Locus 1997

Sequence ID 3R_DroMel_CAF1
Location 5,657,426 – 5,657,517
Length 91
Max. P 0.819748
window3268 window3269

overview

Window 8

Location 5,657,426 – 5,657,517
Length 91
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.12
Mean single sequence MFE -24.78
Consensus MFE -14.16
Energy contribution -14.08
Covariance contribution -0.08
Combinations/Pair 1.18
Mean z-score -2.07
Structure conservation index 0.57
SVM decision value 0.68
SVM RNA-class probability 0.819748
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5657426 91 + 27905053
AGA--GGAA----GCUUAUUACAAGCGACAACAAGCAAUGUAAAUGUAAAUGCCAACUGGCAGUGAGAAAUGGCCAAC-GGCA--------GCACUUG-------------GCCAAGAA-
.((--(...----.))).((((..((........))..............((((....))))))))....(((((((.-(...--------...))))-------------))))....- ( -22.10)
>DroPse_CAF1 2415 102 + 1
GGG--GGAAGCCGGCUUAUUAUAAGCGACAACAAGCAAUGU------AAAUGCCAACUGGCAGUGAGAAAUGGCCAAA-GGCG--------ACAGGCGACAGGCGCCAGGCGCCAGGAG-
..(--(....))((((..((((..((........)).....------...((((....)))))))).....))))...-((((--------...((((.....))))...)))).....- ( -31.80)
>DroSim_CAF1 11053 91 + 1
AGA--GGAA----GCUUAUUACAAGCGACAACAAGCAAUGUAAAUGUAAAUGCCAACUGGCAGUGAGCAAUGGCCAAC-GGCA--------GCACUUG-------------GCCAAGAA-
...--....----((((((((((.((........))..))))........((((....))))))))))..(((((((.-(...--------...))))-------------))))....- ( -25.90)
>DroEre_CAF1 8720 91 + 1
AAA--GGAA----GCAUAUUACAAGCGACAACAAGCAAUGUAAAUGUAAAUGCCAACUGGCAGUGAGAAAUGGCCAAC-GGCA--------GCACUUG-------------GCCAAGAA-
...--....----((((.(((((.((........))..)))))))))...((((....))))........(((((((.-(...--------...))))-------------))))....- ( -23.20)
>DroYak_CAF1 11227 91 + 1
AAA--GGAA----GCAUAUUACGAGCGACAACAAGCAAUGUAAAUGUAAAUGCCAACUGGCAGUGAGAAAUGGCCAAC-GGCA--------GCACUUG-------------GCCAAGAA-
...--....----((((.(((((.((........))..)))))))))...((((....))))........(((((((.-(...--------...))))-------------))))....- ( -22.50)
>DroAna_CAF1 10607 97 + 1
AGAUGGGAA----GCUUAUUAUAAGCGACAACAAGCAAUGU------AAAUGCCAACUGGCAGUGAGAAAUGGCCAAAAGGCAACCGGGCCGGGCUGG-------------AGCGAGGAG
.........----((((.((((..((........)).....------...((((....)))))))).....((((....(((......))).)))).)-------------)))...... ( -23.20)
>consensus
AGA__GGAA____GCUUAUUACAAGCGACAACAAGCAAUGUAAAUGUAAAUGCCAACUGGCAGUGAGAAAUGGCCAAC_GGCA________GCACUUG_____________GCCAAGAA_
.....((.................((........))..(((.........((((...((((.((.....)).))))...))))........)))..................))...... (-14.16 = -14.08 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 5,657,426 – 5,657,517
Length 91
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.12
Mean single sequence MFE -22.77
Consensus MFE -13.72
Energy contribution -14.38
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.60
SVM decision value 0.27
SVM RNA-class probability 0.661574
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5657426 91 - 27905053
-UUCUUGGC-------------CAAGUGC--------UGCC-GUUGGCCAUUUCUCACUGCCAGUUGGCAUUUACAUUUACAUUGCUUGUUGUCGCUUGUAAUAAGC----UUCC--UCU
-....((((-------------(((.((.--------...)-))))))))........((((....))))..............((((((((.......))))))))----....--... ( -21.10)
>DroPse_CAF1 2415 102 - 1
-CUCCUGGCGCCUGGCGCCUGUCGCCUGU--------CGCC-UUUGGCCAUUUCUCACUGCCAGUUGGCAUUU------ACAUUGCUUGUUGUCGCUUAUAAUAAGCCGGCUUCC--CCC
-.....((((.(.((((.....)))).).--------))))-...((((.........((((....))))...------.....(((((((((.....))))))))).))))...--... ( -32.00)
>DroSim_CAF1 11053 91 - 1
-UUCUUGGC-------------CAAGUGC--------UGCC-GUUGGCCAUUGCUCACUGCCAGUUGGCAUUUACAUUUACAUUGCUUGUUGUCGCUUGUAAUAAGC----UUCC--UCU
-......((-------------(((.((.--------.((.-((.(((....))).)).)))).)))))...............((((((((.......))))))))----....--... ( -21.70)
>DroEre_CAF1 8720 91 - 1
-UUCUUGGC-------------CAAGUGC--------UGCC-GUUGGCCAUUUCUCACUGCCAGUUGGCAUUUACAUUUACAUUGCUUGUUGUCGCUUGUAAUAUGC----UUCC--UUU
-....((((-------------(((.((.--------...)-))))))))............((..((((((((((...(((........)))....))))).))))----)..)--).. ( -20.20)
>DroYak_CAF1 11227 91 - 1
-UUCUUGGC-------------CAAGUGC--------UGCC-GUUGGCCAUUUCUCACUGCCAGUUGGCAUUUACAUUUACAUUGCUUGUUGUCGCUCGUAAUAUGC----UUCC--UUU
-....((((-------------(((.((.--------...)-))))))))........((((....))))....(((((((...((........))..)))).))).----....--... ( -17.90)
>DroAna_CAF1 10607 97 - 1
CUCCUCGCU-------------CCAGCCCGGCCCGGUUGCCUUUUGGCCAUUUCUCACUGCCAGUUGGCAUUU------ACAUUGCUUGUUGUCGCUUAUAAUAAGC----UUCCCAUCU
..((..((.-------------...))..))...((.((((..(((((...........)))))..))))...------.....(((((((((.....)))))))))----...)).... ( -23.70)
>consensus
_UUCUUGGC_____________CAAGUGC________UGCC_GUUGGCCAUUUCUCACUGCCAGUUGGCAUUUACAUUUACAUUGCUUGUUGUCGCUUGUAAUAAGC____UUCC__UCU
......................................(((.((((((...........)))))).)))...............((((((((.......))))))))............. (-13.72 = -14.38 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:45 2006