Locus 9920

Sequence ID	3R_DroMel_CAF1
Location	26,525,619 – 26,525,731
Length	112
Max. P	0.937431

overview

Window 5

Location	26,525,619 – 26,525,731
Length	112
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	80.27
Mean single sequence MFE	-27.55
Consensus MFE	-19.78
Energy contribution	-20.39
Covariance contribution	0.61
Combinations/Pair	1.04
Mean z-score	-2.18
Structure conservation index	0.72
SVM decision value	1.09
SVM RNA-class probability	0.913347
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26525619 112 + 27905053
CU-GGCCAUCCUCUUCCGCCGGCGAUUGCAA-AAUGCUCA-ACAUU-UUAUUGAAAUUCAAUUAAAGCCGUAUUUCAAUAAUUGGUCACGCAUGGUGCGCAUUUCCGUGCC-AG-UCC
((-(((.............(((.(((((((.-.((((...-((...-((((((((((..............))))))))))...))...))))..)))).))).))).)))-))-... ( -27.28)
>DroVir_CAF1 144646 101 + 1
----------AUUUUU-C-GAGGAAAUGCAA-AAUGCUGA-ACAUU-UUAUUGAAAUUCAAUUAAAGUCGUAUUUCAAUAAUUGGACACGCAUGGUGCGCAUUUCCGUGC--UGCUCG
----------......-(-(((.....(((.-.((((((.-.((..-((((((((((.(.((....)).).)))))))))).))..)).))))..)))((((....))))--..)))) ( -26.20)
>DroGri_CAF1 255332 106 + 1
-CGAAC---AAA-----G-UAGGAAAUGCAA-AAUGCUGAAACAUU-UUAUUGAAAUUCAAUUAAAGUCGUAUUUCAAUAAUUGGACACGCAUGGUGCCCAUUUCCGUGCACAGUUCG
-(((((---...-----(-(((((((((((.-.((((((...((..-((((((((((.(.((....)).).)))))))))).))..)).))))..)))..)))))).)))...))))) ( -29.00)
>DroWil_CAF1 122832 111 + 1
---UGCCAGU-UUUUCGGAUAGGAAAUGCAA-AAUGCUAA-ACAUUUUUAUUGAAAUUCAAUUAAAGUCGUAUUUCAAUAAUUGGUCACGCAUGGUGCGCAUUUCCGUGCUCCG-GAC
---.......-..((((((..((((((((..-.((((...-((....((((((((((.(.((....)).).))))))))))...))...)))).....))))))))....))))-)). ( -30.00)
>DroMoj_CAF1 146214 109 + 1
-A-GAC---AAUUUUU-G-GAGGAAAUGCGA-AAUGCUGAAACAUU-UUAUUGAAAUUCAAUUAAAGUCGUAUUUCAAUAAUUGGCCACGCAUGGUGCGCAUUUCCGUGCCGUGCUCG
-.-...---.......-(-(.(((((((((.-.((((((...((..-((((((((((.(.((....)).).)))))))))).))..)).))))....)))))))))...))....... ( -30.50)
>DroAna_CAF1 111161 108 + 1
C------UUCCUUUUCCGCUACCGAAUGCAAAAAUGCUCA-ACAUU-UUAUUGAAAUUCAAUUAAAGUCGUAUUUCAAUAAUUGGUCACGCAUGGUGCGCAUUUCCGUGCC-AG-UCC
.------..........((.(((((..(((....)))...-.....-((((((((((.(.((....)).).)))))))))))))))...)).(((..((......))..))-).-... ( -22.30)
>consensus
_____C___AAUUUUC_G_UAGGAAAUGCAA_AAUGCUGA_ACAUU_UUAUUGAAAUUCAAUUAAAGUCGUAUUUCAAUAAUUGGUCACGCAUGGUGCGCAUUUCCGUGCC_AG_UCC
.....................((((((((....((((.....((...((((((((((..............)))))))))).)).....)))).....))))))))............ (-19.78 = -20.39 +   0.61)

