Locus 7677

Sequence ID	X_DroMel_CAF1
Location	19,140,699 – 19,140,854
Length	155
Max. P	0.697266

overview

Window 8

Location	19,140,699 – 19,140,815
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.82
Mean single sequence MFE	-31.38
Consensus MFE	-21.61
Energy contribution	-22.42
Covariance contribution	0.81
Combinations/Pair	1.03
Mean z-score	-2.30
Structure conservation index	0.69
SVM decision value	0.10
SVM RNA-class probability	0.584128
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19140699 116 - 22224390
CAAACAGUGGCUACCAAAAGGCA---GUCUACCGGCCGUAAAUGUU-UUUACGGCAUCAUCUCCAUUCCCGACAUCUUUGUUAGGCCAAUGCAAAUACUCCUUUAUGGUGUGUGAAUAUA
.......(.((((((((((((.(---((......((((((((....-))))))))........((((((..(((....)))..))..)))).....)))))))).))))).)).)..... ( -29.80)
>DroSec_CAF1 11714 117 - 1
CAAACAGUGGCUACCAAAAGGCAGUAGUCUACCGGCCGUAAAUGUUUUUUACGGCAUCAUCUCCAUUC-CGACAUCUUUGUUAGGCCAAUGCAAAUACUCCUUUAUGGUGUGUUAA--CA
.......((((((((((((((.((((........((((((((.....))))))))........(((((-(((((....)))).))..))))....))))))))).))))).)))).--.. ( -31.00)
>DroSim_CAF1 10409 117 - 1
CAAACAGUGGCUACCAAAAGGUAGUAGUCUACCGGCCGUAAAUGUUUUUUACGGCAUCAUCUCCAUUC-CGACAUCUUUGUUAGGCCAAUGCAAAUACUCCUUUAUGGUGUGUUAA--CA
....((.(((((.......(((((....))))).((((((((.....)))))))).............-.((((....)))).))))).))..(((((.((.....)).)))))..--.. ( -33.60)
>DroYak_CAF1 5391 114 - 1
CACACAGUGGCUACCAAAAGGCA---GUCUACCGGCCGUAAAUGCUUUUAUGGCCCUCAUCUCUGUUC-CCACAUCUUUGUUAGGCCAAUGCAAAUACUCCUUUAUGGUGUGUGAA--UA
((((((.(((((....(((((((---(......(((((((((....))))))))).......))))..-......))))....)))))...........((.....))))))))..--.. ( -31.12)
>consensus
CAAACAGUGGCUACCAAAAGGCA___GUCUACCGGCCGUAAAUGUUUUUUACGGCAUCAUCUCCAUUC_CGACAUCUUUGUUAGGCCAAUGCAAAUACUCCUUUAUGGUGUGUGAA__CA
....((.(((((..((((((((....))))....((((((((.....)))))))).....................))))...))))).))...((((.((.....)).))))....... (-21.61 = -22.42 +   0.81)

alignment

secondary structure

dotplot

Window 9

Location	19,140,739 – 19,140,854
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.86
Mean single sequence MFE	-34.60
Consensus MFE	-20.77
Energy contribution	-22.65
Covariance contribution	1.88
Combinations/Pair	1.06
Mean z-score	-2.03
Structure conservation index	0.60
SVM decision value	0.34
SVM RNA-class probability	0.697266
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19140739 115 + 22224390
CAAAGAUGUCGGGAAUGGAGAUGAUGCCGUAAA-AACAUUUACGGCCGGUAGAC---UGCCUUUUGGUAGCCACUGUUUGCCACGGUUUGUGGCUCUACAUACAUACGUACAUAC-AUUU
.....((((((.(.(((.(((....((((((((-....))))))))((((.(.(---((((....)))))).))))...(((((.....)))))))).))).)...)).))))..-.... ( -35.20)
>DroSec_CAF1 11752 118 + 1
CAAAGAUGUCG-GAAUGGAGAUGAUGCCGUAAAAAACAUUUACGGCCGGUAGACUACUGCCUUUUGGUAGCCACUGUUUGCCACGGUUUGUGGUUCUACAUACAUACAUACAUCC-AUAU
...........-..(((((.(((..((((((((.....)))))))).(((((((..(((((....))))).....)))))))...((.((((....)))).))...)))...)))-)).. ( -35.60)
>DroSim_CAF1 10447 119 + 1
CAAAGAUGUCG-GAAUGGAGAUGAUGCCGUAAAAAACAUUUACGGCCGGUAGACUACUACCUUUUGGUAGCCACUGUUUGCCACGGUUUGUGGUUCUACAUACAUACAUACAUCCUAUGA
...........-..((((.((((..((((((((.....)))))))).(((((((..(((((....))))).....)))))))...((.((((....)))).)).......)))))))).. ( -34.70)
>DroYak_CAF1 5429 99 + 1
CAAAGAUGUGG-GAACAGAGAUGAGGGCCAUAAAAGCAUUUACGGCCGGUAGAC---UGCCUUUUGGUAGCCACUGUGUGCCUCGUUUUGUGGUUCUAUCGAC-----------------
....(((...(-((((.((((((((((((.((((....)))).)))((((.(.(---((((....)))))).))))....)))))))))...))))))))...----------------- ( -32.90)
>consensus
CAAAGAUGUCG_GAAUGGAGAUGAUGCCGUAAAAAACAUUUACGGCCGGUAGAC___UGCCUUUUGGUAGCCACUGUUUGCCACGGUUUGUGGUUCUACAUACAUACAUACAUCC_AU_U
...(((.((((.((((.(.......((((((((.....)))))))).(((((((..(((((....))))).....))))))).).)))).)))))))....................... (-20.77 = -22.65 +   1.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:44:54 2006