Locus 9977

Sequence ID	3R_DroMel_CAF1
Location	26,695,897 – 26,696,013
Length	116
Max. P	0.742476

overview

Window 5

Location	26,695,897 – 26,695,987
Length	90
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	81.30
Mean single sequence MFE	-24.97
Consensus MFE	-17.96
Energy contribution	-18.85
Covariance contribution	0.89
Combinations/Pair	1.23
Mean z-score	-1.68
Structure conservation index	0.72
SVM decision value	0.45
SVM RNA-class probability	0.742476
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26695897 90 - 27905053
UUCGCAA-AUCCGAACGAAAAUCCGCAAUUGAGCAAGCCAAUUCAA------------UCGAUUGCGAUUGCCGCAAAAGUGGGUGCACAAAGGCACGCGGAG-----
(((((..-...............(((((((((..............------------)))))))))....((((....))))((((......))))))))).----- ( -26.54)
>DroSec_CAF1 2296 90 - 1
UUCGCAA-AUCCGAACGAAAAUCCGCAAUUGAGCAAGCCAAUUCCA------------UCGAUUGCGAUUGCCGCAAAAGUGGGUGCACAAAGGCACGCGGAG-----
(((((..-...............(((((((((..............------------)))))))))....((((....))))((((......))))))))).----- ( -26.54)
>DroEre_CAF1 2304 90 - 1
UUCGCAA-AUCCGAACGAAAAUCCGCAAUUGAGCAAGCCAAUUCAA------------UCGAUUGCGAUUGCCGCAAAAGUGGGUGCACAAAGGCACGCGGAG-----
(((((..-...............(((((((((..............------------)))))))))....((((....))))((((......))))))))).----- ( -26.54)
>DroYak_CAF1 2317 90 - 1
UUCGCAA-AUGCGAACGAAAAUCCGCAAUUGAGCAAGCAAAUUCAA------------UCGAUUGCGAUUGCCGCAAAAGUGGGUGCAGAAAGGCAAGCGGAG-----
(((((..-..)))))......(((((.................(((------------(((....))))))((((....)))).(((......))).))))).----- ( -26.00)
>DroAna_CAF1 18889 90 - 1
UUCGCAAAACCCGAACUAAAAUCCGCAAUUGGCUUGCUCAAACCAA------------UCCAAUUCGAUUGCCGCAA-AGUGGGUGCAAAAAGGCACGUGAAG-----
(((((..................((.((((((.(((.......)))------------.))))))))....((((..-.))))((((......))))))))).----- ( -20.30)
>DroPer_CAF1 18451 108 - 1
UUCGCAAAAGCCGAACGAAAAUCCGCCAUUGAGUAAGCGAAUCCGAGUCGUAGUCCACGCGAUUGCGAUUGCCACAAAAGUGGGUGCAAAAAAGUACUAGCAAAACAA
(((((....(((((.((......))...))).))..)))))....((((((((((.....)))))))))).((((....))))((((......))))........... ( -23.90)
>consensus
UUCGCAA_AUCCGAACGAAAAUCCGCAAUUGAGCAAGCCAAUUCAA____________UCGAUUGCGAUUGCCGCAAAAGUGGGUGCACAAAGGCACGCGGAG_____
(((((..................(((((((((..........................)))))))))....((((....))))((((......)))))))))...... (-17.96 = -18.85 +   0.89)

alignment

secondary structure

dotplot

Window 6

Location	26,695,923 – 26,696,013
Length	90
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	82.34
Mean single sequence MFE	-20.73
Consensus MFE	-13.00
Energy contribution	-14.09
Covariance contribution	1.08
Combinations/Pair	1.10
Mean z-score	-1.76
Structure conservation index	0.63
SVM decision value	-0.04
SVM RNA-class probability	0.513604
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26695923 90 - 27905053
----CAGGCAAAUUCUCGACUCUUACCUCUUUCGCAA-AUCCGAACGAAAAUCCGCAAUUGAGCAAGCCAAUUCAA------------UCGAUUGCGAUUGCCGCAA
----..(((((................((.((((...-...)))).)).....(((((((((..............------------))))))))).))))).... ( -20.94)
>DroSec_CAF1 2322 90 - 1
----CAGGCAAAUUCUCGACUCUUACCUCUUUCGCAA-AUCCGAACGAAAAUCCGCAAUUGAGCAAGCCAAUUCCA------------UCGAUUGCGAUUGCCGCAA
----..(((((................((.((((...-...)))).)).....(((((((((..............------------))))))))).))))).... ( -20.94)
>DroEre_CAF1 2330 90 - 1
----CAGGCAAAUUCUCGACUCUUACCUCUUUCGCAA-AUCCGAACGAAAAUCCGCAAUUGAGCAAGCCAAUUCAA------------UCGAUUGCGAUUGCCGCAA
----..(((((................((.((((...-...)))).)).....(((((((((..............------------))))))))).))))).... ( -20.94)
>DroYak_CAF1 2343 90 - 1
----CAGGUAAAUUCUCGACUUUUACCUCUUUCGCAA-AUGCGAACGAAAAUCCGCAAUUGAGCAAGCAAAUUCAA------------UCGAUUGCGAUUGCCGCAA
----..(((((................((.(((((..-..))))).)).....(((((((((..............------------))))))))).))))).... ( -23.24)
>DroAna_CAF1 18914 95 - 1
GUGUCAGGCAAAUUCUUGACUUUUACCUCUUUCGCAAAACCCGAACUAAAAUCCGCAAUUGGCUUGCUCAAACCAA------------UCCAAUUCGAUUGCCGCAA
......(((((...................((((.......))))........((.((((((.(((.......)))------------.)))))))).))))).... ( -15.70)
>DroPer_CAF1 18482 107 - 1
AUGGCCAGCACAUUCUUGACUUUUACCUCUUUCGCAAAAGCCGAACGAAAAUCCGCCAUUGAGUAAGCGAAUCCGAGUCGUAGUCCACGCGAUUGCGAUUGCCACAA
.((((..((..((((............((.(((((....).)))).))............))))..)).......((((((((((.....))))))))))))))... ( -22.65)
>consensus
____CAGGCAAAUUCUCGACUCUUACCUCUUUCGCAA_AUCCGAACGAAAAUCCGCAAUUGAGCAAGCCAAUUCAA____________UCGAUUGCGAUUGCCGCAA
......(((((................((.((((.......)))).)).....(((((((((..........................))))))))).))))).... (-13.00 = -14.09 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:46:14 2006