Locus 1182

Sequence ID	3L_DroMel_CAF1
Location	3,372,731 – 3,372,961
Length	230
Max. P	0.983950

overview

Window 7

Location	3,372,731 – 3,372,851
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.00
Mean single sequence MFE	-33.56
Consensus MFE	-33.34
Energy contribution	-33.74
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.75
Structure conservation index	0.99
SVM decision value	1.96
SVM RNA-class probability	0.983950
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3372731 120 + 23771897
GUUAAGCCGCACGCACUAAAACCGAGCCAAAGACCAAGACGACGGACUUCGAGGAGAAGGCCUUUGUAUUUGGUUUAUUUGUCUGGUUUUUUGUGUACAGGUUUUCUUUUAUUCAUUAUU
...(((((..(((((..(((((((..(.((((((((((((((.((.((((.....)))).)).)))).)))))))).)).)..))))))).)))))...)))))................ ( -35.50)
>DroSec_CAF1 39864 120 + 1
GUUAAGCCGCACGCACUAAAACCGAGCCAAAGACCAAGACGACGGACUUCGAGGAGAAGGCCUUUGUAUUUGCUUCAUUUGUCUGGUUUUUUGUGUACAGGUUUUCUUUUAUUCAUUAUU
...(((((..(((((..((((((.((.((((((.((((((((.((.((((.....)))).)).)))).))))..)).)))).)))))))).)))))...)))))................ ( -30.20)
>DroSim_CAF1 37587 120 + 1
GUUAAGCCGCACGCACUAAAACCGAGCCAAAGACCAAGACGACGGACUUCGAGGAGAAGGCCUUUGUAUUUGGUUUAUUUGUCUGGUUUUUUGUGUACAGGUUUUCUUUUAUUCAUUAUU
...(((((..(((((..(((((((..(.((((((((((((((.((.((((.....)))).)).)))).)))))))).)).)..))))))).)))))...)))))................ ( -35.50)
>DroEre_CAF1 39305 120 + 1
GUUAAGCCGCACGCACUAAAACCGAGCCAAAGACCAAGACGACGGACUUCGAGGAGAAGGCCUUUGUAUUUGGUUUAUUUGUCUGGUUUUUUGUGUACAGGUUUUCUUUUAUUCAUUAUU
...(((((..(((((..(((((((..(.((((((((((((((.((.((((.....)))).)).)))).)))))))).)).)..))))))).)))))...)))))................ ( -35.50)
>DroYak_CAF1 38602 120 + 1
GUUAAGCCGCACGCACUAAAACCGAGCCAAAGACCAAGACGACGGACUGCGAGGAGAAGGCCUUUGUAUUUGGUUUAUUUGUCUGGUUUUUUGUGUACAGGUUUUCUUUUAUUCAUUAUU
...(((((..(((((..(((((((..(.((((((((((((((.((.((.(.....).)).)).)))).)))))))).)).)..))))))).)))))...)))))................ ( -31.10)
>consensus
GUUAAGCCGCACGCACUAAAACCGAGCCAAAGACCAAGACGACGGACUUCGAGGAGAAGGCCUUUGUAUUUGGUUUAUUUGUCUGGUUUUUUGUGUACAGGUUUUCUUUUAUUCAUUAUU
...(((((..(((((..((((((.((.(((((((((((((((.((.((((.....)))).)).)))).)))))))..)))).)))))))).)))))...)))))................ (-33.34 = -33.74 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	3,372,731 – 3,372,851
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.00
Mean single sequence MFE	-26.37
Consensus MFE	-25.34
Energy contribution	-25.74
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.23
Structure conservation index	0.96
SVM decision value	0.06
SVM RNA-class probability	0.562197
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3372731 120 - 23771897
AAUAAUGAAUAAAAGAAAACCUGUACACAAAAAACCAGACAAAUAAACCAAAUACAAAGGCCUUCUCCUCGAAGUCCGUCGUCUUGGUCUUUGGCUCGGUUUUAGUGCGUGCGGCUUAAC
....................((((((.((.((((((((.((((...(((((..((...((.((((.....)))).))...)).))))).)))).)).))))))..)).))))))...... ( -27.50)
>DroSec_CAF1 39864 120 - 1
AAUAAUGAAUAAAAGAAAACCUGUACACAAAAAACCAGACAAAUGAAGCAAAUACAAAGGCCUUCUCCUCGAAGUCCGUCGUCUUGGUCUUUGGCUCGGUUUUAGUGCGUGCGGCUUAAC
....................((((((.((.((((((...(....).........((((((((....(..((.....))..)....))))))))....))))))..)).))))))...... ( -25.30)
>DroSim_CAF1 37587 120 - 1
AAUAAUGAAUAAAAGAAAACCUGUACACAAAAAACCAGACAAAUAAACCAAAUACAAAGGCCUUCUCCUCGAAGUCCGUCGUCUUGGUCUUUGGCUCGGUUUUAGUGCGUGCGGCUUAAC
....................((((((.((.((((((((.((((...(((((..((...((.((((.....)))).))...)).))))).)))).)).))))))..)).))))))...... ( -27.50)
>DroEre_CAF1 39305 120 - 1
AAUAAUGAAUAAAAGAAAACCUGUACACAAAAAACCAGACAAAUAAACCAAAUACAAAGGCCUUCUCCUCGAAGUCCGUCGUCUUGGUCUUUGGCUCGGUUUUAGUGCGUGCGGCUUAAC
....................((((((.((.((((((((.((((...(((((..((...((.((((.....)))).))...)).))))).)))).)).))))))..)).))))))...... ( -27.50)
>DroYak_CAF1 38602 120 - 1
AAUAAUGAAUAAAAGAAAACCUGUACACAAAAAACCAGACAAAUAAACCAAAUACAAAGGCCUUCUCCUCGCAGUCCGUCGUCUUGGUCUUUGGCUCGGUUUUAGUGCGUGCGGCUUAAC
....................((((((.((.((((((((................((((((((....(..((.....))..)....)))))))).)).))))))..)).))))))...... ( -24.03)
>consensus
AAUAAUGAAUAAAAGAAAACCUGUACACAAAAAACCAGACAAAUAAACCAAAUACAAAGGCCUUCUCCUCGAAGUCCGUCGUCUUGGUCUUUGGCUCGGUUUUAGUGCGUGCGGCUUAAC
....................((((((.((.((((((((.((((...(((((..((...((.((((.....)))).))...)).))))).)))).)).))))))..)).))))))...... (-25.34 = -25.74 +   0.40)

