Locus 7083

Sequence ID 2L_DroMel_CAF1
Location 19,812,327 – 19,812,517
Length 190
Max. P 0.999955
window11310 window11311 window11312 window11313 window11314

overview

Window 0

Location 19,812,327 – 19,812,447
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.17
Mean single sequence MFE -28.41
Consensus MFE -23.14
Energy contribution -23.58
Covariance contribution 0.44
Combinations/Pair 1.14
Mean z-score -1.73
Structure conservation index 0.81
SVM decision value 0.90
SVM RNA-class probability 0.878482
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19812327 120 + 22407834
UGCUGGUGUUAAGUCACUCUGGUUUCUCUUCAAUUGUCGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACACUCUAAUGAGUCUAAACACAAUUUUUAUUGAGGCCU
....(((.((((.......(((((((((((((.....((...((((((((.(.......).)))))))).)))))))))))))((((....)))).......)).......)))).))). ( -26.64)
>DroGri_CAF1 74884 119 + 1
UUGAGGUGAUAAUUCACUCUGGCUUCUCUUCAGUUGUCGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAGCGCUCUAAUGAGUCUAAACUCAAUUUUU-UAAGCGCCU
(((((((((....))))....(((((((((((.....((...((((((((.(.......).)))))))).)))))))))))))((((....)))).....))))).....-......... ( -30.40)
>DroSec_CAF1 80061 120 + 1
UGGUGGUGUAAGGUCACUCUGGUUUCUCUUCAAUUGUCGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGAAACACUCUAAUGAGUCUAAACUCAAUUUUUAUUGAGGCCU
.(((((((......))))...(((((((((((.....((...((((((((.(.......).)))))))).)))))))))))))((((....)))).....((((((....))))))))). ( -30.50)
>DroSim_CAF1 81533 118 + 1
UGCUGGUGUUA--UCACUCUGGUUUCUCUUCAAUUGUCGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACACUCUAAUGAGUCUAAACUCAAUUUUUAUUGAGGCCU
....(((....--........(((((((((((.....((...((((((((.(.......).)))))))).)))))))))))))((((....)))).....((((((....))))))))). ( -28.10)
>DroYak_CAF1 88823 120 + 1
UGCUAAUGUAAAGUCACUCUGGUUUCUCUUCAAUUGUCGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACACUCUAAUGAGUCUAAACUCAAUUUUUAUUAGGGCCU
.(((...((((((........(((((((((((.....((...((((((((.(.......).)))))))).))))))))))))).......(((((....)))))..))))))...))).. ( -26.40)
>consensus
UGCUGGUGUUAAGUCACUCUGGUUUCUCUUCAAUUGUCGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACACUCUAAUGAGUCUAAACUCAAUUUUUAUUGAGGCCU
....((((......))))...(((((((((((.....((...((((((((.(.......).)))))))).)))))))))))))((((....)))).....((((((....)))))).... (-23.14 = -23.58 +   0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,812,367 – 19,812,484
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.78
Mean single sequence MFE -28.10
Consensus MFE -26.21
Energy contribution -26.03
Covariance contribution -0.19
Combinations/Pair 1.22
Mean z-score -2.15
Structure conservation index 0.93
SVM decision value 1.82
SVM RNA-class probability 0.978620
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19812367 117 + 22407834
AUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACACUCUAAUGAGUCUAAACACAAUUUUUAUUGAGGCCUGAUAACUUAUGCUAUCGGGCCAAUG---AAUUAUAUAUUU
..((((((((.(.......).))))))))..(((...((....((((....))))))...)))....((((((..(((((((((.(....).)))))))))))))---)).......... ( -25.80)
>DroGri_CAF1 74924 119 + 1
AUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAGCGCUCUAAUGAGUCUAAACUCAAUUUUU-UAAGCGCCUGGCGGCAUUUGCAGCCGGGCCAAUUUGUAAAUACAUAUAU
