Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007382.1 Hibiscus syriacus cultivar Beakdansim tig00019835_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: 74950
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4096 original size:24 final size:23
Alignment explanation
Indices: 4067--4117 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 23
4057 TAAACTCGTT
4067 AATATTTTTAAACTCAAATAAA-AA
1 AATA-TTTTAAA-TCAAATAAAGAA
*
4091 AATA-TTTAAATCAATTAAAGAA
1 AATATTTTAAATCAAATAAAGAA
4113 AATAT
1 AATAT
4118 AAATCCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 8 0.33
22 12 0.50
24 4 0.17
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (23 bp):
AATATTTTAAATCAAATAAAGAA
Found at i:4109 original size:21 final size:23
Alignment explanation
Indices: 4073--4117 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
4063 CGTTAATATT
4073 TTTAAACTCAAATAAA-AAAATA
1 TTTAAACTCAAATAAAGAAAATA
*
4095 TTTAAA-TCAATTAAAGAAAATA
1 TTTAAACTCAAATAAAGAAAATA
4117 T
1 T
4118 AAATCCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (23 bp):
TTTAAACTCAAATAAAGAAAATA
Found at i:4122 original size:20 final size:20
Alignment explanation
Indices: 4074--4122 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
4064 GTTAATATTT
4074 TTAAACTCAAATAAAAAAATA
1 TTAAA-TCAAATAAAAAAATA
*
4095 TTTAAATCAATTAAAGAAAATA
1 -TTAAATCAAATAAA-AAAATA
4117 -TAAATC
1 TTAAATC
4123 CTAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 6 0.24
21 8 0.32
22 11 0.44
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (20 bp):
TTAAATCAAATAAAAAAATA
Found at i:6140 original size:27 final size:27
Alignment explanation
Indices: 6110--6161 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
6100 TAGTATGATA
* *
6110 ATGTCGTGTCCTTGTATATAGAGATGG
1 ATGTAGTGTCCTTGTATATAAAGATGG
* *
6137 ATGTAGTGTCTTTGTGTATAAAGAT
1 ATGTAGTGTCCTTGTATATAAAGAT
6162 AGACCGAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (27 bp):
ATGTAGTGTCCTTGTATATAAAGATGG
Found at i:6373 original size:140 final size:140
Alignment explanation
Indices: 6116--6395 Score: 373
Period size: 140 Copynumber: 2.0 Consensus size: 140
6106 GATAATGTCG
* * * * *
6116 TGTCCTTGTATATAGAGATGGATGTAGTGTCTTTGTGTATAAAGATAGACCGAAAGAGGCGAGTG
1 TGTCCTTATATATAGAGATGGATGTAGTGTCTTTGTGTACAAAGATAAACCGAAAGAGACGAGTA
* * *
6181 GGATAGATCGAAGAGAGACAATATGTAATTTACCATAGTATGATAATGTCGTGTTCTTGTGTAGA
66 GGATAGACCGAAGAGAGACAATATGTAATTTACCATAGTATGATAATATCGTGTCCTTGTGTAGA
*
6246 TAGATAGACC
131 TAGACAGACC
* * ** *
6256 TGTCCTTATGTATAGAGATGGATGTCA-TGTCTTTGTGTACAGAGATAAACCGAGGGAGACGGGT
1 TGTCCTTATATATAGAGATGGATGT-AGTGTCTTTGTGTACAAAGATAAACCGAAAGAGACGAGT
* * * * *
6320 AGGATGGACCGAGGAGAGATAATATGTAGTTTACCATAGTATGATAATATCGTGTCCTTGTGTAT
65 AGGATAGACCGAAGAGAGACAATATGTAATTTACCATAGTATGATAATATCGTGTCCTTGTGTAG
6385 ATAGACAGACC
130 ATAGACAGACC
6396 GAGAAGTACA
Statistics
Matches: 120, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
140 119 0.99
141 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (140 bp):
TGTCCTTATATATAGAGATGGATGTAGTGTCTTTGTGTACAAAGATAAACCGAAAGAGACGAGTA
GGATAGACCGAAGAGAGACAATATGTAATTTACCATAGTATGATAATATCGTGTCCTTGTGTAGA
TAGACAGACC
Found at i:6638 original size:52 final size:52
Alignment explanation
Indices: 6573--6676 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 52
6563 CCCTAAATTT
* *
6573 TTATAAATTTAAATTT-ACCTTATCAAATTTAAAAAAATTCAAATTCGTCACTC
1 TTATAAATCTAAATTTGACC-TATCAAATTTAAAAAAACTC-AATTCGTCACTC
* *
6626 TTAT-AATCTAAATTTGTCCTATGAAATTTAAAAAAACTCAATTCGTCACTC
1 TTATAAATCTAAATTTGACCTATCAAATTTAAAAAAACTCAATTCGTCACTC
6677 CAACATAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
51 12 0.26
52 28 0.61
53 6 0.13
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.38
Consensus pattern (52 bp):
TTATAAATCTAAATTTGACCTATCAAATTTAAAAAAACTCAATTCGTCACTC
Found at i:7235 original size:2 final size:2
Alignment explanation
Indices: 7230--7256 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7220 AAAAAAAAAA
