Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005023.1 Hibiscus syriacus cultivar Beakdansim tig00011273_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 46824
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2496 original size:215 final size:214
Alignment explanation
Indices: 2131--2610 Score: 524
Period size: 213 Copynumber: 2.2 Consensus size: 214
2121 TTAGATCAAC
* * * *
2131 CCGATTTCCTCAACGAGAAGGAACAACGTCATCTGC-AACAAATAATTTTACCTGAAGGTGACCA
1 CCGATTTCCTCAACGAGAAAGAACAACGTCATCT-CTAGCAAACAA-TTTACCTGAAGGCGACCA
* * * *
2195 CCTCTTAACACGGATAAGCAGCGTCATCTTTAACACCAAATTATCTCTAGATTGACCCGATCTCC
64 CATCTTAACACAGATAAGCAGCGTCATCTTCAACACCAAATTATCTCTAGATTAACCCGATCTCC
* * * * *
2260 TCAACACTAAGGAGAAGTGTCATTCTCAGATAACCAGACTTCCTCAACGCGAATGAA-CCGAATT
129 TCAACACGAAGCAGAAGTGTCATCCTCAG-T-ACCAGACTTCCTAAACGCGAAGGAATCC-AATT
2324 GTCTCCAAATTATCTCCAGATTGA
191 GTCTCCAAATTATCTCCAGATTGA
* * *
2348 CCTGATTTCCTCAACGAGAAAGAACAACATCATCTCTAGTAAACAATTTACCT-AA-GCG-CCAT
1 CC-GATTTCCTCAACGAGAAAGAACAACGTCATCTCTAGCAAACAATTTACCTGAAGGCGACCAC
* * * * *
2410 ATCTTTAACACAGATGAGTAGTGTCATCTTCAACACCAAATTAT-TTTCAGATTAACCTGATCTC
65 ATC-TTAACACAGATAAGCAGCGTCATCTTCAACACCAAATTATCTCT-AGATTAACCCGATCTC
* * ** * * *
2474 CTCAACGCGAAGCAGCAGTGTCATCCTCAGTATTAGGCTTCCTAAACGCGAAGGAATTCTATTGT
128 CTCAACACGAAGCAGAAGTGTCATCCTCAGTACCAGACTTCCTAAACGCGAAGGAATCCAATTGT
* *
2539 CACCAAATTATTTCCAGATTGA
193 CTCCAAATTATCTCCAGATTGA
* * *
2561 CACAACTTCTTCAACGAG-AAGAAGCAACGTCATCTCTAGCAAACAATTTA
1 C-CGATTTCCTCAACGAGAAAGAA-CAACGTCATCTCTAGCAAACAATTTA
2611 TTTCAAAATA
Statistics
Matches: 221, Mismatches: 35, Indels: 18
0.81 0.13 0.07
Matches are distributed among these distances:
212 5 0.02
213 82 0.37
214 10 0.05
215 76 0.34
216 2 0.01
217 10 0.05
218 36 0.16
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (214 bp):
CCGATTTCCTCAACGAGAAAGAACAACGTCATCTCTAGCAAACAATTTACCTGAAGGCGACCACA
TCTTAACACAGATAAGCAGCGTCATCTTCAACACCAAATTATCTCTAGATTAACCCGATCTCCTC
AACACGAAGCAGAAGTGTCATCCTCAGTACCAGACTTCCTAAACGCGAAGGAATCCAATTGTCTC
CAAATTATCTCCAGATTGA
Found at i:8835 original size:44 final size:44
Alignment explanation
Indices: 8783--8878 Score: 165
Period size: 44 Copynumber: 2.2 Consensus size: 44
8773 ACAATATAAA
8783 CAAAAGATAAAGAAATTAAAAATAAAGTATGATAATCAAGAAAT
1 CAAAAGATAAAGAAATTAAAAATAAAGTATGATAATCAAGAAAT
* * *
8827 GAAAAGATAAATAACTTAAAAATAAAGTATGATAATCAAGAAAT
1 CAAAAGATAAAGAAATTAAAAATAAAGTATGATAATCAAGAAAT
8871 CAAAAGAT
1 CAAAAGAT
8879 CTTCCTTGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.21
Consensus pattern (44 bp):
CAAAAGATAAAGAAATTAAAAATAAAGTATGATAATCAAGAAAT
Found at i:8840 original size:23 final size:23
Alignment explanation
Indices: 8802--8878 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 23
8792 AAGAAATTAA
*
8802 AAAT-AAAG-TATGATAATCAAG
1 AAATAAAAGATATAATAATCAAG
*
8823 AAATGAAAAGATA-AATAACTTAA-
1 AAAT-AAAAGATATAATAA-TCAAG
*
8846 AAAT-AAAG-TATGATAATCAAG
1 AAATAAAAGATATAATAATCAAG
8867 AAATCAAAAGAT
1 AAAT-AAAAGAT
8879 CTTCCTTGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 15
0.69 0.06 0.24
Matches are distributed among these distances:
20 5 0.12
21 16 0.37
23 16 0.37
24 6 0.14
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.22
Consensus pattern (23 bp):
