Locus 661

Sequence ID 2L_DroMel_CAF1
Location 1,962,926 – 1,963,118
Length 192
Max. P 0.827833
window1081 window1082 window1083

overview

Window 1

Location 1,962,926 – 1,963,045
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.20
Mean single sequence MFE -40.00
Consensus MFE -24.75
Energy contribution -27.28
Covariance contribution 2.53
Combinations/Pair 1.09
Mean z-score -1.61
Structure conservation index 0.62
SVM decision value 0.70
SVM RNA-class probability 0.827833
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1962926 119 - 22407834
AUUAAUAUGCCUCAAUUCUGUCGCAGGACAUGUGCAA-AUACUGCUCGCAUGUCCUUGAGCGCGUGCCGUGCGUCCUUAGGAGACCUUUGGGCGUCUUUAAAAGGGGGCGUAGCGCCUGC
.....((((((((.......(((.((((((((((((.-....)))..))))))))))))(((((...)))))((((..(((...)))..))))...........))))))))........ ( -43.00)
>DroSec_CAF1 5350 119 - 1
AUUAAUAUGCCUCAAUUCUGUCGCAGGACAUGUGCAA-AUACUGCUCGCAUGUCCUUGAGCGCGUGCCGCGCGUCCUUAGGAGACCUUUGGGCGUCUUCAAAAGGGGGCGUAGCGCCUGC
........((((((..........((((((((((((.-....)))..))))))))))))).))((((..(((.(((((.(((((((.....).))))))..))))).)))..)))).... ( -47.10)
>DroSim_CAF1 9540 100 - 1
AUUAAUAUGCCUCAAUUCUGUCGCAGGACAUGUG--------------------CUUGAGCGCGUGCCGCGCGUCCUUAGGAGACCUUUGGGCGUCUUCAAAAGGGGGCGUAGCGCCUGC
.....((((((((.........((.((.((((((--------------------(....)))))))))))((((((..(((...)))..)))))).........))))))))........ ( -38.80)
>DroEre_CAF1 14546 119 - 1
AUUAAUUUGCCUCAAUCCUGUCGCAGGACAUGUGCAA-AUACCACUCGCAUGUUCUUGAGCGCGUGCCGCGCGUCCUUAGGCGACCUUUGGGCGUCUUCAAAAGGGGGCGUGGCGCCUGC
........((((((((((((...)))))((((((...-........))))))...))))).))(((((((((.((((((((((.((....)))))))....))))).))))))))).... ( -49.60)
>DroYak_CAF1 12379 94 - 1
AUUAAUAUGCCUCAAUCCUGUCGCAGGACAUGUGCAA-AUACCACUCGCAUGUCCUUGAGCGCGUGCC-------------------------GUCUUCAAAAGUGGGCGUAGCGCCUGC
.......(((..((....))..)))(((((((((...-........)))))))))...((.((((..(-------------------------((((........)))))..)))))).. ( -28.90)
>DroAna_CAF1 35553 96 - 1
AUUAA------------------CAGGACAUGUGCAAAAUCCUACCCGCAUGUCCUUGAGCGCGUGCCUCGCGUCCUUAGAAAA----UAGGCGUCAUCC--GGGGGGCGUAGCGCCUGC
.....------------------.((((((((((............))))))))))...(((.((((..(((.((((..((..(----(....))..)).--.)))))))..)))).))) ( -32.60)
>consensus
AUUAAUAUGCCUCAAUUCUGUCGCAGGACAUGUGCAA_AUACUACUCGCAUGUCCUUGAGCGCGUGCCGCGCGUCCUUAGGAGACCUUUGGGCGUCUUCAAAAGGGGGCGUAGCGCCUGC
....................(((.((((((((((............)))))))))))))((((.(((.....((((..((.....))..))))((((((....))))))))))))).... (-24.75 = -27.28 +   2.53) 

