Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004153.1 Hibiscus syriacus cultivar Beakdansim tig00009082_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: 67030
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:11569 original size:35 final size:35
Alignment explanation
Indices: 11531--11643 Score: 129
Period size: 35 Copynumber: 3.2 Consensus size: 35
11521 GGTAAGGGAT
* * *
11531 TGGTGGTTATATAGGCGTGAAATGGTGATAGAAGT
1 TGGTGATTATATAGGCGTGAAATGGTGATGGAAGA
* * * *
11566 TGGTGATGATATGGGCTTGCAATGGTGATGGAAGA
1 TGGTGATTATATAGGCGTGAAATGGTGATGGAAGA
*
11601 TGGTGATGT-TATCGGCGTGAAAATGGTGATGGAAGA
1 TGGTGAT-TATATAGGCGTG-AAATGGTGATGGAAGA
11637 TGGTGAT
1 TGGTGAT
11644 GTTATAGTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
35 43 0.66
36 22 0.34
ACGTcount: A:0.27, C:0.04, G:0.39, T:0.30
Consensus pattern (35 bp):
TGGTGATTATATAGGCGTGAAATGGTGATGGAAGA
Found at i:11629 original size:36 final size:35
Alignment explanation
Indices: 11544--11648 Score: 147
Period size: 35 Copynumber: 3.0 Consensus size: 35
11534 TGGTTATATA
* * * *
11544 GGCGTGAAATGGTGATAGAAGTTGGTGATGATATG
1 GGCGTGAAATGGTGATGGAAGATGGTGATGTTATC
* *
11579 GGCTTGCAATGGTGATGGAAGATGGTGATGTTATC
1 GGCGTGAAATGGTGATGGAAGATGGTGATGTTATC
11614 GGCGTGAAAATGGTGATGGAAGATGGTGATGTTAT
1 GGCGTG-AAATGGTGATGGAAGATGGTGATGTTAT
11649 AGTTAGTATC
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
35 34 0.56
36 27 0.44
ACGTcount: A:0.27, C:0.05, G:0.39, T:0.30
Consensus pattern (35 bp):
GGCGTGAAATGGTGATGGAAGATGGTGATGTTATC
Found at i:12972 original size:17 final size:17
Alignment explanation
Indices: 12934--12973 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
12924 TTTATTAGAG
12934 TAATGAACTAGTTAAAT
1 TAATGAACTAGTTAAAT
*
12951 GAATGAACTAGATT-AAT
1 TAATGAACTAG-TTAAAT
12968 TAATGA
1 TAATGA
12974 CCTAACTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (17 bp):
TAATGAACTAGTTAAAT
Found at i:14234 original size:33 final size:32
Alignment explanation
Indices: 14168--14230 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
14158 AAAAAATTAA
* *
14168 AAGAAAGAAATGATTAAAATGGAATATGGAAG
1 AAGAAAGAAATGATTAAAATAGAAAATGGAAG
14200 AAGAAAGGAAATGA-TAAGAA-AGAAAATGGAA
1 AAGAAA-GAAATGATTAA-AATAGAAAATGGAA
14231 AGAAATGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 18 0.67
33 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.14
Consensus pattern (32 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGAAG
Found at i:14424 original size:14 final size:14
Alignment explanation
Indices: 14391--14433 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
14381 TATGGGCGTG
*
14391 AATGGTGATGG-AG
1 AATGGTGATGGAAA
*
14404 GATGGTGATGGAAA
1 AATGGTGATGGAAA
14418 AATGGTGAT-GAAA
1 AATGGTGATGGAAA
14431 AAT
1 AAT
14434 AGTATCTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.37, T:0.23
Consensus pattern (14 bp):
AATGGTGATGGAAA
Found at i:18256 original size:13 final size:14
Alignment explanation
Indices: 18238--18273 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
18228 ATGGGCGTGA
*
18238 ATGGTGATGG-AGG
1 ATGGTGATGGAAAG
18251 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
18265 ATGGTGATG
1 ATGGTGATG
18274 AAAAATAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.28, C:0.00, G:0.47, T:0.25
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:18276 original size:13 final size:13
Alignment explanation
Indices: 18238--18276 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
18228 ATGGGCGTGA
* *
18238 ATGGTGATGGAGG
1 ATGGTGATGAAAG
18251 ATGGTGATGGAAAG
1 ATGGTGAT-GAAAG
18265 ATGGTGATGAAA
1 ATGGTGATGAAA
18277 AATAGTATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.44, T:0.23
Consensus pattern (13 bp):
ATGGTGATGAAAG
Found at i:18647 original size:19 final size:20
Alignment explanation
Indices: 18609--18651 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
