Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000537.1 Hibiscus syriacus cultivar Beakdansim tig00001039_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: 60237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5043 original size:28 final size:28
Alignment explanation
Indices: 4980--5045 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
4970 AACTTTAAAG
* *
4980 TGACAATCAAGATTTAGGTTCAATCAGG
1 TGACAATCAAGATTTAGGCTCAATCAGA
*
5008 TGTCAATCAAGATTTAGGCTCAATCAGA
1 TGACAATCAAGATTTAGGCTCAATCAGA
*
5036 TGAGAATCAA
1 TGACAATCAA
5046 AGTGAATTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (28 bp):
TGACAATCAAGATTTAGGCTCAATCAGA
Found at i:10078 original size:2 final size:2
Alignment explanation
Indices: 10073--10102 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10063 AAATTATAAC
10073 TA 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 TA
10103 AAAGAAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14167 original size:5 final size:5
Alignment explanation
Indices: 14159--14197 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
14149 GATAAGATAA
* *
14159 AATAT AATAC AATAT AATAT AATAT AATA- AAGAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
14198 TCTAAATCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 3 0.10
5 26 0.90
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (5 bp):
AATAT
Found at i:16754 original size:18 final size:18
Alignment explanation
Indices: 16728--16767 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16718 AAATAATATA
* *
16728 AAATTCTAAATCCTAATT
1 AAATACTAAAACCTAATT
*
16746 AAATACTAAAACCTATTT
1 AAATACTAAAACCTAATT
16764 AAAT
1 AAAT
16768 TAAAATACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATACTAAAACCTAATT
Found at i:16780 original size:62 final size:62
Alignment explanation
Indices: 16671--16793 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 62
16661 TAAAACATCT
* *
16671 TAAATCCTAATTAAAACGCTTAAAACTATTTGAACTAAAATATCTAAAA-ATAATATAAAATTC
1 TAAATCCTAATTAAAAC-CTTAAAACTATTTAAACTAAAATACCTAAAACA-AATATAAAATTC
*
16734 TAAATCCTAATTAAATA-C-TAAAACCTATTTAAATTAAAATACCTAAAACAAATATAAAAT
1 TAAATCCTAATTAAA-ACCTTAAAA-CTATTTAAACTAAAATACCTAAAACAAATATAAAAT
16794 ATAAAAATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
61 5 0.09
62 32 0.59
63 16 0.30
64 1 0.02
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.31
Consensus pattern (62 bp):
TAAATCCTAATTAAAACCTTAAAACTATTTAAACTAAAATACCTAAAACAAATATAAAATTC
Found at i:16791 original size:25 final size:23
Alignment explanation
Indices: 16742--16791 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 23
16732 TCTAAATCCT
** *
16742 AATTAAATACTAAAACCTATTTA
1 AATTAAATACTAAAACAAATATA
16765 AATTAAAATACCTAAAACAAATATA
1 AATT-AAATA-CTAAAACAAATATA
16790 AA
1 AA
16792 ATATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 4 0.18
24 5 0.23
25 13 0.59
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (23 bp):
AATTAAATACTAAAACAAATATA
Found at i:16824 original size:32 final size:32
Alignment explanation
Indices: 16771--16833 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
16761 TTTAAATTAA
16771 AATACCTAAAACAAATATAAAATA-TAAAAAT
1 AATACCTAAAACAAATATAAAATACTAAAAAT
*
16802 AATATCCTAAAACTTAAT-TAAAATACTAAAAA
1 AATA-CCTAAAAC-AAATATAAAATACTAAAAA
16834 CCTATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 4 0.14
32 15 0.54