AAATAAAAGATATAATAATCAAG
Found at i:8870 original size:21 final size:21
Alignment explanation
Indices: 8802--8870 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
8792 AAGAAATTAA
8802 AAATAAAGTATGATAATCAAG
1 AAATAAAGTATGATAATCAAG
* *
8823 AAATGAAAAG-ATAAATAACTTAA-
1 AAAT--AAAGTAT-GATAA-TCAAG
8846 AAATAAAGTATGATAATCAAG
1 AAATAAAGTATGATAATCAAG
8867 AAAT
1 AAAT
8871 CAAAAGATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
20 3 0.08
21 16 0.42
22 4 0.11
23 12 0.32
24 3 0.08
ACGTcount: A:0.61, C:0.04, G:0.12, T:0.23
Consensus pattern (21 bp):
AAATAAAGTATGATAATCAAG
Found at i:9812 original size:5 final size:5
Alignment explanation
Indices: 9793--9832 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
9783 TTTTCACCTC
* *
9793 TTTTCA TTTTA TTTTG TTTTA TTTTA GTTTA TTTTA TTTT
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
9833 TGTGGAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:12438 original size:24 final size:25
Alignment explanation
Indices: 12411--12504 Score: 91
Period size: 26 Copynumber: 3.6 Consensus size: 25
12401 AAAACTATAA
12411 ATATAAACTATATAATTTATA-TAT
1 ATATAAACTATATAATTTATAGTAT
* *
12435 ATATAAACTATATAGTTTATATAATTAT
1 ATATAAACTATATA-ATT-TAT-AGTAT
* *
12463 ATTAATAAACTATATAGTTCATTAGTAT
1 A-T-ATAAACTATATAATTTA-TAGTAT
12491 ATATAAACTATATA
1 ATATAAACTATATA
12505 TACTATATAG
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
24 14 0.24
25 2 0.03
26 15 0.25
27 2 0.03
28 10 0.17
29 4 0.07
30 12 0.20
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (25 bp):
ATATAAACTATATAATTTATAGTAT
Found at i:12457 original size:26 final size:27
Alignment explanation
Indices: 12411--12504 Score: 106
Period size: 30 Copynumber: 3.5 Consensus size: 27
12401 AAAACTATAA
*
12411 ATATAAACTATATA-ATT-TATA-TAT
1 ATATAAACTATATAGTTTATATAGTAT
*
12435 ATATAAACTATATAGTTTATATAATTAT
1 ATATAAACTATATAGTTTATAT-AGTAT
*
12463 ATTAATAAACTATATAGTTCAT-TAGTAT
1 A-T-ATAAACTATATAGTTTATATAGTAT
12491 ATATAAACTATATA
1 ATATAAACTATATA
12505 TACTATATAG
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
24 14 0.23
25 2 0.03
26 15 0.25
27 2 0.03
28 9 0.15
29 2 0.03
30 17 0.28
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (27 bp):
ATATAAACTATATAGTTTATATAGTAT
Found at i:12458 original size:56 final size:56
Alignment explanation
Indices: 12398--12504 Score: 139
Period size: 54 Copynumber: 1.9 Consensus size: 56
12388 GTATACAATA
* *
12398 TATAAAACTATAA-ATATAAACTATATAATTTA-TA-TATATATAAACTATATAGTT
1 TATATAACTATAATA-ATAAACTATATAATTCATTAGTATATATAAACTATATAGTT
* * *
12452 TATATAATTATATTAATAAACTATATAGTTCATTAGTATATATAAACTATATA
1 TATATAACTATAATAATAAACTATATAATTCATTAGTATATATAAACTATATA
12505 TACTATATAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
54 25 0.56
55 3 0.07
56 17 0.38
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (56 bp):
TATATAACTATAATAATAAACTATATAATTCATTAGTATATATAAACTATATAGTT
Found at i:12493 original size:2 final size:2
Alignment explanation
Indices: 12488--12665 Score: 73
Period size: 2 Copynumber: 86.0 Consensus size: 2
12478 AGTTCATTAG
* * *
12488 TA TA TA TA AA CTA TA TA TA CTA TA TA GTT TA CA TA TA TA CTA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA
* * *
12532 TA TA TA TA TA TA TA GTT TA T- TA -A TGA -A CTA TA TA AA GTA TT
