Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005233.1 Hibiscus syriacus cultivar Beakdansim tig00011847_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: 64092
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:97 original size:18 final size:18
Alignment explanation
Indices: 71--117 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
61 TTCTGACTCC
* *
71 TCGTTGTCATCATCGTCG
1 TCGTCGTCATCATCGTCA
*
89 TCGTCGTCACCATCGTCA
1 TCGTCGTCATCATCGTCA
107 TCGTCGTCATC
1 TCGTCGTCATC
118 GTCCTGAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.34, G:0.19, T:0.34
Consensus pattern (18 bp):
TCGTCGTCATCATCGTCA
Found at i:113 original size:9 final size:9
Alignment explanation
Indices: 71--120 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
61 TTCTGACTCC
*
71 TCGTTGTCA
1 TCGTCGTCA
* *
80 TCATCGTCG
1 TCGTCGTCA
89 TCGTCGTCA
1 TCGTCGTCA
* *
98 CCATCGTCA
1 TCGTCGTCA
107 TCGTCGTCA
1 TCGTCGTCA
116 TCGTC
1 TCGTC
121 CTGAGAGGTA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.12, C:0.34, G:0.20, T:0.34
Consensus pattern (9 bp):
TCGTCGTCA
Found at i:480 original size:18 final size:18
Alignment explanation
Indices: 454--493 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
444 AAAGGCGATG
*
454 GCGGTATCATATATGGTT
1 GCGGCATCATATATGGTT
472 GCGGCATCATATATGGTT
1 GCGGCATCATATATGGTT
490 GCGG
1 GCGG
494 TGGCTGCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.33
Consensus pattern (18 bp):
GCGGCATCATATATGGTT
Found at i:2096 original size:111 final size:111
Alignment explanation
Indices: 1964--2185 Score: 372
Period size: 111 Copynumber: 2.0 Consensus size: 111
1954 TTACAAAAAA
* * *
1964 TTAATTCTTAATTTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* * * *
2029 AATTAAAACGTTAAAATGTTACCGTATCGGTAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTGACCGTATCAGCAAAGTGTAGAGATAT
2075 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
2140 AATTAAAACGTTAAAATGTGACCGTATCAGCAAATTGTAGAGATAT
66 AATTAAAACGTTAAAATGTGACCGTATCAGCAAAGTGTAGAGATAT
2186 ATGATTTCCA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTGACCGTATCAGCAAAGTGTAGAGATAT
Found at i:2290 original size:17 final size:17
Alignment explanation
Indices: 2239--2293 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 17
2229 CTGTAAAAGA
*
2239 ATTATATTAGT-AAAAT
1 ATTATAATAGTAAAAAT
*
2255 ATTA-AATA--AAACAAA
1 ATTATAATAGTAAA-AAT
2270 ATTATAATAGTAAAAAT
1 ATTATAATAGTAAAAAT
2287 ATTATAA
1 ATTATAA
2294 AATATACCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
14 2 0.06
15 9 0.29
16 8 0.26
17 9 0.29
18 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
ATTATAATAGTAAAAAT
Found at i:2338 original size:20 final size:19
Alignment explanation
Indices: 2310--2348 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
2300 CCTTAAAAAG
*
2310 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGA-AAATTT
2330 AGAGAATTTGAGAAAATTT
1 AGAGAATTTGAGAAAATTT
2349 GGTGTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (19 bp):
AGAGAATTTGAGAAAATTT
Found at i:15924 original size:12 final size:13
Alignment explanation
Indices: 15902--15934 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
15892 ATATTTCTTC
*
15902 TTGTTTTTGTTTG
1 TTGTGTTTGTTTG
15915 TT-TGTTTGTTTG
1 TTGTGTTTGTTTG
15927 TTGTGTTT
1 TTGTGTTT
15935 AAACTGTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (13 bp):
TTGTGTTTGTTTG
Found at i:18212 original size:5 final size:5
Alignment explanation
Indices: 18204--18233 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
18194 GGAAAAGGCC
18204 AAATG AAATG AAATG AAATG AAATG AAATG
1 AAATG AAATG AAATG AAATG AAATG AAATG
18234 CCTAGTACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (5 bp):
AAATG
Found at i:18325 original size:74 final size:74
Alignment explanation
Indices: 18240--18397 Score: 235
Period size: 74 Copynumber: 2.1 Consensus size: 74
18230 AATGCCTAGT
* **
18240 ACAGAAAACACAGACAAAAGAAAGTACTTCTAACTCTCAGCAATACAACACAGATTTACTTGTTC
1 ACAGAAAACACAGACAAAAGAAAGTACTTCAAACTCAAAGCAATACAACACAGATTTACTTGTTC
*
18305 AAGAATCGA
66 AAGAATCAA
** * * *
18314 ACAGAAAACACAGTGAAAAGAAAGTACTTCAAACTCAAAGCTATATAACACTGATTTACTTGTTC
1 ACAGAAAACACAGACAAAAGAAAGTACTTCAAACTCAAAGCAATACAACACAGATTTACTTGTTC
18379 AAGAATCAA
66 AAGAATCAA
18388 ACAGAAAACA
1 ACAGAAAACA
18398 AAGATTAGCT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (74 bp):
ACAGAAAACACAGACAAAAGAAAGTACTTCAAACTCAAAGCAATACAACACAGATTTACTTGTTC
AAGAATCAA
Found at i:22778 original size:18 final size:18
Alignment explanation
Indices: 22739--22779 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
22729 GAGCCACATT
* * *
22739 TGTTGCTGTTGATGTTGT
1 TGTTGCTGATGATGATGA
22757 TGTTGCTGATGATGATGA
1 TGTTGCTGATGATGATGA
22775 TGTTG
1 TGTTG
22780 TTGAAAGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.05, G:0.34, T:0.49
Consensus pattern (18 bp):
TGTTGCTGATGATGATGA
Found at i:28068 original size:35 final size:35
Alignment explanation
Indices: 28022--28091 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
28012 TTCATTTAGG
28022 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
28057 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
