Locus 4916

Sequence ID X_DroMel_CAF1
Location 12,798,572 – 12,798,708
Length 136
Max. P 0.999983
window8016 window8017 window8018 window8019

overview

Window 6

Location 12,798,572 – 12,798,674
Length 102
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 71.88
Mean single sequence MFE -26.38
Consensus MFE -14.79
Energy contribution -15.47
Covariance contribution 0.69
Combinations/Pair 1.12
Mean z-score -3.46
Structure conservation index 0.56
SVM decision value 4.71
SVM RNA-class probability 0.999941
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12798572 102 + 22224390
AAACAAACACAGUGGCCAAACGCAGU---UUCACU--GCCCAUGAAAAUGGAAUCCAAUUUCCAUGU-----ACUUUUUUUUU----UUGCCACUGCCACUGCCAUUUCCGUGUUU
....((((((((((((.(((.((((.---....))--))........((((((......))))))..-----.........))----).))))))((....)).......)))))) ( -25.80)
>DroSim_CAF1 4857 101 + 1
AAACAAACACAGUGGCCAAGCGCAGU---UUCACU--GCCCAUGAAAAUGGAAUCCAAUUUCCAUGU------CUUUUUUUUU----UGGCCACUGCCACUGCCAUUUCCGUGUUU
....((((((((((((((((.((((.---....))--))........((((((......))))))..------........))----))))))))((....)).......)))))) ( -32.00)
>DroYak_CAF1 5640 94 + 1
AA----ACACAGUGGCCAAACGCAGU---UUCACU--GCCCAUGAAAAUGGAAUCCAAUUUCCAUGU-----ACUUUUUUUUUUUUUCGGCCACUGCCACUGCCA--------CUU
..----...((((((((....((((.---....))--))........((((((......))))))..-----................)))))))).........--------... ( -27.80)
>DroAna_CAF1 5191 108 + 1
AA------GCAGUGU-CAGAAGCAGUAGAGACACUUGGGCAAUG-AAAUGGAAUCCAAUUUCCAUCUUAUAUACGUAUUUUUUUUUGUAUAUACAUACAUAUCUAGUUUGGUGUUU
((------(((((((-(............)))))(..(((....-..((((((......))))))..((((((((..........))))))))............)))..)))))) ( -19.90)
>consensus
AA____ACACAGUGGCCAAACGCAGU___UUCACU__GCCCAUGAAAAUGGAAUCCAAUUUCCAUGU_____ACUUUUUUUUU____UGGCCACUGCCACUGCCAUUUCCGUGUUU
.........((((((((......(((......)))............((((((......)))))).......................)))))))).................... (-14.79 = -15.47 +   0.69)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,798,572 – 12,798,674
Length 102
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 71.88
Mean single sequence MFE -31.88
Consensus MFE -18.86
Energy contribution -19.18
Covariance contribution 0.31
Combinations/Pair 1.20
Mean z-score -4.01
Structure conservation index 0.59
SVM decision value 5.32
SVM RNA-class probability 0.999983
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12798572 102 - 22224390
AAACACGGAAAUGGCAGUGGCAGUGGCAA----AAAAAAAAAGU-----ACAUGGAAAUUGGAUUCCAUUUUCAUGGGC--AGUGAA---ACUGCGUUUGGCCACUGUGUUUGUUU
....(((((....((((((((...(((..----...........-----.(((((((((.((...))))))))))).((--((....---.)))))))..)))))))).))))).. ( -32.90)
>DroSim_CAF1 4857 101 - 1
AAACACGGAAAUGGCAGUGGCAGUGGCCA----AAAAAAAAAG------ACAUGGAAAUUGGAUUCCAUUUUCAUGGGC--AGUGAA---ACUGCGCUUGGCCACUGUGUUUGUUU
............(((((..((((((((((----(.........------.(((((((((.((...))))))))))).((--((....---.))))..)))))))))))..))))). ( -37.60)
>DroYak_CAF1 5640 94 - 1
AAG--------UGGCAGUGGCAGUGGCCGAAAAAAAAAAAAAGU-----ACAUGGAAAUUGGAUUCCAUUUUCAUGGGC--AGUGAA---ACUGCGUUUGGCCACUGUGU----UU
...--------........((((((((((((.............-----.(((((((((.((...))))))))))).((--((....---.)))).))))))))))))..----.. ( -35.40)
>DroAna_CAF1 5191 108 - 1
AAACACCAAACUAGAUAUGUAUGUAUAUACAAAAAAAAAUACGUAUAUAAGAUGGAAAUUGGAUUCCAUUU-CAUUGCCCAAGUGUCUCUACUGCUUCUG-ACACUGC------UU
...............(((((((((((............)))))))))))((((((((......))))))))-....((...((((((............)-)))))))------.. ( -21.60)
>consensus
AAACACGGAAAUGGCAGUGGCAGUGGCCA____AAAAAAAAAGU_____ACAUGGAAAUUGGAUUCCAUUUUCAUGGGC__AGUGAA___ACUGCGUUUGGCCACUGUGU____UU
.............((((((((...(((.......................(((((((((.((...))))))))))).....(((......)))..)))..))))))))........ (-18.86 = -19.18 +   0.31)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,798,605 – 12,798,708
