Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005399.1 Hibiscus syriacus cultivar Beakdansim tig00012374_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: 110401
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:4454 original size:3 final size:3
Alignment explanation
Indices: 4446--4482 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
4436 CTAGCCGCAC
4446 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4483 GGGAAAAGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:9630 original size:16 final size:17
Alignment explanation
Indices: 9593--9633 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
9583 TTAAAATAAA
* *
9593 ATATTATATTTAAATTC
1 ATATTTTATTTAAATAC
9610 A-ATTTTATTT-AATAC
1 ATATTTTATTTAAATAC
9625 ATATTTTAT
1 ATATTTTAT
9634 ATTTTTCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 15 0.71
17 1 0.05
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTTTATTTAAATAC
Found at i:11720 original size:58 final size:58
Alignment explanation
Indices: 11651--11767 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
11641 ATATGGATAT
11651 ATGATTCTATTTCCCGAAGGGGAAATTAAAAAAAAAAAATTGGGAAAGTAAATTTATA
1 ATGATTCTATTTCCCGAAGGGGAAATTAAAAAAAAAAAATTGGGAAAGTAAATTTATA
*
11709 ATGATTCTATTTCCCGAAGGGGAAATTTAAAAAAAAAAATTGGGAAAGTAAATTTATA
1 ATGATTCTATTTCCCGAAGGGGAAATTAAAAAAAAAAAATTGGGAAAGTAAATTTATA
11767 A
1 A
11768 AATTATAAGG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (58 bp):
ATGATTCTATTTCCCGAAGGGGAAATTAAAAAAAAAAAATTGGGAAAGTAAATTTATA
Found at i:17023 original size:2 final size:2
Alignment explanation
Indices: 17016--17049 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17006 CCATCTTTCA
17016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17050 TTAATAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47158 original size:60 final size:61
Alignment explanation
Indices: 47039--47209 Score: 180
Period size: 60 Copynumber: 2.9 Consensus size: 61
47029 TAATCTGCAA
* * *
47039 TCTAAATTAGTCTCTAAA-TTTTTAA-ATTTCGAATTTCATCCTCAAACTATGACTATCAT
1 TCTAAATTAGTCGCTAAACTTTTGAACATTTCGAATTTCATCCCCAAACTATGACTATCAT
*
47098 TCTAAATTAGTC-CATAAACTTTTGAACATTTTG-A-TTCAATCCCCAAACTATGAACT-TCAT
1 TCTAAATTAGTCGC-TAAACTTTTGAACATTTCGAATTTC-ATCCCCAAACTATG-ACTATCAT
* *
47158 TCTAAATTAG-CGCCCAAACTTTTTGAACATTT-GAATTTGAT-CCCAAACTATG
1 TCTAAATTAGTCG-CTAAAC-TTTTGAACATTTCGAATTTCATCCCCAAACTATG
47210 CATATATACT
Statistics
Matches: 97, Mismatches: 5, Indels: 19
0.80 0.04 0.16
Matches are distributed among these distances:
58 1 0.01
59 20 0.21
60 50 0.52
61 24 0.25
62 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (61 bp):
TCTAAATTAGTCGCTAAACTTTTGAACATTTCGAATTTCATCCCCAAACTATGACTATCAT
Found at i:49385 original size:16 final size:16
Alignment explanation
Indices: 49364--49396 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
49354 TATGTTCATG
49364 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
49380 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
49396 A
1 A
49397 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:49783 original size:14 final size:14
Alignment explanation
Indices: 49762--49805 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
49752 GTCATCTGTT
49762 CAAACATAAATGAA
1 CAAACATAAATGAA
*
49776 CGAACATAAATGAA
1 CAAACATAAATGAA
* *
49790 CAAAAATAAACGAA
1 CAAACATAAATGAA
49804 CA
1 CA
49806 TATAATCGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.64, C:0.16, G:0.09, T:0.11
Consensus pattern (14 bp):
CAAACATAAATGAA
Found at i:49796 original size:24 final size:26
Alignment explanation
Indices: 49764--49816 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
49754 CATCTGTTCA
* *
49764 AACATAAATGAACGAACATA-AAT-G
1 AACAAAAATAAACGAACATATAATCG
49788 AACAAAAATAAACGAACATATAATCG
1 AACAAAAATAAACGAACATATAATCG
49814 AAC
1 AAC
49817 GTTCACGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 18 0.72
25 3 0.12
26 4 0.16
ACGTcount: A:0.60, C:0.15, G:0.09, T:0.15
Consensus pattern (26 bp):
AACAAAAATAAACGAACATATAATCG
Found at i:49827 original size:10 final size:10
Alignment explanation
Indices: 49812--49838 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
49802 AACATATAAT
49812 CGAACGTTCA
1 CGAACGTTCA
49822 CGAACGTTCA
1 CGAACGTTCA
49832 CGAACGT
1 CGAACGT
49839 AAATGAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.19
Consensus pattern (10 bp):
CGAACGTTCA
Found at i:61349 original size:3 final size:3
Alignment explanation
Indices: 61341--61375 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
61331 CTTTATGATT
* *
61341 TTA TTA TTA TTA TTA TTA TCA TTA TCA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
61376 TTTTGCATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:64745 original size:12 final size:11
Alignment explanation
Indices: 64717--64755 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
64707 TTGTTAACAT
64717 ATTTTAAGTAA
1 ATTTTAAGTAA
64728 ATTTTAAGTAA
1 ATTTTAAGTAA
64739 TATTTTAAGTAA
1 -ATTTTAAGTAA
64751 ATTTT
1 ATTTT
64756 TACCGGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (11 bp):
ATTTTAAGTAA
Found at i:64756 original size:12 final size:12
