Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007447.1 Hibiscus syriacus cultivar Beakdansim tig00020355_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: 105336
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1770 original size:18 final size:19
Alignment explanation
Indices: 1733--1771 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1723 ACCGACGAGT
*
1733 AGTATCGGTACTCCTCAAGG
1 AGTATCGATACT-CTCAAGG
1753 AGTATCGATACT-TCAAGG
1 AGTATCGATACTCTCAAGG
1771 A
1 A
1772 AAATCTTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (19 bp):
AGTATCGATACTCTCAAGG
Found at i:1846 original size:22 final size:21
Alignment explanation
Indices: 1818--1878 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
1808 CGGTACTGTT
*
1818 GAACAGTATCAATACTAAGCAA
1 GAACAGTATCGATACTAAG-AA
*
1840 GAACAGTATCGATACT-AGAT
1 GAACAGTATCGATACTAAGAA
*
1860 GAACACTATCGATACTAAG
1 GAACAGTATCGATACTAAG
1879 TGCACAGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 4 0.11
22 15 0.43
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.21
Consensus pattern (21 bp):
GAACAGTATCGATACTAAGAA
Found at i:11470 original size:20 final size:21
Alignment explanation
Indices: 11432--11472 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11422 AAACCATTCA
11432 GGGGGGAATCGGTACCCCCTT
1 GGGGGGAATCGGTACCCCCTT
* *
11453 GGGGGGAATCGTTTCCCCCT
1 GGGGGGAATCGGTACCCCCT
11473 GAGCAATCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.29, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTT
Found at i:14155 original size:21 final size:23
Alignment explanation
Indices: 14107--14166 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
14097 ATTCCCCTGT
14107 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
* **
14130 AGGGGGAATTTGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
14151 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGGTTCCC
14167 TATGCACCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 4 0.14
21 11 0.38
22 3 0.10
23 11 0.38
ACGTcount: A:0.18, C:0.23, G:0.35, T:0.23
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:18013 original size:21 final size:21
Alignment explanation
Indices: 17979--18019 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17969 GAGTTTGTTT
*
17979 TCATTTTTCAATTTTGAAAAC
1 TCATTTTTCAATTTTAAAAAC
18000 TCATTTTT-ATATTTTAAAAA
1 TCATTTTTCA-ATTTTAAAAA
18020 TAATTTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAAAC
Found at i:19967 original size:20 final size:19
Alignment explanation
Indices: 19942--19979 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
19932 CGTTATACAA
*
19942 GGGGGGAATTGGTATCCCTG
1 GGGGGGAATCGGT-TCCCTG
19962 GGGGGGAATCGGTTCCCT
1 GGGGGGAATCGGTTCCCT
19980 CCGAGCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.13, C:0.18, G:0.45, T:0.24
Consensus pattern (19 bp):
GGGGGGAATCGGTTCCCTG
Found at i:24150 original size:31 final size:31
Alignment explanation
Indices: 24078--24152 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
24068 AACGTCCAAG
* * *
24078 TGACCAAAACATAATAAAACGATAACATAAG
1 TGACCAAAACTTAATAAAACAATAACATAAA
**
24109 TGACCAAAACTTAATAAAACAATAATGTAAA
1 TGACCAAAACTTAATAAAACAATAACATAAA
24140 TGACCAAAACTTA
1 TGACCAAAACTTA
24153 TGTTTTTTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (31 bp):
TGACCAAAACTTAATAAAACAATAACATAAA
Found at i:25619 original size:21 final size:21
Alignment explanation
Indices: 25593--25632 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25583 TAAAGCTTAC
25593 ATGATA-ATCTACAATATTGAT
1 ATGATAGATC-ACAATATTGAT
*
25614 ATGATAGATCATAATATTG
1 ATGATAGATCACAATATTG
25633 TTGTGACAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.38
