Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001996.1 Hibiscus syriacus cultivar Beakdansim tig00004087_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: 60647
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7700 original size:2 final size:2
Alignment explanation
Indices: 7693--7786 Score: 188
Period size: 2 Copynumber: 47.0 Consensus size: 2
7683 TATTAAAGAG
7693 TA TA TA TA TA TA 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 TA TA TA TA TA TA
7735 TA TA TA TA TA TA 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 TA TA TA TA TA TA
7777 TA TA TA TA TA
1 TA TA TA TA TA
7787 GATACGACTC
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10137 original size:2 final size:2
Alignment explanation
Indices: 10130--10156 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10120 TCTTTTTAAA
10130 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
10157 CCCCTATCCG
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:10484 original size:24 final size:24
Alignment explanation
Indices: 10369--10484 Score: 128
Period size: 24 Copynumber: 4.8 Consensus size: 24
10359 CATAAATCAG
* * *
10369 GTCAAGTATCATATAAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* *
10393 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
* *
10417 GTCAAGTATCAGATCAAAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
10441 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
*
10465 GTCAAGTATTAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
10485 TCAAATCGAA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
23 5 0.06
24 71 0.91
25 2 0.03
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:10500 original size:48 final size:48
Alignment explanation
Indices: 10402--10502 Score: 116
Period size: 48 Copynumber: 2.1 Consensus size: 48
10392 GGTCAAGTAA
** *
10402 CAGATCAGAATCCAAGTCAAGTATCAGATCAAAATCTATGTCAGATAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAAAATCTAAATCAGAAAT
* * *
10450 CAGATCAGAATCCATGTCAAGTATTAGATCAGAAT-TCAAATC-GAAAAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAAAATCT-AAATCAG-AAAT
10498 CAGAT
1 CAGAT
10503 AAAATATTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 2 0.04
48 43 0.96
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.25
Consensus pattern (48 bp):
CAGATCAGAATCCAAGTCAAGTATCAGATCAAAATCTAAATCAGAAAT
Found at i:11645 original size:17 final size:18
Alignment explanation
Indices: 11611--11645 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11601 TTCTATCCTG
*
11611 TCTTATTATTTAATTCCA
1 TCTTATCATTTAATTCCA
11629 TCTTATCATTT-ATTCCA
1 TCTTATCATTTAATTCCA
11646 GACCTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.20, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCCA
Found at i:12966 original size:13 final size:13
Alignment explanation
Indices: 12948--12972 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12938 GTTAACGGGT
12948 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
12961 CGGGTCGGGTCA
1 CGGGTCGGGTCA
12973 GGTTATGACC
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:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:14006 original size:12 final size:12
Alignment explanation
Indices: 13989--14014 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13979 CTCAAAGGAC
13989 TTGGGTATCATA
1 TTGGGTATCATA
14001 TTGGGTATCATA
1 TTGGGTATCATA
14013 TT
1 TT
14015 AGTCATATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (12 bp):
TTGGGTATCATA
Found at i:14078 original size:2 final size:2
Alignment explanation
Indices: 14071--14096 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14061 AAATAAATAC
14071 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
14097 TTAACCGGGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15069 original size:14 final size:15
Alignment explanation
Indices: 15047--15093 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
15037 TATAAGGTAA
*
15047 TTTTGTTATAATT-T
1 TTTTATTATAATTAT
*
15061 TTTTATTATACTTAT
1 TTTTATTATAATTAT
*
15076 TGTTTATTATGATTAT
1 T-TTTATTATAATTAT
15092 TT
1 TT
15094 GAAAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.41
15 3 0.11
16 13 0.48
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:18423 original size:19 final size:19
Alignment explanation
Indices: 18399--18472 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
