Locus 477

Sequence ID	3R_DroMel_CAF1
Location	1,791,813 – 1,791,937
Length	124
Max. P	0.951861

overview

Window 1

Location	1,791,813 – 1,791,919
Length	106
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	82.90
Mean single sequence MFE	-18.45
Consensus MFE	-16.70
Energy contribution	-16.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	0.91
SVM decision value	0.27
SVM RNA-class probability	0.663427
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1791813 106 + 27905053
--GCAU-CAGGAGAUGAAAA----AACGAAAACAAAAUAUUAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAA
--((..-((((((((((...----.............((((.((((.((((...(((....)))..)))).)))))))).(((.....)))))))))))))....))...... ( -20.20)
>DroVir_CAF1 119854 102 + 1
AAGAAUA-------AAUAAA----AAUAAAGAGAAAAUAUCAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAA
..((((.-------......----......((.......))..(((....)))))))..((..((((((.....((((.((((.....)))).))))....)))))).))... ( -16.80)
>DroGri_CAF1 105488 90 + 1
AAGA-----------------------ACCGAGAAUAUAACAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAA
....-----------------------...............(((....((((......))))((((((.....((((.((((.....)))).))))....)))))).))).. ( -16.70)
>DroWil_CAF1 101605 102 + 1
--GAAU-AAGAAG---CGAA----AACGAAAA-AAAAUAUUAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAA
--....-.....(---(...----........-........(((((....)))))........((((((.....((((.((((.....)))).))))....)))))).))... ( -18.30)
>DroMoj_CAF1 111958 109 + 1
ACGAAUACAAGAAAUAUAUA----UAUAAAGAGAAAAUAUCAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAA
..((((...((((.((((((----(((.........)))).))))).))))..))))..((..((((((.....((((.((((.....)))).))))....)))))).))... ( -18.90)
>DroAna_CAF1 93275 110 + 1
--GCAU-CAGGAGCUGAAAAAAAAAAUGAAAACAAAAUAUUAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAA
--((.(-(((...))))...............((.......(((((....))))).....)).((((((.....((((.((((.....)))).))))....)))))).))... ( -19.80)
>consensus
__GAAU_CAGGAG_U_AAAA____AAUAAAAAGAAAAUAUCAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAA
..........................................(((....((((......))))((((((.....((((.((((.....)))).))))....)))))).))).. (-16.70 = -16.70 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	1,791,813 – 1,791,919
Length	106
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	82.90
Mean single sequence MFE	-22.44
Consensus MFE	-19.70
Energy contribution	-19.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.42
Structure conservation index	0.88
SVM decision value	1.41
SVM RNA-class probability	0.951169
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1791813 106 - 27905053
UUUGCUGCGGAACAGGAAAUGAGCACCUGCUGCUUAUUUAUAUUUUCCGCUCACUUGAAUGUAAAAUUACAUAAUAUUUUGUUUUCGUU----UUUUCAUCUCCUG-AUGC--
......((((((.(..(((((((((.....)))))))))...).))))))......(((..((((((........))))))..)))...----....((((....)-))).-- ( -24.20)
>DroVir_CAF1 119854 102 - 1
UUUGCUGCGGAACAGGAAAUGAGCACCUGCUGCUUAUUUAUAUUUUCCGCUCACUUGAAUGUAAAAUUACAUGAUAUUUUCUCUUUAUU----UUUAUU-------UAUUCUU
......((((((.(..(((((((((.....)))))))))...).))))))......(((((.(((((.....((.....)).....)))----))....-------))))).. ( -21.00)
>DroGri_CAF1 105488 90 - 1
UUUGCUGCGGAACAGGAAAUGAGCACCUGCUGCUUAUUUAUAUUUUCCGCUCACUUGAAUGUAAAAUUACAUGUUAUAUUCUCGGU-----------------------UCUU
......((((((.(..(((((((((.....)))))))))...).))))))..(((.((((((((.........))))))))..)))-----------------------.... ( -22.40)