((((((.....(((((((.(((..(....)..)))))))).))(((..(((((((....)))))....))-..)))(((((((.((....)).)))))))..))))))............ ( -30.30)
>DroSim_CAF1 81571 117 + 1
AUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACACUCUAAUGAGUCUAAACUCAAUUUUUAUUGAGGCCUGAUAACUUAUGUUAUCGGGCCAAUU---AAUUAUAUAUUU
..((((((((.(.......).))))))))......((((.....))))..(((((....)))))...........(((((((((((....)))))))))))....---............ ( -30.80)
>DroYak_CAF1 88863 117 + 1
AUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACACUCUAAUGAGUCUAAACUCAAUUUUUAUUAGGGCCUGACAGCUUAUGUUAUUGGGCCAAUA---GAUAAUACAUUU
..((((((((.(.......).))))))))..(((.((((.....))))..(((((....)))))...(((((...((((..(.(((....))).)..)))).)))---))...))).... ( -25.50)
>consensus
AUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACACUCUAAUGAGUCUAAACUCAAUUUUUAUUAAGGCCUGACAACUUAUGCUAUCGGGCCAAUU___AAUUAUAUAUUU
..((((((((.(.......).))))))))..(((.((((.....))))..(((((....)))))...........(((((((((((....)))))))))))............))).... (-26.21 = -26.03 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,812,367 – 19,812,484
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.78
Mean single sequence MFE -25.82
Consensus MFE -22.94
Energy contribution -23.12
Covariance contribution 0.19
Combinations/Pair 1.17
Mean z-score -1.62
Structure conservation index 0.89
SVM decision value 0.57
SVM RNA-class probability 0.786274
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19812367 117 - 22407834
AAAUAUAUAAUU---CAUUGGCCCGAUAGCAUAAGUUAUCAGGCCUCAAUAAAAAUUGUGUUUAGACUCAUUAGAGUGUUCCUCUCCACGGAAAUCUUUAGUAAAAGGCGAAAGAUUUAU
......((((.(---(...((((.((((((....)))))).))))..........((((.(((..(((....(((...((((.......)))).)))..))).))).))))..)).)))) ( -26.30)
>DroGri_CAF1 74924 119 - 1
AUAUAUGUAUUUACAAAUUGGCCCGGCUGCAAAUGCCGCCAGGCGCUUA-AAAAAUUGAGUUUAGACUCAUUAGAGCGCUCCUCUCCACGGAAAUCUUUAGUAAAAGGCGAAAGAUUUAU
......................(((((.((....)).))).(((((((.-......(((((....)))))...))))))).........))((((((((.((.....)).)))))))).. ( -29.30)
>DroSim_CAF1 81571 117 - 1
AAAUAUAUAAUU---AAUUGGCCCGAUAACAUAAGUUAUCAGGCCUCAAUAAAAAUUGAGUUUAGACUCAUUAGAGUGUUCCUCUCCACGGAAAUCUUUAGUAAAAGGCGAAAGAUUUAU
............---....((((.((((((....)))))).))))............(((...(.((((....)))).)..))).......((((((((.((.....)).)))))))).. ( -27.20)
>DroYak_CAF1 88863 117 - 1
AAAUGUAUUAUC---UAUUGGCCCAAUAACAUAAGCUGUCAGGCCCUAAUAAAAAUUGAGUUUAGACUCAUUAGAGUGUUCCUCUCCACGGAAAUCUUUAGUAAAAGGCGAAAGAUUUAU
..........((---((..((((..(((........)))..))))...........(((((....))))).))))(((........)))..((((((((.((.....)).)))))))).. ( -20.50)
>consensus
AAAUAUAUAAUU___AAUUGGCCCGAUAACAUAAGCUAUCAGGCCCCAAUAAAAAUUGAGUUUAGACUCAUUAGAGUGUUCCUCUCCACGGAAAUCUUUAGUAAAAGGCGAAAGAUUUAU
...................((((.((((((....)))))).))))...........(((((....)))))..((((.....))))......((((((((.((.....)).)))))))).. (-22.94 = -23.12 +   0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,812,407 – 19,812,517
Length 110
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 67.21
Mean single sequence MFE -24.90
Consensus MFE -19.98
Energy contribution -19.73
Covariance contribution -0.25
Combinations/Pair 1.40
Mean z-score -3.19
Structure conservation index 0.80
SVM decision value 4.84
SVM RNA-class probability 0.999955
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19812407 110 + 22407834