1 TA TA TA TA TA TA TA -TA TA TA TA TA T-A TA -TA TA TA TA -TA TA
* * * *
12573 TA TA T- TG TA TG TA CTA TA TA TA TA TA AA CTA TA TA AA T- TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
12615 GTT TA TA TT TA TA TA T- TA TA T- TA TA TA TA TA TA AA CTA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
12657 TA CTA TA TA
1 TA -TA TA TA
12666 ACTTACATAT
Statistics
Matches: 131, Mismatches: 25, Indels: 40
0.67 0.13 0.20
Matches are distributed among these distances:
1 7 0.05
2 107 0.82
3 17 0.13
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12516 original size:35 final size:34
Alignment explanation
Indices: 12433--12553 Score: 105
Period size: 30 Copynumber: 3.7 Consensus size: 34
12423 TAATTTATAT
* *
12433 ATATATAAACTATATAGTTTA-TATA-AT--TAT
1 ATATATATACTATATAGTTTATTATATATACTAA
* *
12463 AT-TAATAAACTATATAGTTCATTAGTATATA-TAA
1 ATAT-ATATACTATATAGTTTATTA-TATATACTAA
* *
12497 ACTATATATACTATATAGTTTA-CATATATACTAT
1 A-TATATATACTATATAGTTTATTATATATACTAA
12531 ATATATATA-TATATAGTTTATTA
1 ATATATATACTATATAGTTTATTA
12554 ATGAACTATA
Statistics
Matches: 75, Mismatches: 7, Indels: 15
0.77 0.07 0.15
Matches are distributed among these distances:
29 1 0.01
30 18 0.24
31 2 0.03
32 13 0.17
33 17 0.23
34 7 0.09
35 16 0.21
36 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (34 bp):
ATATATATACTATATAGTTTATTATATATACTAA
Found at i:12628 original size:33 final size:34
Alignment explanation
Indices: 12488--12630 Score: 100
Period size: 33 Copynumber: 4.2 Consensus size: 34
12478 AGTTCATTAG
*
12488 TATATATAAACTATATATACTATATAGTTTAC-ATA
1 TATATATAAACTATATA-AAT-TATAGTTTACTATA
* * *
12523 TATACTATATA-TATATATA-TATAGTTTATTA-A
1 TATA-TATAAACTATATAAATTATAGTTTACTATA
* * * * *
12555 TGAACTATATAAAGTATTTATATTGTA-TGTACTATA
1 T--A-TATATAAACTATATAAATTATAGTTTACTATA
*
12591 TATATATAAACTATATAAATTATAGTTTA-TATT
1 TATATATAAACTATATAAATTATAGTTTACTATA
12624 TATATAT
1 TATATAT
12631 TATATTATAT
Statistics
Matches: 84, Mismatches: 15, Indels: 20
0.71 0.13 0.17
Matches are distributed among these distances:
32 11 0.13
33 29 0.35
34 10 0.12
35 24 0.29
36 10 0.12
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (34 bp):
TATATATAAACTATATAAATTATAGTTTACTATA
Found at i:12711 original size:27 final size:27
Alignment explanation
Indices: 12681--12733 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
12671 CATATGAACT
*
12681 ATATATAAAAACTATATATTATAGTTG
1 ATATATAAAAACTATATAATATAGTTG
* * *
12708 ATATTTATATACTATATAATATAGTT
1 ATATATAAAAACTATATAATATAGTT
12734 TATACTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (27 bp):
ATATATAAAAACTATATAATATAGTTG
Found at i:12742 original size:27 final size:27
Alignment explanation
Indices: 12691--12745 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
12681 ATATATAAAA
* *
12691 ACTATATATTATAGTTGATATTTATAT
1 ACTATATAATATAGTTGATACTTATAT
*
12718 ACTATATAATATAGTTTATACTTATAT
1 ACTATATAATATAGTTGATACTTATAT
12745 A
1 A
12746 ATTTATACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (27 bp):
ACTATATAATATAGTTGATACTTATAT
Found at i:12752 original size:27 final size:27
Alignment explanation
Indices: 12693--12757 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
12683 ATATAAAAAC
* * *
