Locus 5993

Sequence ID X_DroMel_CAF1
Location 15,398,075 – 15,398,309
Length 234
Max. P 0.930754
window9747 window9748 window9749 window9750

overview

Window 7

Location 15,398,075 – 15,398,180
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.69
Mean single sequence MFE -24.65
Consensus MFE -19.17
Energy contribution -19.30
Covariance contribution 0.13
Combinations/Pair 1.08
Mean z-score -2.06
Structure conservation index 0.78
SVM decision value 1.20
SVM RNA-class probability 0.930007
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15398075 105 + 22224390
CUCCACCCCCCC------CCCCU-A-CCCCCUGUUGCUUGUCAUUUGCUGCUUCAUAUUUCUUCAUUGCCAUAAUGAAGCCCAAAACAGA-------ACAGGGCAAACUGCAAUAACAAG
............------.....-.-..(((((((.((.((..((((..(((((((.................))))))).)))))))))-------))))))................. ( -19.13)
>DroSec_CAF1 44084 103 + 1
----ACUCCCAC------CCC-------CUCUGUUGCUUGUCAUUUGCUGCUUCAUAUUUAUUCAUUGCCAUAAUGAAGCCCAAAACAGAAGGCAAAACAGGGCAAACUGCAAUAACAAG
----........------.((-------((...((((((....((((..(((((((.................))))))).)))).....))))))...))))................. ( -20.13)
>DroEre_CAF1 35340 113 + 1
UUCCAAUCCCCC------UUCUGGACGCCCCUGUUGCUUGUCAUUUGCUGCUUCAUAUUUCUUCAUUGCCACAAUGAAGCCCAAAACAGAAGGCA-AACAGGGCAAACUGCAAUAACAGG
.((((.......------...)))).((((.((((((((....((((..(((((((.................))))))).)))).....)))).-))))))))...(((......))). ( -27.53)
>DroYak_CAF1 26902 120 + 1
UUCCAAAACCCCCCUGUUUUUUGGACGCCCCUGUUGCUUGUCAUUUGCUGCUUCAUAUUUCUUCAUUGCCAUAAUGAAGCCCAAAACAGAAGGCAAAACAGGGCGAAUUGCAAUAACAGG
............((((((..(((.((((((.((((((((....((((..(((((((.................))))))).)))).....)))))..))))))))...).))).)))))) ( -31.83)
>consensus
UUCCAAUCCCCC______CCCUG_A_GCCCCUGUUGCUUGUCAUUUGCUGCUUCAUAUUUCUUCAUUGCCAUAAUGAAGCCCAAAACAGAAGGCA_AACAGGGCAAACUGCAAUAACAAG
.............................(((((((.((((..(((((.(((((((.................)))))))((..................)))))))..))))))))))) (-19.17 = -19.30 +   0.13)

