Locus 4520

Sequence ID	2R_DroMel_CAF1
Location	14,814,229 – 14,814,589
Length	360
Max. P	0.999788

overview

Window 5

Location	14,814,229 – 14,814,349
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.83
Mean single sequence MFE	-48.02
Consensus MFE	-46.34
Energy contribution	-46.18
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-2.39
Structure conservation index	0.97
SVM decision value	4.08
SVM RNA-class probability	0.999788
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14814229 120 + 20766785
UCCCGCCAGCCGCAGCGGGAGCUAUGAGCAGCUGGAGCUGCUGGAUCACGCAACGCAUCCACAGCAACAACAGGAAGCCAGCAGUGGCAAGGCCAAGCCGAGCUGCCAUUGCACCAACAU
((((((........))))))((.(((.((((((((.((((((((.....((...)).(((............)))..))))))))(((...)))...)).))))))))).))........ ( -47.10)
>DroSec_CAF1 16076 120 + 1
UCCCGCCAGCCGCAGCGGGAGCUAUGAGCAGCUGGAGCUGUUGGAUCACGCAACGCAUCCACAGCAGCAACAGGAGGCCACCAGUGGCAAGGCCAAGCCUAGCUGUCAUUGCACCAACAU
((((((........))))))((.((((.(((((((.(((((((((((.......).)))))..)))))....((..((((....))))....))....))))))))))).))........ ( -48.70)
>DroSim_CAF1 10349 120 + 1
UCCCGCCAGCCGCAGCGGGAGCUAUGAGCAGCUGGAGCUGCUGGAUCACGCAACGCAUCCACAGCAGCAACAGGAGGCCACCAGUGGCAAGGCCAAGCCUAGCUGUCAUUGCACCAACAU
((((((........))))))((.((((.(((((((.(((((((......((...)).....)))))))....((..((((....))))....))....))))))))))).))........ ( -50.20)
>DroEre_CAF1 8953 120 + 1
UCCCGCCAGCCGCAGCGGGAGCUAUGAGCAGCUGGAGCUGCUGGAUCACGCAACGCAUCCACAGCAGGAACAGGAAGCCACCAGUGGCAAGGCCAAGCCGAGCUGUCAUUGCACCAACAU
((((((........))))))((.((((.(((((((.((((.((((((.......).))))))))).......((..((((....))))....))...)).))))))))).))........ ( -45.70)
>DroYak_CAF1 10223 120 + 1
UCCCGCUAGCCGCAGCGGGAGCUAUGAGCAGCUGGAGCUGCUGGAUCACGCAACGCAUCCACAGCAGGAACAGGAGGCCACCAGUGGCAAGGCCAAGCCGAGCUGUCAUUGCACCAACAU
(((((((......)))))))((.((((.(((((((.((((.((((((.......).))))))))).......((..((((....))))....))...)).))))))))).))........ ( -48.40)
>consensus
UCCCGCCAGCCGCAGCGGGAGCUAUGAGCAGCUGGAGCUGCUGGAUCACGCAACGCAUCCACAGCAGCAACAGGAGGCCACCAGUGGCAAGGCCAAGCCGAGCUGUCAUUGCACCAACAU
((((((........))))))((.(((.((((((((.((((.((((((.......).))))))))).......((..((((....))))....))...)).))))))))).))........ (-46.34 = -46.18 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	14,814,269 – 14,814,389
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-36.88
Consensus MFE	-34.98
Energy contribution	-34.94
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.67
Structure conservation index	0.95
SVM decision value	2.07
SVM RNA-class probability	0.987185
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14814269 120 + 20766785
CUGGAUCACGCAACGCAUCCACAGCAACAACAGGAAGCCAGCAGUGGCAAGGCCAAGCCGAGCUGCCAUUGCACCAACAUUAGUAUUAUGCACCUGUUUCAUGAGAUGAAGCAGGAGUUC
.........(((..((.(((............))).))..(((((((((.(((...)))....)))))))))................))).((((((((((...))))))))))..... ( -38.30)
>DroSec_CAF1 16116 120 + 1
UUGGAUCACGCAACGCAUCCACAGCAGCAACAGGAGGCCACCAGUGGCAAGGCCAAGCCUAGCUGUCAUUGCACCAACAUUAGUAUUAUGCACCUGUUUCAUGAGAUGAAACAGGAGUUC
.........(((..(((...(((((...........((((....)))).((((...)))).)))))...)))....((....))....))).((((((((((...))))))))))..... ( -36.50)
>DroSim_CAF1 10389 120 + 1
CUGGAUCACGCAACGCAUCCACAGCAGCAACAGGAGGCCACCAGUGGCAAGGCCAAGCCUAGCUGUCAUUGCACCAACAUUAGUAUUAUGCACCUGUUUCAUGAGAUGAAACAGGAGUUC
.........(((..(((...(((((...........((((....)))).((((...)))).)))))...)))....((....))....))).((((((((((...))))))))))..... ( -36.50)
>DroEre_CAF1 8993 120 + 1
CUGGAUCACGCAACGCAUCCACAGCAGGAACAGGAAGCCACCAGUGGCAAGGCCAAGCCGAGCUGUCAUUGCACCAACAUUAGUAUUAUGCACCUGUUUCAUGAGAUGAAGCAGGAGUUC
.........(((..(((...(((((.((....((..((((....))))....))...))..)))))...)))....((....))....))).((((((((((...))))))))))..... ( -36.00)
>DroYak_CAF1 10263 120 + 1
CUGGAUCACGCAACGCAUCCACAGCAGGAACAGGAGGCCACCAGUGGCAAGGCCAAGCCGAGCUGUCAUUGCACCAACAUUAGUAUUAUGCACCUGUUUCAUGAGAUGAAGCAGGAGUUC
.........(((..(((...(((((.((....((..((((....))))....))...))..)))))...)))....((....))....))).((((((((((...))))))))))..... ( -37.10)
>consensus
CUGGAUCACGCAACGCAUCCACAGCAGCAACAGGAGGCCACCAGUGGCAAGGCCAAGCCGAGCUGUCAUUGCACCAACAUUAGUAUUAUGCACCUGUUUCAUGAGAUGAAGCAGGAGUUC
.........(((..(((...(((((...........((((....))))..(((...)))..)))))...)))....((....))....))).((((((((((...))))))))))..... (-34.98 = -34.94 +  -0.04)