alignment

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secondary structure

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dotplot

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Window 2

Location 1,962,966 – 1,963,085
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.57
Mean single sequence MFE -41.47
Consensus MFE -30.24
Energy contribution -31.52
Covariance contribution 1.28
Combinations/Pair 1.10
Mean z-score -2.12
Structure conservation index 0.73
SVM decision value 0.55
SVM RNA-class probability 0.778896
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1962966 119 - 22407834
UUUGGAGGCGUAUUCGCUGGUGUGCGUCGCAUAUGUAGCAAUUAAUAUGCCUCAAUUCUGUCGCAGGACAUGUGCAA-AUACUGCUCGCAUGUCCUUGAGCGCGUGCCGUGCGUCCUUAG
....((((((((((.((((((((((...)))))).))))....)))))))))).......(((.((((((((((((.-....)))..))))))))))))(((((...)))))........ ( -44.40)
>DroSec_CAF1 5390 119 - 1
UUUGGAGGCGUGUUCGCUGGUGUGCGUCGCAUAUGUAGCAAUUAAUAUGCCUCAAUUCUGUCGCAGGACAUGUGCAA-AUACUGCUCGCAUGUCCUUGAGCGCGUGCCGCGCGUCCUUAG
....((((((((((.((((((((((...)))))).))))....)))))))))).......(((.((((((((((((.-....)))..))))))))))))(((((...)))))........ ( -46.30)
>DroSim_CAF1 9580 100 - 1
UUUGGAGGCGUGUUCGCUGGUGUGCGUCGCAUAUGUAGCAAUUAAUAUGCCUCAAUUCUGUCGCAGGACAUGUG--------------------CUUGAGCGCGUGCCGCGCGUCCUUAG
....((((((((((.((((((((((...)))))).))))....))))))))))......(.(((.((.((((((--------------------(....)))))))))..))).)..... ( -39.70)
>DroEre_CAF1 14586 119 - 1
UUUGGAGGCGUGUUCGCUGGUGUGCGUCGCAUAUGUAGCAAUUAAUUUGCCUCAAUCCUGUCGCAGGACAUGUGCAA-AUACCACUCGCAUGUUCUUGAGCGCGUGCCGCGCGUCCUUAG
...(((.(((((.....((((((.....((((((((.((((.....))))......((((...))))))))))))..-))))))...((((((.(....).))))))))))).))).... ( -42.80)
>DroYak_CAF1 12406 107 - 1
UUUGGAGGCGUGCACGCUGGUGUGCGUCGCAUAUGUAGCAAUUAAUAUGCCUCAAUCCUGUCGCAGGACAUGUGCAA-AUACCACUCGCAUGUCCUUGAGCGCGUGCC------------
..(((.((((..(((....)))..))))((((((((.(((.......)))......((((...))))))))))))..-...)))...((((((.(....).)))))).------------ ( -38.20)
>DroAna_CAF1 35587 102 - 1
UUUGGAGGCGUGUUCGCUGGUGUGUGUCGCAUAUGUAGCAAUUAA------------------CAGGACAUGUGCAAAAUCCUACCCGCAUGUCCUUGAGCGCGUGCCUCGCGUCCUUAG
....((((((((((((((((((((.....))))).))))......------------------.((((((((((............)))))))))).))))))..))))).......... ( -37.40)
>consensus
UUUGGAGGCGUGUUCGCUGGUGUGCGUCGCAUAUGUAGCAAUUAAUAUGCCUCAAUUCUGUCGCAGGACAUGUGCAA_AUACUACUCGCAUGUCCUUGAGCGCGUGCCGCGCGUCCUUAG
...((..((((((((((((((((((...)))))).)))).........................((((((((((............)))))))))).)))))))).))............ (-30.24 = -31.52 +   1.28) 

alignment

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secondary structure

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dotplot

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Window 3

Location 1,963,006 – 1,963,118
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.62
Mean single sequence MFE -32.90
Consensus MFE -20.81
Energy contribution -23.28
Covariance contribution 2.48
Combinations/Pair 1.12
Mean z-score -1.53
Structure conservation index 0.63
SVM decision value 0.07
SVM RNA-class probability 0.566525
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1963006 112 - 22407834
-CCUUGUGCCACAUUCCUAGC-----UCGC-CUCGCAGUUUUUGGAGGCGUAUUCGCUGGUGUGCGUCGCAUAUGUAGCAAUUAAUAUGCCUCAAUUCUGUCGCAGGACAUGUGCAA-AU
-.....(((.((((((((.((-----....-...((((......((((((((((.((((((((((...)))))).))))....))))))))))....)))).)))))).))))))).-.. ( -35.40)
>DroSec_CAF1 5430 111 - 1
--CGUGUGCCACAUUCCUAGC-----UCUC-CUCGCAGUUUUUGGAGGCGUGUUCGCUGGUGUGCGUCGCAUAUGUAGCAAUUAAUAUGCCUCAAUUCUGUCGCAGGACAUGUGCAA-AU
--....(((.((((((((.((-----....-...((((......((((((((((.((((((((((...)))))).))))....))))))))))....)))).)))))).))))))).-.. ( -35.40)
>DroSim_CAF1 9606 108 - 1
UCCUUGUUCCACAUUCCUAGC-----UCGC-CUCGCAGUUUUUGGAGGCGUGUUCGCUGGUGUGCGUCGCAUAUGUAGCAAUUAAUAUGCCUCAAUUCUGUCGCAGGACAUGUG------
.........(((((((((.((-----....-...((((......((((((((((.((((((((((...)))))).))))....))))))))))....)))).)))))).)))))------ ( -33.50)
>DroEre_CAF1 14626 109 - 1
----UGUUCCACAUUCCUAGC-----UCGC-CUCGCACUUUUUGGAGGCGUGUUCGCUGGUGUGCGUCGCAUAUGUAGCAAUUAAUUUGCCUCAAUCCUGUCGCAGGACAUGUGCAA-AU
----.....((((...(((((-----.(((-(((.((.....)))))))).....)))))))))....((((((((.((((.....))))......((((...))))))))))))..-.. ( -35.70)
>DroYak_CAF1 12434 118 - 1
-CUUUAUUCUAGAUUCCUAGCCUAGAUCGCCCUGGCAUCUUUUGGAGGCGUGCACGCUGGUGUGCGUCGCAUAUGUAGCAAUUAAUAUGCCUCAAUCCUGUCGCAGGACAUGUGCAA-AU
-.......((((....))))((.((((.((....))))))...)).((((..(((....)))..))))((((((((.(((.......)))......((((...))))))))))))..-.. ( -37.80)
>DroAna_CAF1 35627 89 - 1
-CC-UGAUCCAGAUUUCUAAU-----AUAU-U-----UUUUUUGGAGGCGUGUUCGCUGGUGUGUGUCGCAUAUGUAGCAAUUAA------------------CAGGACAUGUGCAAAAU
-..-.((..((.((((((((.-----....-.-----....)))))((((....))))))).))..))((((((((..(......------------------..).))))))))..... ( -19.60)
>consensus
_CCUUGUUCCACAUUCCUAGC_____UCGC_CUCGCAGUUUUUGGAGGCGUGUUCGCUGGUGUGCGUCGCAUAUGUAGCAAUUAAUAUGCCUCAAUUCUGUCGCAGGACAUGUGCAA_AU
.........(((((((((.((.......((....))........((((((((((.((((((((((...)))))).))))....)))))))))).........)))))).)))))...... (-20.81 = -23.28 +   2.48) 

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 09:42:16 2006