Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004482.1 Hibiscus syriacus cultivar Beakdansim tig00009877_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: 71844
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2801 original size:2 final size:2
Alignment explanation
Indices: 2794--2824 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2784 TTATTAATAC
2794 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 T
2825 GCTGATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26944 original size:2 final size:2
Alignment explanation
Indices: 26937--26962 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26927 CCCGAGCGAG
26937 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
26963 GCTACACACT
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):
TC
Found at i:34485 original size:12 final size:12
Alignment explanation
Indices: 34446--34492 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
34436 AACTTTATAA
34446 AATTAAAATTTT
1 AATTAAAATTTT
* *
34458 TATTAATAA-TTG
1 AATTAA-AATTTT
34470 AATTAAAATTTT
1 AATTAAAATTTT
*
34482 AATTATAATTT
1 AATTAAAATTT
34493 GAGAATTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
11 2 0.07
12 24 0.86
13 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
AATTAAAATTTT
Found at i:34494 original size:24 final size:24
Alignment explanation
Indices: 34446--34491 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
34436 AACTTTATAA
*
34446 AATTAAAATTTTTATTAATAATTG
1 AATTAAAATTTTAATTAATAATTG
34470 AATTAAAATTTTAATT-ATAATT
1 AATTAAAATTTTAATTAATAATT
34492 TGAGAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
AATTAAAATTTTAATTAATAATTG
Found at i:38739 original size:10 final size:10
Alignment explanation
Indices: 38724--38748 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38714 TTTATCACAC
38724 CAAATTTTCT
1 CAAATTTTCT
38734 CAAATTTTCT
1 CAAATTTTCT
38744 CAAAT
1 CAAAT
38749 ACTCTATCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (10 bp):
CAAATTTTCT
Found at i:38833 original size:17 final size:18
Alignment explanation
Indices: 38796--38836 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
38786 ATATTATGTA
*
38796 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
38814 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
38831 TTTACT
1 TTTACT
38837 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:44085 original size:28 final size:28
Alignment explanation
Indices: 44054--44109 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
44044 GATATAATCG
*
44054 GAAAA-TCTTATATAATTTTAAATATTTT
1 GAAAATTCTTATAAAATTTT-AATATTTT
*
44082 GAAAATTTTTATAAAATTTTAATATTTT
1 GAAAATTCTTATAAAATTTTAATATTTT
44110 TTATAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (28 bp):
GAAAATTCTTATAAAATTTTAATATTTT
Found at i:44110 original size:29 final size:30
Alignment explanation
Indices: 44061--44119 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
44051 TCGGAAAATC
*
44061 TTATATAATTTTAAATATTTTGA-AAATTT
1 TTATAAAATTTTAAATATTTTGATAAATTT
*
44090 TTATAAAATTTT-AATATTTTTTATAAATTT
1 TTATAAAATTTTAAATA-TTTTGATAAATTT
44120 ATCTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.15
29 16 0.62
30 6 0.23
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (30 bp):
TTATAAAATTTTAAATATTTTGATAAATTT
Found at i:47691 original size:38 final size:38
Alignment explanation
Indices: 47644--47759 Score: 205
Period size: 38 Copynumber: 3.1 Consensus size: 38
47634 GTGGAAACAC
* * *
47644 GGTCGTTCCTCTGTAATGCTATCAACTCCCGCAGTGGT
1 GGTCGTTCCTCTGTAATGGTATCAGCTCCTGCAGTGGT
47682 GGTCGTTCCTCTGTAATGGTATCAGCTCCTGCAGTGGT
1 GGTCGTTCCTCTGTAATGGTATCAGCTCCTGCAGTGGT
47720 GGTCGTTCCTCTGTAATGGTATCAGCTCCTGCAGTGGT
1 GGTCGTTCCTCTGTAATGGTATCAGCTCCTGCAGTGGT
47758 GG
1 GG
47760 AAACACGGTC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 75 1.00
ACGTcount: A:0.14, C:0.25, G:0.28, T:0.33
Consensus pattern (38 bp):
GGTCGTTCCTCTGTAATGGTATCAGCTCCTGCAGTGGT
Found at i:47711 original size:20 final size:20
Alignment explanation
Indices: 47688--47749 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
47678 TGGTGGTCGT
47688 TCCTCTGTAATGGTATCAGC
1 TCCTCTGTAATGGTATCAGC