alignment

secondary structure

dotplot

Window 7

Location	14,814,309 – 14,814,429
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.17
Mean single sequence MFE	-39.62
Consensus MFE	-34.96
Energy contribution	-35.32
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-2.25
Structure conservation index	0.88
SVM decision value	2.49
SVM RNA-class probability	0.994509
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14814309 120 + 20766785
GCAGUGGCAAGGCCAAGCCGAGCUGCCAUUGCACCAACAUUAGUAUUAUGCACCUGUUUCAUGAGAUGAAGCAGGAGUUCCCCACGAUACCCGAUGCCAUAGUGACGCAAUGCGUCAAUG
(((((((((.(((...)))....))))))))).....((((.((((..(((.((((((((((...)))))))))).).....))..))))..))))......((((((...))))))... ( -41.90)
>DroSec_CAF1 16156 120 + 1
CCAGUGGCAAGGCCAAGCCUAGCUGUCAUUGCACCAACAUUAGUAUUAUGCACCUGUUUCAUGAGAUGAAACAGGAGUUCCCCACGAUACCGGAUGCCAUUGUGACGCAAUGCGUCAAUG
.((((((((((((...)))).(.((((..((((...((....))....))))((((((((((...))))))))))..........)))).)...))))))))((((((...))))))... ( -40.10)
>DroSim_CAF1 10429 120 + 1
CCAGUGGCAAGGCCAAGCCUAGCUGUCAUUGCACCAACAUUAGUAUUAUGCACCUGUUUCAUGAGAUGAAACAGGAGUUCCCCACGAUACCCGACGCCAUUGUGACGCAAUGCGUCAAUG
.(((((((.((((...))))....(((..((((...((....))....))))((((((((((...)))))))))).................))))))))))((((((...))))))... ( -40.10)
>DroEre_CAF1 9033 120 + 1
CCAGUGGCAAGGCCAAGCCGAGCUGUCAUUGCACCAACAUUAGUAUUAUGCACCUGUUUCAUGAGAUGAAGCAGGAGUUCCCCACGAUACCCGAUGCCAUAGUGACGCAAUGCGUCAAUG
...((((((.(((...)))(((((.....((((...((....))....))))((((((((((...)))))))))))))))..............))))))..((((((...))))))... ( -38.00)
>DroYak_CAF1 10303 120 + 1
CCAGUGGCAAGGCCAAGCCGAGCUGUCAUUGCACCAACAUUAGUAUUAUGCACCUGUUUCAUGAGAUGAAGCAGGAGUUCCCCACGAUACCCGAUGCCAUAGUGACGCAAUGCGUCAAUG
...((((((.(((...)))(((((.....((((...((....))....))))((((((((((...)))))))))))))))..............))))))..((((((...))))))... ( -38.00)
>consensus
CCAGUGGCAAGGCCAAGCCGAGCUGUCAUUGCACCAACAUUAGUAUUAUGCACCUGUUUCAUGAGAUGAAGCAGGAGUUCCCCACGAUACCCGAUGCCAUAGUGACGCAAUGCGUCAAUG
...((((((.(((...)))(((((.....((((...((....))....))))((((((((((...)))))))))))))))..............))))))..((((((...))))))... (-34.96 = -35.32 +   0.36)