33 9 0.32
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.25
Consensus pattern (32 bp):
AATACCTAAAACAAATATAAAATACTAAAAAT
Found at i:16876 original size:77 final size:74
Alignment explanation
Indices: 16715--16888 Score: 183
Period size: 77 Copynumber: 2.3 Consensus size: 74
16705 CTAAAATATC
* * * * * *
16715 TAAAA-ATAATATAAAATTCTAAATCCTAATTAAATACTAAAACCTATTTAAATTAAAATACCTA
1 TAAAATATAAAATAATATCCTAAAACTTAATTAAATACTAAAACCTATTTAAACTAAAATACCTA
*
16779 AAACAAATA
66 AAAAAAATA
16788 TAAAATATAAAAATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATA-
1 TAAAATAT-AAAATAATATCCTAAAACTTAATT-AAATACT-AAAACCTATTTAAACTAAAATAC
16852 C-AAAGATAAAATA
63 CTAAA-A-AAAATA
** * *
16865 TAATGTTTAAAATATTATCCTAAA
1 TAAAATATAAAATAATATCCTAAA
16889 CTTGATTTTA
Statistics
Matches: 84, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
73 5 0.06
74 2 0.02
75 22 0.26
76 24 0.29
77 31 0.37
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.30
Consensus pattern (74 bp):
TAAAATATAAAATAATATCCTAAAACTTAATTAAATACTAAAACCTATTTAAACTAAAATACCTA
AAAAAAATA
Found at i:22692 original size:21 final size:21
Alignment explanation
Indices: 22627--22692 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
22617 GCTTTGGAAT
**
22627 TTTTCCTGGGATGTAAATAGC
1 TTTTCCTGGGATGTAACCAGC
* *
22648 TTGTCCTGGGACGTAACCAGC
1 TTTTCCTGGGATGTAACCAGC
*
22669 TTTTCTTGGGATGTAACCAGC
1 TTTTCCTGGGATGTAACCAGC
22690 TTT
1 TTT
22693 CTTTTGAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (21 bp):
TTTTCCTGGGATGTAACCAGC
Found at i:27408 original size:2 final size:2
Alignment explanation
Indices: 27401--27429 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27391 ATACTCACAT
27401 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 T
27430 CATACTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29511 original size:2 final size:2
Alignment explanation
Indices: 29504--29528 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29494 CTCCATGCTT
29504 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 T
29529 TAGAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34026 original size:14 final size:13
Alignment explanation
Indices: 33990--34056 Score: 66
Period size: 13 Copynumber: 5.2 Consensus size: 13
33980 TAATAATTTG
33990 TAAATAAAAA-AA
1 TAAATAAAAATAA
*
34002 TAAAAAAAAATAA
1 TAAATAAAAATAA
34015 TAAAGTAAAAATAAA
1 TAAA-TAAAAAT-AA
* *
34030 CAAAT-AAAATAG
1 TAAATAAAAATAA
*
34042 TATATAAAAATAA
1 TAAATAAAAATAA
34055 TA
1 TA
34057 TTAATATTGA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
12 13 0.30
13 19 0.43
14 7 0.16
15 5 0.11
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (13 bp):
TAAATAAAAATAA
Found at i:34114 original size:13 final size:13
Alignment explanation
Indices: 34098--34122 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34088 AAAATAAATA
34098 AATAAAAAATAGG
1 AATAAAAAATAGG
34111 AATAAAAAATAG
1 AATAAAAAATAG
34123 TAAATACTCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
AATAAAAAATAGG
Found at i:36167 original size:103 final size:99
Alignment explanation
Indices: 35978--36175 Score: 238
Period size: 103 Copynumber: 2.0 Consensus size: 99
35968 TATTGTTCCA
* * *
35978 AGTCCAATATCTTTCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGACTCTGGAACTGGAAAATTGTTTGTTGACAAC
** *
36043 CAGTCGCCCCTTCGCTGTGAAGTTGAGCTTCTCG
66 CAACCACCCCTTCGCTGTGAAGTTGAGCTTCTCG
*
