Locus 6950

Sequence ID X_DroMel_CAF1
Location 17,415,235 – 17,415,364
Length 129
Max. P 0.979726
window11355 window11356 window11357

overview

Window 5

Location 17,415,235 – 17,415,338
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.80
Mean single sequence MFE -22.36
Consensus MFE -12.87
Energy contribution -12.76
Covariance contribution -0.11
Combinations/Pair 1.28
Mean z-score -2.51
Structure conservation index 0.58
SVM decision value 0.79
SVM RNA-class probability 0.852221
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17415235 103 + 22224390
UCUCUU-GGCC-CGGUGUUU------UGCUAUUAU--UUUCUUAACAGUUAGCGGGCAGCAUACUG---UUUUUUUGUAUAAUU--U--UUUAAUGCCUUUCCUAACUGGAUUGGCAAUU
......-.(((-((.((...------.(((.(((.--.....))).))))).)))))...((((..---.......))))....--.--.....((((..(((.....)))..))))... ( -24.40)
>DroSec_CAF1 8908 104 + 1
UCUCUU-GGCC-CGGUGUUU------UGCUAUUAU--UUUCUUUACAGUUAGCGGGCAGCAUACUG---UUU-UUUGUAUACUU--UUUUUUAAUGCCUUUCCUAACUGGAUUGGCAAUU
......-.(((-((.((..(------((.((....--......))))).)).)))))((.((((..---...-...)))).)).--........((((..(((.....)))..))))... ( -23.70)
>DroSim_CAF1 8984 104 + 1
UCUCUU-GGCC-CGAUGUUU------UGCUAUUAU--UUUCUUUACAGUUAGCGGGCAGCAUACUG---UUU-UUUGUAUAAUU--UUUUUUAAUGCCUUUCCUAACUGGAUUGGCAAUU
......-.(((-((.(((..------.........--.......))).....)))))...((((..---...-...))))....--........((((..(((.....)))..))))... ( -22.47)
>DroEre_CAF1 8809 104 + 1
UCUCUU-CGCC-CGGUGUUC------UGCUAUUAU--UUUCUAUACAGUUAUCGAGCAGCUUACUGUGGUUU--UUUUAUAAUU----UUUUAAUGCCUUUCUUAACUGGAUUGGCAAUU
......-.(((-(((((..(------((((.....--...((....))......)))))..))))).)))..--..........----......((((..(((.....)))..))))... ( -23.84)
>DroYak_CAF1 8740 106 + 1
UCUCGG-CGCCCCGGUGUUU------UGCUAUUAU--UUUCUUUACAGUUAGCGAGCAGCUUACUG---UUU--UUUUAUACUUUUUUUUUUAAUGCCUUUCUUAACUGGAUUGGCAAUU
....((-(((....))))).------.........--.......(((((.(((.....))).))))---)..--....................((((..(((.....)))..))))... ( -21.80)
>DroAna_CAF1 8800 99 + 1
UCUAUUUGGCC-CGCUUUACCAUUAUUAUUAUUAUUUUUUCUUUACAGUUAGUGAGCAGAGUAGUG---UUG-C--------UU--U------UUGCCUUUCUUAACUGGAUUGGCAAUU
.((((((.((.-((((..................................)))).)).))))))..---...-.--------..--.------(((((..(((.....)))..))))).. ( -17.98)
>consensus
UCUCUU_GGCC_CGGUGUUU______UGCUAUUAU__UUUCUUUACAGUUAGCGAGCAGCAUACUG___UUU_UUUGUAUAAUU__U_UUUUAAUGCCUUUCCUAACUGGAUUGGCAAUU
............((((((........(((((..................)))))......))))))............................((((..(((.....)))..))))... (-12.87 = -12.76 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,415,265 – 17,415,364
Length 99
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.42
Mean single sequence MFE -27.20
Consensus MFE -16.67
Energy contribution -17.12
Covariance contribution 0.44
Combinations/Pair 1.11
Mean z-score -3.81
Structure conservation index 0.61
SVM decision value 1.84
SVM RNA-class probability 0.979726
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17415265 99 + 22224390
CUUAACAGUUAGCGGGCAGCAUACUG---UUUUUUUGUAUAAUU--U--UUUAAUGCCUUUCCUAACUGGAUUGGCAAUUG--------CG------CCUGGCUGUAUAUUAAAUCAUUU
....((((((((.(.((((.((((..---.......))))....--.--.....((((..(((.....)))..)))).)))--------).------))))))))).............. ( -28.10)
>DroSec_CAF1 8938 98 + 1
CUUUACAGUUAGCGGGCAGCAUACUG---UUU-UUUGUAUACUU--UUUUUUAAUGCCUUUCCUAACUGGAUUGGCAAUUG----------------CCUGGCUGUAUAUUAAAUCAUUU
...((((((...(((((((.((((..---...-...))))....--........((((..(((.....)))..)))).)))----------------))))))))))............. ( -28.30)
>DroSim_CAF1 9014 98 + 1
CUUUACAGUUAGCGGGCAGCAUACUG---UUU-UUUGUAUAAUU--UUUUUUAAUGCCUUUCCUAACUGGAUUGGCAAUUG----------------CCUGGCUGUAUAUUAAAUCAUUU
...((((((...(((((((.((((..---...-...))))....--........((((..(((.....)))..)))).)))----------------))))))))))............. ( -28.30)