12693 TATATATTATAGTTGATATTTATATAC
1 TATATAATATAGTTGATACTTATATAA
*
12720 TATATAATATAGTTTATACTTATATAA
1 TATATAATATAGTTGATACTTATATAA
* *
12747 TTTATACTATA
1 TATATAATATA
12758 TAAATTCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (27 bp):
TATATAATATAGTTGATACTTATATAA
Found at i:12763 original size:15 final size:15
Alignment explanation
Indices: 12726--12760 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12716 ATACTATATA
*
12726 ATATAGTTTATACTT
1 ATATAATTTATACTT
12741 ATATAATTTATAC-T
1 ATATAATTTATACTT
12755 ATATAA
1 ATATAA
12761 ATTCAAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (15 bp):
ATATAATTTATACTT
Found at i:12875 original size:29 final size:29
Alignment explanation
Indices: 12814--12898 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
12804 ACATTAATTA
*
12814 ATAAACTATTTATATAATATATACTGCATAT
1 ATAAACTA--TATATAATATATACTGCACAT
* **
12845 ATAAACTATATATAATATATATTTTACAT
1 ATAAACTATATATAATATATACTGCACAT
* *
12874 ATGAACTATAGTTTATATATATACT
1 ATAAACTATA-TATA-ATATATACT
12899 ATATACTATA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
29 26 0.58
30 3 0.07
31 16 0.36
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (29 bp):
ATAAACTATATATAATATATACTGCACAT
Found at i:12890 original size:25 final size:24
Alignment explanation
Indices: 12862--12918 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
12852 ATATATAATA
12862 TATATTTTAC-ATATGAACTATAGTT
1 TATATTTTACTATAT--ACTATAGTT
*
12887 TATATATATACTATATACTATAGTT
1 TATAT-TTTACTATATACTATAGTT
*
12912 GATATTT
1 TATATTT
12919 ATATACTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 1 0.04
25 18 0.67
26 4 0.15
27 4 0.15
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (24 bp):
TATATTTTACTATATACTATAGTT
Found at i:12902 original size:27 final size:26
Alignment explanation
Indices: 12878--13078 Score: 136
Period size: 25 Copynumber: 7.8 Consensus size: 26
12868 TTACATATGA
12878 ACTATAGTT-TATATATATACTATAT
1 ACTATAGTTATATATATATACTATAT
*
12903 ACTATAGTTGATATTTATATACTATAT
1 ACTATAGTT-ATATATATATACTATAT
* *
12930 A-T-TA-TTATGTATATAAACTATAT
1 ACTATAGTTATATATATATACTATAT
* *
12953 ATTATTTAGTT-TACATATGAATTA-TATAT
1 ACTA--TAGTTATATATAT--A-TACTATAT
* * *
12982 A-AAAACTATATATATATATA-TATAT
1 ACTATAGT-TATATATATATACTATAT
13007 ACTATAGGTTATATATA-A-ACTATAT
1 ACTATA-GTTATATATATATACTATAT
*
13032 ACTATAGTTGATATTTATATACTATAT
1 ACTATAGTT-ATATATATATACTATAT
* *
13059 AATATAATT-TATACTATATA
1 ACTATAGTTATATA-TATATA
13079 AATTCAAAGT
Statistics
Matches: 139, Mismatches: 18, Indels: 37
0.72 0.09 0.19
Matches are distributed among these distances:
23 15 0.11
24 7 0.05
25 40 0.29
26 21 0.15
27 39 0.28
28 9 0.06
29 7 0.05
30 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (26 bp):
ACTATAGTTATATATATATACTATAT
Found at i:12921 original size:25 final size:27
Alignment explanation
Indices: 12878--13064 Score: 75
Period size: 27 Copynumber: 7.2 Consensus size: 27
12868 TTACATATGA
*
12878 ACTATAGTTTATA-T-ATATACTATAT
1 ACTATAGTTGATATTAATATACTATAT
*
12903 ACTATAGTTGATATTTATATACTATAT
1 ACTATAGTTGATATTAATATACTATAT
* *
12930 A-T-TATTATGTATATAAACTATA-TAT-T
1 ACTATAGT-TG-ATATTAA-TATACTATAT
* * * *
12956 A-TTTAGTTTACATATGAATTATA-TATAAAA
1 ACTATAG-TT-GATATTAA-TATACTAT--AT
12986 ACTATA--T-ATA-T-ATATA-TATAT