18599 GAAACCCCTT
18609 TGAAAACACATAATTTTTAA
1 TGAAAACACATAATTTTTAA
*
18629 TGAAAATACATAA-TTTTAA
1 TGAAAACACATAATTTTTAA
18648 TGAA
1 TGAA
18652 GATAAATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (20 bp):
TGAAAACACATAATTTTTAA
Found at i:22967 original size:18 final size:18
Alignment explanation
Indices: 22944--22982 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
22934 TAGTCTTATA
22944 TTCGTCTAAAAGAAGGGG
1 TTCGTCTAAAAGAAGGGG
22962 TTCGTCTAAAAGAAGGGG
1 TTCGTCTAAAAGAAGGGG
22980 TTC
1 TTC
22983 CTCTTGGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.26
Consensus pattern (18 bp):
TTCGTCTAAAAGAAGGGG
Found at i:23513 original size:17 final size:17
Alignment explanation
Indices: 23491--23532 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
23481 TATTACAATT
23491 ATGAACTAGTTAAATGA
1 ATGAACTAGTTAAATGA
* *
23508 ATGAACTAGTTTAATTA
1 ATGAACTAGTTAAATGA
23525 ATGAACTA
1 ATGAACTA
23533 ACTATATGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (17 bp):
ATGAACTAGTTAAATGA
Found at i:25703 original size:10 final size:10
Alignment explanation
Indices: 25688--25712 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25678 GTGACTCATT
25688 AGCTATTTGG
1 AGCTATTTGG
25698 AGCTATTTGG
1 AGCTATTTGG
25708 AGCTA
1 AGCTA
25713 AGAACCAACA
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:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (10 bp):
AGCTATTTGG
Found at i:28311 original size:23 final size:23
Alignment explanation
Indices: 28276--28320 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
28266 AAATCCAGCA
28276 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATCAAAGCACTCAAAAG
* *
28299 AAGAAATTGAAAGCACTCAAAA
1 AAGAAAATCAAAGCACTCAAAA
28321 AGAAAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.16, G:0.13, T:0.11
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCAAAAG
Found at i:32526 original size:17 final size:17
Alignment explanation
Indices: 32504--32560 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
32494 TTATTACATT
32504 AATGAACTAGTTAAATG
1 AATGAACTAGTTAAATG
* *
32521 AATGAACTAGTTTAATT
1 AATGAACTAGTTAAATG
* * *
32538 AATAAACTAATTATATGG
1 AATGAACTAGTTAAAT-G
32556 AATGA
1 AATGA
32561 TCTAAGATGC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 27 0.87
18 4 0.13
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.33
Consensus pattern (17 bp):
AATGAACTAGTTAAATG
Found at i:39646 original size:13 final size:14
Alignment explanation
Indices: 39628--39656 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39618 GATGTAGTCT
39628 TTTTCTT-TTTTTG
1 TTTTCTTCTTTTTG
39641 TTTTCTTCTTTTTG
1 TTTTCTTCTTTTTG
39655 TT
1 TT
39657 GCTTTTGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (14 bp):
TTTTCTTCTTTTTG
Found at i:40070 original size:35 final size:36
Alignment explanation
Indices: 40041--40168 Score: 179
Period size: 36 Copynumber: 3.6 Consensus size: 36
40031 TTGGTTGTTA
* * *
40041 TATAGGCGTG-AAATGGTGATAGAAGTTGGTGATGA
1 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
* * *
40076 TATGGGCATG-CAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
*
40111 TATAGGTGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
40147 TATAGGCGTGAAAATGGTGATG
1 TATAGGCGTGAAAATGGTGATG
40169 TTATAGGTAG
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 36 0.44
36 45 0.56
ACGTcount: A:0.30, C:0.03, G:0.38, T:0.29
Consensus pattern (36 bp):
TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
Found at i:40106 original size:13 final size:13
Alignment explanation
Indices: 40088--40145 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
40078 TGGGCATGCA
40088 ATGGTGATGGAAG
1 ATGGTGATGGAAG
** *
40101 ATGGTGATGTTAT
1 ATGGTGATGGAAG
*
40114 A-GGTG-T-GAAA
1 ATGGTGATGGAAG
40124 ATGGTGATGGAAG
1 ATGGTGATGGAAG
40137 ATGGTGATG
1 ATGGTGATG
40146 TTATAGGCGT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 2 0.06
