Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009400.1 Hibiscus syriacus cultivar Beakdansim tig00113327_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: 56336
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:639 original size:18 final size:19
Alignment explanation
Indices: 600--639 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
590 TTCATCCTGA
**
600 AAATTAAAAAAAAAATCCG
1 AAATTAAAAAAAAAATAAG
619 AAATTAAAAAAAAAA-AAG
1 AAATTAAAAAAAAAATAAG
637 AAA
1 AAA
640 AGAAAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (19 bp):
AAATTAAAAAAAAAATAAG
Found at i:7785 original size:19 final size:20
Alignment explanation
Indices: 7749--7788 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
7739 GAATAATAAT
7749 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
* *
7769 ATAAG-AATGATATGAAATA
1 ATAAGTAATGAAAAGAAATA
7788 A
1 A
7789 GGAAATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:11981 original size:13 final size:12
Alignment explanation
Indices: 11965--12021 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 12
11955 TTTTTTGAAC
11965 TTCTCTTTTTCTT
1 TTCT-TTTTTCTT
11978 TTCTTTTCTTCTT
1 TTCTTTT-TTCTT
11991 TTCTTTTTT-TT
1 TTCTTTTTTCTT
* ** *
12002 ATGATTTTTCTC
1 TTCTTTTTTCTT
12014 TTCTTTTT
1 TTCTTTTT
12022 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
11 8 0.23
12 11 0.31
13 16 0.46
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:12325 original size:19 final size:20
Alignment explanation
Indices: 12289--12328 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
12279 GAATAATAAT
12289 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
* *
12309 ATAAG-AATGATATGAAATA
1 ATAAGTAATGAAAAGAAATA
12328 A
1 A
12329 GGAAATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:16165 original size:35 final size:35
Alignment explanation
Indices: 16119--16211 Score: 141
Period size: 35 Copynumber: 2.7 Consensus size: 35
16109 TGGTAATGGA
*
16119 ATGGTGATGATATAGGTGTGAAATAGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATAGTGATAGAAG
* * * *
16154 ATGGTGATGATATAGGCATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATAGTGATAGAAG
16189 ATGGTGATGATATAGGCGTGAAA
1 ATGGTGATGATATAGGCGTGAAA
16212 ATGGTGATGA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.34, C:0.03, G:0.35, T:0.27
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATAGTGATAGAAG
Found at i:17750 original size:17 final size:17
Alignment explanation
Indices: 17728--17761 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17718 GTGTTTGGGC
17728 GCCAATTTGATGTCACA
1 GCCAATTTGATGTCACA
17745 GCCAATTTGATGTCACA
1 GCCAATTTGATGTCACA
17762 TGAAGTGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (17 bp):
GCCAATTTGATGTCACA
Found at i:20882 original size:15 final size:15
Alignment explanation
Indices: 20846--20875 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20836 GTGATTCAAC
20846 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
20860 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
20875 T
1 T
20876 CTTTTTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:24771 original size:12 final size:12
Alignment explanation
Indices: 24754--24778 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24744 TCATACCCTT
24754 GTAGATCAAGAA
1 GTAGATCAAGAA
24766 GTAGATCAAGAA
1 GTAGATCAAGAA
24778 G
1 G
24779 ATCAGTGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.28, T:0.16
Consensus pattern (12 bp):
GTAGATCAAGAA
Found at i:26367 original size:10 final size:11
Alignment explanation
Indices: 26346--26371 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
26336 TATTTTATTA
26346 TTTTGCCTTTT
1 TTTTGCCTTTT
26357 TTTTGCCTTTT
1 TTTTGCCTTTT
26368 TTTT
1 TTTT
26372 TTGTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTGCCTTTT
Found at i:26378 original size:10 final size:10
Alignment explanation
Indices: 26365--26391 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
26355 TTTTTTGCCT
26365 TTTTTTTTTG
1 TTTTTTTTTG
26375 TTTTTTTTTG
1 TTTTTTTTTG
26385 TTTTTTT
1 TTTTTTT
26392 GAAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:26378 original size:11 final size:11
Alignment explanation
Indices: 26353--26391 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
26343 TTATTTTGCC
26353 TTTTTTTTGCCTT
1 TTTTTTTTG--TT
26366 TTTTTTTTG-T
1 TTTTTTTTGTT
26376 TTTTTTTTGTT
1 TTTTTTTTGTT
26387 TTTTT
1 TTTTT
26392 GAAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.40
11 6 0.24
13 9 0.36
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:35946 original size:13 final size:14
Alignment explanation