1 ACTATAGTTGATATTAATATACTATAT
*
13007 ACTATAGGTT-ATA-T-ATAAACTATAT
1 ACTATA-GTTGATATTAATATACTATAT
*
13032 ACTATAGTTGATATTTATATACTATAT
1 ACTATAGTTGATATTAATATACTATAT
*
13059 AATATA
1 ACTATA
13065 ATTTATACTA
Statistics
Matches: 128, Mismatches: 15, Indels: 36
0.72 0.08 0.20
Matches are distributed among these distances:
21 7 0.05
23 7 0.05
24 13 0.10
25 29 0.23
26 11 0.09
27 51 0.40
28 6 0.05
30 1 0.01
31 3 0.02
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (27 bp):
ACTATAGTTGATATTAATATACTATAT
Found at i:13031 original size:52 final size:51
Alignment explanation
Indices: 12887--13032 Score: 118
Period size: 52 Copynumber: 2.8 Consensus size: 51
12877 AACTATAGTT
* * ** *
12887 TATATATATACTATATACTATA-GTTGATATTTATATACTATATATTATTATGTA
1 TATATATATA-TATATACTATAGGTT-ATA--TATAAACTATATATAAAAATATA
* * * * * *
12941 TATAAACTATATAT-TA-TTTAGTTTACATATGAATTATATATAAAAACTATA
1 TATATA-TATATATATACTATAGGTTATATATAAACTATATATAAAAA-TATA
12992 TATATATATATATATACTATAGGTTATATATAAACTATATA
1 TATATATATATATATACTATAGGTTATATATAAACTATATA
13033 CTATAGTTGA
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
50 20 0.29
51 10 0.14
52 24 0.34
53 4 0.06
54 8 0.11
55 4 0.06
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (51 bp):
TATATATATATATATACTATAGGTTATATATAAACTATATATAAAAATATA
Found at i:13093 original size:2 final size:2
Alignment explanation
Indices: 12887--13078 Score: 53
Period size: 2 Copynumber: 93.0 Consensus size: 2
12877 AACTATAGTT
*
12887 TA TA TA TA TA CTA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA
1 TA TA TA TA TA -TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA
* * * * *
12931 T- TA T- TA TG TA TA TA AA CTA TA TA T- TA TT TA GTT TA CA TA TGA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA T-A
* * **
12973 -A T- TA TA TA TA AA AA CTA TA TA TA TA TA TA TA TA TA CTA TA GG
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
13015 T- TA TA TA TA AA CTA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA
*
13058 TA -A TA TA -A TT TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA
13079 AATTCAAAGT
Statistics
Matches: 141, Mismatches: 23, Indels: 52
0.65 0.11 0.24
Matches are distributed among these distances:
1 10 0.07
2 108 0.77
3 23 0.16
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:13183 original size:20 final size:20
Alignment explanation
Indices: 13150--13232 Score: 55
Period size: 20 Copynumber: 4.0 Consensus size: 20
13140 ATTTATATAG
13150 TATATACTAAATATATAAACTA
1 TATATACT--ATATATAAACTA
**
13172 TATATACTATATAATTTAC-A
1 TATATACTATAT-ATAAACTA
*
13192 TATGA-ACTATATATAAA-AA
1 TAT-ATACTATATATAAACTA
**
13211 GTATATTTTATATATAAACTA
1 -TATATACTATATATAAACTA
13232 T
1 T
13233 CTACTATATT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
19 5 0.10
20 29 0.60
21 6 0.12
22 8 0.17
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (20 bp):
TATATACTATATATAAACTA
Found at i:14065 original size:16 final size:16
Alignment explanation
Indices: 14046--14093 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
14036 TATATAGTAA
14046 ATACTAATTATATAAT
1 ATACTAATTATATAAT
* *
14062 ATAC--ACTATGTAAT
1 ATACTAATTATATAAT
*
14076 ATACTAATTATTTAAT
1 ATACTAATTATATAAT
14092 AT
1 AT