11 5 0.14
12 5 0.14
13 23 0.66
ACGTcount: A:0.29, C:0.00, G:0.41, T:0.29
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:44181 original size:25 final size:25
Alignment explanation
Indices: 44153--44200 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
44143 TTTTTTGAAA
44153 TTTTGGC-TTTTTTGTTTTGTTTTTT
1 TTTTGGCTTTTTTTGTTTT-TTTTTT
44178 TTTTGGCTTTTTTTGTTTTTTTT
1 TTTTGGCTTTTTTTGTTTTTTTT
44201 AAATAGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.00, C:0.04, G:0.15, T:0.81
Consensus pattern (25 bp):
TTTTGGCTTTTTTTGTTTTTTTTTT
Found at i:46879 original size:16 final size:16
Alignment explanation
Indices: 46858--46889 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46848 TGCATATGAT
46858 GTCCAAATCATTCACC
1 GTCCAAATCATTCACC
46874 GTCCAAATCATTCACC
1 GTCCAAATCATTCACC
46890 AAGCTACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.38, G:0.06, T:0.25
Consensus pattern (16 bp):
GTCCAAATCATTCACC
Found at i:56136 original size:36 final size:35
Alignment explanation
Indices: 56040--56151 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
56030 TTGGTGGTTA
* * * *
56040 TATAAGCGTGAAATGGTGATAGAAGTTGGTGATGA
1 TATAGGCGTAAAATGGTGATAGAAGATGGTGATGT
** *
56075 TATAGGCGTGCAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTAAAATGGTGATAGAAGATGGTGATGT
56110 TATAGGCGTAAAAATGGTGATAGAAGATGGTGATGT
1 TATAGGCGT-AAAATGGTGATAGAAGATGGTGATGT
56146 TATAGG
1 TATAGG
56152 TAGTATCTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 39 0.57
36 29 0.43
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.29
Consensus pattern (35 bp):
TATAGGCGTAAAATGGTGATAGAAGATGGTGATGT
Found at i:61879 original size:19 final size:20
Alignment explanation
Indices: 61855--61897 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
61845 AGCATTTATC
*
61855 TTCATT-AAAATTATGTATT
1 TTCATTCAAAATCATGTATT
*
61874 TTCATTCAAAATCATGTGTT
1 TTCATTCAAAATCATGTATT
61894 TTCA
1 TTCA
61898 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTCAAAATCATGTATT
Found at i:62697 original size:7 final size:6
Alignment explanation
Indices: 62678--62729 Score: 63
Period size: 6 Copynumber: 8.7 Consensus size: 6
62668 CAAAAGCAAC
*
62678 AAAAAG AAAAAG AAAGAAG AAAAA- AAGAA- AAAAAG AAAAAAG AAAAAG
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG
62726 AAAA
1 AAAA
62730 TACTCCTACA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 8 0.20
6 21 0.51
7 12 0.29
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:62702 original size:15 final size:14
Alignment explanation
Indices: 62684--62729 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 14
62674 CAACAAAAAG
62684 AAAAAGAAAGAAGAA
1 AAAAAGAAA-AAGAA
*
62699 AAAAAGAAAAAAAGA
1 AAAAAGAAAAAGA-A
62714 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
62728 AA
1 AA
62730 TACTCCTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 6 0.21
15 22 0.79
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:62711 original size:29 final size:31
Alignment explanation
Indices: 62669--62729 Score: 92
Period size: 29 Copynumber: 2.0 Consensus size: 31
62659 GTGCTACAAC
62669 AAAAGCAACAAAAAG-AAAAAGAAAGAAGAAA
1 AAAAGCAACAAAAAGAAAAAAGAAA-AAGAAA
62700 AAAAG-AA-AAAAAGAAAAAAGAAAAAGAAA
1 AAAAGCAACAAAAAGAAAAAAGAAAAAGAAA
62729 A
1 A
62730 TACTCCTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 13 0.45
30 11 0.38
31 5 0.17
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (31 bp):
AAAAGCAACAAAAAGAAAAAAGAAAAAGAAA
Found at i:62988 original size:24 final size:23
Alignment explanation
Indices: 62956--63000 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
62946 TTTCATTTCC
62956 TTATTCTTTCAT-CTTTTCTTATT
1 TTATTCTTT-ATCCTTTTCTTATT
62979 TTATTACTTTATCCTTTTCTTA
1 TTATT-CTTTATCCTTTTCTTA
63001 ACCTTTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.67
Consensus pattern (23 bp):
TTATTCTTTATCCTTTTCTTATT
Done.