Locus 3007

Sequence ID	3L_DroMel_CAF1
Location	8,652,460 – 8,652,643
Length	183
Max. P	0.987322

overview

Window 1

Location	8,652,460 – 8,652,553
Length	93
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	86.27
Mean single sequence MFE	-32.60
Consensus MFE	-27.39
Energy contribution	-27.78
Covariance contribution	0.39
Combinations/Pair	1.07
Mean z-score	-1.87
Structure conservation index	0.84
SVM decision value	0.41
SVM RNA-class probability	0.726336
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8652460 93 - 23771897
GCAUGUUU---GCAACACUUCA-AAGCAACAUUUGCGCAAUCCCGGCGAAUGAUGUGAAAUGUC---UACGCGCAUGCGCACAACGCCUGCGCAUGUGUG-----------------
(((....)---)).(((.(((.-..(((.(((((((.(......)))))))).)))))).))).---..((((((((((((.......))))))))))))----------------- ( -33.30)
>DroSec_CAF1 40379 93 - 1
GCAUGUUU---GCAACACUUCA-AAGCAACAUUUGCGCAAUCCCGGCGAAUGAUGUGAAAUGUC---UACGCGCAUGCGCACAACGCCUGCGCAUGUGUG-----------------
(((....)---)).(((.(((.-..(((.(((((((.(......)))))))).)))))).))).---..((((((((((((.......))))))))))))----------------- ( -33.30)
>DroSim_CAF1 40751 93 - 1
GCAUGUUU---GCAACACUUCA-AAGCAACAUUUGCGCAAUCCCGGCGAAUGAUGUGAAAUGUC---UACGCGCAUGCGCACAACGCCUGCGCAUGUGUG-----------------
(((....)---)).(((.(((.-..(((.(((((((.(......)))))))).)))))).))).---..((((((((((((.......))))))))))))----------------- ( -33.30)
>DroEre_CAF1 41827 93 - 1
GCAUGUUU---GCAACACUUCA-AGGCAACAUUUGCGCAAUCCCGGCGAAUGAUGUGAAAUGUC---AACGCGCAUGCGCACAACGCCUGCGCAUGUGUG-----------------
(((....)---)).(((.(((.-..(((.(((((((.(......)))))))).)))))).))).---..((((((((((((.......))))))))))))----------------- ( -33.30)
>DroYak_CAF1 41599 110 - 1
GCAUGUUU---GCAACACUUCA-AAGCAACAUUUGCGCAAUCCCGGCGAAUGAUGUGAAAUGUC---UACGCGCAUGCGCACAACGCCUGCGCCUGUGUGAGUUGGAUGAGUUGUGG
......(.---.((((.(((((-(.(((.(((((((.(......)))))))).)))........---..((((((.(((((.......))))).))))))..))))).).))))..) ( -34.20)
>DroPer_CAF1 43617 99 - 1
GCAUGUUCUCGGUGGCACUUCUUGGGCAACAUUGGCGUUAUCCUGGCGAAUGAUGUGAAAUGUCCUUUUUGCGCAUGC-CACAACGCCUGCGCAUGUGUC-----------------
.............(((((....((.(((.....((((((....((((..(((.((..(((......)))..)))))))-)).))))))))).)).)))))----------------- ( -28.20)
>consensus
GCAUGUUU___GCAACACUUCA_AAGCAACAUUUGCGCAAUCCCGGCGAAUGAUGUGAAAUGUC___UACGCGCAUGCGCACAACGCCUGCGCAUGUGUG_________________
..............(((.(((....(((.(((((((.(......)))))))).)))))).)))......((((((((((((.......))))))))))))................. (-27.39 = -27.78 +   0.39)