>DroEre_CAF1 8839 98 + 1
CUAUACAGUUAUCGAGCAGCUUACUGUGGUUU--UUUUAUAAUU----UUUUAAUGCCUUUCUUAACUGGAUUGGCAAUUG----------------CCUGGCUGUAUAUUAAAUCAUUU
.((((((((((....((((....))))(((..--.....(((..----..))).((((..(((.....)))..))))...)----------------))))))))))))........... ( -22.10)
>DroYak_CAF1 8771 99 + 1
CUUUACAGUUAGCGAGCAGCUUACUG---UUU--UUUUAUACUUUUUUUUUUAAUGCCUUUCUUAACUGGAUUGGCAAUUG----------------CCUGGCUGUAUAUUAAAUCAUUU
...((((((((((((((((....)))---)))--....................((((..(((.....)))..))))...)----------------.)))))))))............. ( -23.80)
>DroAna_CAF1 8839 100 + 1
CUUUACAGUUAGUGAGCAGAGUAGUG---UUG-C--------UU--U------UUGCCUUUCUUAACUGGAUUGGCAAUUGGUGUGCUGCGCUACUAACUGGUCGCAUAUUAAAUCAUUU
.....((((((((.(((...((((..---(.(-(--------(.--.------(((((..(((.....)))..)))))..))))..)))))))))))))))................... ( -32.60)
>consensus
CUUUACAGUUAGCGAGCAGCAUACUG___UUU_UUUGUAUAAUU__U_UUUUAAUGCCUUUCCUAACUGGAUUGGCAAUUG________________CCUGGCUGUAUAUUAAAUCAUUU
...(((((((((....(((....)))............................((((..(((.....)))..)))).....................)))))))))............. (-16.67 = -17.12 +   0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,415,265 – 17,415,364
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.42
Mean single sequence MFE -19.45
Consensus MFE -9.39
Energy contribution -9.62
Covariance contribution 0.22
Combinations/Pair 1.14
Mean z-score -2.44
Structure conservation index 0.48
SVM decision value 0.27
SVM RNA-class probability 0.662090
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17415265 99 - 22224390
AAAUGAUUUAAUAUACAGCCAGG------CG--------CAAUUGCCAAUCCAGUUAGGAAAGGCAUUAAA--A--AAUUAUACAAAAAAA---CAGUAUGCUGCCCGCUAACUGUUAAG
.......((((((...(((..((------((--------(...((((..(((.....)))..)))).....--.--....((((.......---..)))))).))).)))...)))))). ( -20.50)
>DroSec_CAF1 8938 98 - 1
AAAUGAUUUAAUAUACAGCCAGG----------------CAAUUGCCAAUCCAGUUAGGAAAGGCAUUAAAAAA--AAGUAUACAAA-AAA---CAGUAUGCUGCCCGCUAACUGUAAAG
.............(((((.(.((----------------(...((((..(((.....)))..))))........--.(((((((...-...---..)))))))))).)....)))))... ( -23.70)
>DroSim_CAF1 9014 98 - 1
AAAUGAUUUAAUAUACAGCCAGG----------------CAAUUGCCAAUCCAGUUAGGAAAGGCAUUAAAAAA--AAUUAUACAAA-AAA---CAGUAUGCUGCCCGCUAACUGUAAAG
..(((((((........(((.((----------------(....)))..(((.....)))..)))........)--)))))).....-..(---((((..((.....))..))))).... ( -20.19)
>DroEre_CAF1 8839 98 - 1
AAAUGAUUUAAUAUACAGCCAGG----------------CAAUUGCCAAUCCAGUUAAGAAAGGCAUUAAAA----AAUUAUAAAA--AAACCACAGUAAGCUGCUCGAUAACUGUAUAG
...........(((((((((.((----------------(....)))..((.......))..))).......----..........--......(((....))).........)))))). ( -14.90)
>DroYak_CAF1 8771 99 - 1
AAAUGAUUUAAUAUACAGCCAGG----------------CAAUUGCCAAUCCAGUUAAGAAAGGCAUUAAAAAAAAAAGUAUAAAA--AAA---CAGUAAGCUGCUCGCUAACUGUAAAG
...........(((((.(((.((----------------(....)))..((.......))..))).((......))..)))))...--..(---((((.(((.....))).))))).... ( -17.90)
>DroAna_CAF1 8839 100 - 1
AAAUGAUUUAAUAUGCGACCAGUUAGUAGCGCAGCACACCAAUUGCCAAUCCAGUUAAGAAAGGCAA------A--AA--------G-CAA---CACUACUCUGCUCACUAACUGUAAAG
...................((((((((.(.((((........(((((..((.......))..)))))------.--.(--------(-...---..))...)))).)))))))))..... ( -19.50)
>consensus
AAAUGAUUUAAUAUACAGCCAGG________________CAAUUGCCAAUCCAGUUAAGAAAGGCAUUAAAA_A__AAUUAUACAAA_AAA___CAGUAUGCUGCCCGCUAACUGUAAAG
.............(((((.........................((((..((.......))..))))............................(((....)))........)))))... ( -9.39 =  -9.62 +   0.22)

alignment

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secondary structure

Postscript

dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:34 2006