alignment

secondary structure

dotplot

Window 8

Location	14,814,429 – 14,814,549
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-38.12
Consensus MFE	-34.80
Energy contribution	-34.60
Covariance contribution	-0.20
Combinations/Pair	1.06
Mean z-score	-2.01
Structure conservation index	0.91
SVM decision value	2.60
SVM RNA-class probability	0.995658
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14814429 120 + 20766785
AGAAUUGCCAUCAGCGCGAAAACUGUAUCCAGAUGUUGAGGAAGGAGCUCGCGCUUCAUCCUAUCCCAGUGCAGAGCUAUCCGGCAAAGGUGCUGCAGCAACAGCAGCAGCAACACCACC
....(((((.((((((......(((....))).))))))(((...((((((((((............))))).))))).)))))))).((((((((.((....)).)))))...)))... ( -40.40)
>DroSec_CAF1 16276 120 + 1
AGAAUUGCCAUCAGCGCGAAAACUGUAUCCAGAUGUUGAGGAAGGAGCUCGCGCUCCAUCCCAUCCCAGUUCAAAGUUAUCCGGCAAAGGUGCUGCAGCAACAGCAGCAACAACACCACC
....(((((.((((((......(((....))).))))))(((.(((((....))))).))).....................))))).(.((((((.......)))))).)......... ( -33.60)
>DroSim_CAF1 10549 120 + 1
AGAAUUGCCAUCAGCGCGAAAACUGUAUCCAGAUGUUGAGGAAGGAGCUCGCGCUCCAUCCCAUCCCAGUUCAAAGUUAUCCGGCAAAGGUGCUGCAGCAACAGCAGCAGCAACACCACC
....(((((.((((((......(((....))).))))))(((.(((((....))))).))).....................))))).((((((((.((....)).)))))...)))... ( -37.00)
>DroEre_CAF1 9153 120 + 1
AGAAUUGCCAUCAGCGCGAAAACUGUAUCCAGAUGUUGAGGAAGGAGCUUGCGCUCCAUCCCAUCCCAGUUCAAAGUUAUCCGGCGAAGGUGUUGCAGCAACAGCAGCAGCAACACCACC
....(((((.((((((......(((....))).))))))(((.(((((....))))).))).....................))))).((((((((.((.......)).))))))))... ( -39.80)
>DroYak_CAF1 10423 120 + 1
AGAAUUGCCAUCAGCGCGAAAACUGUAUCCAGAUGUUGAGGAAGGAGCUCGCGCUCCAUCCCAUCCCAGUUCAAAGUUAUCCGGCGAAGGUGUUGCAGCAACAGCAGCAGCAACACCACC
....(((((.((((((......(((....))).))))))(((.(((((....))))).))).....................))))).((((((((.((.......)).))))))))... ( -39.80)
>consensus
AGAAUUGCCAUCAGCGCGAAAACUGUAUCCAGAUGUUGAGGAAGGAGCUCGCGCUCCAUCCCAUCCCAGUUCAAAGUUAUCCGGCAAAGGUGCUGCAGCAACAGCAGCAGCAACACCACC
....(((((.((((((......(((....))).))))))(((.(((((....))))).))).....................))))).((((.(((.((.......)).))).))))... (-34.80 = -34.60 +  -0.20)

