Locus 8049

Sequence ID 3R_DroMel_CAF1
Location 21,627,237 – 21,627,462
Length 225
Max. P 0.993066
window12952 window12953 window12954 window12955 window12956

overview

Window 2

Location 21,627,237 – 21,627,345
Length 108
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 84.75
Mean single sequence MFE -22.20
Consensus MFE -15.50
Energy contribution -15.82
Covariance contribution 0.32
Combinations/Pair 1.10
Mean z-score -1.88
Structure conservation index 0.70
SVM decision value 0.34
SVM RNA-class probability 0.697059
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21627237 108 - 27905053
----------AAAA-CGACGGCAAACCAAGUGUCAAGUUGAAAUAAACUUUAAGACACACUUGACAUAUUGCCAGUUGCUCGCUUCCAGCUCACAACAUAAUUUUCCAUUAGUUGGAUA
----------....-(((((((((.....(((((((((((...............)).))))))))).))))).((((...((.....))...))))..............)))).... ( -23.66)
>DroSec_CAF1 116643 108 - 1
----------AAAA-CGACGGCAAACCAAGUGUCAAGUUGAAAUAAACUUUAAGACAGACUUGACAUAUUGCCAGUUGCUCGCUUCCAGCUCACAACAUAAUUUUCCAUUAGUUGGAUA
----------....-(((((((((.....((((((((((..................)))))))))).))))).((((...((.....))...))))..............)))).... ( -25.27)
>DroSim_CAF1 113197 96 - 1
----------A-------------AUCAAGUGUCAAGUUGAAAUAAACUUUAAGACAGACUUGACAUAUUGCCAGUUGCUCGCUUUCAGCUCACAACAUAAUUUUCCAUUAGUUGGAUA
----------.-------------.....((((((((((..................)))))))))).......((((...((.....))...)))).......((((.....)))).. ( -19.07)
>DroYak_CAF1 113415 119 - 1
AAAAAAAAAAAACACCGAUAGCAAACCAAGUGUCAAGUUGAAAUAAACUUUAAGACAGACUUGACAUAUUGCCAGUUGCUCGCUUCCAGUUCACAACAUAAUUUUCCAUUAGUUGGAUA
..............(((((.((((.....((((((((((..................)))))))))).))))..((((...((.....))...))))..............)))))... ( -20.27)
>DroAna_CAF1 95743 99 - 1
----------A---------GCA-GUCCAGCGACAACUUGAAGCAAACUUUAGGACAGACUUGACAUAUUGCUAGUUGCUCGCUUCCAGCUCACAACAUAAUUUUCCAUUAGUUGGAUA
----------.---------...-....((((((((((...(((((...(((((.....)))))....)))))))))).)))))(((((((...................))))))).. ( -22.71)
>consensus
__________AA_A_CGA__GCAAACCAAGUGUCAAGUUGAAAUAAACUUUAAGACAGACUUGACAUAUUGCCAGUUGCUCGCUUCCAGCUCACAACAUAAUUUUCCAUUAGUUGGAUA
.............................((((((((((....(........)....)))))))))).......((((...((.....))...)))).......((((.....)))).. (-15.50 = -15.82 +   0.32)