Indices: 35922--35967 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
35912 GAACTTCTCT
35922 TTTTCTTTCTTTTC
1 TTTTCTTTCTTTTC
35936 TTTTC-TTCTTTTC
1 TTTTCTTTCTTTTC
*
35949 TGATTT-TTTCTCTTC
1 T--TTTCTTTCTTTTC
35964 TTTT
1 TTTT
35968 TGCACTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 12 0.43
14 5 0.18
15 11 0.39
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTTCTTTCTTTTC
Found at i:40462 original size:19 final size:20
Alignment explanation
Indices: 40421--40471 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
40411 GAAACCCCTT
*
40421 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
40441 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
40460 TGAAGATACATG
1 TGAAAATACATG
40472 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:41207 original size:20 final size:21
Alignment explanation
Indices: 41169--41208 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
41159 GATCATCTAG
* *
41169 AAGCTAAGATAACATGTATAT
1 AAGCTAAGATAAAAGGTATAT
41190 AAGCT-AGATAAAAGGTATA
1 AAGCTAAGATAAAAGGTATA
41209 GGACGTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.25
Consensus pattern (21 bp):
AAGCTAAGATAAAAGGTATAT
Found at i:41411 original size:30 final size:31
Alignment explanation
Indices: 41371--41430 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
41361 ACATTCTGCT
**
41371 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
41402 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
41431 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:43541 original size:36 final size:35
Alignment explanation
Indices: 43450--43558 Score: 139
Period size: 35 Copynumber: 3.1 Consensus size: 35
43440 GGTGGTTATG
* * *
43450 TAGGCGTGAAATGGTGATAGAAGATGGTAATGATA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
** * *
43485 TATACGTGCAATGGTAATGGAAGATGGTGATGTTA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
43520 TAGGCGTGAAAATGGTGATGGAAGATGGTGATGTT-
1 TAGGCGTG-AAATGGTGATGGAAGATGGTGATGTTA
43555 TAGG
1 TAGG
43559 TAGTATCTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
35 38 0.61
36 24 0.39
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.28
Consensus pattern (35 bp):
TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
Found at i:47726 original size:36 final size:35
Alignment explanation
Indices: 47634--47743 Score: 141
Period size: 35 Copynumber: 3.1 Consensus size: 35
47624 TGGTGGTTAC
* * * *
47634 ATAGGCGTGAAATGGTTATAGAAGATGGTAATGAT
1 ATAGGCGTGAAATGGTAATGGAAGATGGTGATGTT
*
47669 ATAGGCGTGCAATGGTAATGGAAGATGGTGATGTT
1 ATAGGCGTGAAATGGTAATGGAAGATGGTGATGTT
* *
47704 ATAGGCATGAAAATGGTGATGGAAGATGGTGATGTT
1 ATAGGCGTG-AAATGGTAATGGAAGATGGTGATGTT
47740 -TAGG
1 ATAGG
47744 TAGTATCTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
35 42 0.64
36 24 0.36
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.28
Consensus pattern (35 bp):
ATAGGCGTGAAATGGTAATGGAAGATGGTGATGTT
Found at i:54624 original size:6 final size:6
Alignment explanation
Indices: 54613--54652 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
54603 GATGTAGGAG
*
54613 TCTTTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTT
54653 CTTGTTGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 19 0.63
7 6 0.20
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:54655 original size:13 final size:12
Alignment explanation
Indices: 54613--54652 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 12
54603 GATGTAGGAG
54613 TCTTTTTC-TTT
1 TCTTTTTCTTTT
*
54624 TCTTTTTGTTTT
1 TCTTTTTCTTTT
54636 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
54649 TCTT
1 TCTT
54653 CTTGTTGCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 7 0.28
12 7 0.28
13 11 0.44
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:54657 original size:25 final size:23
Alignment explanation
Indices: 54613--54658 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
54603 GATGTAGGAG
*
54613 TCTTTTTCTTTTCTTTTTGTTTT
1 TCTTTTTCTTTTCTTCTTGTTTT
54636 TCTTCTTTCTTTTTCTTCTTGTT
1 TCTT-TTTC-TTTTCTTCTTGTT
54659 GCAGTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 4 0.20
25 12 0.60
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.78
Consensus pattern (23 bp):
TCTTTTTCTTTTCTTCTTGTTTT
Found at i:55498 original size:19 final size:20
Alignment explanation
Indices: 55451--55501 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
55441 GAAATCCCTT
**
55451 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
55471 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
55490 TGAAGATACATG
1 TGAAAATACATG
55502 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Done.