36077 AGTCTAATATCCTTCG-CTGTGAAGTTGAAATTGACTCTGAAAGAAACT-GAAAAGTTGTTTGTT
1 AGTCCAATATCCTTCGTC-GTGAAGTTGAAATTGACTCTG---G-AACTGGAAAA-TTGTTTGTT
* * *
36140 GACAAGCAACCACCTCTTCGTTGTGAAGTTGAGCTT
60 GACAACCAACCACCCCTTCGCTGTGAAGTTGAGCTT
36176 GTGTTGTCTT
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
98 1 0.01
99 34 0.41
102 5 0.06
103 43 0.52
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (99 bp):
AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGACTCTGGAACTGGAAAATTGTTTGTTGACAAC
CAACCACCCCTTCGCTGTGAAGTTGAGCTTCTCG
Found at i:36323 original size:69 final size:66
Alignment explanation
Indices: 36236--36363 Score: 166
Period size: 69 Copynumber: 1.9 Consensus size: 66
36226 AAATTGGGAA
* *
36236 GCCCCTTCCTCGTAAAGTTGAGCCTCGAATGGCACGATATCCTCCGTCGTGGAGTTGAAATCGCG
1 GCCCCTTCATCGTAAAGTTGAGCCTCGAATGG---GATATCCTCCGTCGTGAAGTTGAAATCGCG
36301 GATG
63 GATG
* * * * *
36305 GCCCCTTCATCGTGAAGTTGAGCCTTGACTTGGATATCCTTCGTCGTGAAGTTGAAATC
1 GCCCCTTCATCGTAAAGTTGAGCCTCGAATGGGATATCCTCCGTCGTGAAGTTGAAATC
36364 CAAGTATTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
66 25 0.48
69 27 0.52
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (66 bp):
GCCCCTTCATCGTAAAGTTGAGCCTCGAATGGGATATCCTCCGTCGTGAAGTTGAAATCGCGGAT
G
Found at i:42315 original size:20 final size:21
Alignment explanation
Indices: 42243--42310 Score: 136
Period size: 21 Copynumber: 3.2 Consensus size: 21
42233 CTAGAACCCC
42243 GGGGGGTATCGATTCTCCTAT
1 GGGGGGTATCGATTCTCCTAT
42264 GGGGGGTATCGATTCTCCTAT
1 GGGGGGTATCGATTCTCCTAT
42285 GGGGGGTATCGATTCTCCTAT
1 GGGGGGTATCGATTCTCCTAT
42306 GGGGG
1 GGGGG
42311 AATCGGTTCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.13, C:0.18, G:0.38, T:0.31
Consensus pattern (21 bp):
GGGGGGTATCGATTCTCCTAT
Found at i:47428 original size:21 final size:21
Alignment explanation
Indices: 47386--47429 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
47376 CCGTTATACA
*
47386 AGGGGGAATCGGTACCCCCTG
1 AGGGGGAATCAGTACCCCCTG
* *
47407 AGGGGGAATCAGTTCCCTCTG
1 AGGGGGAATCAGTACCCCCTG
47428 AG
1 AG
47430 CATACTGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.36, T:0.18
Consensus pattern (21 bp):
AGGGGGAATCAGTACCCCCTG
Found at i:47491 original size:23 final size:23
Alignment explanation
Indices: 47462--47516 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
47452 AACCATTCAT
47462 GGGGGAATCAGTACCCCCTATGG
1 GGGGGAATCAGTACCCCCTATGG
47485 GGGGGAATCAGTACCCCCTATGG
1 GGGGGAATCAGTACCCCCTATGG
47508 GGGGGAATC
1 GGGGGAATC
47517 GGTTCCCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.24, G:0.38, T:0.16
Consensus pattern (23 bp):
GGGGGAATCAGTACCCCCTATGG
Found at i:56952 original size:2 final size:2
Alignment explanation
Indices: 56947--56975 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
56937 AAAAAAAAGA
56947 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 A
56976 ATAATTGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57039 original size:16 final size:18
Alignment explanation
Indices: 57018--57060 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
57008 GTAAAAATAA
57018 AAAAATAAAATT-ATA-T
1 AAAAATAAAATTAATATT
*
57034 AAAAATAATATTAATATT
1 AAAAATAAAATTAATATT
*
57052 GAAAATAAA
1 AAAAATAAA
57061 TAACAATGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 11 0.50
17 3 0.14
18 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAATAAAATTAATATT
Done.