14094 CAAATACAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.46
16 14 0.54
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (16 bp):
ATACTAATTATATAAT
Found at i:14261 original size:18 final size:18
Alignment explanation
Indices: 14211--14278 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
14201 TAGCAAAAAT
* * *
14211 TATACACTATATGATATAT
1 TATATACTATATG-CATAC
14230 TATATATCTAATATGCCA-AC
1 TATATA-CT-ATATG-CATAC
14250 TATATACTATATGCATAC
1 TATATACTATATGCATAC
*
14268 TATATATTATA
1 TATATACTATA
14279 CACATGCCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
17 2 0.05
18 17 0.41
19 7 0.17
20 9 0.22
21 6 0.15
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.41
Consensus pattern (18 bp):
TATATACTATATGCATAC
Found at i:14811 original size:14 final size:14
Alignment explanation
Indices: 14779--14811 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
14769 TTGAAGATTT
*
14779 ATAACATAAGAATC
1 ATAATATAAGAATC
14793 ATAATATAAGAATC
1 ATAATATAAGAATC
14807 ATAAT
1 ATAAT
14812 TAATATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.27
Consensus pattern (14 bp):
ATAATATAAGAATC
Found at i:15065 original size:16 final size:16
Alignment explanation
Indices: 15020--15065 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
15010 CATTTACAGA
15020 TCAGGTTGAAAACATG
1 TCAGGTTGAAAACATG
* * * *
15036 TTATGTTCATAACATG
1 TCAGGTTGAAAACATG
15052 TCAGGTTGAAAACA
1 TCAGGTTGAAAACA
15066 AGTCGGGTAA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (16 bp):
TCAGGTTGAAAACATG
Found at i:28266 original size:3 final size:3
Alignment explanation
Indices: 28260--28330 Score: 63
Period size: 3 Copynumber: 23.7 Consensus size: 3
28250 TATTATTTAT
* * * * * * *
28260 TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA TTA TTA TTA TTA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28308 TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TA
28331 TTCAAATGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.94
4 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:28633 original size:33 final size:35
Alignment explanation
Indices: 28568--28633 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 35
28558 TTGAACAAGC
* *
28568 TCTTCTCATTGTGAACTTCTTCTTCTTCAAATGAAT
1 TCTTCTCATTATGAACTTC-TCTTCTGCAAATGAAT
*
28604 TCTTCTCATTATGAAC-TC-CTTCTGGAAATG
1 TCTTCTCATTATGAACTTCTCTTCTGCAAATG
28634 CTGATGATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 10 0.37
35 2 0.07
36 15 0.56
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.44
Consensus pattern (35 bp):
TCTTCTCATTATGAACTTCTCTTCTGCAAATGAAT
Found at i:28810 original size:113 final size:113
Alignment explanation
Indices: 28670--29535 Score: 1473
Period size: 113 Copynumber: 7.7 Consensus size: 113
28660 ATAGAGTCAT
*
28670 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
28735 ATTATGAACTTTCTCTGGAAAAGTTGATACATCGAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
*
28783 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
28848 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
28896 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
28961 ATTATGAACTATCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
29009 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