>DroWil_CAF1 101605 102 - 1
UUUGCUGCGGAACAGGAAAUGAGCACCUGCUGCUUAUUUAUAUUUUCCGCUCACUUGAAUGUAAAAUUACAUAAUAUUUU-UUUUCGUU----UUCG---CUUCUU-AUUC--
...((.((((((.(..(((((((((.....)))))))))...).))))))........(((((....)))))........-........----...)---).....-....-- ( -21.20)
>DroMoj_CAF1 111958 109 - 1
UUUGCUGCGGAACAGGAAAUGAGCACCUGCUGCUUAUUUAUAUUUUCCGCUCACUUGAAUGUAAAAUUACAUGAUAUUUUCUCUUUAUA----UAUAUAUUUCUUGUAUUCGU
(((((.((((((.(..(((((((((.....)))))))))...).))))))((....))..)))))..((((.(((((............----...)))))...))))..... ( -20.86)
>DroAna_CAF1 93275 110 - 1
UUUGCUGCGGAACAGGAAAUGAGCACCUGCUGCUUAUUUAUAUUUUCCGCUCACUUGAAUGUAAAAUUACAUAAUAUUUUGUUUUCAUUUUUUUUUUCAGCUCCUG-AUGC--
...(((((((((.(..(((((((((.....)))))))))...).)))))).....((((..((((((........))))))..))))...........))).....-....-- ( -25.00)
>consensus
UUUGCUGCGGAACAGGAAAUGAGCACCUGCUGCUUAUUUAUAUUUUCCGCUCACUUGAAUGUAAAAUUACAUAAUAUUUUCUCUUCAUU____UUUA_A_CUCCUG_AUUC__
......((((((.(..(((((((((.....)))))))))...).))))))........(((((....)))))......................................... (-19.70 = -19.70 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	1,791,839 – 1,791,937
Length	98
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	87.69
Mean single sequence MFE	-23.10
Consensus MFE	-21.43
Energy contribution	-21.52
Covariance contribution	0.08
Combinations/Pair	1.04
Mean z-score	-1.81
Structure conservation index	0.93
SVM decision value	1.42
SVM RNA-class probability	0.951861
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1791839 98 + 27905053
AAAAUAUUAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAACAUGGUACAGUCA--------GCAUA--------------
....((((((((....((((......))))((((((.....((((.((((.....)))).))))....)))))).....))))))))......--------.....-------------- ( -21.40)
>DroVir_CAF1 119876 97 + 1
AAAAUAUCAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAACAUGGUACACUC---------GCACA--------------
....((((((((....((((......))))((((((.....((((.((((.....)))).))))....)))))).....)))))))).....---------.....-------------- ( -23.50)
>DroPse_CAF1 92391 106 + 1
AAAAUAUUAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAACAUGGUACAGCCAGCCAGCGAGCACA--------------
........(((((....)))))....(((.((((((.....((((.((((.....)))).))))....)))))).((.....(((.....)))....))...))).-------------- ( -23.40)
>DroGri_CAF1 105498 97 + 1
AAUAUAACAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAACAUGCUACAGUA---------GCACA--------------
........(((((....)))))....(((.((((((.....((((.((((.....)))).))))....))))))((((....))))......---------.))).-------------- ( -21.50)
>DroMoj_CAF1 111987 111 + 1
AAAAUAUCAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAACAUGGCACAGUA---------GCACAAGUACUCUGGCACA
.......(((((....((((......))))((((((.....((((.((((.....)))).))))....)))))).....)))))((.(((.(---------(........)))))))... ( -25.40)
>DroPer_CAF1 94963 106 + 1
AAAAUAUUAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAACAUGGUACAGCCAGCCAGCGAGCACA--------------
........(((((....)))))....(((.((((((.....((((.((((.....)))).))))....)))))).((.....(((.....)))....))...))).-------------- ( -23.40)
>consensus
AAAAUAUCAUGUAAUUUUACAUUCAAGUGAGCGGAAAAUAUAAAUAAGCAGCAGGUGCUCAUUUCCUGUUCCGCAGCAAACAUGGUACAGUC_________GCACA______________
....((((((((....((((......))))((((((.....((((.((((.....)))).))))....)))))).....))))))))................................. (-21.43 = -21.52 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:10 2006