* * * *
47708 T-C-CTGCAGTGGTGGTC-GT
1 TCCTCTGTAATGGT-ATCAGC
47726 TCCTCTGTAATGGTATCAGC
1 TCCTCTGTAATGGTATCAGC
47746 TCCT
1 TCCT
47750 GCAGTGGTGG
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
18 10 0.33
19 6 0.20
20 14 0.47
ACGTcount: A:0.15, C:0.26, G:0.24, T:0.35
Consensus pattern (20 bp):
TCCTCTGTAATGGTATCAGC
Found at i:49318 original size:31 final size:31
Alignment explanation
Indices: 49280--49346 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
49270 AAAAAAAACA
*
49280 TAAGATTTAGTCACTTTTGTTTTGTTTTAAT
1 TAAGATTTAGTCACTTTCGTTTTGTTTTAAT
*
49311 TAAGATTTGGTCACTTTCGTTTTGTTTTAAT
1 TAAGATTTAGTCACTTTCGTTTTGTTTTAAT
49342 TAAGA
1 TAAGA
49347 AATGATCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.24, C:0.07, G:0.15, T:0.54
Consensus pattern (31 bp):
TAAGATTTAGTCACTTTCGTTTTGTTTTAAT
Found at i:49356 original size:31 final size:31
Alignment explanation
Indices: 49290--49356 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
49280 TAAGATTTAG
* ** *
49290 TCACTTTTGTTTTGTTTTAATTAAGATTTGG
1 TCACTTTCGTTTTGTTTTAATTAAGAAATGA
49321 TCACTTTCGTTTTGTTTTAATTAAGAAATGA
1 TCACTTTCGTTTTGTTTTAATTAAGAAATGA
49352 TCACT
1 TCACT
49357 GAAGATTAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.52
Consensus pattern (31 bp):
TCACTTTCGTTTTGTTTTAATTAAGAAATGA
Found at i:50963 original size:19 final size:19
Alignment explanation
Indices: 50935--50982 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
50925 GCGATTTTGA
*
50935 AAAATATGTTGCAATAGTT
1 AAAATGTGTTGCAATAGTT
*
50954 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCAATAGTT
50973 AAAATGTGTT
1 AAAATGTGTT
50983 ACGAGAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.38
Consensus pattern (19 bp):
AAAATGTGTTGCAATAGTT
Found at i:50991 original size:19 final size:19
Alignment explanation
Indices: 50950--50991 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
50940 ATGTTGCAAT
* *
50950 AGTTAAAATGTGTTGCGAT
1 AGTTAAAATGTGTTACGAG
50969 AGTTAAAATGTGTTACGAG
1 AGTTAAAATGTGTTACGAG
50988 AGTT
1 AGTT
50992 TGAAAAACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (19 bp):
AGTTAAAATGTGTTACGAG
Found at i:51028 original size:19 final size:19
Alignment explanation
Indices: 51004--51040 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
50994 AAAAACGTGT
51004 TGTTGCGATAGCGAAAAAG
1 TGTTGCGATAGCGAAAAAG
*
51023 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGCGAAAAA
51041 TCCAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.30, T:0.24
Consensus pattern (19 bp):
TGTTGCGATAGCGAAAAAG
Found at i:51439 original size:41 final size:41
Alignment explanation
Indices: 51382--51499 Score: 209
Period size: 41 Copynumber: 2.9 Consensus size: 41
51372 TCCGCGCGGA
*
51382 TATCGCGTTGCGATAGTCAGAATCGTGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTAT
*
51423 TATCGCGTTGCGATAGTCAGAATTGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTAT
*
51464 TATCGCGTTGCGATAGTCATAATCGCGTTGCGATTT
1 TATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTT
51500 ACATATTCGC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTAT
Found at i:51509 original size:20 final size:20
Alignment explanation
Indices: 51383--51497 Score: 108
Period size: 20 Copynumber: 5.7 Consensus size: 20
51373 CCGCGCGGAT
*
51383 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCATA
* * *
51403 ATCGTGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCATA
*
51424 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCATA
* * *
51444 ATTGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCATA
51465 ATCGCGTTGCGATAGTCATA
1 ATCGCGTTGCGATAGTCATA
51485 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
51498 TTACATATTC
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
19 6 0.08
20 38 0.51
21 24 0.32
22 6 0.08
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCATA
Found at i:51569 original size:40 final size:40
Alignment explanation
Indices: 51525--51656 Score: 151
Period size: 40 Copynumber: 3.3 Consensus size: 40
51515 AATAGTCAAA
51525 ATCGCGTTGCGAATCTGGAAACTGATTTGCGATACTGGAG
1 ATCGCGTTGCGAATCTGGAAACTGATTTGCGATACTGGAG
* ** * * * ** *
51565 ATCGCGTTGCG-ATTTACATATTCGCA-TTGCGATAGTCAAA
