Locus 5197

Sequence ID	3R_DroMel_CAF1
Location	13,618,738 – 13,618,870
Length	132
Max. P	0.951728

overview

Window 0

Location	13,618,738 – 13,618,832
Length	94
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	84.18
Mean single sequence MFE	-36.18
Consensus MFE	-25.61
Energy contribution	-26.95
Covariance contribution	1.34
Combinations/Pair	1.18
Mean z-score	-2.33
Structure conservation index	0.71
SVM decision value	0.21
SVM RNA-class probability	0.634369
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13618738 94 + 27905053
AUAUCCGCGAGACGUCUCGGGAUUGUCCCAUU-------GCGAGGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUUGCUCGGA--------G
...((((.(((....)))(((.....)))...-------((((((((....((((.(((((..((......))..)))))...)))))))))))).))))--------. ( -37.10)
>DroSec_CAF1 67715 94 + 1
AUAUCCGCGAGACGUCUCGGGAUUGUCCCAUU-------GCGAGGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUCGCUCGGA--------G
...((((.(((....)))(((.....)))...-------((((((((....((((.(((((..((......))..)))))...)))))))))))).))))--------. ( -39.20)
>DroSim_CAF1 61334 94 + 1
AUAUCCGCGAGACGUCUCGGGAUUGUCCCAUU-------GCGAGGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUCGCUCGGA--------G
...((((.(((....)))(((.....)))...-------((((((((....((((.(((((..((......))..)))))...)))))))))))).))))--------. ( -39.20)
>DroEre_CAF1 58986 94 + 1
AUAUCCGCGAGACGUCUCGGGAUUGUCCCAUU-------GCGAAGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUUACUUGGA--------G
...((((((((....)))(((.....)))...-------)).((((.....((((.(((((..((......))..)))))...))))......)))))))--------. ( -33.70)
>DroYak_CAF1 60331 102 + 1
AUAUCCGCGAGACGUCUCGGGAUUGUCCCAUU-------GCGAAGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCAGCUUAACUUGGAUGAACAGAG
.((((((((((....)))(((.....)))...-------)).(((((.((.((((.(((((..((......))..)))))...))))))...))))))))))....... ( -35.70)
>DroAna_CAF1 58210 89 + 1
AUAUCCCCAAGACGUCUCGGGAUUGUCUCUUUUUUUUGUGCACUGGGCCUAGAUCGAGUUGGCUCGAUAAAGGUGCAGCUGCAGU------------GGA--------A
...(((.(.(((((((....)).)))))..........(((((((.((((..((((((....))))))..)))).))).))))).------------)))--------. ( -32.20)
>consensus
AUAUCCGCGAGACGUCUCGGGAUUGUCCCAUU_______GCGAGGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUCGCUCGGA________G
...((((((((....)))(((.....)))..........))((((((....((((.(((((..((......))..)))))...))))))))))....)))......... (-25.61 = -26.95 +   1.34)

alignment

secondary structure

dotplot

Window 1

Location	13,618,738 – 13,618,832
Length	94
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	84.18
Mean single sequence MFE	-28.15
Consensus MFE	-21.49
Energy contribution	-21.38
Covariance contribution	-0.11
Combinations/Pair	1.09
Mean z-score	-1.57
Structure conservation index	0.76
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13618738 94 - 27905053
C--------UCCGAGCAAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACCUCGC-------AAUGGGACAAUCCCGAGACGUCUCGCGGAUAU
.--------..((((....((((((.(((....))).....))))))....))))...........((((-------...(((.....)))(((....))))))).... ( -27.80)
>DroSec_CAF1 67715 94 - 1
C--------UCCGAGCGAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACCUCGC-------AAUGGGACAAUCCCGAGACGUCUCGCGGAUAU
.--------..((((....((((((.(((....))).....))))))....))))...........((((-------...(((.....)))(((....))))))).... ( -27.80)
>DroSim_CAF1 61334 94 - 1
C--------UCCGAGCGAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACCUCGC-------AAUGGGACAAUCCCGAGACGUCUCGCGGAUAU
.--------..((((....((((((.(((....))).....))))))....))))...........((((-------...(((.....)))(((....))))))).... ( -27.80)
>DroEre_CAF1 58986 94 - 1
C--------UCCAAGUAAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACUUCGC-------AAUGGGACAAUCCCGAGACGUCUCGCGGAUAU
.--------(((.......((((((.(((....))).....)))))).(.....).....)))..(((((-------...(((.....)))(((....))))))))... ( -25.70)
>DroYak_CAF1 60331 102 - 1
CUCUGUUCAUCCAAGUUAAGCUGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACUUCGC-------AAUGGGACAAUCCCGAGACGUCUCGCGGAUAU
........(((((((((.(((((.....)))))...(((..(((((......)))))..)))))))).((-------...(((.....)))(((....))))))))).. ( -30.80)
>DroAna_CAF1 58210 89 - 1
U--------UCC------------ACUGCAGCUGCACCUUUAUCGAGCCAACUCGAUCUAGGCCCAGUGCACAAAAAAAAGAGACAAUCCCGAGACGUCUUGGGGAUAU
.--------...------------..((((.(((..(((..((((((....))))))..)))..)))))))................(((((((....))))))).... ( -29.00)
>consensus
C________UCCGAGCAAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACCUCGC_______AAUGGGACAAUCCCGAGACGUCUCGCGGAUAU
.........(((..............(((....)))(((..(((((......)))))..)))...................)))..((((((((....)))).)))).. (-21.49 = -21.38 +  -0.11)

