Locus 6580

Sequence ID	3L_DroMel_CAF1
Location	17,443,937 – 17,444,116
Length	179
Max. P	0.891084

overview

Window 5

Location	17,443,937 – 17,444,051
Length	114
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	80.70
Mean single sequence MFE	-45.25
Consensus MFE	-28.60
Energy contribution	-29.72
Covariance contribution	1.12
Combinations/Pair	1.29
Mean z-score	-1.71
Structure conservation index	0.63
SVM decision value	0.26
SVM RNA-class probability	0.658043
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17443937 114 - 23771897
UCGAGCCAAAGCCCGAUUGGAGAACGAGGUGGUUCUCCUGCGGAGCGAGGUGUCCUCGCUGCGCUCCAAGCACAACCAACAUCGUAAGUAUCGGCAGGAGCAGGUGGUUCUGCA
..((((((..(((((...(((((((......)))))))..)))(((((((...)))))))))(((((..((...((..((...))..))....)).)))))...)))))).... ( -45.20)
>DroSec_CAF1 3082 114 - 1
UCGGGCCAAAGCCCGAUUGGAGAACGAGGUGGUUCUCCUGCGUGGCGAGGUGUCCUCGCUGCGCUCCAAGCACAACCAACAUCGUAAGUAUCGGCAGGAGCAGGCGGUUCUACA
((((((....))))))..(((((((......)))))))((((..((((((...))))))..)(((((..((...((..((...))..))....)).)))))..)))........ ( -46.30)
>DroSim_CAF1 3530 114 - 1
UCGGGCCAAAGCCCGAUUGGAGAACGAGGUGGUUCUCCUGCGUGGCGAGGUGUCCUCGCUGCGCUCCAAGCACAAUCAGCAUCGUAAGUAUCGGCAGGAGCAGGCGGUUCUACA
((((((....))))))..(((((((......)))))))((((..((((((...))))))..)(((((..((.......)).(((.......)))..)))))..)))........ ( -48.80)
>DroEre_CAF1 3281 114 - 1
CCGGGCCAAAGCCCGUUUGGAAAACGAGGUGGUUCUCCUGCGACGCGAGGUGGCCUCACUGCGCUCCAGGCAUAUCCAGCAUCGUAAGUAUCGACAGGAACAGGCGGUUCUACA
((((((....))))(((((....(((((.(((....((((.((.(((.((((....)))).))))))))).....))).).))))..((....)).....)))))))....... ( -37.10)
>DroYak_CAF1 3286 114 - 1
UCGGGCCAAAGCCCGACUGGAAAACGAGGUGGUCCUCCUUCGCCGCGAGGUGGCCUCACUGCGCUCCAAGCAUAUCAAACAUCGUAAGUAUCGCCAGAAUCAGGCGGUGCUACA
((((((....))))))...((....(((((((....))..((((....)))))))))..(((.......)))..)).......(((.((((((((.......))))))))))). ( -43.60)
>DroAna_CAF1 3027 114 - 1
UCGCGCCAAGGCGCGACUGGAACACGAGAUAACCAUCUUACGCCGCGAGGUGGCCAGGCUGCGCGCCAAACAGGACCAGCGACGACGUGACAAGCUGGAGAAGGAUGUGGCGCA
..((((((.((((((.((((.....(((((....))))).((((....)))).))))....))))))........(((((.............))))).........)))))). ( -50.52)
>consensus
UCGGGCCAAAGCCCGAUUGGAAAACGAGGUGGUUCUCCUGCGCCGCGAGGUGGCCUCGCUGCGCUCCAAGCACAACCAACAUCGUAAGUAUCGGCAGGAGCAGGCGGUUCUACA
((((((....))))))(((((....((((....))))..((((.((((((...)))))).)))))))))..............((.((.((((.(.......).)))).)))). (-28.60 = -29.72 +   1.12)