alignment

secondary structure

dotplot

Window 6

Location	26,525,619 – 26,525,731
Length	112
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	80.27
Mean single sequence MFE	-28.62
Consensus MFE	-20.11
Energy contribution	-21.00
Covariance contribution	0.89
Combinations/Pair	1.07
Mean z-score	-2.47
Structure conservation index	0.70
SVM decision value	1.26
SVM RNA-class probability	0.937431
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26525619 112 - 27905053
GGA-CU-GGCACGGAAAUGCGCACCAUGCGUGACCAAUUAUUGAAAUACGGCUUUAAUUGAAUUUCAAUAA-AAUGU-UGAGCAUU-UUGCAAUCGCCGGCGGAAGAGGAUGGCC-AG
...-((-(((.(((..((..(((..((((..(((...((((((((((.(((......))).))))))))))-...))-)..)))).-.))).))..))).(....)......)))-)) ( -32.50)
>DroVir_CAF1 144646 101 - 1
CGAGCA--GCACGGAAAUGCGCACCAUGCGUGUCCAAUUAUUGAAAUACGACUUUAAUUGAAUUUCAAUAA-AAUGU-UCAGCAUU-UUGCAUUUCCUC-G-AAAAAU----------
......--....(((((((((....((((.((..((.((((((((((.(((......))).))))))))))-..)).-.)))))).-.)))))))))..-.-......---------- ( -26.40)
>DroGri_CAF1 255332 106 - 1
CGAACUGUGCACGGAAAUGGGCACCAUGCGUGUCCAAUUAUUGAAAUACGACUUUAAUUGAAUUUCAAUAA-AAUGUUUCAGCAUU-UUGCAUUUCCUA-C-----UUU---GUUCG-
(((((.(((...((((((((((((.....))))))..((((((((((.(((......))).))))))))))-(((((....)))))-....))))))))-)-----...---)))))- ( -28.80)
>DroWil_CAF1 122832 111 - 1
GUC-CGGAGCACGGAAAUGCGCACCAUGCGUGACCAAUUAUUGAAAUACGACUUUAAUUGAAUUUCAAUAAAAAUGU-UUAGCAUU-UUGCAUUUCCUAUCCGAAAA-ACUGGCA---
...-((((....(((((((((....((((..(((...((((((((((.(((......))).))))))))))....))-)..)))).-.)))))))))..))))....-.......--- ( -30.60)
>DroMoj_CAF1 146214 109 - 1
CGAGCACGGCACGGAAAUGCGCACCAUGCGUGGCCAAUUAUUGAAAUACGACUUUAAUUGAAUUUCAAUAA-AAUGUUUCAGCAUU-UCGCAUUUCCUC-C-AAAAAUU---GUC-U-
.......((...(((((((((....((((..(((...((((((((((.(((......))).))))))))))-...)))...)))).-.))))))))).)-)-.......---...-.- ( -29.00)
>DroAna_CAF1 111161 108 - 1
GGA-CU-GGCACGGAAAUGCGCACCAUGCGUGACCAAUUAUUGAAAUACGACUUUAAUUGAAUUUCAAUAA-AAUGU-UGAGCAUUUUUGCAUUCGGUAGCGGAAAAGGAA------G
..(-((-((..(((((((((((.....))..(((...((((((((((.(((......))).))))))))))-...))-)..)))))))))...))))).............------. ( -24.40)
>consensus
CGA_CU_GGCACGGAAAUGCGCACCAUGCGUGACCAAUUAUUGAAAUACGACUUUAAUUGAAUUUCAAUAA_AAUGU_UCAGCAUU_UUGCAUUUCCUA_C_GAAAAUG___G_____
............(((((((((....((((.....((.((((((((((.(((......))).))))))))))...)).....))))...)))))))))..................... (-20.11 = -21.00 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:44:54 2006