alignment

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secondary structure

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Window 3

Location 21,627,277 – 21,627,382
Length 105
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 77.68
Mean single sequence MFE -20.80
Consensus MFE -10.86
Energy contribution -11.30
Covariance contribution 0.44
Combinations/Pair 1.17
Mean z-score -2.68
Structure conservation index 0.52
SVM decision value 2.37
SVM RNA-class probability 0.993066
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21627277 105 - 27905053
CAAAAAUGCUAUCUCGAAAAAAGAAGGCACAAAAAAA-------------AAAA-CGACGGCAAACCAAGUGUCAAGUUGAAAUAAACUUUAAGACACACUUGACAUAUUGCCAGUUGC
......((((.(((.......))).))))........-------------....-(((((((((.....(((((((((((...............)).))))))))).))))).)))). ( -22.46)
>DroSec_CAF1 116683 106 - 1
CAAAAAUGCUAUCUCGCAAAAAGAAGGCAAAAAGAAAA------------AAAA-CGACGGCAAACCAAGUGUCAAGUUGAAAUAAACUUUAAGACAGACUUGACAUAUUGCCAGUUGC
......((((.(((.......))).)))).........------------....-(((((((((.....((((((((((..................)))))))))).))))).)))). ( -24.37)
>DroSim_CAF1 113237 94 - 1
CAAAAAUGCUAUCUCGCAAAAAGGAGGCAAAAAGAAAA------------A-------------AUCAAGUGUCAAGUUGAAAUAAACUUUAAGACAGACUUGACAUAUUGCCAGUUGC
......(((......))).......(((((...((...------------.-------------.))..((((((((((..................)))))))))).)))))...... ( -19.57)
>DroYak_CAF1 113455 118 - 1
CAAAAAUGCUAUCUCGCAAAAAGA-GGCAAAAAUACAAAAAAAAAAAAAAAACACCGAUAGCAAACCAAGUGUCAAGUUGAAAUAAACUUUAAGACAGACUUGACAUAUUGCCAGUUGC
......(((((((((.......))-((...........................)))))))))......((((((((((..................))))))))))............ ( -18.60)
>DroAna_CAF1 95783 96 - 1
CAGAAAUUCUGGCUGGCAGAGAGAAGUGACCAAAAAA-------------A---------GCA-GUCCAGCGACAACUUGAAGCAAACUUUAGGACAGACUUGACAUAUUGCUAGUUGC
(((.....)))((((((((.(..((((..........-------------.---------...-(((....)))..(((((((....)))))))....))))..)...))))))))... ( -19.00)
>consensus
CAAAAAUGCUAUCUCGCAAAAAGAAGGCAAAAAAAAAA____________AA_A_CGA__GCAAACCAAGUGUCAAGUUGAAAUAAACUUUAAGACAGACUUGACAUAUUGCCAGUUGC
......((((.(((.......))).))))........................................((((((((((....(........)....))))))))))............ (-10.86 = -11.30 +   0.44)

alignment

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secondary structure

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Window 4

Location 21,627,317 – 21,627,422
Length 105
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 68.63
Mean single sequence MFE -21.87
Consensus MFE -13.72
Energy contribution -14.19
Covariance contribution 0.47
Combinations/Pair 1.06
Mean z-score -1.73
Structure conservation index 0.63
SVM decision value 2.28
SVM RNA-class probability 0.991606
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21627317 105 + 27905053
AACUUGACACUUGGUUUGCCGUCGUUUU-UUUUUUUGUGCCUUCUUUUUUCGAGAUAGCAUUUUUGCUGUCGAUUUUUCGAAGGGGAAGAUUUGACAGCUGCACUU
.............((..((.((((..((-((((......(((((.........(((((((....)))))))((....)))))))))))))..)))).)).)).... ( -25.60)
>DroSim_CAF1 113277 92 + 1
AACUUGACACUUGAU------------UUUUUCUUUUUGCCUCCUUUUUGCGAGAUAGCAUUUUUGCUGUCGAUUUUUCG--GGGGAAGAUUUGACAGCUGCACUU
....((.((.(((.(------------(...((((....(((((.........(((((((....)))))))((....)))--))))))))...))))).))))... ( -20.80)
>DroAna_CAF1 95823 81 + 1
AAGUUGUCGCUGGAC-UGC--------U-UUUUUUGGUCACUUCUCUCUGCCAGCCAGAAUUUCUGCUGUCGAUUU---------------UUGACAGCUGCACUU
.((((((((.(.(((-.((--------.-..(((((((..(........)...))))))).....)).))).)...---------------.))))))))...... ( -19.20)
>consensus
AACUUGACACUUGAU_UGC________U_UUUUUUUGUGCCUUCUUUUUGCGAGAUAGCAUUUUUGCUGUCGAUUUUUCG__GGGGAAGAUUUGACAGCUGCACUU
.........((((.....................................))))...........((((((((.(((((......))))).))))))))....... (-13.72 = -14.19 +   0.47)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,627,317 – 21,627,422
Length 105
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 68.63
Mean single sequence MFE -17.17
Consensus MFE -11.39
Energy contribution -11.28
Covariance contribution -0.11
Combinations/Pair 1.18
Mean z-score -1.49
Structure conservation index 0.66
SVM decision value 1.79
SVM RNA-class probability 0.977261
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21627317 105 - 27905053
AAGUGCAGCUGUCAAAUCUUCCCCUUCGAAAAAUCGACAGCAAAAAUGCUAUCUCGAAAAAAGAAGGCACAAAAAAA-AAAACGACGGCAAACCAAGUGUCAAGUU
..((((.((((((.....(((......))).....)))))).......((.(((.......))))))))).......-........((((.......))))..... ( -18.40)
>DroSim_CAF1 113277 92 - 1
AAGUGCAGCUGUCAAAUCUUCCCC--CGAAAAAUCGACAGCAAAAAUGCUAUCUCGCAAAAAGGAGGCAAAAAGAAAAA------------AUCAAGUGUCAAGUU
...(((.((((((.....(((...--.))).....)))))).....(((......)))........)))..........------------............... ( -14.70)
>DroAna_CAF1 95823 81 - 1
AAGUGCAGCUGUCAA---------------AAAUCGACAGCAGAAAUUCUGGCUGGCAGAGAGAAGUGACCAAAAAA-A--------GCA-GUCCAGCGACAACUU
...(((.((((((..---------------.....)))))).....(((((.....)))))................-.--------)))-(((....)))..... ( -18.40)
>consensus
AAGUGCAGCUGUCAAAUCUUCCCC__CGAAAAAUCGACAGCAAAAAUGCUAUCUCGCAAAAAGAAGGCACAAAAAAA_A________GCA_AUCAAGUGUCAAGUU
..((((.((((((......................)))))).....((((.(((.......))).))))...........................))).)..... (-11.39 = -11.28 +  -0.11)

