Locus 1307

Sequence ID	3R_DroMel_CAF1
Location	3,839,583 – 3,839,802
Length	219
Max. P	0.703648

overview

Window 5

Location	3,839,583 – 3,839,700
Length	117
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	79.49
Mean single sequence MFE	-45.00
Consensus MFE	-33.91
Energy contribution	-32.45
Covariance contribution	-1.46
Combinations/Pair	1.42
Mean z-score	-1.25
Structure conservation index	0.75
SVM decision value	0.36
SVM RNA-class probability	0.703648
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3839583 117 - 27905053
GACUUGCAUGAGCCGGCGCUGGAGCUCCUGAUUCAGCUGCAGUGCGUUGGCGGCGCUCGGCUUCGCUGUGUUCUGCAAGAGGGCCGAAAUCUCGUCCAUAAGCUGCUGCUGGUUUAU
.......((((((((((((((((........)))))).(((((....((((((...((((((((..(((.....))).)).))))))....))).)))...))))).)))))))))) ( -45.90)
>DroVir_CAF1 4075 117 - 1
CACCUGCUCCAGCCGCCGCUGCAGCUCCUGGUUCAGUCUCAAUGCAUUUGUAUCGCAUGGCUCGGCACUGGCUGCCAGCAGCGUUGUGAUUUCCUGCAGCAGUUGUUGGUGGCUCAG
....(((.(.(((((..((((.(((.....)))))))..).((((.........)))))))).))))(((((..(((((((((((((........))))).))))))))..)).))) ( -43.90)
>DroSec_CAF1 4730 117 - 1
CACUUGCAUGAGCCGGCGCUGGAGCUCCUGAUUCAGUUGCAGUGCAUUCGCGGCGCUCGGCUCCGUUGUGGUCUGCAAGAGGGCCGAAAUCUCGUCCAGAAGCUGCUGCUGGCUUAU
.......((((((((((((((.((((........)))).))))))....((((((((((((((..((((.....))))..)))))))..(((.....))).)).))))))))))))) ( -48.20)
>DroSim_CAF1 4409 117 - 1
CACUUGCAUGAGCCGGCGCUGGAGCUCCUGAUUCAGUUGCAGUGCAUUGGCGGCGCUCGGCUCCGUUGUGGUCUGCAAGAGGGCCGAAAUCUCCUCCAAAAGCUGCUGCUGGCUUAU
.......((((((((((((((((........)))))).(((((...((((.((.(.(((((((..((((.....))))..)))))))...).)).))))..))))).)))))))))) ( -50.30)
>DroEre_CAF1 4193 117 - 1
AACUUGCAUGAGCCGUCGCUGGAGCUCCUGAUUCAGCUGCAGUGCGUUGGCAUCGCUCGGUUCUAAGGUGCUCUGCAAUAGGACCGAAAUCUCGUCCAUAAGCUGCUGCUGGUUUAU
.......(((((((...((((((........)))))).(((((((..((((.....(((((((((...(((...))).)))))))))......).)))...)).))))).))))))) ( -39.70)
>DroYak_CAF1 4093 117 - 1
GACCUGCAUGAGCCGGCGUUGGAGCUCCUGGUUCAACUGCAAUGCGUUGGCGUCGCUCCGUUCCGACGUGCUCUGCAAUAGGGCAGAGAUCUCGUUCAUAAGCUGCUGCUGGUUUAU
.......((((((((((((((((.(....).)))))).(((..((..((((((((........)))))).((((((......))))))........))...))))).)))))))))) ( -42.00)
>consensus
CACUUGCAUGAGCCGGCGCUGGAGCUCCUGAUUCAGCUGCAGUGCAUUGGCGGCGCUCGGCUCCGAUGUGGUCUGCAAGAGGGCCGAAAUCUCGUCCAUAAGCUGCUGCUGGCUUAU
.......((((((((((((((((.(....).)))))).(((((((....)).....(((((((.....((.....))...)))))))..............))))).)))))))))) (-33.91 = -32.45 +  -1.46)

alignment

secondary structure

dotplot

Window 6

Location	3,839,700 – 3,839,802
Length	102
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	81.28
Mean single sequence MFE	-41.21
Consensus MFE	-28.30
Energy contribution	-28.19
Covariance contribution	-0.11
Combinations/Pair	1.38
Mean z-score	-1.59
Structure conservation index	0.69
SVM decision value	0.28
SVM RNA-class probability	0.666643
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3839700 102 - 27905053
---CGGGCCG---AAAUGGGAACGAGGUCGCAGCCGGCGCACCAGGAUGUCCUCGUUCCGAGAGAAGCGGGCCCUUACUACUUGUAACAUGGCCAGAAUUUUGGUCCG
---(((((((---((((.(((((((((..(((.((((....)).)).))))))))))))..........((((.((((.....))))...))))...))))))))))) ( -45.20)
>DroSec_CAF1 4847 102 - 1
---CGGGCCG---AAAUGGGAACGAGGUCGCAGCCGGCGCACCAGGAUGUCCUCGUUCCGGGAGAAGCGGGCCCUUACUACUUGUAACAUGGCCAGAAUUUUGGUCCG
---(((((((---((((.(((((((((..(((.((((....)).)).))))))))))))..........((((.((((.....))))...))))...))))))))))) ( -45.20)
>DroSim_CAF1 4526 102 - 1
---CGGGCCG---AAAUGGGAACGAGGUCGCAGCCGGCGCACCAGGAUGUCCUCGUUCCGGGAGAAGCGGGCCCUUACUACUUGUAACAUGGCCAGAAUUUUGGUCCG
---(((((((---((((.(((((((((..(((.((((....)).)).))))))))))))..........((((.((((.....))))...))))...))))))))))) ( -45.20)
>DroEre_CAF1 4310 102 - 1
---CGGGCCG---AAAUGGGAGCGAGGUCUCAGCCGGCGCACCAGGAUGUCCUCGUUUCGAGAGAAGCGGGCUCUAACUACUUGUAGCAUGGCCAGGAUUUUGGUCCG
---(((((((---((.(((..(((.(((....)))..))).)))....(((((((((((....))))))((((....(((....)))...)))))))))))))))))) ( -43.00)
>DroYak_CAF1 4210 102 - 1
---CGGGCCG---AAAUGGGAGCGAGGUCUAAGCCGGCGCACCAGGAUGUCCUCGUUCCGAGAGAAGCGGGUCCUAACUACUUGCAACAUGGCCAGGAUUUUAGUCCG
---..(((((---.....(((((((((.(....((((....)).))..).))))))))).......((((((.......))))))....))))).((((....)))). ( -39.60)
>DroPer_CAF1 4463 108 - 1
AAGCCUGCUGUUACAUUGGGUGCGCGGCUUUAGGCGGCGGAUUAAAAUCUCCUCGUUCCGUGCAUAUCGAGCCCGGACAGAUUUCAGCAACGCUAGAACCUUUGCGCG
..((.(((((....(((..((.((.(((((.(.(((.((((...............)))))))...).))))))).)).)))..)))))..((..........)))). ( -29.06)
>consensus
___CGGGCCG___AAAUGGGAACGAGGUCGCAGCCGGCGCACCAGGAUGUCCUCGUUCCGAGAGAAGCGGGCCCUUACUACUUGUAACAUGGCCAGAAUUUUGGUCCG
....(((((.......(.(((((((((.(....((((....)).))..).))))))))).)........)))))................((((((....)))))).. (-28.30 = -28.19 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:26 2006