alignment

secondary structure

dotplot

Window 9

Location	14,814,429 – 14,814,549
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.67
Mean single sequence MFE	-46.74
Consensus MFE	-44.27
Energy contribution	-44.47
Covariance contribution	0.20
Combinations/Pair	1.06
Mean z-score	-2.37
Structure conservation index	0.95
SVM decision value	3.88
SVM RNA-class probability	0.999681
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14814429 120 - 20766785
GGUGGUGUUGCUGCUGCUGUUGCUGCAGCACCUUUGCCGGAUAGCUCUGCACUGGGAUAGGAUGAAGCGCGAGCUCCUUCCUCAACAUCUGGAUACAGUUUUCGCGCUGAUGGCAAUUCU
...((((((((.((.......)).)))))))).((((((..((((...((..((((..((((....((....))))))..))))....(((....))).....)))))).)))))).... ( -42.50)
>DroSec_CAF1 16276 120 - 1
GGUGGUGUUGUUGCUGCUGUUGCUGCAGCACCUUUGCCGGAUAACUUUGAACUGGGAUGGGAUGGAGCGCGAGCUCCUUCCUCAACAUCUGGAUACAGUUUUCGCGCUGAUGGCAAUUCU
...((((((((.((.......)).)))))))).((((((.........((((((((((((((.(((((....))))).)))....))))).....)))))).........)))))).... ( -46.67)
>DroSim_CAF1 10549 120 - 1
GGUGGUGUUGCUGCUGCUGUUGCUGCAGCACCUUUGCCGGAUAACUUUGAACUGGGAUGGGAUGGAGCGCGAGCUCCUUCCUCAACAUCUGGAUACAGUUUUCGCGCUGAUGGCAAUUCU
...((((((((.((.......)).)))))))).((((((.........((((((((((((((.(((((....))))).)))....))))).....)))))).........)))))).... ( -48.27)
>DroEre_CAF1 9153 120 - 1
GGUGGUGUUGCUGCUGCUGUUGCUGCAACACCUUCGCCGGAUAACUUUGAACUGGGAUGGGAUGGAGCGCAAGCUCCUUCCUCAACAUCUGGAUACAGUUUUCGCGCUGAUGGCAAUUCU
((.((((((((.((.......)).)))))))).))((((.........((((((((((((((.(((((....))))).)))....))))).....)))))).........))))...... ( -48.37)
>DroYak_CAF1 10423 120 - 1
GGUGGUGUUGCUGCUGCUGUUGCUGCAACACCUUCGCCGGAUAACUUUGAACUGGGAUGGGAUGGAGCGCGAGCUCCUUCCUCAACAUCUGGAUACAGUUUUCGCGCUGAUGGCAAUUCU
((.((((((((.((.......)).)))))))).))((((.........((((((((((((((.(((((....))))).)))....))))).....)))))).........))))...... ( -47.87)
>consensus
GGUGGUGUUGCUGCUGCUGUUGCUGCAGCACCUUUGCCGGAUAACUUUGAACUGGGAUGGGAUGGAGCGCGAGCUCCUUCCUCAACAUCUGGAUACAGUUUUCGCGCUGAUGGCAAUUCU
...((((((((.((.......)).))))))))...((((.........((((((((((((((.(((((....))))).)))....))))).....)))))).........))))...... (-44.27 = -44.47 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	14,814,469 – 14,814,589
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.83
Mean single sequence MFE	-38.66
Consensus MFE	-33.58
Energy contribution	-33.34
Covariance contribution	-0.24
Combinations/Pair	1.14
Mean z-score	-1.96
Structure conservation index	0.87
SVM decision value	2.10
SVM RNA-class probability	0.987967
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14814469 120 + 20766785
GAAGGAGCUCGCGCUUCAUCCUAUCCCAGUGCAGAGCUAUCCGGCAAAGGUGCUGCAGCAACAGCAGCAGCAACACCACCAGAAUAGGCAGGCCAAGCCUCCCACGCCGCUCAAGCCGUC
...((((((((((((............))))).)))))...((((...((((((((.((....)).)))))...))).........((.((((...)))).))..))))......))... ( -41.20)
>DroSec_CAF1 16316 120 + 1
GAAGGAGCUCGCGCUCCAUCCCAUCCCAGUUCAAAGUUAUCCGGCAAAGGUGCUGCAGCAACAGCAGCAACAACACCACCAGAAUAGGCAGGCCAAGCCUCCCACGCCGCUCAAGCCGUC
((.(((((....))))).)).....................((((...(.((((((.......)))))).)..........((...(((((((...)))).....)))..))..)))).. ( -33.60)
>DroSim_CAF1 10589 120 + 1
GAAGGAGCUCGCGCUCCAUCCCAUCCCAGUUCAAAGUUAUCCGGCAAAGGUGCUGCAGCAACAGCAGCAGCAACACCACCAGAAUAGGCAGGCCAAGCCUCCCACGCCGCUCAAGCCGUC
((.(((((....))))).)).....................((((...((((((((.((....)).)))))...)))....((...(((((((...)))).....)))..))..)))).. ( -37.00)
>DroEre_CAF1 9193 120 + 1
GAAGGAGCUUGCGCUCCAUCCCAUCCCAGUUCAAAGUUAUCCGGCGAAGGUGUUGCAGCAACAGCAGCAGCAACACCACCAGAACAGGCAGGCCAAGCCUCCUACGCCCCUUAAGCCGUC
((.(((((....))))).)).....................((((...((((((((.((.......)).))))))))........(((.((((...)))))))...........)))).. ( -40.00)
>DroYak_CAF1 10463 120 + 1
GAAGGAGCUCGCGCUCCAUCCCAUCCCAGUUCAAAGUUAUCCGGCGAAGGUGUUGCAGCAACAGCAGCAGCAACACCACCAGAACAGGCAGGCCAAGCCUCCCACGCCGCUCAAACCGUC
((.(((((....))))).)).....................(((((..((((((((.((.......)).)))))))).........((.((((...)))).)).)))))........... ( -41.50)
>consensus
GAAGGAGCUCGCGCUCCAUCCCAUCCCAGUUCAAAGUUAUCCGGCAAAGGUGCUGCAGCAACAGCAGCAGCAACACCACCAGAAUAGGCAGGCCAAGCCUCCCACGCCGCUCAAGCCGUC
((.(((((....))))).))...............(((...((((...((((.(((.((.......)).))).)))).........((.((((...)))).))..))))....))).... (-33.58 = -33.34 +  -0.24)