alignment

secondary structure

dotplot

Window 9

Location	3,372,851 – 3,372,961
Length	110
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	92.63
Mean single sequence MFE	-41.27
Consensus MFE	-38.83
Energy contribution	-38.64
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-1.68
Structure conservation index	0.94
SVM decision value	0.91
SVM RNA-class probability	0.880504
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3372851 110 - 23771897
CUCAGCGCAUUUUCGCCCAGUGUAUUCCACAUAAAGCGUAGCACGGUAGCCGAGCUACAGGUUCGAGUGCCGCUGUGUGU------GUGUGUGUGGACGAUGACGCUGGUAAAA-AA
....(((......)))(((((((..((((((((..((...((((((((..(((((.....)))))..))))).)))..))------...)))))))).....))))))).....-.. ( -41.20)
>DroSec_CAF1 39984 109 - 1
CUCUGCGCAUUUUCGCCCAGUGUAUUCCACAUAAAGCGUAGCACGGUAGCCGAGCUACAGGUUCGAGUGCCGCUGUGUGU------GUGUGUGUGGACGAUGACGCUGGUAAAA--A
....(((......)))(((((((..((((((((..((...((((((((..(((((.....)))))..))))).)))..))------...)))))))).....))))))).....--. ( -41.00)
>DroSim_CAF1 37707 115 - 1
CUGCGCGCAUUUUCGCCCAGUGUAUUCCGCAUAAAGCGUAGCACGGUAGCCGAGCUACAGGUUCGAGUGCCGCUGUGUGUGUCUGUGUGUGUGUGGACGAUGACGCUGGUAAAA--A
....(((......)))(((((((..((((((((..(((..((((((..(((((((.....)))))...))..)))))).....)))...)))))))).....))))))).....--. ( -41.50)
>DroYak_CAF1 38722 117 - 1
CUCUGCGCAUUUUCGCCCAGUGUAUUCCACAUAAAGCGUAGCACGGUAGCCGAGCUACAGGUUCGAGUGCGGCUGUGUGUGUGUACUUGUGUGUGGACGAUGACGCUGGUAAAAAAA
....(((......)))(((((((..((((((((....(((((.(((...))).))))).....((((((((((.....)).)))))))))))))))).....)))))))........ ( -41.40)
>consensus
CUCUGCGCAUUUUCGCCCAGUGUAUUCCACAUAAAGCGUAGCACGGUAGCCGAGCUACAGGUUCGAGUGCCGCUGUGUGU______GUGUGUGUGGACGAUGACGCUGGUAAAA__A
....(((......)))(((((((..((((((((.......((((((..(((((((.....)))))...))..))))))...........)))))))).....)))))))........ (-38.83 = -38.64 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:23 2006