Length 103
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 66.46
Mean single sequence MFE -12.80
Consensus MFE -6.38
Energy contribution -6.12
Covariance contribution -0.25
Combinations/Pair 1.22
Mean z-score -1.74
Structure conservation index 0.50
SVM decision value 0.73
SVM RNA-class probability 0.834450
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12798605 103 + 22224390
CCCAUGAAAAUGGAAUCCAAUUUCCAUGU-----ACUUUUUUUUU----UUGCCACUGCCACUGCCAUUUCCGUGUUU---UUUCUCGCCA-UUCUUUCUUA--UAUCUAUUUUUUUU
.....((((((((((......))))))..-----...........----.......................(((...---.....)))..-...))))...--.............. (  -8.10)
>DroSim_CAF1 4890 97 + 1
CCCAUGAAAAUGGAAUCCAAUUUCCAUGU------CUUUUUUUUU----UGGCCACUGCCACUGCCAUUUCCGUGUUUU--UUUCUCGCCG-CUCUUUCUUA--UAUCUUUU------
..((((...((((((......))))))..------..........----((((....))))..........))))....--..........-..........--........------ ( -12.80)
>DroYak_CAF1 5669 94 + 1
CCCAUGAAAAUGGAAUCCAAUUUCCAUGU-----ACUUUUUUUUUUUUUCGGCCACUGCCACUGCCA--------CUU---UUCCGUGUUU-CUUUUUUCUUGAUAUCUUU-------
..((.((((((((((......))))))..-----................(((....))).....((--------(..---....)))...-....)))).))........------- ( -13.20)
>DroAna_CAF1 5222 111 + 1
GCAAUG-AAAUGGAAUCCAAUUUCCAUCUUAUAUACGUAUUUUUUUUUGUAUAUACAUACAUAUCUAGUUUGGUGUUUUUUUUUUUUGCCAGCUUUGUUUUG--UAUUCUUU----UU
......-..((((((......))))))..((((((((..........)))))))).(((((.((..((((.((((...........))))))))..))..))--))).....----.. ( -17.10)
>consensus
CCCAUGAAAAUGGAAUCCAAUUUCCAUGU_____ACUUUUUUUUU____UGGCCACUGCCACUGCCAUUUCCGUGUUU___UUUCUCGCCA_CUCUUUCUUA__UAUCUUUU______
.........((((((......)))))).......................(((....))).......................................................... ( -6.38 =  -6.12 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,798,605 – 12,798,708
Length 103
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 66.46
Mean single sequence MFE -15.08
Consensus MFE -9.99
Energy contribution -9.05
Covariance contribution -0.94
Combinations/Pair 1.33
Mean z-score -1.98
Structure conservation index 0.66
SVM decision value 2.87
SVM RNA-class probability 0.997507
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12798605 103 - 22224390
AAAAAAAAUAGAUA--UAAGAAAGAA-UGGCGAGAAA---AAACACGGAAAUGGCAGUGGCAGUGGCAA----AAAAAAAAAGU-----ACAUGGAAAUUGGAUUCCAUUUUCAUGGG
..............--..........-..........---...((.((((((((((((..(.(((....----...........-----.))).)..))))....)))))))).)).. ( -12.49)
>DroSim_CAF1 4890 97 - 1
------AAAAGAUA--UAAGAAAGAG-CGGCGAGAAA--AAAACACGGAAAUGGCAGUGGCAGUGGCCA----AAAAAAAAAG------ACAUGGAAAUUGGAUUCCAUUUUCAUGGG
------........--..........-..........--....((.((((((((.(((..((((..(((----..........------...)))..)))).))))))))))).)).. ( -14.82)
>DroYak_CAF1 5669 94 - 1
-------AAAGAUAUCAAGAAAAAAG-AAACACGGAA---AAG--------UGGCAGUGGCAGUGGCCGAAAAAAAAAAAAAGU-----ACAUGGAAAUUGGAUUCCAUUUUCAUGGG
-------.......((..........-...(((....---..)--------)).....(((....)))))..............-----.(((((((((.((...))))))))))).. ( -16.20)
>DroAna_CAF1 5222 111 - 1
AA----AAAGAAUA--CAAAACAAAGCUGGCAAAAAAAAAAAACACCAAACUAGAUAUGUAUGUAUAUACAAAAAAAAAUACGUAUAUAAGAUGGAAAUUGGAUUCCAUUU-CAUUGC
..----........--.............((((......................(((((((((((............)))))))))))((((((((......))))))))-..)))) ( -16.80)
>consensus
______AAAAGAUA__UAAAAAAAAG_UGGCAAGAAA___AAACACGGAAAUGGCAGUGGCAGUGGCCA____AAAAAAAAAGU_____ACAUGGAAAUUGGAUUCCAUUUUCAUGGG
.........................................................((((....)))).....................(((((((((.((...))))))))))).. ( -9.99 =  -9.05 +  -0.94)

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 11:36:00 2006