Locus 9045

Sequence ID	3R_DroMel_CAF1
Location	24,194,397 – 24,194,504
Length	107
Max. P	0.987824

overview

Window 7

Location	24,194,397 – 24,194,504
Length	107
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	77.01
Mean single sequence MFE	-31.69
Consensus MFE	-14.88
Energy contribution	-17.22
Covariance contribution	2.33
Combinations/Pair	1.11
Mean z-score	-2.98
Structure conservation index	0.47
SVM decision value	2.09
SVM RNA-class probability	0.987824
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24194397 107 + 27905053
GAACGA--------GGCACAUGCAAUCGCUUUU--CAUUGCAUGUGUCUGUCUGCUCUGUGAAUUGAAAUUUUUCCAGCGCCGCGCUGUUCUUUCUAUUUAUUUGCUGC--UUUUUUUU
.....(--------((((((((((((.......--.)))))))))))))((..((...((((((.((((......(((((...)))))...)))).))))))..)).))--........ ( -30.20)
>DroPse_CAF1 18417 118 + 1
GAAAGAGCUGCCCCGCCGCUUUCAAUCGGAUUGCACAUUGCAUGUGUCUGU-UGCUCUACGAAUUGAAAUUUUUUCAACAUCCCGGGGUUUCUCGUAUUUAUUUUUGUAGUUUCCUUUU
....(((..((((((.((....(((.((((((((.....)))...))))))-)).....))..(((((.....))))).....))))))..)))......................... ( -24.60)
>DroSec_CAF1 17261 105 + 1
GAACGA--------GGCACAUGCAAUCUCGUUU--CAUUGCAUGUGUCUGUCUGCGCUGUGAAUUGAAAUUUUUCCAGCGCCGCGCUGUUCUUUCUAUUUAUUUGCCGC--UUUUU--U
((((((--------((((((((((((.......--.)))))))))))))((..((((((.(((.........))))))))).))..)))))..................--.....--. ( -34.30)
>DroEre_CAF1 20331 109 + 1
GGACGA--------GGCACAUGCAAUCGCGUUU--CAUUGCAUGUGUCUGUCUGCGCUGUGAAUUGAAAUUUUUUCAGCGCCGCGCUGUGCUUUCUAUUUAUUUGCCGGGGUUUUUUUU
((((.(--------((((((((((((.......--.)))))))))))))))))((((((.(((........))).)))))).((.(((.((.............))))).))....... ( -39.42)
>DroYak_CAF1 18349 102 + 1
-----A--------GGCACAUGCAAUCGCGUUU--CAUUGCAUGUGUCUGUCUGCGCUGUGAAUUGAAAUUUUUUCAGCGCCGCGCUGUUCUUUCUAUUUAUUUGCCGG--UUUUUUUU
-----(--------((((((((((((.......--.)))))))))))))..(((.((.((((((.((((......(((((...)))))...)))).))))))..)))))--........ ( -32.20)
>DroPer_CAF1 18350 118 + 1
GGAAGAGCUGCCCCGCCGCCUGCAAUCGGAUUGCACAUUGCAUGUGUCUGU-UGCUCUACGAAUUGAAAUUUUUUCAACAUCCCGGGGUUUUUCGUAUUUAUUUUUGUAGUUUCCUUUU
(((((((..((((((.((...((((.((((((((.....)))...))))))-)))....))..(((((.....))))).....))))))..)))....((((....)))).)))).... ( -29.40)
>consensus
GAACGA________GGCACAUGCAAUCGCGUUU__CAUUGCAUGUGUCUGUCUGCGCUGUGAAUUGAAAUUUUUUCAGCGCCGCGCUGUUCUUUCUAUUUAUUUGCCGA__UUUUUUUU
..............((((((((((((..........)))))))))))).....((...((((((.((((......((((.....))))...)))).))))))..))............. (-14.88 = -17.22 +   2.33)

alignment

secondary structure

dotplot

Window 8

Location	24,194,397 – 24,194,504
Length	107
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	77.01
Mean single sequence MFE	-25.84
Consensus MFE	-10.74
Energy contribution	-12.02
Covariance contribution	1.28
Combinations/Pair	1.07
Mean z-score	-2.25
Structure conservation index	0.42
SVM decision value	0.36
SVM RNA-class probability	0.704090
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24194397 107 - 27905053
AAAAAAAA--GCAGCAAAUAAAUAGAAAGAACAGCGCGGCGCUGGAAAAAUUUCAAUUCACAGAGCAGACAGACACAUGCAAUG--AAAAGCGAUUGCAUGUGCC--------UCGUUC
........--...((.....(((.((((...(((((...)))))......)))).)))......)).(((((.((((((((((.--.......)))))))))).)--------).))). ( -24.10)
>DroPse_CAF1 18417 118 - 1
AAAAGGAAACUACAAAAAUAAAUACGAGAAACCCCGGGAUGUUGAAAAAAUUUCAAUUCGUAGAGCA-ACAGACACAUGCAAUGUGCAAUCCGAUUGAAAGCGGCGGGGCAGCUCUUUC
...((....))..............(((...((((((..(((((.....................))-)))..)...(((.....)))..(((........))))))))...))).... ( -24.60)
>DroSec_CAF1 17261 105 - 1
A--AAAAA--GCGGCAAAUAAAUAGAAAGAACAGCGCGGCGCUGGAAAAAUUUCAAUUCACAGCGCAGACAGACACAUGCAAUG--AAACGAGAUUGCAUGUGCC--------UCGUUC
.--.....--(((.....................))).(((((((((.........))).)))))).(((((.((((((((((.--.......)))))))))).)--------).))). ( -29.20)
>DroEre_CAF1 20331 109 - 1
AAAAAAAACCCCGGCAAAUAAAUAGAAAGCACAGCGCGGCGCUGAAAAAAUUUCAAUUCACAGCGCAGACAGACACAUGCAAUG--AAACGCGAUUGCAUGUGCC--------UCGUCC
...........((((..................)).))((((((................)))))).(((((.((((((((((.--.......)))))))))).)--------).))). ( -28.26)
>DroYak_CAF1 18349 102 - 1
AAAAAAAA--CCGGCAAAUAAAUAGAAAGAACAGCGCGGCGCUGAAAAAAUUUCAAUUCACAGCGCAGACAGACACAUGCAAUG--AAACGCGAUUGCAUGUGCC--------U-----
........--..(((.......................((((((................))))))........(((((((((.--.......))))))))))))--------.----- ( -25.09)
>DroPer_CAF1 18350 118 - 1
AAAAGGAAACUACAAAAAUAAAUACGAAAAACCCCGGGAUGUUGAAAAAAUUUCAAUUCGUAGAGCA-ACAGACACAUGCAAUGUGCAAUCCGAUUGCAGGCGGCGGGGCAGCUCUUCC
...((....))....................(((((....((((((.....))))))((((...(((-((.(((((((...)))))...)).).))))..))))))))).......... ( -23.80)
>consensus
AAAAAAAA__CCGGCAAAUAAAUAGAAAGAACAGCGCGGCGCUGAAAAAAUUUCAAUUCACAGAGCAGACAGACACAUGCAAUG__AAACGCGAUUGCAUGUGCC________UCGUUC
...............................(((((...))))).............................((((((((((..........))))))))))................ (-10.74 = -12.02 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:25:28 2006