AACACUCUAAUGAGUCUAAACACAAUUUUUAUUGAGGCCUGAUAACUUAUGCUAUCGGGCCAAUG---AAUUAUAUAUUUUA--AAAAUGU-UAGUUACAUCUUAAUGA---ACUUGUA
...((((....))))......((((..(((((((((((((((((.(....).))))))))).(((---(((((.(((((...--..)))))-))))).))).)))))))---).)))). ( -25.90)
>DroGri_CAF1 74964 105 + 1
AGCGCUCUAAUGAGUCUAAACUCAAUUUUU-UAAGCGCCUGGCGGCAUUUGCAGCCGGGCCAAUUUGUAAAUACAUAUAUCAUUAAAAUUUGCUG----AUCU---------AAUUGUA
((.((((....)))))).....(((((...-..((((((((((.((....)).))))))).....(((....)))................))).----....---------))))).. ( -26.30)
>DroSim_CAF1 81611 112 + 1
AACACUCUAAUGAGUCUAAACUCAAUUUUUAUUGAGGCCUGAUAACUUAUGUUAUCGGGCCAAUU---AAUUAUAUAUUUU---CAAAUUU-UAGUUACAUUUUAAUGAAUAACUUGUA
.(((......(((((....)))))...(((((((((((((((((((....)))))))))))...(---(((((...(((..---..)))..-))))))....)))))))).....))). ( -27.90)
>DroYak_CAF1 88903 85 + 1
AACACUCUAAUGAGUCUAAACUCAAUUUUUAUUAGGGCCUGACAGCUUAUGUUAUUGGGCCAAUA---GAUAAUACAUUUUA-------------------------------CUUAGA
.....((((((((((....)))))...(((((...((((..(.(((....))).)..)))).)))---))............-------------------------------.))))) ( -19.50)
>consensus
AACACUCUAAUGAGUCUAAACUCAAUUUUUAUUAAGGCCUGACAACUUAUGCUAUCGGGCCAAUU___AAUUAUAUAUUUUA__AAAAUUU_UAG____AUCU_________ACUUGUA
...((((....))))....................(((((((((((....))))))))))).......................................................... (-19.98 = -19.73 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,812,407 – 19,812,517
Length 110
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 67.21
Mean single sequence MFE -21.39
Consensus MFE -15.01
Energy contribution -15.20
Covariance contribution 0.19
Combinations/Pair 1.33
Mean z-score -1.84
Structure conservation index 0.70
SVM decision value 2.62
SVM RNA-class probability 0.995797
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19812407 110 - 22407834
UACAAGU---UCAUUAAGAUGUAACUA-ACAUUUU--UAAAAUAUAUAAUU---CAUUGGCCCGAUAGCAUAAGUUAUCAGGCCUCAAUAAAAAUUGUGUUUAGACUCAUUAGAGUGUU
.......---.....(((((((.....-)))))))--..(((((((.....---....((((.((((((....)))))).))))...........)))))))..((((....))))... ( -23.05)
>DroGri_CAF1 74964 105 - 1
UACAAUU---------AGAU----CAGCAAAUUUUAAUGAUAUAUGUAUUUACAAAUUGGCCCGGCUGCAAAUGCCGCCAGGCGCUUA-AAAAAUUGAGUUUAGACUCAUUAGAGCGCU
((((...---------..((----((...........))))...))))........(((((..(((.......))))))))((((((.-......(((((....)))))...)))))). ( -24.50)
>DroSim_CAF1 81611 112 - 1
UACAAGUUAUUCAUUAAAAUGUAACUA-AAAUUUG---AAAAUAUAUAAUU---AAUUGGCCCGAUAACAUAAGUUAUCAGGCCUCAAUAAAAAUUGAGUUUAGACUCAUUAGAGUGUU
((((..(((.....)))..)))).(((-((.....---.............---....((((.((((((....)))))).))))(((((....))))).)))))((((....))))... ( -24.40)
>DroYak_CAF1 88903 85 - 1
UCUAAG-------------------------------UAAAAUGUAUUAUC---UAUUGGCCCAAUAACAUAAGCUGUCAGGCCCUAAUAAAAAUUGAGUUUAGACUCAUUAGAGUGUU
(((((.-------------------------------..............---....((((..(((........)))..))))...........(((((....))))))))))..... ( -13.60)
>consensus
UACAAGU_________AGAU____CUA_AAAUUUU__UAAAAUAUAUAAUU___AAUUGGCCCGAUAACAUAAGCUAUCAGGCCCCAAUAAAAAUUGAGUUUAGACUCAUUAGAGUGUU
..........................................................((((.((((((....)))))).))))...........(((((....))))).......... (-15.01 = -15.20 +   0.19)

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 12:27:09 2006