alignment

secondary structure

dotplot

Window 2

Location	8,652,553 – 8,652,643
Length	90
Sequences	6
Columns	92
Reading direction	forward
Mean pairwise identity	76.15
Mean single sequence MFE	-32.37
Consensus MFE	-24.27
Energy contribution	-24.22
Covariance contribution	-0.05
Combinations/Pair	1.46
Mean z-score	-3.48
Structure conservation index	0.75
SVM decision value	2.07
SVM RNA-class probability	0.987322
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8652553 90 + 23771897
GAAUCCUAAACUCGGUUCACA-ACU-UCGUUGGCUUAGUUUCCUGGCUUAUAUCCUGGAAACCCGUCGACGAGGCUAAGGACCUUCAUCAGA
.............(((((...-.((-((((((((...((((((.((.......)).))))))..))))))))))....)))))......... ( -28.80)
>DroSec_CAF1 40472 89 + 1
GAAUCCUAAA-UCGGUUCACG-GCU-UCGUUGGCUUAGUUUCCUGGCUUAUACCCUGGAAACCCGCUGGCGAGGCUAAAAACCUUCAUCAGA
..........-..((((...(-(((-((((..((...((((((.((.......)).))))))..))..))))))))...))))......... ( -32.00)
>DroSim_CAF1 40844 89 + 1
GAAUCCUAAA-UCGGUUCACG-GCUUUCGUGGGCUUAGUUUCCUGGCUUAUACCCUG-AAACACGCUGGCGAGGCUAAGAACCUUCAUCAGA
..........-..(((((..(-((((.(((.(((...(((((..((......))..)-))))..))).))))))))..)))))......... ( -27.60)
>DroEre_CAF1 41920 89 + 1
GAGUCCUAAC-UCGGUCCACG-GCU-UCGUCGGCUUAGUUUCCUGGCUUACAUCCGGGAAACCCGCCGGCGAGGCUACGGACCUCCAUCAGA
((((....))-))(((((..(-(((-((((((((...(((((((((.......)))))))))..))))))))))))..)))))......... ( -48.20)
>DroYak_CAF1 41709 90 + 1
GAAUCCUAAC-UCGGUCCACGGGCU-UCGUCGGCUCAGUUUCCUCGCUUAUAUCCUGGAAACCAGCCGGCGAGACUAAGGACCUUCAUCAGA
..........-..(((((...((..-(((((((((..((((((.............)))))).)))))))))..))..)))))......... ( -34.42)
>DroAna_CAF1 38597 79 + 1
UAA---GAAA-UCGGUUGAGA-ACC-UCCCAGG-----GUUCCACAUCUAUUCCCAGGAAUAAUCCCUGCGAGGUCA-GGACC-UCAUCUCA
...---....-..((((..((-.((-((.((((-----(.........(((((....)))))..))))).)))))).-.))))-........ ( -23.20)
>consensus
GAAUCCUAAA_UCGGUUCACG_GCU_UCGUCGGCUUAGUUUCCUGGCUUAUACCCUGGAAACCCGCCGGCGAGGCUAAGGACCUUCAUCAGA
.............(((((....(((.((((((((...((((((.((.......)).))))))..)))))))))))...)))))......... (-24.27 = -24.22 +  -0.05)

alignment

secondary structure

dotplot

Window 3

Location	8,652,553 – 8,652,643
Length	90
Sequences	6
Columns	92
Reading direction	reverse
Mean pairwise identity	76.15
Mean single sequence MFE	-30.87
Consensus MFE	-14.71
Energy contribution	-16.91
Covariance contribution	2.20
Combinations/Pair	1.12
Mean z-score	-2.05
Structure conservation index	0.48
SVM decision value	0.58
SVM RNA-class probability	0.787821
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8652553 90 - 23771897
UCUGAUGAAGGUCCUUAGCCUCGUCGACGGGUUUCCAGGAUAUAAGCCAGGAAACUAAGCCAACGA-AGU-UGUGAACCGAGUUUAGGAUUC
(((((....(((.(.((((.((((.(...(((((((.((.......)).)))))))....).))))-.))-)).).)))....))))).... ( -24.30)
>DroSec_CAF1 40472 89 - 1
UCUGAUGAAGGUUUUUAGCCUCGCCAGCGGGUUUCCAGGGUAUAAGCCAGGAAACUAAGCCAACGA-AGC-CGUGAACCGA-UUUAGGAUUC
(((((....(((((...((.(((...((.(((((((..(((....))).)))))))..))...)))-.))-...)))))..-.))))).... ( -27.20)
>DroSim_CAF1 40844 89 - 1
UCUGAUGAAGGUUCUUAGCCUCGCCAGCGUGUUU-CAGGGUAUAAGCCAGGAAACUAAGCCCACGAAAGC-CGUGAACCGA-UUUAGGAUUC
(((((....(((((...((.(((...((..((((-(..(((....)))..)))))...))...)))..))-...)))))..-.))))).... ( -25.90)
>DroEre_CAF1 41920 89 - 1
UCUGAUGGAGGUCCGUAGCCUCGCCGGCGGGUUUCCCGGAUGUAAGCCAGGAAACUAAGCCGACGA-AGC-CGUGGACCGA-GUUAGGACUC
((((((...((((((..((.(((.((((.(((((((.((.......)).)))))))..)))).)))-.))-..))))))..-)))))).... ( -43.30)
>DroYak_CAF1 41709 90 - 1
UCUGAUGAAGGUCCUUAGUCUCGCCGGCUGGUUUCCAGGAUAUAAGCGAGGAAACUGAGCCGACGA-AGCCCGUGGACCGA-GUUAGGAUUC
((((((...(((((...(..(((.((((((((((((.(........)..))))))).))))).)))-..)....)))))..-)))))).... ( -36.60)
>DroAna_CAF1 38597 79 - 1
UGAGAUGA-GGUCC-UGACCUCGCAGGGAUUAUUCCUGGGAAUAGAUGUGGAAC-----CCUGGGA-GGU-UCUCAACCGA-UUUC---UUA
.(((((..-(((..-.((((((.(((((....((((.............)))))-----)))).))-)))-)....))).)-))))---... ( -27.92)
>consensus
UCUGAUGAAGGUCCUUAGCCUCGCCGGCGGGUUUCCAGGAUAUAAGCCAGGAAACUAAGCCAACGA_AGC_CGUGAACCGA_UUUAGGAUUC
(((((....(((((......(((..(((..((((((.((.......)).))))))...)))..)))........)))))....))))).... (-14.71 = -16.91 +   2.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:16 2006