Locus 23

Sequence ID 4_DroMel_CAF1
Location 225,898 – 226,040
Length 142
Max. P 0.999916
window38 window39 window40 window41

overview

Window 8

Location 225,898 – 226,017
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 74.14
Mean single sequence MFE -25.75
Consensus MFE -12.90
Energy contribution -12.80
Covariance contribution -0.10
Combinations/Pair 1.25
Mean z-score -2.67
Structure conservation index 0.50
SVM decision value 1.31
SVM RNA-class probability 0.940129
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 225898 119 + 1281640
AUUUCAAUACCAAUAUUUACGAAAUAAGCAUUAGUGCACUAGUGCAAAGCAAGAUAUUGGCUUUUCCACU-UCAGAUGAAACAGAAUACGUACAUGUAUUCAGAUGUGUACACAUAAGCA
..........((((((((.........(((((((....)))))))......))))))))(((((((...(-((....)))...)))...((((((((......))))))))....)))). ( -23.26)
>DroPse_CAF1 3573 108 + 1
AUUU-----CCAUUAUAUACGGA-UGGGUAUGCAUCCA------UCAAACAAGUUAUUGGCUUUAACACAUGCACAUUGAACUAAAUAUGUGCAUGUAUUAAUAUGUAUACAUGCACGCA
....-----............((-(((((....)))))------)).....((((..((((..........)).))...))))......((((((((((........))))))))))... ( -27.00)
>DroPer_CAF1 4938 108 + 1
AUUU-----CCAUUAUAUACGGA-UGGGUAUGCAUCCA------UCAAACAAGUUAUUGGCUUUAACACAUGCACAUUGAACUAAAUAUGUGCAUGUAUUAAUAUGUAUACAUGCACGCA
....-----............((-(((((....)))))------)).....((((..((((..........)).))...))))......((((((((((........))))))))))... ( -27.00)
>consensus
AUUU_____CCAUUAUAUACGGA_UGGGUAUGCAUCCA______UCAAACAAGUUAUUGGCUUUAACACAUGCACAUUGAACUAAAUAUGUGCAUGUAUUAAUAUGUAUACAUGCACGCA
........................(((((....)))))..............((...((.......))...))...............(((((((((((........))))))))))).. (-12.90 = -12.80 +  -0.10)

alignment

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secondary structure

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Window 9

Location 225,898 – 226,017
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 74.14
Mean single sequence MFE -30.10
Consensus MFE -13.83
Energy contribution -16.67
Covariance contribution 2.84
Combinations/Pair 1.12
Mean z-score -3.29
Structure conservation index 0.46
SVM decision value 1.41
SVM RNA-class probability 0.951230
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 225898 119 - 1281640
UGCUUAUGUGUACACAUCUGAAUACAUGUACGUAUUCUGUUUCAUCUGA-AGUGGAAAAGCCAAUAUCUUGCUUUGCACUAGUGCACUAAUGCUUAUUUCGUAAAUAUUGGUAUUGAAAU
(((.((((((((..(....)..)))))))).)))(((..((((....))-))..)))..((((((((.((((...(((.(((....))).))).......))))))))))))........ ( -27.30)
>DroPse_CAF1 3573 108 - 1
UGCGUGCAUGUAUACAUAUUAAUACAUGCACAUAUUUAGUUCAAUGUGCAUGUGUUAAAGCCAAUAACUUGUUUGA------UGGAUGCAUACCCA-UCCGUAUAUAAUGG-----AAAU
...((((((.(((.....(((((((((((((((..........)))))))))))))))...(((........))))------)).)))))).....-(((((.....))))-----)... ( -31.50)
>DroPer_CAF1 4938 108 - 1
UGCGUGCAUGUAUACAUAUUAAUACAUGCACAUAUUUAGUUCAAUGUGCAUGUGUUAAAGCCAAUAACUUGUUUGA------UGGAUGCAUACCCA-UCCGUAUAUAAUGG-----AAAU
...((((((.(((.....(((((((((((((((..........)))))))))))))))...(((........))))------)).)))))).....-(((((.....))))-----)... ( -31.50)
>consensus
UGCGUGCAUGUAUACAUAUUAAUACAUGCACAUAUUUAGUUCAAUGUGCAUGUGUUAAAGCCAAUAACUUGUUUGA______UGGAUGCAUACCCA_UCCGUAUAUAAUGG_____AAAU
........(((((((...(((((((((((((((..........))))))))))))))).......................((((........))))...)))))))............. (-13.83 = -16.67 +   2.84)