18389 ATGTTTGGAT
*
18399 GGTATCGATACCCCTAGTA
1 GGTATCGATACCCCCAGTA
18418 GGTATCGATACCCCCATGCTA
1 GGTATCGATACCCCCA-G-TA
*
18439 TGGTATCGATACCCCCCAATA
1 -GGTATCGATA-CCCCCAGTA
*
18460 GGTACCGATACCC
1 GGTATCGATACCC
18473 TCAGGCATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
19 18 0.38
20 10 0.21
21 4 0.08
22 10 0.21
23 6 0.12
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (19 bp):
GGTATCGATACCCCCAGTA
Found at i:20384 original size:21 final size:21
Alignment explanation
Indices: 20358--20397 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20348 AAGACTCTAT
20358 TTTCAAAATACAAAAATGATG
1 TTTCAAAATACAAAAATGATG
**
20379 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
20398 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATG
Found at i:24241 original size:21 final size:21
Alignment explanation
Indices: 24215--24314 Score: 82
Period size: 23 Copynumber: 4.6 Consensus size: 21
24205 TGTGCATAGA
24215 GTATCGATACCCCTT-ATACAG
1 GTATCGATACCCCTTGATA-AG
24236 GTATCGATACCCCCTTTGAATAA-
1 GTATCGATA-CCCC-TTG-ATAAG
*
24259 GTATTGATACCCCTTGA-ATAG
1 GTATCGATACCCCTTGATA-AG
*
24280 GTATCGATACCCTCTTTGA-ATG
1 GTATCGATACCC-C-TTGATAAG
24302 TGTATCGATACCC
1 -GTATCGATACCC
24315 TCCCTTATGG
Statistics
Matches: 67, Mismatches: 3, Indels: 16
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.01
20 2 0.03
21 23 0.34
22 10 0.15
23 27 0.40
24 1 0.01
25 3 0.04
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (21 bp):
GTATCGATACCCCTTGATAAG
Found at i:24267 original size:23 final size:23
Alignment explanation
Indices: 24236--24338 Score: 99
Period size: 21 Copynumber: 4.7 Consensus size: 23
24226 CCTTATACAG
24236 GTATCGATACCCCCTTTGAATAA
1 GTATCGATACCCCCTTTGAATAA
* *
24259 GTATTGATA-CCCC-TTGAATAG
1 GTATCGATACCCCCTTTGAATAA
* **
24280 GTATCGATACCCTCTTTGAATGT
1 GTATCGATACCCCCTTTGAATAA
* *
24303 GTATCGATACCCTCCCTT--AT-G
1 GTATCGATACCC-CCTTTGAATAA
24324 GTATCGATACCCCCT
1 GTATCGATACCCCCT
24339 GTCGGGTTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
20 2 0.03
21 27 0.40
22 9 0.13
23 26 0.39
24 3 0.04
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (23 bp):
GTATCGATACCCCCTTTGAATAA
Found at i:24282 original size:44 final size:43
Alignment explanation
Indices: 24214--24338 Score: 146
Period size: 44 Copynumber: 2.8 Consensus size: 43
24204 TTGTGCATAG
*
24214 AGTATCGATACCCCTTATACAGGTATCGATACCCCCTTTGAATA
1 AGTATCGATACCCCTTA-ATAGGTATCGATACCCCCTTTGAATA
* * *
24258 AGTATTGATACCCCTTGAATAGGTATCGATACCCTCTTTGAATG
1 AGTATCGATACCCCTT-AATAGGTATCGATACCCCCTTTGAATA
*
24302 TGTATCGATACCCTCCCTT-AT-GGTATCGATACCCCCT
1 AGTATCGATA--C-CCCTTAATAGGTATCGATACCCCCT
24339 GTCGGGTTTA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
44 61 0.87
45 3 0.04
46 1 0.01
47 5 0.07
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (43 bp):
AGTATCGATACCCCTTAATAGGTATCGATACCCCCTTTGAATA
Found at i:24329 original size:21 final size:21
Alignment explanation
Indices: 24235--24335 Score: 75
Period size: 23 Copynumber: 4.6 Consensus size: 21
24225 CCCTTATACA
24235 GGTATCGATACCC-CCTTTGAAT
1 GGTATCGATACCCTCC-TT-AAT
* *
24257 AAGTATTGATA-CC-CCTTGAAT
1 -GGTATCGATACCCTCCTT-AAT
*
24278 AGGTATCGATACCCTCTTTGAAT
1 -GGTATCGATACCCTCCTT-AAT
24301 GTGTATCGATACCCTCCCTT-AT
1 G-GTATCGATACCCT-CCTTAAT
24323 GGTATCGATACCC
1 GGTATCGATACCC
24336 CCTGTCGGGT
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
21 27 0.40
22 10 0.15
23 28 0.41
24 3 0.04
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (21 bp):
GGTATCGATACCCTCCTTAAT
Found at i:25036 original size:21 final size:21
Alignment explanation
Indices: 25010--25056 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
25000 CGGTCTAACC
25010 ATCCTCCAAACT-TTCCTCAAA
1 ATCCTCC-AACTATTCCTCAAA
*
25031 ATCCTCCACCTATTCCTCAAA
1 ATCCTCCAACTATTCCTCAAA
*
25052 TTCCT
1 ATCCT
25057 AATCCTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.32
Consensus pattern (21 bp):
ATCCTCCAACTATTCCTCAAA
Found at i:26985 original size:24 final size:24
Alignment explanation
Indices: 26956--27005 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
26946 TGGTGGTTGA
*
26956 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
26980 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
27004 TT
1 TT
27006 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:30274 original size:23 final size:23