alignment

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secondary structure

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Window 8

Location 15,398,180 – 15,398,290
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.66
Mean single sequence MFE -17.85
Consensus MFE -11.51
Energy contribution -12.07
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -1.62
Structure conservation index 0.64
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15398180 110 + 22224390
GGAAAAAACCAAAAAUAAAA-AUA---------AAGGAGCAAAAAAAGGACAUCCAUGCGAGCAAAGUAACACGUAAAUUAAUCGCAAUUGCAAAAGUUAUUUGUUACCCCCUGCAAUUU
((......))..........-...---------..(((.(........)...))).(((.((....((((((.((((.......((....)).....)))).))))))...))))).... ( -13.60)
>DroSec_CAF1 44187 98 + 1
GGGAAAAACCAAAAAA-------A---------AAGGA--UAAAAAAGGACAUCCA-GCGGGCAAAGUAACACGUAUAUUAAUCGCAAUUGCAAAAGUUAUUUGUUACCCCCUGCAA---
((......))......-------.---------..(((--(..........)))).-(((((....((((((.(((........((....))......))).))))))..)))))..--- ( -19.04)
>DroEre_CAF1 35453 115 + 1
GG-AAAAACCAAAGCCAAAA-AAAAGGGGGGAAAAGGA--AAAAAAUAGACAACCA-GCGGGCAAAGUAACACGUAAAUUAAUCGCAAUUGCAAAAGUUAUUUGUUACCCCCUGCAAUUU
((-.....))..........-....((..(........--..........)..)).-(((((....((((((.((((.......((....)).....)))).))))))..)))))..... ( -18.57)
>DroYak_CAF1 27022 116 + 1
AG-AAAAACGAAAAAAAAAAUGAAAAAGGGGGAAAGCA--AAAAAAAGGACAACCA-UUGGGCGAAGUAACACGUAAAUUAAUCGCAAUUGCAAAAGUUAUUUGUUACCCCCUGCAAUUU
..-.................((....((((((..((((--((.....((....)).-....((((..(((........))).))))..............)))))).)))))).)).... ( -20.20)
>consensus
GG_AAAAACCAAAAAAAAAA_AAA_________AAGGA__AAAAAAAGGACAACCA_GCGGGCAAAGUAACACGUAAAUUAAUCGCAAUUGCAAAAGUUAUUUGUUACCCCCUGCAAUUU
.........................................................(((((....((((((.((((.......((....)).....)))).))))))..)))))..... (-11.51 = -12.07 +   0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,398,210 – 15,398,309
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 90.36
Mean single sequence MFE -22.46
Consensus MFE -18.21
Energy contribution -18.78
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.45
Structure conservation index 0.81
SVM decision value 0.04
SVM RNA-class probability 0.555220
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15398210 99 + 22224390
AAAAAAAGGACAUCCAUGCGAGCAAAGUAACACGUAAAUUAAUCGCAAUUGCAAAAGUUAUUUGUUACCCCCUGCAAUUUACAAGGGAUUUCCCCGGGG
.......((....))...........((((((.((((.......((....)).....)))).))))))((((((.......)).(((.....))))))) ( -18.80)
>DroSec_CAF1 44209 93 + 1
UAAAAAAGGACAUCCA-GCGGGCAAAGUAACACGUAUAUUAAUCGCAAUUGCAAAAGUUAUUUGUUACCCCCUGCAA-----GGGGGAUUUCCCCGGGG
............(((.-(((((....((((((.(((........((....))......))).))))))..)))))..-----.((((....))))))). ( -25.44)
>DroEre_CAF1 35489 98 + 1
AAAAAAUAGACAACCA-GCGGGCAAAGUAACACGUAAAUUAAUCGCAAUUGCAAAAGUUAUUUGUUACCCCCUGCAAUUUACAAGGGAUUUCCCGGGGG
..........(..((.-(((((....((((((.((((.......((....)).....)))).))))))..))))).........(((....)))))..) ( -23.80)
>DroYak_CAF1 27059 98 + 1
AAAAAAAGGACAACCA-UUGGGCGAAGUAACACGUAAAUUAAUCGCAAUUGCAAAAGUUAUUUGUUACCCCCUGCAAUUUACAAGGGAUUUCCCAGGGG
.............((.-(((((.((.((((((.((((.......((....)).....)))).)))))).((((..........)))).)).))))))). ( -21.80)
>consensus
AAAAAAAGGACAACCA_GCGGGCAAAGUAACACGUAAAUUAAUCGCAAUUGCAAAAGUUAUUUGUUACCCCCUGCAAUUUACAAGGGAUUUCCCCGGGG
.............((..(((((....((((((.((((.......((....)).....)))).))))))..))))).........(((....))).)).. (-18.21 = -18.78 +   0.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,398,210 – 15,398,309
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 90.36
Mean single sequence MFE -26.48
Consensus MFE -21.99
Energy contribution -22.43
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -2.17
Structure conservation index 0.83
SVM decision value 1.21
SVM RNA-class probability 0.930754
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15398210 99 - 22224390
CCCCGGGGAAAUCCCUUGUAAAUUGCAGGGGGUAACAAAUAACUUUUGCAAUUGCGAUUAAUUUACGUGUUACUUUGCUCGCAUGGAUGUCCUUUUUUU
....(((((.((((..(((.(((((((((((...........)))))))))))((((.((((......))))..))))..))).)))).)))))..... ( -25.70)
>DroSec_CAF1 44209 93 - 1
CCCCGGGGAAAUCCCCC-----UUGCAGGGGGUAACAAAUAACUUUUGCAAUUGCGAUUAAUAUACGUGUUACUUUGCCCGC-UGGAUGUCCUUUUUUA
((.((((.(((..((((-----.....))))((((((.(((....((((....))))....)))...))))))))).)))).-.))............. ( -25.80)
>DroEre_CAF1 35489 98 - 1
CCCCCGGGAAAUCCCUUGUAAAUUGCAGGGGGUAACAAAUAACUUUUGCAAUUGCGAUUAAUUUACGUGUUACUUUGCCCGC-UGGUUGUCUAUUUUUU
((..((((....(((((((.....)))))))((((((..(((...((((....)))).....)))..))))))....)))).-.))............. ( -27.70)
>DroYak_CAF1 27059 98 - 1
CCCCUGGGAAAUCCCUUGUAAAUUGCAGGGGGUAACAAAUAACUUUUGCAAUUGCGAUUAAUUUACGUGUUACUUCGCCCAA-UGGUUGUCCUUUUUUU
((..((((....(((((((.....)))))))((((((..(((...((((....)))).....)))..))))))....)))).-.))............. ( -26.70)
>consensus
CCCCGGGGAAAUCCCUUGUAAAUUGCAGGGGGUAACAAAUAACUUUUGCAAUUGCGAUUAAUUUACGUGUUACUUUGCCCGC_UGGAUGUCCUUUUUUU
.....(((....(((((((.....)))))))((((((..(((...((((....)))).....)))..))))))....)))....((....))....... (-21.99 = -22.43 +   0.44)

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 12:01:41 2006