alignment

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secondary structure

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dotplot

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Window 0

Location 225,938 – 226,040
Length 102
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 71.27
Mean single sequence MFE -27.07
Consensus MFE -14.91
Energy contribution -15.67
Covariance contribution 0.76
Combinations/Pair 1.15
Mean z-score -3.21
Structure conservation index 0.55
SVM decision value 4.53
SVM RNA-class probability 0.999916
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 225938 102 + 1281640
AGUGCAAAGCAAGAUAUUGGCUUUUCCACU-UCAGAUGAAACAGAAUACGUACAUGUAUUCAGAUGUGUACACAUAAGCAAUAUAUGU-------UUAUAUACUUAUGU----------U
.(((((...(..((...(((.....)))..-))..........(((((((....))))))).)...)))))(((((((..(((((...-------.))))).)))))))----------. ( -21.00)
>DroPse_CAF1 3605 115 + 1
----UCAAACAAGUUAUUGGCUUUAACACAUGCACAUUGAACUAAAUAUGUGCAUGUAUUAAUAUGUAUACAUGCACGCA-UAUGUGCAUUAAAGAUACAUACAUAUGUGUACUUAUUUG
----.((((.((((......(((((....((((((((((.........(((((((((((........)))))))))))))-.)))))))))))))((((((....)))))))))).)))) ( -30.10)
>DroPer_CAF1 4970 115 + 1
----UCAAACAAGUUAUUGGCUUUAACACAUGCACAUUGAACUAAAUAUGUGCAUGUAUUAAUAUGUAUACAUGCACGCA-UAUGUGCAUUAAAGAUACAUACAUAUGUGUACUUAUUUG
----.((((.((((......(((((....((((((((((.........(((((((((((........)))))))))))))-.)))))))))))))((((((....)))))))))).)))) ( -30.10)
>consensus
____UCAAACAAGUUAUUGGCUUUAACACAUGCACAUUGAACUAAAUAUGUGCAUGUAUUAAUAUGUAUACAUGCACGCA_UAUGUGCAUUAAAGAUACAUACAUAUGUGUACUUAUUUG
.........(((....)))...........(((((((...........(((((((((((........)))))))))))...((((((.........))))))...)))))))........ (-14.91 = -15.67 +   0.76)

alignment

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secondary structure

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dotplot

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Window 1

Location 225,938 – 226,040
Length 102
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 71.27
Mean single sequence MFE -33.37
Consensus MFE -17.87
Energy contribution -19.10
Covariance contribution 1.23
Combinations/Pair 1.17
Mean z-score -5.33
Structure conservation index 0.54
SVM decision value 3.59
SVM RNA-class probability 0.999422
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 225938 102 - 1281640
A----------ACAUAAGUAUAUAA-------ACAUAUAUUGCUUAUGUGUACACAUCUGAAUACAUGUACGUAUUCUGUUUCAUCUGA-AGUGGAAAAGCCAAUAUCUUGCUUUGCACU
.----------(((((((((((((.-------...)))).)))))))))(((((............)))))((((((..((((....))-))..)))((((.........)))))))... ( -21.30)
>DroPse_CAF1 3605 115 - 1
CAAAUAAGUACACAUAUGUAUGUAUCUUUAAUGCACAUA-UGCGUGCAUGUAUACAUAUUAAUACAUGCACAUAUUUAGUUCAAUGUGCAUGUGUUAAAGCCAAUAACUUGUUUGA----
(((((((((.........(((((((.....((((((...-...))))))..)))))))(((((((((((((((..........)))))))))))))))........))))))))).---- ( -39.40)
>DroPer_CAF1 4970 115 - 1
CAAAUAAGUACACAUAUGUAUGUAUCUUUAAUGCACAUA-UGCGUGCAUGUAUACAUAUUAAUACAUGCACAUAUUUAGUUCAAUGUGCAUGUGUUAAAGCCAAUAACUUGUUUGA----
(((((((((.........(((((((.....((((((...-...))))))..)))))))(((((((((((((((..........)))))))))))))))........))))))))).---- ( -39.40)
>consensus
CAAAUAAGUACACAUAUGUAUGUAUCUUUAAUGCACAUA_UGCGUGCAUGUAUACAUAUUAAUACAUGCACAUAUUUAGUUCAAUGUGCAUGUGUUAAAGCCAAUAACUUGUUUGA____
............(((((((((((.........(((.....)))((((((((((........))))))))))............))))))))))).......................... (-17.87 = -19.10 +   1.23)

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 09:31:45 2006