alignment

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secondary structure

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Window 6

Location 21,627,345 – 21,627,462
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.06
Mean single sequence MFE -20.54
Consensus MFE -13.91
Energy contribution -14.06
Covariance contribution 0.15
Combinations/Pair 1.15
Mean z-score -2.26
Structure conservation index 0.68
SVM decision value 0.98
SVM RNA-class probability 0.893563
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21627345 117 - 27905053
UCAAGCAAUUGAACAGCGACCAAACUUCCACACAAAUCCCAAGUGCAGCUGUCAAAUCUUCCCCUUCGAAAAAUCGACAGCAAAAAUGCUAUCUCGAAAAAAGAAGGCACAAAAAAA---
((((....))))(((((......((((.............))))...)))))..........(((((......((((.((((....))))...)))).....)))))..........--- ( -20.62)
>DroSec_CAF1 116751 116 - 1
UCAAGCAAUUGAACAGCGACCAAACUUCCACACAAAUCCCAAGUGCAGCUGUCAAAUCUUCCCC--CGAAAAAUCGACAGCAAAAAUGCUAUCUCGCAAAAAGAAGGCAAAAAGAAAA--
((((....))))...((((...........(((.........)))..((((((.....(((...--.))).....))))))............)))).....................-- ( -18.10)
>DroSim_CAF1 113293 116 - 1
UCAAGCAAUUGAACAGCGACCAAACUUCCACACAAAUCCCAAGUGCAGCUGUCAAAUCUUCCCC--CGAAAAAUCGACAGCAAAAAUGCUAUCUCGCAAAAAGGAGGCAAAAAGAAAA--
((((....))))............(((((..................((((((.....(((...--.))).....)))))).....(((......)))....)))))...........-- ( -20.90)
>DroYak_CAF1 113534 117 - 1
UCAAGCAAUUGAACAGCGACCAAACUUCCACACAAAUCCCAAGUGCAGCUGUCAAAUCUUCCUC--CGAAAAAUCGACAGCAAAAAUGCUAUCUCGCAAAAAGA-GGCAAAAAUACAAAA
((((....))))..((((............(((.........)))..((((((.....(((...--.))).....)))))).....)))).((((.......))-))............. ( -18.50)
>DroAna_CAF1 95842 100 - 1
UUCAGCAAUUGAACAGGGAA-AAACUU-UGGAGAAGCCCGAAGUGCAGCUGUCAA---------------AAAUCGACAGCAGAAAUUCUGGCUGGCAGAGAGAAGUGACCAAAAAA---
.(((((....(((.......-..((((-(((......)))))))...((((((..---------------.....)))))).....)))..))))).....................--- ( -24.60)
>consensus
UCAAGCAAUUGAACAGCGACCAAACUUCCACACAAAUCCCAAGUGCAGCUGUCAAAUCUUCCCC__CGAAAAAUCGACAGCAAAAAUGCUAUCUCGCAAAAAGAAGGCAAAAAAAAAA__
((((....))))...................................((((((.....(((......))).....)))))).....((((.(((.......))).))))........... (-13.91 = -14.06 +   0.15)

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 13:01:17 2006