29074 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
29122 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
29187 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
29235 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * **
29300 ATTATGAACTCTAC-CTGGAAATGCTGATCCATCGAATGATGAATTCAA
66 ATTATGAACT-TTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
* * *
29348 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTACCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * **
29413 ATTATGAACTTTCTCTGGAAATGTTGATCCATCGAATGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
* *
29461 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
29526 ATTATAAACT
66 ATTATGAACT
29536 CTACCTGGAA
Statistics
Matches: 729, Mismatches: 22, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
112 2 0.00
113 725 0.99
114 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
Found at i:29688 original size:76 final size:76
Alignment explanation
Indices: 29562--29743 Score: 285
Period size: 76 Copynumber: 2.4 Consensus size: 76
29552 TAAGAAGAAA
* * * *
29562 AAACATTC-TGCACTGTAGGGCTTACAGCTGACTCGAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 AAACA-TCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
29626 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* * *
29638 AAACATCATGCACTGTAGGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCTCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
29703 AGGCTTTTTGG
66 AGGCTTTTTGG
29714 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
29744 TGGGAAATAG
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
75 2 0.02
76 95 0.98
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:30446 original size:22 final size:22
Alignment explanation
Indices: 30418--30494 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
30408 CATAAAGCTT
30418 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
30440 TCATCTTTAAAAAGAGAACCTA
1 TCATCTTTGAAAAGAGAATCTA
30462 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
30484 TCATCTTTGAA
1 TCATCTTTGAA
30495 GAGTGTAGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:30940 original size:50 final size:50
Alignment explanation
Indices: 30865--30960 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
30855 TCACTGGTTC
* * * * * *
30865 GTAAAACATTTGACAATATATTCATCTTTTCCTGTGGTTTCTGCCCAGAT
1 GTAAAACATTTAAAAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
*
30915 GTAAAACATTTAAAAACACATTCATCCTTTCTTGTGGCTTCTGCCC
1 GTAAAACATTTAAAAACACATTCATCCTTTCCTGTGGCTTCTGCCC
30961 GAAGTTATGG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (50 bp):
GTAAAACATTTAAAAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
Found at i:33307 original size:114 final size:114
Alignment explanation
Indices: 33107--33331 Score: 353
Period size: 114 Copynumber: 2.0 Consensus size: 114
33097 ATCATGCAGA
* * * * *
33107 TCATCTTTCAATTCCAATGATTGGTTCTGGGGTTTCTACCGAACCAGATCAGATAACTCACATAA
1 TCATCTTTCAAATCCAATGATTGGTTCTGGGGTTTCTAACAAACCAGATCAGATAACTCAAAGAA
*
33172 CACATCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAAT
66 CACATCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTACGAGAAAAT
* *
33221 TCATCTTTCAAATCCAATGATTGGTTTTGGGG-TTCATAACAAATCAGATCAGATAACTCAAAGA
