Locus 4206

Sequence ID 2R_DroMel_CAF1
Location 13,829,836 – 13,829,971
Length 135
Max. P 0.760070
window6760 window6761 window6762

overview

Window 0

Location 13,829,836 – 13,829,943
Length 107
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 84.28
Mean single sequence MFE -17.57
Consensus MFE -16.00
Energy contribution -16.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.28
Structure conservation index 0.91
SVM decision value 0.50
SVM RNA-class probability 0.760070
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13829836 107 - 20766785
GCCCACACAAACGAUGAAAACUAUGGCGUUGGGCGAAAAGUUUUUAGUUCAACGGGGUAGCGAAAAAUAUAA-AAGGAAAACUAUAUGUGUGUACAAAAAAAAAAAAA--
(..((((((...........((((..((((((((............))))))))..))))............-.((.....))...))))))..).............-- ( -20.00)
>DroEre_CAF1 131045 91 - 1
GCCCACACAAACG---------AUGGCGUUGGGCGAAAAGUUUUUAGUUCAACGGGGUAGCGAAAAAUAUAAAAAGGAAAACUAUAUGUGUGUAUAUACA----------
...((((((....---------((((((((((((............))))))))..(((........)))...........)))).))))))........---------- ( -16.40)
>DroYak_CAF1 135104 100 - 1
GCCCACACAAACG---------AUGGCGUUGGGCAAAAAGUUUUUAGUUCAACGGGGUAGCGAAAAAUAUAAAAAGGAAAACUAUAUGUGUGUAUAAAAAAAAAGAC-GA
...((((((....---------((((((((((((.(((....))).))))))))..(((........)))...........)))).))))))...............-.. ( -16.30)
>consensus
GCCCACACAAACG_________AUGGCGUUGGGCGAAAAGUUUUUAGUUCAACGGGGUAGCGAAAAAUAUAAAAAGGAAAACUAUAUGUGUGUAUAAAAAAAAA_A____
...((((((.................((((((((.(((....))).))))))))....................((.....))...)))))).................. (-16.00 = -16.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,829,866 – 13,829,971
Length 105
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 82.88
Mean single sequence MFE -23.94
Consensus MFE -18.08
Energy contribution -19.20
Covariance contribution 1.11
Combinations/Pair 1.09
Mean z-score -1.72
Structure conservation index 0.76
SVM decision value 0.27
SVM RNA-class probability 0.662631
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13829866 105 + 20766785
UCCUU-UUAUAUUUUUCGCUACCCCGUUGAACUAAAAACUUUU-CGCCCAACGCCAUAGUUUUCAUCGUUUGUGUGGGCGGGGUAAAUGCGUUUUUGAUGCUG---UUUU
.....-...((((...((((((((((((........)))....-.(((((.(((....(.......)....))))))))))))))...))).....))))...---.... ( -25.20)
>DroSec_CAF1 130420 104 + 1
UCCUU-UUAUAUUUUUCGCUACCCCGUUGAACUAAAAACUUUU-CGCCCAACGCCAUCGUUUUCAUCGUUUGUGUGGGCGGGGUAAAUGCGUUUUUGAUGCUG---UUU-
.....-...((((...((((((((((((........)))....-.(((((.(((...((.......))...))))))))))))))...))).....))))...---...- ( -27.50)
>DroSim_CAF1 135671 104 + 1
UCCUU-UUAUAUUUUUCGCUACCCCGUUGAACUAAAAACUUUU-CGCCCAACGCCAUCGUUUUCAUCGUUUGUGUGGGCGGGGUAAAUGCGUUUUUGAUGCUG---UUU-
.....-...((((...((((((((((((........)))....-.(((((.(((...((.......))...))))))))))))))...))).....))))...---...- ( -27.50)
>DroEre_CAF1 131067 96 + 1
UCCUUUUUAUAUUUUUCGCUACCCCGUUGAACUAAAAACUUUU-CGCCCAACGCCAU---------CGUUUGUGUGGGCGGGGUAAAUGCGUUUUUGAUGCUG---UUU-
.........((((...((((((((((((........)))....-.(((((.(((...---------.....))))))))))))))...))).....))))...---...- ( -26.00)
>DroYak_CAF1 135135 99 + 1
