Locus 4909

Sequence ID	X_DroMel_CAF1
Location	12,781,757 – 12,781,848
Length	91
Max. P	0.997752

overview

Window 6

Location	12,781,757 – 12,781,848
Length	91
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	80.94
Mean single sequence MFE	-36.44
Consensus MFE	-25.04
Energy contribution	-25.52
Covariance contribution	0.48
Combinations/Pair	1.31
Mean z-score	-3.27
Structure conservation index	0.69
SVM decision value	2.92
SVM RNA-class probability	0.997752
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12781757 91 + 22224390
-AAAUAGACCGGAAGUCCUCGAAAGGCGACUGCUUGCAAGCAGUGGCCUCUCAUAUCC-------GGUCUGCCCUAUGCAAGCAGUU-UGCCAUCGAGAC
-.....((.(....)))(((((..((((((((((((((.((((..(((..........-------)))))))....))))))))).)-)))).))))).. ( -35.90)
>DroSec_CAF1 5119 90 + 1
-AAA-AGACCGGAAGUCCUCGAACAGCGACUGCUUGCAAGCAGUGCCUGGCCAUAUCC-------GGCCUGGCCAAUGCAAGCUGUU-UGCCAUCGAGAC
-...-.((.(....)))(((((...(((((.(((((((....(.(((.((((......-------)))).))))..))))))).).)-)))..))))).. ( -35.40)
>DroSim_CAF1 6825 90 + 1
-AAA-AGACCGGAAGUCCUCGAACAGCGACUGCUUGCAAGCAGUGCCUGGCCAUAUCC-------GGCCUGGCCAAUGCAAGCAGUU-UGCCAUCGAGAC
-...-.((.(....)))(((((...(((((((((((((....(.(((.((((......-------)))).))))..))))))))).)-)))..))))).. ( -40.00)
>DroEre_CAF1 5352 97 + 1
CAAU-CGACCGGAAGUUCUCGAAAGGCGACUGCUUGCAAGCAGUGCG-GUCAACAUCCGGAGUCCGGACUGGCCAAUGCAAGCAGUU-UACCAUGCGGAC
...(-(((.(....)...))))..((.(((((((((((.((...))(-((((...(((((...))))).)))))..)))))))))))-..))........ ( -36.20)
>DroYak_CAF1 6662 90 + 1
-AAG-AGACCGGAAGUCAUCGAUGGACAACUGCUUGCAAGCAGUGCG-GUCCAUAUCC-------GGGCUAGACAAUGCAAGCAGUUUUACCAUUGGGAC
-...-.........(((.(((((((..(((((((((((..((((.((-(.......))-------).))).)....)))))))))))...)))))))))) ( -34.70)
>consensus
_AAA_AGACCGGAAGUCCUCGAAAGGCGACUGCUUGCAAGCAGUGCC_GGCCAUAUCC_______GGCCUGGCCAAUGCAAGCAGUU_UGCCAUCGAGAC
......((.(....)))(((((.....(((((((((((......(((.((((.............)))).)))...)))))))))))......))))).. (-25.04 = -25.52 +   0.48)

alignment

secondary structure

dotplot

Window 7

Location	12,781,757 – 12,781,848
Length	91
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	80.94
Mean single sequence MFE	-35.88
Consensus MFE	-21.90
Energy contribution	-23.62
Covariance contribution	1.72
Combinations/Pair	1.24
Mean z-score	-2.58
Structure conservation index	0.61
SVM decision value	1.61
SVM RNA-class probability	0.967441
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12781757 91 - 22224390
GUCUCGAUGGCA-AACUGCUUGCAUAGGGCAGACC-------GGAUAUGAGAGGCCACUGCUUGCAAGCAGUCGCCUUUCGAGGACUUCCGGUCUAUUU-
((((.....(((-(.....))))...))))(((((-------(((..((((((((.((((((....)))))).))))))))......))))))))....- ( -39.80)
>DroSec_CAF1 5119 90 - 1
GUCUCGAUGGCA-AACAGCUUGCAUUGGCCAGGCC-------GGAUAUGGCCAGGCACUGCUUGCAAGCAGUCGCUGUUCGAGGACUUCCGGUCU-UUU-
..(((((((((.-.((.(((((((..((((.((((-------(....))))).))).)....))))))).)).)))).)))))(((.....))).-...- ( -37.00)
>DroSim_CAF1 6825 90 - 1
GUCUCGAUGGCA-AACUGCUUGCAUUGGCCAGGCC-------GGAUAUGGCCAGGCACUGCUUGCAAGCAGUCGCUGUUCGAGGACUUCCGGUCU-UUU-
..(((((((((.-.((((((((((..((((.((((-------(....))))).))).)....)))))))))).)))).)))))(((.....))).-...- ( -42.30)
>DroEre_CAF1 5352 97 - 1
GUCCGCAUGGUA-AACUGCUUGCAUUGGCCAGUCCGGACUCCGGAUGUUGAC-CGCACUGCUUGCAAGCAGUCGCCUUUCGAGAACUUCCGGUCG-AUUG
(((((..((((.-...((....))...))))...))))).((((((.((((.-.((((((((....)))))).))...)))).)...)))))...-.... ( -32.10)
>DroYak_CAF1 6662 90 - 1
GUCCCAAUGGUAAAACUGCUUGCAUUGUCUAGCCC-------GGAUAUGGAC-CGCACUGCUUGCAAGCAGUUGUCCAUCGAUGACUUCCGGUCU-CUU-
......((((...(((((((((((..((..((..(-------((.......)-))..)))).)))))))))))..)))).((.(((.....))))-)..- ( -28.20)
>consensus
GUCUCGAUGGCA_AACUGCUUGCAUUGGCCAGGCC_______GGAUAUGGAC_GGCACUGCUUGCAAGCAGUCGCCGUUCGAGGACUUCCGGUCU_UUU_
.(((((..(((...((((((((((...(((.((((.............)))).)))......)))))))))).)))...)))))................ (-21.90 = -23.62 +   1.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:50 2006