCGCAUUUGUAAUGCACAAA_
.......................................................((((((.(((..(((((((....)))))))..)))..))))))... ( -9.71 = -11.77 +   2.06)

alignment

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secondary structure

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Window 9

Location 18,235,716 – 18,235,817
Length 101
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 74.61
Mean single sequence MFE -24.46
Consensus MFE -8.65
Energy contribution -10.65
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -3.55
Structure conservation index 0.35
SVM decision value 2.83
SVM RNA-class probability 0.997276
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18235716 101 - 23771897
UUUUGUGCAUUACAAAUGCGAAAAUGUUUUCGCAAAUAUUUGCACAGUUGUGGAGUGGAAUUAACCCCCUCCACGUUCAACAUUUUUAAAACCAAUGCAAU
..(((((((.......(((((((....)))))))......)))))))..((((((.((........))))))))........................... ( -28.12)
>DroSec_CAF1 18333 100 - 1
-UUUGUGCAUUACAAAUGCGAAAAUGUUUUCGCAAAUAUUUGCACAGUUGUGGAGUGGAAUUAACCCUCUCCACACACAACAUUUUUAAAACCCAUGGAAU
-..((((((.......(((((((....)))))))......))))))(((((((((.((.......)).))))))).))....................... ( -29.82)
>DroSim_CAF1 24356 99 - 1
--UUGUGCAUUACAAAUGCGAAAAUGUUUCCGCAAAUAUUUGCACAGUUGUGGAGUGGAAUUAACCCCCUCCACACACAACAUUUUUAAAACCAAUGCAAU
--((((((((.....))))(((((((((...((((....))))...(((((((((.((........))))))))).))))))))))).........)))). ( -27.70)
>DroEre_CAF1 18461 94 - 1
-UUUGUGCAUUACAAAUGCGAAAAUGUUUUCGCAAAUAUUUGCACAGUUGUG-----GUAUUAACUCUCUCCACGCUCAACAUUUUUAAAGCCAG-AAUAU
-..((((((.......(((((((....)))))))......))))))(((.((-----((.((((.....................)))).)))).-))).. ( -20.62)
>DroYak_CAF1 25127 95 - 1
-UUUGUGCAUUACAAAUGCGAAAAUGUUUUCGCAAAUAUUUGCACAGUUGUG-----GGAUUAACUCCCUCCACGCAAAACAUUUUUAAAGCCAAUACUAU
-..((((((.......(((((((....)))))))......))))))((.(.(-----(((.....)))).).))........................... ( -22.22)
>DroAna_CAF1 23165 80 - 1
--------------AUUGUGAAAAAAAUG-CUGAAAUAUUUGCACAGUUGGU-----GGCUUAAAAA-UGCCACAAAAAACUGAUCCCAAAUGUGGAUUGU
--------------.............((-(..........)))(((((.((-----(((.......-.)))))....)))))(((((....).))))... ( -18.30)
>consensus
_UUUGUGCAUUACAAAUGCGAAAAUGUUUUCGCAAAUAUUUGCACAGUUGUG_____GAAUUAACCCCCUCCACACACAACAUUUUUAAAACCAAUACAAU
..(((((((.......(((((((....)))))))......)))))))...................................................... ( -8.65 = -10.65 +   2.00)