Consensus pattern (21 bp):
ATGATAGATCACAATATTGAT
Found at i:25786 original size:26 final size:27
Alignment explanation
Indices: 25732--25787 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
25722 ATTTGAGAAC
* * *
25732 TTATTTAATTTTTAAAATATTAAGGTA
1 TTATTTAATATTTAAAATATAAAAGTA
*
25759 TTATTTAA-ATTTAAAATATAAAATTA
1 TTATTTAATATTTAAAATATAAAAGTA
25785 TTA
1 TTA
25788 ATATATTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (27 bp):
TTATTTAATATTTAAAATATAAAAGTA
Found at i:30470 original size:21 final size:21
Alignment explanation
Indices: 30444--30483 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
30434 CAGAACCCTA
*
30444 GGGGGGTATCGGTTCCCCTGT
1 GGGGGGAATCGGTTCCCCTGT
30465 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGGTTCCCCT
30484 TCAAAGGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.25, G:0.42, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCCTGT
Found at i:30513 original size:21 final size:23
Alignment explanation
Indices: 30465--30515 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
30455 GTTCCCCTGT
*
30465 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGCTCCCCTTCAA
*
30488 AGGGGGAATCGGCT-CCC-TCAA
1 GGGGGGAATCGGCTCCCCTTCAA
30509 GGGGGGA
1 GGGGGGA
30516 TCGATTCTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.40
22 3 0.12
23 12 0.48
ACGTcount: A:0.20, C:0.24, G:0.41, T:0.16
Consensus pattern (23 bp):
GGGGGGAATCGGCTCCCCTTCAA
Found at i:36004 original size:22 final size:21
Alignment explanation
Indices: 35975--36030 Score: 94
Period size: 22 Copynumber: 2.6 Consensus size: 21
35965 AACCATTCAG
35975 GGGGGAATCGGTACCCCCTTA
1 GGGGGAATCGGTACCCCCTTA
35996 GGGGAGAATCGGTACCCCCTTA
1 GGGG-GAATCGGTACCCCCTTA
36018 GGTGGGAATCGGT
1 GG-GGGAATCGGT
36031 TCCCTCTGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.12
22 27 0.82
23 2 0.06
ACGTcount: A:0.20, C:0.23, G:0.38, T:0.20
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTTA
Found at i:39846 original size:23 final size:23
Alignment explanation
Indices: 39792--39846 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
39782 TAAGAATAAT
*
39792 TATGTCTTTGTGACACATTTATT
1 TATGTCTTTGTGACACATTTATC
* * *
39815 TATGCCTTTGTGGCACGTTTATC
1 TATGTCTTTGTGACACATTTATC
*
39838 TCTGTCTTT
1 TATGTCTTT
39847 TGGTAGTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.15, C:0.18, G:0.16, T:0.51
Consensus pattern (23 bp):
TATGTCTTTGTGACACATTTATC
Found at i:40976 original size:16 final size:16
Alignment explanation
Indices: 40955--41015 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
40945 TGATCACTAG
*
40955 TTAT-TATATATGATGT
1 TTATATATATAT-ATAT
*
40971 TTAT-TATGTATATAT
1 TTATATATATATATAT
*
40986 ATATATATATATATAT
1 TTATATATATATATAT
*
41002 ATATATATATATAT
1 TTATATATATATAT
41016 GATGTTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.15
16 34 0.85
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
TTATATATATATATAT
Found at i:40984 original size:2 final size:2
Alignment explanation
Indices: 40979--41015 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
40969 GTTTATTATG
40979 TA 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 TA T
41016 GATGTTATTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43226 original size:2 final size:2
Alignment explanation
Indices: 43219--43245 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43209 TGAATTTGAG
43219 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
43246 ATTTTAAGAT
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:43269 original size:19 final size:19
Alignment explanation
Indices: 43245--43281 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
43235 ATATATATAT
*