28092 CCTGTACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.31, G:0.31, T:0.17
Consensus pattern (35 bp):
GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
Found at i:28093 original size:20 final size:20
Alignment explanation
Indices: 28021--28084 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
28011 TTTCATTTAG
28021 GGGGGAATCGATACCCCCCA
1 GGGGGAATCGATACCCCCCA
*
28041 GGGGGAATCTG-T---TCCC-
1 GGGGGAATC-GATACCCCCCA
28057 -GGGGAATCGATACCCCCCA
1 GGGGGAATCGATACCCCCCA
28076 GGGGGAATC
1 GGGGGAATC
28085 TGTTCCCCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
14 1 0.03
15 9 0.26
17 3 0.09
18 3 0.09
20 18 0.51
21 1 0.03
ACGTcount: A:0.22, C:0.30, G:0.34, T:0.14
Consensus pattern (20 bp):
GGGGGAATCGATACCCCCCA
Found at i:36063 original size:20 final size:20
Alignment explanation
Indices: 36027--36064 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36017 ATCCTATTTT
**
36027 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
36047 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
36065 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:38217 original size:11 final size:11
Alignment explanation
Indices: 38187--38222 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
38177 TATTTAAACG
38187 GGTATTGGGCC
1 GGTATTGGGCC
*
38198 GGATATTGGGTC
1 GG-TATTGGGCC
38210 GGTATTGGGCC
1 GGTATTGGGCC
38221 GG
1 GG
38223 GAATCGAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.11, C:0.14, G:0.47, T:0.28
Consensus pattern (11 bp):
GGTATTGGGCC
Found at i:38296 original size:24 final size:25
Alignment explanation
Indices: 38236--38296 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
38226 TCGAGCCGGG
38236 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
38259 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
38283 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
38297 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:38374 original size:13 final size:13
Alignment explanation
Indices: 38330--38361 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
38320 TTTAATATTT
38330 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
38343 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
38356 ATCGGG
1 ATCGGG
38362 TAATCGGGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.53, T:0.16
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:42654 original size:2 final size:2
Alignment explanation
Indices: 42643--42675 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
42633 AAATTTATTA
42643 AT AT -T 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
42676 TTATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:42735 original size:13 final size:13
Alignment explanation
Indices: 42691--42722 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
42681 TTTAATATTT
42691 ATCGGGGCGGATA
1 ATCGGGGCGGATA
*
42704 ATCGGGGCGGGTA
1 ATCGGGGCGGATA
42717 ATCGGG
1 ATCGGG
42723 TAATCGGGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.16, G:0.50, T:0.16
Consensus pattern (13 bp):
ATCGGGGCGGATA
Found at i:42779 original size:6 final size:6
Alignment explanation
Indices: 42768--42792 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42758 AAATGGGTTT
42768 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
42793 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:43376 original size:22 final size:23
Alignment explanation
Indices: 43330--43393 Score: 89
Period size: 22 Copynumber: 2.8 Consensus size: 23
43320 ACAAGGAATA
43330 TGCCACAAGAG-CAGAGAAAAAGTG
1 TGCCACAAGAGACAGAG--AAAGTG
43354 TGCCACAAGAGA-AGAGAAAGTG
1 TGCCACAAGAGACAGAGAAAGTG
43376 TGCCACAAG-GACAGAGAA
1 TGCCACAAGAGACAGAGAA
43394 TCTTATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.05
22 21 0.55
24 15 0.39
ACGTcount: A:0.45, C:0.17, G:0.30, T:0.08
Consensus pattern (23 bp):
TGCCACAAGAGACAGAGAAAGTG
Found at i:45678 original size:46 final size:46
Alignment explanation
Indices: 45622--45709 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
45612 TTAACAGGTA
*
45622 CCTGTCTATTGTGGTAATAATGCAAAACTATGTTGCAGCATCTGGT
1 CCTGTCTATTGTGATAATAATGCAAAACTATGTTGCAGCATCTGGT
* *
45668 CCTGTTTATTGTGATAATAATGCAAAACTATGTTGCTGCATC
1 CCTGTCTATTGTGATAATAATGCAAAACTATGTTGCAGCATC
45710 CTATTGTCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (46 bp):
CCTGTCTATTGTGATAATAATGCAAAACTATGTTGCAGCATCTGGT
Found at i:51094 original size:2 final size:2
Alignment explanation
Indices: 51089--51115 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51079 TAATATAAGA
51089 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
51116 AATGTTGTTG
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:63555 original size:37 final size:38
Alignment explanation
Indices: 63509--63583 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 38
63499 TTATATTTTT
*
63509 TAATATTTAAGATGATAATAA-TTGAAT-ATTAAAATAAA
1 TAATATTTAACA--ATAATAATTTGAATGATTAAAATAAA
*
63547 TAAT-TTTAACAATAATAATTTTAATGATTAAAATAAA
1 TAATATTTAACAATAATAATTTGAATGATTAAAATAAA
63584 AACAACTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 7 0.21
36 5 0.15
37 17 0.52
38 4 0.12
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (38 bp):
TAATATTTAACAATAATAATTTGAATGATTAAAATAAA
Done.