Alignment explanation
Indices: 64718--64757 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
64708 TGTTAACATA
64718 TTTTAAGTAAA-
1 TTTTAAGTAAAT
64729 TTTTAAGT-AAT
1 TTTTAAGTAAAT
64740 ATTTTAAGTAAAT
1 -TTTTAAGTAAAT
64753 TTTTA
1 TTTTA
64758 CCGGTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 2 0.08
11 8 0.31
12 13 0.50
13 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (12 bp):
TTTTAAGTAAAT
Found at i:65114 original size:18 final size:17
Alignment explanation
Indices: 65079--65111 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
65069 TTTATTAGGT
65079 TGTAATTTTCATGATTA
1 TGTAATTTTCATGATTA
*
65096 TGTAATTTTTATGATT
1 TGTAATTTTCATGATT
65112 TATTGTATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (17 bp):
TGTAATTTTCATGATTA
Found at i:70094 original size:20 final size:19
Alignment explanation
Indices: 70069--70108 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
70059 TGGTTCACAT
70069 AATGTAAGATTACCAGTGGA
1 AATGTAAGATTACCA-TGGA
70089 AATGTAAGATTACCATGGA
1 AATGTAAGATTACCATGGA
70108 A
1 A
70109 TAAGATTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (19 bp):
AATGTAAGATTACCATGGA
Found at i:70114 original size:16 final size:19
Alignment explanation
Indices: 70072--70117 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
70062 TTCACATAAT
70072 GTAAGATTACCAGTGGAAA
1 GTAAGATTACCAGTGGAAA
70091 TGTAAGATTACCA-TGG-AA
1 -GTAAGATTACCAGTGGAAA
70109 -TAAGATTAC
1 GTAAGATTAC
70118 TGGAATGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.35
18 2 0.08
19 3 0.12
20 12 0.46
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (19 bp):
GTAAGATTACCAGTGGAAA
Found at i:70333 original size:37 final size:37
Alignment explanation
Indices: 70260--70334 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
70250 GTTGTAAAAT
*
70260 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
70297 ATTTATATAATTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
70334 A
1 A
70335 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:71718 original size:2 final size:2
Alignment explanation
Indices: 71711--71740 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
71701 TTGAGGCCCA
71711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71741 TGAATAGAAA
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):
AT
Found at i:72770 original size:16 final size:16
Alignment explanation
Indices: 72743--72781 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
72733 GTTTATTTCA
*
72743 GAATGA-TTAAATGTT
1 GAATGATTTAAATATT
72758 GAATGATTTAAATATT
1 GAATGATTTAAATATT
72774 GAATGATT
1 GAATGATT
72782 CAGAGACTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (16 bp):
GAATGATTTAAATATT
Found at i:72868 original size:27 final size:27
Alignment explanation
Indices: 72835--72900 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
72825 GATAATGACT
*
72835 CTGAATCATTCAGAATGTAC-TTCTGTG
1 CTGAATCATTCAGAATATACTTTC-GTG
72862 CTGAATCATTCAGAATATACTTTCGTG
1 CTGAATCATTCAGAATATACTTTCGTG
*
72889 CTAAATCATTCA
1 CTGAATCATTCA
72901 ACACTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 33 0.92
28 3 0.08
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (27 bp):
CTGAATCATTCAGAATATACTTTCGTG
Found at i:84950 original size:17 final size:18
Alignment explanation
Indices: 84928--84961 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
84918 CAATAAATTT
84928 AATTATTATT-ATTTATA
1 AATTATTATTAATTTATA
*
84945 AATTATTTTTAATTTAT
1 AATTATTATTAATTTAT
84962 TTTATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTATTATTAATTTATA
Found at i:84981 original size:27 final size:27
Alignment explanation
Indices: 84925--84983 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
84915 ATTCAATAAA
*
84925 TTTAATTATTATTATTTATAAATTATT
1 TTTAATTATTATTATTTATAAATTAAT
*
84952 TTTAATTTATT-TTATTT-TAATTTTAAT
1 TTTAA-TTATTATTATTTATAA-ATTAAT
84979 TTTAA
1 TTTAA
84984 ATAATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 3 0.11
27 20 0.71
28 5 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTAATTATTATTATTTATAAATTAAT
Found at i:86666 original size:2 final size:2
Alignment explanation
Indices: 86659--86686 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
86649 GAAATATCTC
86659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
86687 TAATAATAAA
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):
AT
Found at i:95308 original size:21 final size:21
Alignment explanation
Indices: 95284--95327 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
95274 TGGTAAAATG
*
95284 TTATCTAAAATATTATTATTT
1 TTATCTAAAATATTAATATTT
*
95305 TTATTTAAAATATTAATATTT
1 TTATCTAAAATATTAATATTT
95326 TT
1 TT
95328 TAATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATCTAAAATATTAATATTT
Found at i:108753 original size:20 final size:21
Alignment explanation
Indices: 108728--108767 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
108718 TTAATCAGTA
108728 TGAATCACAAAT-AAATTAAT
1 TGAATCACAAATAAAATTAAT
*
108748 TGAATCACAATTAAAATTAA
1 TGAATCACAAATAAAATTAA
108768 CTGTGTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (21 bp):
TGAATCACAAATAAAATTAAT
Done.