Alignment explanation
Indices: 30231--30283 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
30221 TGTTTGTTTG
** *
30231 TTTATTTTTATTTGTTTTATTTC
1 TTTATTTTTATTTGTAATATTAC
30254 TTTATTTTTAATTT-TAATATTAC
1 TTTATTTTT-ATTTGTAATATTAC
30277 TTT-TTTT
1 TTTATTTT
30284 AGGACAAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 18 0.69
24 4 0.15
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTATTTTTATTTGTAATATTAC
Found at i:33043 original size:16 final size:16
Alignment explanation
Indices: 33015--33047 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33005 CACGTGAGGA
33015 TTATCTTATTTTTATT
1 TTATCTTATTTTTATT
33031 TTAT-TTATCTTTTATT
1 TTATCTTAT-TTTTATT
33047 T
1 T
33048 ATTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATCTTATTTTTATT
Found at i:34404 original size:21 final size:21
Alignment explanation
Indices: 34375--34429 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
34365 TTACACTATA
* *
34375 GGTATCGATACCCTATGAAGG
1 GGTACCGATACCCTATGAAAG
34396 GGTACCGATACCCTATGAAAG
1 GGTACCGATACCCTATGAAAG
* *
34417 GGTGCTGATACCC
1 GGTACCGATACCC
34430 CCCGTTTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (21 bp):
GGTACCGATACCCTATGAAAG
Found at i:37768 original size:9 final size:9
Alignment explanation
Indices: 37754--37787 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
37744 TAAGTAAAAT
37754 ATTAAATAA
1 ATTAAATAA
37763 ATTAAAT-A
1 ATTAAATAA
*
37771 CTTAAATAA
1 ATTAAATAA
37780 ATTAAATA
1 ATTAAATA
37788 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:37786 original size:17 final size:17
Alignment explanation
Indices: 37750--37788 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
37740 TAATTAAGTA
37750 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
37766 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
37783 AAATAC
1 AAATAC
37789 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:38220 original size:29 final size:29
Alignment explanation
Indices: 38174--38252 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
38164 TACTGCTAAG
** *
38174 GGTGTTAGATCGGGAAATATAGTTTGACC
1 GGTGTTAGATCGAAAAATATAGTCTGACC
*
38203 GGTGTTAGATCAAAAAATATAGTCTGACC
1 GGTGTTAGATCGAAAAATATAGTCTGACC
* *
38232 GATGTTAGATCGATAAATATA
1 GGTGTTAGATCGAAAAATATA
38253 CCGATCACTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.30
Consensus pattern (29 bp):
GGTGTTAGATCGAAAAATATAGTCTGACC
Found at i:40014 original size:31 final size:31
Alignment explanation
Indices: 39907--40015 Score: 83
Period size: 31 Copynumber: 3.7 Consensus size: 31
39897 TATTATTTTT
*
39907 AAAATATTAAAATAATT-TA-TTTATT-AT-
1 AAAATATTAATATAATTATATTTTATTAATA
* *
39934 TAAATATT-AT-T-TTTATAATTTTATTAATA
1 AAAATATTAATATAATTAT-ATTTTATTAATA
* *
39963 AAAATATTAATATTAGTATATTTTATTGAAATA
1 AAAATATTAATATAATTATATTTTATT--AATA
39996 AAAATATT-ATA-AATTATATT
1 AAAATATTAATATAATTATATT
40016 AATTATTTAG
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
24 2 0.03
25 2 0.03
26 2 0.03
27 13 0.20
28 2 0.03
29 7 0.11
30 2 0.03
31 16 0.25
32 6 0.09
33 12 0.19
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.50
Consensus pattern (31 bp):
AAAATATTAATATAATTATATTTTATTAATA
Found at i:40095 original size:23 final size:23
Alignment explanation
Indices: 40046--40096 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
40036 GTATTATATT
**
40046 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
40069 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
40092 ATATT
1 ATATT
40097 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:48348 original size:20 final size:20
Alignment explanation
Indices: 48323--48360 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
48313 CCTGACTTGT
*
48323 TTGGAAGACCTGTAAATCGG
1 TTGGAAGACCTGAAAATCGG
48343 TTGGAAGACCTGAAAATC
1 TTGGAAGACCTGAAAATC
48361 AATTCCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (20 bp):
TTGGAAGACCTGAAAATCGG
Found at i:48741 original size:20 final size:20
Alignment explanation
Indices: 48716--48758 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
48706 TCTAAAGGCT
48716 CATTTAGAACCATGTAGATG
1 CATTTAGAACCATGTAGATG
* * *
48736 CATTTAGAATCATTTAGTTG
1 CATTTAGAACCATGTAGATG
48756 CAT
1 CAT
48759 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (20 bp):
CATTTAGAACCATGTAGATG
Done.