7230 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
7257 CATAACCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15721 original size:2 final size:2
Alignment explanation
Indices: 15714--15739 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15704 TTCCCGTATA
15714 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
15740 GTAGTAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20915 original size:2 final size:2
Alignment explanation
Indices: 20908--20944 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20898 TGTGTTTTTA
20908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20945 ATTTTAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27892 original size:17 final size:14
Alignment explanation
Indices: 27860--27888 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27850 AAACGGTCCC
27860 TTATTATAGGATAT
1 TTATTATAGGATAT
27874 TTATTATAGGATAT
1 TTATTATAGGATAT
27888 T
1 T
27889 ATTTTATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TTATTATAGGATAT
Found at i:27951 original size:60 final size:57
Alignment explanation
Indices: 27869--27993 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 57
27859 CTTATTATAG
* *
27869 GATATTTATTATAGGATATTATTTTATTGAGTCATTT-GATTATTAAAAGTTATAAAAT
1 GATATTTATTATAGGATATTATTTT-GTGAG-CATTTCGATTATTAAAAGTTAAAAAAT
* * *
27927 GATACTTTAATTATAGTATGTTATTTTGTGAGGATTTCGATTATTAAAAGTTAAAAAAT
1 GATA-TTT-ATTATAGGATATTATTTTGTGAGCATTTCGATTATTAAAAGTTAAAAAAT
27986 GATCATTT
1 GAT-ATTT
27994 TACTATTTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
58 8 0.14
59 33 0.57
60 17 0.29
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (57 bp):
GATATTTATTATAGGATATTATTTTGTGAGCATTTCGATTATTAAAAGTTAAAAAAT
Found at i:33579 original size:22 final size:23
Alignment explanation
Indices: 33541--33587 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
33531 TATCACATTA
*
33541 ATGTGATGAGTTTTAATAAAAAT
1 ATGTAATGAGTTTTAATAAAAAT
33564 ATGTAATGA-TTTTAATAAAAAT
1 ATGTAATGAGTTTTAATAAAAAT
33586 AT
1 AT
33588 TTTTATTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGTAATGAGTTTTAATAAAAAT
Found at i:33640 original size:17 final size:17
Alignment explanation
Indices: 33615--33648 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
33605 ATCATGATAT
33615 AATAAATTTTAATAAAA
1 AATAAATTTTAATAAAA
* *
33632 AATATATTTTATTAAAA
1 AATAAATTTTAATAAAA
33649 TTTATCACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAAATTTTAATAAAA
Found at i:36778 original size:20 final size:20
Alignment explanation
Indices: 36753--36790 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
36743 TGATGAATCA
36753 TTTATTATGAAATTTATGTT
1 TTTATTATGAAATTTATGTT
36773 TTTATTATGAAATTTATG
1 TTTATTATGAAATTTATG
36791 AATTTATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (20 bp):
TTTATTATGAAATTTATGTT
Found at i:36796 original size:20 final size:20
Alignment explanation
Indices: 36752--36797 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
36742 ATGATGAATC
*
36752 ATTTATTATGAAATTTATGT
1 ATTTATTATGAAATTTATGA
*
36772 TTTTATTATGAAATTTATGA
1 ATTTATTATGAAATTTATGA
36792 ATTTAT
1 ATTTAT
36798 CTAATTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (20 bp):
ATTTATTATGAAATTTATGA
Found at i:37370 original size:11 final size:11
Alignment explanation
Indices: 37354--37390 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
37344 TAGATTTTTA
37354 TAAAATATCTT
1 TAAAATATCTT
*
37365 TAAAAT-T-TA
1 TAAAATATCTT
37374 TAAAATATCTT
1 TAAAATATCTT
37385 TAAAAT
1 TAAAAT
37391 TTATAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 7 0.32
10 2 0.09
11 13 0.59
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (11 bp):
TAAAATATCTT
Found at i:37375 original size:20 final size:20
Alignment explanation
Indices: 37350--37398 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
37340 AATTTAGATT
37350 TTTATAAAATATCTTTAAAA
1 TTTATAAAATATCTTTAAAA
37370 TTTATAAAATATCTTTAAAA
1 TTTATAAAATATCTTTAAAA
37390 TTTATAAAA