1 TCATCTTTCAAATCCAATGATTGGTTCTGGGGTTTC-TAACAAACCAGATCAGATAACTCAAAGA
*
33285 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTACGAGAA
65 ACACATCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTACGAGAA
33332 CATGGCACTT
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 3 0.03
114 98 0.97
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (114 bp):
TCATCTTTCAAATCCAATGATTGGTTCTGGGGTTTCTAACAAACCAGATCAGATAACTCAAAGAA
CACATCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTACGAGAAAAT
Found at i:35476 original size:72 final size:72
Alignment explanation
Indices: 35313--35456 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 72
35303 ATATAATAGT
* * * * *
35313 ATAATAGACTAGCTGAATATTATCCACAAAGTCGGGGCTATTAACCAATTGCTTTAGGGGGATAA
1 ATAACAGACTAGTTGAATATTATCCACAAAGCCAGGGCTATTAACCAATTGCTTTAGGGGGACAA
35378 CTCAAGC
66 CTCAAGC
* *
35385 ATAACAGACTAGTTGAATATTATCCATAAAGCCAGGGCTATTAACCGATTGCTTTAGGGGGACAA
1 ATAACAGACTAGTTGAATATTATCCACAAAGCCAGGGCTATTAACCAATTGCTTTAGGGGGACAA
35450 CTCAAGC
66 CTCAAGC
35457 TTTATTGTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (72 bp):
ATAACAGACTAGTTGAATATTATCCACAAAGCCAGGGCTATTAACCAATTGCTTTAGGGGGACAA
CTCAAGC
Found at i:38334 original size:36 final size:36
Alignment explanation
Indices: 38271--38342 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
38261 TCTTACCATA
* ** *
38271 GACTACTTTTGGTATCAATCTGGCAGGATCTTTGTG
1 GACTACTTTTGGTATCAATATAACAGGATCTCTGTG
*
38307 GACTACTTTTGGTATTAATATAACAGGATCTCTGTG
1 GACTACTTTTGGTATCAATATAACAGGATCTCTGTG
38343 TGCTTTGCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (36 bp):
GACTACTTTTGGTATCAATATAACAGGATCTCTGTG
Found at i:41309 original size:3 final size:3
Alignment explanation
Indices: 41303--41387 Score: 66
Period size: 3 Copynumber: 28.7 Consensus size: 3
41293 TAATATTTAT
* * * * * *
41303 TAA TAA TAA -AA TAA AAA TAA AAA TAA TTA TTA TTA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
41350 TTA TTA TTA TAA TAA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
41388 TTCAAATGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
2 4 0.06
3 65 0.92
4 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:41345 original size:18 final size:18
Alignment explanation
Indices: 41319--41365 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
41309 TAAAATAAAA
*
41319 ATAAAAATAATTATTATT
1 ATAATAATAATTATTATT
41337 ATAATAATAATTATTATT
1 ATAATAATAATTATTATT
*
41355 ATTATAATAAT
1 ATAATAATAAT
41366 AATAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAATAATAATTATTATT
Found at i:41352 original size:21 final size:21
Alignment explanation
Indices: 41318--41371 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
41308 ATAAAATAAA
*
41318 AATAAAAATAATTATTATTAT
1 AATAATAATAATTATTATTAT
*
41339 AATAATAATTATTATTATTAT
1 AATAATAATAATTATTATTAT
41360 AATAATAATAAT
1 AATAATAATAAT
41372 AATAATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAATAATAATTATTATTAT
Found at i:45335 original size:2 final size:2
Alignment explanation
Indices: 45328--45370 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
45318 AGGTCATTAC
45328 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45369 TA
1 TA
45371 AGATGTAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.