Locus 3169

Sequence ID	3R_DroMel_CAF1
Location	8,400,702 – 8,400,803
Length	101
Max. P	0.984373

overview

Window 7

Location	8,400,702 – 8,400,803
Length	101
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	75.99
Mean single sequence MFE	-39.43
Consensus MFE	-23.14
Energy contribution	-26.42
Covariance contribution	3.28
Combinations/Pair	1.23
Mean z-score	-2.33
Structure conservation index	0.59
SVM decision value	1.81
SVM RNA-class probability	0.978488
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8400702 101 + 27905053
GCCAACGCAGCAAGUUGUCUCCAAGGUAUUUUUGCACCAGAUGAAUGACCAGGGGCUCUGCGCCCGGUCAAC-U--GGUGAGAAAAUUCCAAUGGCACUUU-------------UUG
((((..((((....))))......((.(((((..((((((.....(((((..((((.....))))))))).)-)--))))..))))).))..)))).....-------------... ( -35.80)
>DroSec_CAF1 62553 102 + 1
GCCAACGCAGCAAGUUGUCUCCAAGGUAUUUUUGCACCAGAUGAAUGGCCAGGAGCUUUGGGCCCGGUCAGGAA--GGAAAGCAAAUACCAAUGCUGCUUU-------------CUG
......((((((..(((....)))((((((..(((.((.......(((((.((.((.....)))))))))....--))...)))))))))..))))))...-------------... ( -29.20)
>DroSim_CAF1 61720 101 + 1
GCCAACGCAGCAAGUUGUCUCCAAGGUAUUUUUGCACCAGAUGAAUGGCCAGGGGCUCUGGGCCCGGUCAAC-U--GGUGAGGAAAUACCAAUGCUGCUUU-------------CUG
......((((((..(((....)))((((((((..((((((.....(((((.(((.(....).)))))))).)-)--))))..))))))))..))))))...-------------... ( -42.70)
>DroEre_CAF1 64520 101 + 1
GCCACCGCAGCAAGUUGUCUCCAAGGUAUUUUUGCACCAGAUGAAUGGCCAGGUCCUCUGGGCCCGGUCAAC-U--GGUGAGAAAAUACCAAUGCUGCUUU-------------CUG
......((((((..(((....)))((((((((..((((((.....(((((.(((((...))))).))))).)-)--))))..))))))))..))))))...-------------... ( -43.30)
>DroYak_CAF1 64347 103 + 1
GCCACCGCAGCAAGUUGUCUCCAAGGUAUUUUUGCACCAGAUGAAUGGCCAGGGGCUCUGGGCCCGGUCAAC-CUGGGUGGGAAAAUACCAAUGCUGCUUU-------------CUG
......((((((..(((....)))(((((((((.((((....(..(((((.(((.(....).))))))))..-)..)))).)))))))))..))))))...-------------... ( -41.80)
>DroPer_CAF1 65175 107 + 1
ACUGCCGCCGCAAUGUGUCUCUGAGGUGUCUUUGGGGCAAAUGAACGGCCUGGGGCGGACAGACCAGCCAGG----------CGAAGGCCAAGGCCCCGCCCAGCACUUAGAGGCUG
..(((....)))....(((((((((.(((...((((((........(((.(((..(.....).)))))).((----------(....)))...))))))....)))))))))))).. ( -43.80)
>consensus
GCCAACGCAGCAAGUUGUCUCCAAGGUAUUUUUGCACCAGAUGAAUGGCCAGGGGCUCUGGGCCCGGUCAAC_U__GGUGAGAAAAUACCAAUGCUGCUUU_____________CUG
......((((((..(((....)))(((((((((.((((.......(((((..((((.....)))))))))......)))).)))))))))..))))))................... (-23.14 = -26.42 +   3.28)

alignment

secondary structure

dotplot

Window 8

Location	8,400,702 – 8,400,803
Length	101
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	75.99
Mean single sequence MFE	-38.86
Consensus MFE	-20.00
Energy contribution	-22.25
Covariance contribution	2.26
Combinations/Pair	1.22
Mean z-score	-2.60
Structure conservation index	0.51
SVM decision value	1.97
SVM RNA-class probability	0.984373
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8400702 101 - 27905053
CAA-------------AAAGUGCCAUUGGAAUUUUCUCACC--A-GUUGACCGGGCGCAGAGCCCCUGGUCAUUCAUCUGGUGCAAAAAUACCUUGGAGACAACUUGCUGCGUUGGC
...-------------.....((((..((.(((((..((((--(-(.((((((((.((...)).)))))))).....))))))..))))).))(((....)))..........)))) ( -35.60)
>DroSec_CAF1 62553 102 - 1
CAG-------------AAAGCAGCAUUGGUAUUUGCUUUCC--UUCCUGACCGGGCCCAAAGCUCCUGGCCAUUCAUCUGGUGCAAAAAUACCUUGGAGACAACUUGCUGCGUUGGC
(((-------------...((((((..(((((((((...((--....(((...((((..........))))..)))...)).)))..))))))(((....)))..)))))).))).. ( -32.40)
>DroSim_CAF1 61720 101 - 1
CAG-------------AAAGCAGCAUUGGUAUUUCCUCACC--A-GUUGACCGGGCCCAGAGCCCCUGGCCAUUCAUCUGGUGCAAAAAUACCUUGGAGACAACUUGCUGCGUUGGC
(((-------------...((((((..(((((((...((((--(-(.(((...((((.((.....))))))..))).))))))...)))))))(((....)))..)))))).))).. ( -42.40)
>DroEre_CAF1 64520 101 - 1
CAG-------------AAAGCAGCAUUGGUAUUUUCUCACC--A-GUUGACCGGGCCCAGAGGACCUGGCCAUUCAUCUGGUGCAAAAAUACCUUGGAGACAACUUGCUGCGGUGGC
...-------------...((((((..((((((((..((((--(-(.(((...((((.((.....))))))..))).))))))..))))))))(((....)))..))))))...... ( -43.60)
>DroYak_CAF1 64347 103 - 1
CAG-------------AAAGCAGCAUUGGUAUUUUCCCACCCAG-GUUGACCGGGCCCAGAGCCCCUGGCCAUUCAUCUGGUGCAAAAAUACCUUGGAGACAACUUGCUGCGGUGGC
...-------------...((((((..((((((((..((((.((-((.((...((((.((.....))))))..))))))))))..))))))))(((....)))..))))))...... ( -40.00)
>DroPer_CAF1 65175 107 - 1
CAGCCUCUAAGUGCUGGGCGGGGCCUUGGCCUUCG----------CCUGGCUGGUCUGUCCGCCCCAGGCCGUUCAUUUGCCCCAAAGACACCUCAGAGACACAUUGCGGCGGCAGU
..(((.......((..((((((((....))).)))----------))..)).((((((.......))))))........(((.(((..................))).))))))... ( -39.17)
>consensus
CAG_____________AAAGCAGCAUUGGUAUUUUCUCACC__A_GUUGACCGGGCCCAGAGCCCCUGGCCAUUCAUCUGGUGCAAAAAUACCUUGGAGACAACUUGCUGCGGUGGC
...................((((((..(((((((...((((......((.(((((.........))))).)).......))))...)))))))(((....)))..))))))...... (-20.00 = -22.25 +   2.26)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:48 2006