alignment

secondary structure

dotplot

Window 6

Location	17,443,971 – 17,444,089
Length	118
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.01
Mean single sequence MFE	-46.32
Consensus MFE	-34.04
Energy contribution	-33.72
Covariance contribution	-0.33
Combinations/Pair	1.45
Mean z-score	-1.11
Structure conservation index	0.73
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17443971 118 + 23771897
GUUGGUUGUGCUUGGAGCGCAGCGAGGACACCUCGCUCCGCAGGAGAACCACCUCGUUCUCCAAUCGGGCUUUGGCUCGAUCGUGGUAUGGCAUCGCGCUGGACGAA--UGAAAUUUUGG
..(((((.(.((....(((.(((((((...))))))).))))).).)))))..(((((((((((((((((....)))))))((((((.....)))))).)))).)))--)))........ ( -47.00)
>DroSec_CAF1 3116 118 + 1
GUUGGUUGUGCUUGGAGCGCAGCGAGGACACCUCGCCACGCAGGAGAACCACCUCGUUCUCCAAUCGGGCUUUGGCCCGAUCGUGGUAUGGCAUCGCGCUGGACAAA--UCAAAUUUUGG
.((((((((((.....))))((((..((..((..((((((..(((((((......))))))).(((((((....)))))))))))))..))..)).)))).....))--))))....... ( -49.90)
>DroSim_CAF1 3564 118 + 1
GCUGAUUGUGCUUGGAGCGCAGCGAGGACACCUCGCCACGCAGGAGAACCACCUCGUUCUCCAAUCGGGCUUUGGCCCGAUCGUGGUAUGGCAUCGCGCUGGACAAA--UCAAAUUUUGG
..(((((((((.....))))((((..((..((..((((((..(((((((......))))))).(((((((....)))))))))))))..))..)).)))).....))--)))........ ( -49.50)
>DroEre_CAF1 3315 118 + 1
GCUGGAUAUGCCUGGAGCGCAGUGAGGCCACCUCGCGUCGCAGGAGAACCACCUCGUUUUCCAAACGGGCUUUGGCCCGGUCGUGGUACGGCAUCGGGCUGGACGAA--UUAAAUUUUGG
.........(((((..(((..((((((...))))))..))).(((((((......)))))))...)))))((..(((((((((.....))))..)))))..))((((--......)))). ( -47.50)
>DroYak_CAF1 3320 118 + 1
GUUUGAUAUGCUUGGAGCGCAGUGAGGCCACCUCGCGGCGAAGGAGGACCACCUCGUUUUCCAGUCGGGCUUUGGCCCGAUCGUGGUACGGCAUUGGGCUGGAUGAG--UCAAAUUUUGG
(((((((...((...(((.(((((..(((((.....((.(((.((((....)))).))).)).(((((((....))))))).)))))....))))).)))))....)--))))))..... ( -45.80)
>DroAna_CAF1 3061 118 + 1
GCUGGUCCUGUUUGGCGCGCAGCCUGGCCACCUCGCGGCGUAAGAUGGUUAUCUCGUGUUCCAGUCGCGCCUUGGCGCGAUCAUGAAGGGGCAUCC--UUGGGCAAUGUUUAGAUUCGCG
((..(......)..))((.(((....(((.(((((..(((..((((....))))..)))..).(((((((....)))))))...).))))))....--))).))................ ( -38.20)
>consensus
GCUGGUUGUGCUUGGAGCGCAGCGAGGACACCUCGCGACGCAGGAGAACCACCUCGUUCUCCAAUCGGGCUUUGGCCCGAUCGUGGUAUGGCAUCGCGCUGGACAAA__UCAAAUUUUGG
....((((((((((..(((..((((((...))))))..))).(((((((......))))))).(((((((....))))))))).))))))))............................ (-34.04 = -33.72 +  -0.33)

alignment

secondary structure

dotplot

Window 7

Location	17,444,011 – 17,444,116
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.42
Mean single sequence MFE	-35.13
Consensus MFE	-25.23
Energy contribution	-24.71
Covariance contribution	-0.52
Combinations/Pair	1.44
Mean z-score	-1.66
Structure conservation index	0.72
SVM decision value	0.96
SVM RNA-class probability	0.891084
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17444011 105 + 23771897
CAGGAGAACCACCUCGUUCUCCAAUCGGGCUUUGGCUCGAUCGUGGUAUGGCAUCGCGCUGGACGAA--UGAAAUUUUGGUA-GUCCAAAA---------CACACGGCUUG---UCUAUU
..(((((((......))))))).(((((((....)))))))((((((.....)))))).(((((((.--((...((((((..-..))))))---------....))..)))---)))).. ( -34.60)
>DroSec_CAF1 3156 105 + 1
CAGGAGAACCACCUCGUUCUCCAAUCGGGCUUUGGCCCGAUCGUGGUAUGGCAUCGCGCUGGACAAA--UCAAAUUUUGGUA-GUCCAAAA---------CACACGGCUUG---UCUAUU
..(((((((......))))))).(((((((....)))))))((((((.....)))))).(((((((.--.(...((((((..-..))))))---------.....)..)))---)))).. ( -38.80)
>DroSim_CAF1 3604 105 + 1
CAGGAGAACCACCUCGUUCUCCAAUCGGGCUUUGGCCCGAUCGUGGUAUGGCAUCGCGCUGGACAAA--UCAAAUUUUGGUA-GUCCUAAA---------CACACGGCUUG---UCUAUU
..(((((((......))))))).(((((((....)))))))((((((..(((.....)))((((..(--(((.....)))).-))))...)---------).)))).....---...... ( -35.80)
>DroEre_CAF1 3355 108 + 1
CAGGAGAACCACCUCGUUUUCCAAACGGGCUUUGGCCCGGUCGUGGUACGGCAUCGGGCUGGACGAA--UUAAAUUUUGGUA-GUCCAAAA---------CACACUGCUUGUCGUCUAUU
..(((((((......)))))))..((((((..(((((((((((.....))))..)))))(((((..(--(((.....)))).-)))))...---------..))..))))))........ ( -35.70)
>DroYak_CAF1 3360 105 + 1
AAGGAGGACCACCUCGUUUUCCAGUCGGGCUUUGGCCCGAUCGUGGUACGGCAUUGGGCUGGAUGAG--UCAAAUUUUGGUA-GUCCAAAA---------CACACUGCUUG---UCUAGU
...((((....))))(((..((((((((((....)))))))..)))...))).....((((((..((--(....((((((..-..))))))---------......)))..---)))))) ( -37.90)
>DroAna_CAF1 3101 115 + 1
UAAGAUGGUUAUCUCGUGUUCCAGUCGCGCCUUGGCGCGAUCAUGAAGGGGCAUCC--UUGGGCAAUGUUUAGAUUCGCGUACGUACAAAGACAAAAUUUCGCAUGGGUUC---UUUACC
......(((...((((((((((.(((((((....)))))))....((((.....))--)))))...(((((.....((....)).....))))).......)))))))...---...))) ( -28.00)
>consensus
CAGGAGAACCACCUCGUUCUCCAAUCGGGCUUUGGCCCGAUCGUGGUAUGGCAUCGCGCUGGACAAA__UCAAAUUUUGGUA_GUCCAAAA_________CACACGGCUUG___UCUAUU
..(((((((......))))))).(((((((....)))))))((((....(((.....)))((((...................))))...............)))).............. (-25.23 = -24.71 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:56 2006