43245 AATTTTAAGATGTGAATTA
1 AATTTTAAGATATGAATTA
*
43264 AATTTTAATATATGAATT
1 AATTTTAAGATATGAATT
43282 TAAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (19 bp):
AATTTTAAGATATGAATTA
Found at i:51277 original size:20 final size:20
Alignment explanation
Indices: 51248--51287 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
51238 GAGGGTGGTA
51248 GTATTAAGACTAGATGCTCG
1 GTATTAAGACTAGATGCTCG
* *
51268 GTATTGAGACTGGATGCTCG
1 GTATTAAGACTAGATGCTCG
51288 ATCTCAGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (20 bp):
GTATTAAGACTAGATGCTCG
Found at i:59927 original size:90 final size:89
Alignment explanation
Indices: 59811--59984 Score: 294
Period size: 90 Copynumber: 1.9 Consensus size: 89
59801 TCCCGAATAT
* * *
59811 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATAGAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAG
59876 GGTAACTTGGATATAAAAGGATTA
66 GGTAACTTGGATATAAAAGGATTA
59900 TTAAATTCTAATTAATTAAATAGAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTA
1 TTAAATTC-AATTAATTAAATAGAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTA
**
59965 GGGTAACTTGTCTATAAAAG
65 GGGTAACTTGGATATAAAAG
59985 AGTGTGTTAG
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 7 0.09
90 72 0.91
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.37
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATAGAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAG
GGTAACTTGGATATAAAAGGATTA
Found at i:61188 original size:17 final size:17
Alignment explanation
Indices: 61162--61200 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
61152 CCAACTAGTT
*
61162 ATTTTTTTATTTT-TTA
1 ATTTTGTTATTTTATTA
61178 GATTTTGTTATTTTATTA
1 -ATTTTGTTATTTTATTA
61196 ATTTT
1 ATTTT
61201 ATTTAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (17 bp):
ATTTTGTTATTTTATTA
Found at i:61730 original size:21 final size:21
Alignment explanation
Indices: 61706--61746 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
61696 TTCACCACCC
* *
61706 AATAATTTATATATTTTACAG
1 AATAATCTATACATTTTACAG
61727 AATAATCTATACATTTTACA
1 AATAATCTATACATTTTACA
61747 TTTTTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (21 bp):
AATAATCTATACATTTTACAG
Found at i:75833 original size:21 final size:21
Alignment explanation
Indices: 75807--75864 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
75797 CCGCTATACT
75807 TGAATTTTAAATTCATTGCTA
1 TGAATTTTAAATTCATTGCTA
*
75828 TGAATTTTAAATTCATTTCTA
1 TGAATTTTAAATTCATTGCTA
75849 TGAATTTTAAATTCAT
1 TGAATTTTAAATTCAT
75865 ACATATGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (21 bp):
TGAATTTTAAATTCATTGCTA
Found at i:83162 original size:42 final size:41
Alignment explanation
Indices: 83115--83215 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
83105 CTAAAATTTC
* * *
83115 TAAATCATTCGGGCCATCAGTAAGTCTTTCGAGTATGATGA
1 TAAATCATTCGGGCCATCACTAAGTCTTTCGAGCAGGATGA
* * * * *
83156 TTAAATCCTTCGGGTCATCTCTCAGTTTTTCGAGCAGGATGA
1 -TAAATCATTCGGGCCATCACTAAGTCTTTCGAGCAGGATGA
*
83198 TAAGTCATTCGGGCCATC
1 TAAATCATTCGGGCCATC
83216 TATAAGACCT
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 15 0.31
42 33 0.69
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (41 bp):
TAAATCATTCGGGCCATCACTAAGTCTTTCGAGCAGGATGA
Found at i:91681 original size:24 final size:24
Alignment explanation
Indices: 91652--91701 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
91642 CAGTATCATT
91652 AGAGATTGTTGATTGAAACAAATG
1 AGAGATTGTTGATTGAAACAAATG
*
91676 AGAGATTGTTGATTGAAATAAATG
1 AGAGATTGTTGATTGAAACAAATG
91700 AG
1 AG
91702 TTACCGTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.26, T:0.30
Consensus pattern (24 bp):
AGAGATTGTTGATTGAAACAAATG
Done.