1 TTTATAAAA
37399 CTAAACATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTATAAAATATCTTTAAAA
Found at i:37776 original size:2 final size:2
Alignment explanation
Indices: 37769--37803 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
37759 ATTGACAAAT
37769 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37804 TAAAGTTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41508 original size:31 final size:32
Alignment explanation
Indices: 41470--41542 Score: 121
Period size: 31 Copynumber: 2.3 Consensus size: 32
41460 AAGTGACATT
**
41470 ATATTATAAAAGGGACCCAATTGTTTA-TAAA
1 ATATTATAAAAGGGACCCAATTGCCTATTAAA
41501 ATATTATAAAAGGGACCCAATTGCCTATTAAA
1 ATATTATAAAAGGGACCCAATTGCCTATTAAA
41533 ATATTATAAA
1 ATATTATAAA
41543 TGAAAAGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 25 0.64
32 14 0.36
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (32 bp):
ATATTATAAAAGGGACCCAATTGCCTATTAAA
Found at i:48070 original size:21 final size:21
Alignment explanation
Indices: 48041--48080 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
48031 GATAATTTTA
48041 GTGACTAAAACACAAACTTTG
1 GTGACTAAAACACAAACTTTG
* * *
48062 GTGATTAAAATAGAAACTT
1 GTGACTAAAACACAAACTT
48081 ATTGAACCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (21 bp):
GTGACTAAAACACAAACTTTG
Found at i:52527 original size:2 final size:2
Alignment explanation
Indices: 52520--52547 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52510 AGTTGAAATT
52520 TA TA 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
52548 AAATAAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54179 original size:15 final size:16
Alignment explanation
Indices: 54154--54185 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
54144 CATACTTATT
54154 AAAAATAAAAAAATCA
1 AAAAATAAAAAAATCA
54170 AAAAAT-AAAAAATCA
1 AAAAATAAAAAAATCA
54185 A
1 A
54186 TGATCCACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAATAAAAAAATCA
Found at i:61874 original size:13 final size:13
Alignment explanation
Indices: 61856--61881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61846 TACTTTTTAA
61856 GCATATGAAAATT
1 GCATATGAAAATT
61869 GCATATGAAAATT
1 GCATATGAAAATT
61882 AGGGATGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
GCATATGAAAATT
Found at i:63054 original size:31 final size:31
Alignment explanation
Indices: 63016--63077 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
63006 AACATAGAGT
63016 CGAGATCTTTAAAGAATATGCTAATTTCATC
1 CGAGATCTTTAAAGAATATGCTAATTTCATC
63047 CGAGATCTTTAAAGAATATGCTAATTTCATC
1 CGAGATCTTTAAAGAATATGCTAATTTCATC
63078 GTACATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (31 bp):
CGAGATCTTTAAAGAATATGCTAATTTCATC
Found at i:67404 original size:29 final size:29
Alignment explanation
Indices: 67322--67397 Score: 152
Period size: 29 Copynumber: 2.6 Consensus size: 29
67312 ACCCAACCCA
67322 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCTCC
67351 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCTCC
67380 TAGGTCGCCATGCACTCC
1 TAGGTCGCCATGCACTCC
67398 GGGCGACTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.17, C:0.43, G:0.21, T:0.18
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCTCC
Found at i:69729 original size:60 final size:61
Alignment explanation
Indices: 69602--69738 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 61
69592 ATAGTTGGGT
* * *
69602 GACCAATTTGTAACTTTTAATAGTCGAGAGACTTAATAAAGCAACATTCTATAATTAAAGA
1 GACCATTTTGTAACTTTTAATAGTCAAGAGACTTAATAAAGCAACATTCTATAAGTAAAGA
* * * *
69663 -ATCATTTTGTAACTTTTAATAGTCAAGAGATTTAATAAAGCAATA-TC-ATATAGTAAGGA
1 GACCATTTTGTAACTTTTAATAGTCAAGAGACTTAATAAAGCAACATTCTATA-AGTAAAGA
69722 GACCATTTGTGT-ACTTT
1 GACCATTT-TGTAACTTT
69739 ACCCTTTTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
58 3 0.05
59 8 0.12
60 51 0.78
61 3 0.05
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (61 bp):
GACCATTTTGTAACTTTTAATAGTCAAGAGACTTAATAAAGCAACATTCTATAAGTAAAGA
Done.