alignment

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secondary structure

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Window 0

Location 18,235,750 – 18,235,853
Length 103
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 90.03
Mean single sequence MFE -20.58
Consensus MFE -17.06
Energy contribution -16.90
Covariance contribution -0.16
Combinations/Pair 1.06
Mean z-score -2.30
Structure conservation index 0.83
SVM decision value 2.18
SVM RNA-class probability 0.989744
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18235750 103 + 23771897
GGGUUAAUUCCACUCCACAACUGUGCAAAUAUUUGCGAAAACAUUUUCGCAUUUGUAAUGCACAAAAAAAAAAUAGUUUCAUUCAAAAAGAGGAUUUU-UUUGU
(((.....)))..........((((((.(((..(((((((....)))))))..)))..))))))..((((((((...(((.........))).)))))-))).. ( -21.10)
>DroSec_CAF1 18367 97 + 1
GGGUUAAUUCCACUCCACAACUGUGCAAAUAUUUGCGAAAACAUUUUCGCAUUUGUAAUGCACAAA----AAAUAGUUUCAUUCAAAAAGUAGAUUUU-UU--U
(((.....)))..........((((((.(((..(((((((....)))))))..)))..))))))..----............................-..--. ( -19.00)
>DroSim_CAF1 24390 96 + 1
GGGUUAAUUCCACUCCACAACUGUGCAAAUAUUUGCGGAAACAUUUUCGCAUUUGUAAUGCACAA-----AAAUAGUUUCAUUCAAAAAGUGGAUUUU-UU--U
(((.....)))..(((((...((((((.(((..(((((((....)))))))..)))..)))))).-----.....(.......).....)))))....-..--. ( -23.50)
>DroEre_CAF1 18494 93 + 1
GAGUUAAUAC-----CACAACUGUGCAAAUAUUUGCGAAAACAUUUUCGCAUUUGUAAUGCACAAA----AAAUAGUUUCAUUCAAAUAGAGGGUUUUUUU--U
........((-----(.....((((((.(((..(((((((....)))))))..)))..))))))..----...........(((.....))))))......--. ( -18.90)
>DroYak_CAF1 25161 92 + 1
GAGUUAAUCC-----CACAACUGUGCAAAUAUUUGCGAAAACAUUUUCGCAUUUGUAAUGCACAAA----AAAUAGUUUCAUUCAAAAAGAGGGUUUU-UU--U
........((-----(.....((((((.(((..(((((((....)))))))..)))..))))))..----............((.....)))))....-..--. ( -20.40)
>consensus
GGGUUAAUUCCACUCCACAACUGUGCAAAUAUUUGCGAAAACAUUUUCGCAUUUGUAAUGCACAAA____AAAUAGUUUCAUUCAAAAAGAGGAUUUU_UU__U
.....................((((((.(((..(((((((....)))))))..)))..))))))........................................ (-17.06 = -16.90 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,235,750 – 18,235,853
Length 103
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 90.03
Mean single sequence MFE -22.30
Consensus MFE -14.84
Energy contribution -17.04
Covariance contribution 2.20
Combinations/Pair 1.00
Mean z-score -2.66
Structure conservation index 0.67
SVM decision value 0.11
SVM RNA-class probability 0.588833
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18235750 103 - 23771897
ACAAA-AAAAUCCUCUUUUUGAAUGAAACUAUUUUUUUUUUGUGCAUUACAAAUGCGAAAAUGUUUUCGCAAAUAUUUGCACAGUUGUGGAGUGGAAUUAACCC
.((((-((.......)))))).......((((((..(..(((((((.......(((((((....)))))))......)))))))..)..))))))......... ( -23.72)
>DroSec_CAF1 18367 97 - 1
A--AA-AAAAUCUACUUUUUGAAUGAAACUAUUU----UUUGUGCAUUACAAAUGCGAAAAUGUUUUCGCAAAUAUUUGCACAGUUGUGGAGUGGAAUUAACCC
.--..-....((((((((((....))))((((..----.(((((((.......(((((((....)))))))......)))))))..))))))))))........ ( -23.32)
>DroSim_CAF1 24390 96 - 1
A--AA-AAAAUCCACUUUUUGAAUGAAACUAUUU-----UUGUGCAUUACAAAUGCGAAAAUGUUUCCGCAAAUAUUUGCACAGUUGUGGAGUGGAAUUAACCC
.--..-....((((((((((....))))((((..-----(((((((.......((((..........))))......)))))))..))))))))))........ ( -23.22)
>DroEre_CAF1 18494 93 - 1
A--AAAAAAACCCUCUAUUUGAAUGAAACUAUUU----UUUGUGCAUUACAAAUGCGAAAAUGUUUUCGCAAAUAUUUGCACAGUUGUG-----GUAUUAACUC
.--....................(((.(((((..----.(((((((.......(((((((....)))))))......)))))))..)))-----)).))).... ( -20.92)
>DroYak_CAF1 25161 92 - 1
A--AA-AAAACCCUCUUUUUGAAUGAAACUAUUU----UUUGUGCAUUACAAAUGCGAAAAUGUUUUCGCAAAUAUUUGCACAGUUGUG-----GGAUUAACUC
.--..-.................(((..((((..----.(((((((.......(((((((....)))))))......)))))))..)))-----)..))).... ( -20.32)
>consensus
A__AA_AAAAUCCUCUUUUUGAAUGAAACUAUUU____UUUGUGCAUUACAAAUGCGAAAAUGUUUUCGCAAAUAUUUGCACAGUUGUGGAGUGGAAUUAACCC
............................((((((.....(((((((.......(((((((....)))))))......))))))).....))))))......... (-14.84 = -17.04 +   2.20)

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 12:30:01 2006