alignment

secondary structure

dotplot

Window 2

Location	13,618,770 – 13,618,870
Length	100
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	78.97
Mean single sequence MFE	-35.70
Consensus MFE	-26.64
Energy contribution	-27.42
Covariance contribution	0.78
Combinations/Pair	1.30
Mean z-score	-2.19
Structure conservation index	0.75
SVM decision value	1.41
SVM RNA-class probability	0.951728
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13618770 100 + 27905053
GCGAGGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUUGCUCGGA--------G----GAGCUGAGGAGCA-AGGAGCAGGCGAGGAUAACGAUGGG
((...((((((.((((.(((((..((......))..)))))...)))).(((((((((...--------.----))))...))))).-))))))..))............... ( -37.70)
>DroSec_CAF1 67747 100 + 1
GCGAGGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUCGCUCGGA--------G----GAGCAGAGGAGCA-AGGAGCAGGCGAGGAUCACGAUGGG
((...((((((.((((.(((((..((......))..)))))...)))).(((((((((...--------.----))))...))))).-))))))..))............... ( -39.20)
>DroSim_CAF1 61366 100 + 1
GCGAGGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUCGCUCGGA--------G----GAGCAGAGGAGCA-AGGAGCAGGCGAGGAUCACGAUGGG
((...((((((.((((.(((((..((......))..)))))...)))).(((((((((...--------.----))))...))))).-))))))..))............... ( -39.20)
>DroEre_CAF1 59018 101 + 1
GCGAAGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUUACUUGGA--------G----GAGCAGAGGAGCAGAAGAGCAGGCGAAGAUCAGGAUGGG
((...((((((.((((.(((((..((......))..)))))...)))).(((((.......--------)----))))..))))))......))................... ( -30.60)
>DroYak_CAF1 60363 109 + 1
GCGAAGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCAGCUUAACUUGGAUGAACAGAG----AAGCAGAGGAGCAGAGUAGCAGGCGAGGAUCAGGAUGGG
((...((((((.((((.(((((..((......))..)))))...)))).((((...(((......)))..----))))..))))))......))................... ( -32.40)
>DroPer_CAF1 68609 90 + 1
-UGGAGCGCCCAGAUCCAGUGUGAGCGAUAAAGGUGCAGCUGCUG----GCU--GCCCAGA--------GAAUGGGGCGGGGGGGCA-GGGGGCAGGCAGGCAGCA-------
-....(((((...((((.......).)))...))))).(((((((----.((--((((...--------.......((......)).-..)))))).)).))))).------- ( -35.12)
>consensus
GCGAAGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUCGCUCGGA________G____GAGCAGAGGAGCA_AGGAGCAGGCGAGGAUCACGAUGGG
.((..((((((.((((.(((((((((......)))))))))...)))).(((((((((................))))...)))))..))))))...)).............. (-26.64 = -27.42 +   0.78)

alignment

secondary structure

dotplot

Window 3

Location	13,618,770 – 13,618,870
Length	100
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	78.97
Mean single sequence MFE	-23.67
Consensus MFE	-16.17
Energy contribution	-15.97
Covariance contribution	-0.19
Combinations/Pair	1.19
Mean z-score	-1.30
Structure conservation index	0.68
SVM decision value	0.26
SVM RNA-class probability	0.657554
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13618770 100 - 27905053
CCCAUCGUUAUCCUCGCCUGCUCCU-UGCUCCUCAGCUC----C--------UCCGAGCAAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACCUCGC
..........((((....(((((..-.(((....)))..----.--------...)))))..((((((.(((....))).....))))))............))))....... ( -21.60)
>DroSec_CAF1 67747 100 - 1
CCCAUCGUGAUCCUCGCCUGCUCCU-UGCUCCUCUGCUC----C--------UCCGAGCGAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACCUCGC
......((((.....((((((....-.(((..((.((((----.--------...)))))))))......))))..)).(((..(((((......)))))..)))....)))) ( -23.50)
>DroSim_CAF1 61366 100 - 1
CCCAUCGUGAUCCUCGCCUGCUCCU-UGCUCCUCUGCUC----C--------UCCGAGCGAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACCUCGC
......((((.....((((((....-.(((..((.((((----.--------...)))))))))......))))..)).(((..(((((......)))))..)))....)))) ( -23.50)
>DroEre_CAF1 59018 101 - 1
CCCAUCCUGAUCUUCGCCUGCUCUUCUGCUCCUCUGCUC----C--------UCCAAGUAAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACUUCGC
....((((((((......((((.....((......))..----.--------....))))..((((((.(((....))).....)))))).......)))).))))....... ( -22.60)
>DroYak_CAF1 60363 109 - 1
CCCAUCCUGAUCCUCGCCUGCUACUCUGCUCCUCUGCUU----CUCUGUUCAUCCAAGUUAAGCUGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACUUCGC
....((((((((...((((((....((((...((.((((----..((.........))..)))).))...))))..)))........))).......)))).))))....... ( -23.10)
>DroPer_CAF1 68609 90 - 1
-------UGCUGCCUGCCUGCCCCC-UGCCCCCCCGCCCCAUUC--------UCUGGGC--AGC----CAGCAGCUGCACCUUUAUCGCUCACACUGGAUCUGGGCGCUCCA-
-------.(((((.((.((((((..-..................--------...))))--)).----))))))).((.(((..(((.(.......))))..))).))....- ( -27.70)
>consensus
CCCAUCGUGAUCCUCGCCUGCUCCU_UGCUCCUCUGCUC____C________UCCGAGCAAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACCUCGC
...............((((((......(((.....((((................))))..)))......))))..)).(((..(((((......)))))..)))........ (-16.17 = -15.97 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:50 2006