alignment

secondary structure

dotplot

Window 1

Location	14,814,469 – 14,814,589
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.83
Mean single sequence MFE	-50.44
Consensus MFE	-48.26
Energy contribution	-47.38
Covariance contribution	-0.88
Combinations/Pair	1.19
Mean z-score	-1.47
Structure conservation index	0.96
SVM decision value	1.71
SVM RNA-class probability	0.973547
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14814469 120 - 20766785
GACGGCUUGAGCGGCGUGGGAGGCUUGGCCUGCCUAUUCUGGUGGUGUUGCUGCUGCUGUUGCUGCAGCACCUUUGCCGGAUAGCUCUGCACUGGGAUAGGAUGAAGCGCGAGCUCCUUC
.(((.(......).)))(((((.((((((...(((((((..((((((((((.((.......)).))))))))...((.(((....)))))))..))))))).....)).))))))))).. ( -49.40)
>DroSec_CAF1 16316 120 - 1
GACGGCUUGAGCGGCGUGGGAGGCUUGGCCUGCCUAUUCUGGUGGUGUUGUUGCUGCUGUUGCUGCAGCACCUUUGCCGGAUAACUUUGAACUGGGAUGGGAUGGAGCGCGAGCUCCUUC
...((((.((((..(....)..))))))))..(((((((..((((((((((.((.......)).)))))))).....((((....)))).))..)))))))..(((((....)))))... ( -48.80)
>DroSim_CAF1 10589 120 - 1
GACGGCUUGAGCGGCGUGGGAGGCUUGGCCUGCCUAUUCUGGUGGUGUUGCUGCUGCUGUUGCUGCAGCACCUUUGCCGGAUAACUUUGAACUGGGAUGGGAUGGAGCGCGAGCUCCUUC
...((((.((((..(....)..))))))))..(((((((..((((((((((.((.......)).)))))))).....((((....)))).))..)))))))..(((((....)))))... ( -50.40)
>DroEre_CAF1 9193 120 - 1
GACGGCUUAAGGGGCGUAGGAGGCUUGGCCUGCCUGUUCUGGUGGUGUUGCUGCUGCUGUUGCUGCAACACCUUCGCCGGAUAACUUUGAACUGGGAUGGGAUGGAGCGCAAGCUCCUUC
..(((.((((((....((((((((...)))).)))).((((((((((((((.((.......)).))))))))...))))))...)))))).)))......((.(((((....))))).)) ( -51.40)
>DroYak_CAF1 10463 120 - 1
GACGGUUUGAGCGGCGUGGGAGGCUUGGCCUGCCUGUUCUGGUGGUGUUGCUGCUGCUGUUGCUGCAACACCUUCGCCGGAUAACUUUGAACUGGGAUGGGAUGGAGCGCGAGCUCCUUC
..(((((..((.((((.((.((((...)))).)))))((((((((((((((.((.......)).))))))))...))))))...)))..)))))......((.(((((....))))).)) ( -52.20)
>consensus
GACGGCUUGAGCGGCGUGGGAGGCUUGGCCUGCCUAUUCUGGUGGUGUUGCUGCUGCUGUUGCUGCAGCACCUUUGCCGGAUAACUUUGAACUGGGAUGGGAUGGAGCGCGAGCUCCUUC
...((((.((((..(....)..))))))))..(((((((..((((((((((.((.......)).)))))))).....((((....)))).))..)))))))..(((((....)))))... (-48.26 = -47.38 +  -0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:08 2006