UCCUUUUUAUAUUUUUCGCUACCCCGUUGAACUAAAAACUUUU-UGCCCAACGCCAU---------CGUUUGUGUGGGCGGGGUAAAUGCGUUUUUGAUGCUGGUUUUU-
.((....(((......((((((((((((........)))....-.(((((.(((...---------.....))))))))))))))...)))......)))..)).....- ( -26.10)
>DroAna_CAF1 138052 83 + 1
UUAUU-U--UAUUUUU---------GUUGAACUAAAAACUUUUUUGGCCCAUGGUAUAG-----------AGGAGGGGGAGAGUAAAUGCGUUUUUGAUGCUG---UUU-
....(-(--(((((((---------......((((((....))))))(((.........-----------....))).))))))))).(((((...)))))..---...- ( -11.32)
>consensus
UCCUU_UUAUAUUUUUCGCUACCCCGUUGAACUAAAAACUUUU_CGCCCAACGCCAU_G_______CGUUUGUGUGGGCGGGGUAAAUGCGUUUUUGAUGCUG___UUU_
...................(((((((((........)))......(((((.(((.................))))))))))))))...(((((...)))))......... (-18.08 = -19.20 +   1.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,829,866 – 13,829,971
Length 105
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 82.88
Mean single sequence MFE -20.82
Consensus MFE -13.94
Energy contribution -15.49
Covariance contribution 1.56
Combinations/Pair 1.06
Mean z-score -1.96
Structure conservation index 0.67
SVM decision value 0.17
SVM RNA-class probability 0.616743
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13829866 105 - 20766785
AAAA---CAGCAUCAAAAACGCAUUUACCCCGCCCACACAAACGAUGAAAACUAUGGCGUUGGGCG-AAAAGUUUUUAGUUCAACGGGGUAGCGAAAAAUAUAA-AAGGA
....---............(((...(((((((((.....................)))(((((((.-...........))))))))))))))))..........-..... ( -23.90)
>DroSec_CAF1 130420 104 - 1
-AAA---CAGCAUCAAAAACGCAUUUACCCCGCCCACACAAACGAUGAAAACGAUGGCGUUGGGCG-AAAAGUUUUUAGUUCAACGGGGUAGCGAAAAAUAUAA-AAGGA
-...---............(((...((((((((((((.(...((.(....)))...).).))))).-....(((........))))))))))))..........-..... ( -24.10)
>DroSim_CAF1 135671 104 - 1
-AAA---CAGCAUCAAAAACGCAUUUACCCCGCCCACACAAACGAUGAAAACGAUGGCGUUGGGCG-AAAAGUUUUUAGUUCAACGGGGUAGCGAAAAAUAUAA-AAGGA
-...---............(((...((((((((((((.(...((.(....)))...).).))))).-....(((........))))))))))))..........-..... ( -24.10)
>DroEre_CAF1 131067 96 - 1
-AAA---CAGCAUCAAAAACGCAUUUACCCCGCCCACACAAACG---------AUGGCGUUGGGCG-AAAAGUUUUUAGUUCAACGGGGUAGCGAAAAAUAUAAAAAGGA
-...---............(((...(((((((((..........---------..)))(((((((.-...........))))))))))))))))................ ( -24.50)
>DroYak_CAF1 135135 99 - 1
-AAAAACCAGCAUCAAAAACGCAUUUACCCCGCCCACACAAACG---------AUGGCGUUGGGCA-AAAAGUUUUUAGUUCAACGGGGUAGCGAAAAAUAUAAAAAGGA
-..................(((...(((((((((..........---------..)))(((((((.-(((....))).))))))))))))))))................ ( -24.40)
>DroAna_CAF1 138052 83 - 1
-AAA---CAGCAUCAAAAACGCAUUUACUCUCCCCCUCCU-----------CUAUACCAUGGGCCAAAAAAGUUUUUAGUUCAAC---------AAAAAUA--A-AAUAA
-...---..((.........))..................-----------........(((((.((((....)))).)))))..---------.......--.-..... (  -3.90)
>consensus
_AAA___CAGCAUCAAAAACGCAUUUACCCCGCCCACACAAACG_______C_AUGGCGUUGGGCG_AAAAGUUUUUAGUUCAACGGGGUAGCGAAAAAUAUAA_AAGGA
...................(((...(((((((((((........................)))))......(((........))))))))))))................ (-13.94 = -15.49 +   1.56)

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 11:14:18 2006