1 ATCGCGTTGCGAATCTGGAAACT-G-ATTTGCGATACTGGAG
51605 ATCGCGTTGCGAATCTGGAAACTGATTTGCGATACTGGAG
1 ATCGCGTTGCGAATCTGGAAACTGATTTGCGATACTGGAG
51645 ATCGCGTTGCGA
1 ATCGCGTTGCGA
51657 TTTAGAGATC
Statistics
Matches: 70, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
39 7 0.10
40 56 0.80
41 7 0.10
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (40 bp):
ATCGCGTTGCGAATCTGGAAACTGATTTGCGATACTGGAG
Found at i:51572 original size:80 final size:80
Alignment explanation
Indices: 51485--51660 Score: 325
Period size: 80 Copynumber: 2.2 Consensus size: 80
51475 GATAGTCATA
51485 ATCGCGTTGCGATTTACATATTCGCATTAAAATAGTCAAAATCGCGTTGCGAATCTGGAAACTGA
1 ATCGCGTTGCGATTTACATATTCGCATTAAAATAGTCAAAATCGCGTTGCGAATCTGGAAACTGA
51550 TTTGCGATACTGGAG
66 TTTGCGATACTGGAG
***
51565 ATCGCGTTGCGATTTACATATTCGCATTGCGATAGTCAAAATCGCGTTGCGAATCTGGAAACTGA
1 ATCGCGTTGCGATTTACATATTCGCATTAAAATAGTCAAAATCGCGTTGCGAATCTGGAAACTGA
51630 TTTGCGATACTGGAG
66 TTTGCGATACTGGAG
51645 ATCGCGTTGCGATTTA
1 ATCGCGTTGCGATTTA
51661 GAGATCGCAT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 93 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (80 bp):
ATCGCGTTGCGATTTACATATTCGCATTAAAATAGTCAAAATCGCGTTGCGAATCTGGAAACTGA
TTTGCGATACTGGAG
Found at i:51574 original size:20 final size:20
Alignment explanation
Indices: 51551--51676 Score: 62
Period size: 20 Copynumber: 6.3 Consensus size: 20
51541 GGAAACTGAT
51551 TTGCGATACTGGAGATCGCG
1 TTGCGATACTGGAGATCGCG
* ** * *
51571 TTGCGAT-TTACATATTCGCA
1 TTGCGATACTGGAGA-TCGCG
* ** *
51591 TTGCGATAGTCAAAATCGCG
1 TTGCGATACTGGAGATCGCG
* **
51611 TTGCGA-ATCTGGA-AACTGAT
1 TTGCGATA-CTGGAGATC-GCG
51631 TTGCGATACTGGAGATCGCG
1 TTGCGATACTGGAGATCGCG
* * *
51651 TTGCGAT-TTAGAGATCGCA
1 TTGCGATACTGGAGATCGCG
51670 TTGCGAT
1 TTGCGAT
51677 TTTGTTGGTC
Statistics
Matches: 78, Mismatches: 22, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
19 22 0.28
20 50 0.64
21 6 0.08
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (20 bp):
TTGCGATACTGGAGATCGCG
Found at i:51666 original size:19 final size:19
Alignment explanation
Indices: 51642--51678 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
51632 TGCGATACTG
*
51642 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
51661 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
51679 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:51860 original size:2 final size:2
Alignment explanation
Indices: 51855--51883 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
51845 ATTATTAATG
51855 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
51884 AGAATTTTAA
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:57967 original size:42 final size:42
Alignment explanation
Indices: 57908--58040 Score: 239
Period size: 42 Copynumber: 3.2 Consensus size: 42
57898 CCAAAAAAGT
*
57908 ACAATATACAGCATGATAATTAGATATTCACCGCGGCATTCA
1 ACAATATACAGCATGATAATTAGATATTCACTGCGGCATTCA
*
57950 ACAATATACAGCATGATAATTAGATATTCACTGTGGCATTCA
1 ACAATATACAGCATGATAATTAGATATTCACTGCGGCATTCA
*
57992 ACAATATACAGCATGATAATTGGATATTCACTGCGGCATTCA
1 ACAATATACAGCATGATAATTAGATATTCACTGCGGCATTCA
58034 ACAATAT
1 ACAATAT
58041 GATTGATTAC
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (42 bp):
ACAATATACAGCATGATAATTAGATATTCACTGCGGCATTCA
Found at i:71513 original size:94 final size:93
Alignment explanation
Indices: 71347--71530 Score: 289
Period size: 94 Copynumber: 2.0 Consensus size: 93
71337 AATCACTATA
* *
71347 TGATCTATTGACCGACTAATTCAGATAATGTACTATAGAGGCGAGGGCGACCATTCCGACCTAAT
1 TGATCTATTGACCGACTAATTCAGACAATGTACTATAGAGGCGAGGGCGACCATTCAGACCTAAT
71412 TTGCTCCATTCGCAAACATCAAGATTATT
66 TTGCTCCATTCGC-AACATCAAGATTATT
* * * *
71441 TGATTTATTGACCTACTAATTCAGACCATGTACTATAGAGGCGAGGGCGATCATTCAGATCC-AA
1 TGATCTATTGACCGACTAATTCAGACAATGTACTATAGAGGCGAGGGCGACCATTCAGA-CCTAA
71505 TTTGCTCCATTCGCAACATCAAGATT
65 TTTGCTCCATTCGCAACATCAAGATT
71531 CAAACCTCTG
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
93 12 0.14
94 69 0.83
95 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (93 bp):
TGATCTATTGACCGACTAATTCAGACAATGTACTATAGAGGCGAGGGCGACCATTCAGACCTAAT
TTGCTCCATTCGCAACATCAAGATTATT
Done.