Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005776.1 Hibiscus syriacus cultivar Beakdansim tig00013521_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: 84808
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:4089 original size:32 final size:33
Alignment explanation
Indices: 4053--4120 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
4043 GTTGATGAAT
*
4053 GAAGGATGAT-TTAATGGTGATGA-ATGGTAATG
1 GAAGGATGATGTTAATGG-CATGATATGGTAATG
* *
4085 GAAGGATGATGTTATTGGCATGATATGGTGATG
1 GAAGGATGATGTTAATGGCATGATATGGTAATG
4118 GAA
1 GAA
4121 TATGGTGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.32, C:0.01, G:0.35, T:0.31
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCATGATATGGTAATG
Found at i:11549 original size:19 final size:19
Alignment explanation
Indices: 11505--11559 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
11495 GAAATCCCTT
* *
11505 TGAAAATACATGATTTTTAA
1 TGAAAATACATGA-CTCTAA
11525 TGAAAATACATGACTCTAA
1 TGAAAATACATGACTCTAA
*
11544 TTAAAATACATG-CTCT
1 TGAAAATACATGACTCT
11560 TGGCCGAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 4 0.12
19 15 0.47
20 13 0.41
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.35
Consensus pattern (19 bp):
TGAAAATACATGACTCTAA
Found at i:20774 original size:24 final size:21
Alignment explanation
Indices: 20740--20782 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
20730 TGCACAAGAT
*
20740 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
20762 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
20783 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:23650 original size:13 final size:13
Alignment explanation
Indices: 23628--23657 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
23618 ACTAAACACC
23628 TTTC-ACATACCT
1 TTTCAACATACCT
23640 TTTCAACATACCT
1 TTTCAACATACCT
23653 TTTCA
1 TTTCA
23658 TCTTTAGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:26154 original size:19 final size:21
Alignment explanation
Indices: 26111--26162 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
26101 GAAACCCCTT
26111 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
26132 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
26151 TGAAGATACATG
1 TGAAAATACATG
26163 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:28278 original size:14 final size:13
Alignment explanation
Indices: 28259--28300 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
28249 GTGCTTCAAC
28259 TTTCTTTCTTTTCT
1 TTTCTTTCTTTT-T
*
28273 TTTCTTTGTTTTT
1 TTTCTTTCTTTTT
28286 TCTTC-TTCTTTTT
1 T-TTCTTTCTTTTT
28299 TT
1 TT
28301 GAGTGCTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 1 0.04
13 10 0.40
14 14 0.56
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTCTTTCTTTTT
Found at i:28288 original size:16 final size:16
Alignment explanation
Indices: 28267--28300 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
28257 ACTTTCTTTC
28267 TTTTCTT-TTCTTTGTT
1 TTTTCTTCTTCTTT-TT
28283 TTTTCTTCTTCTTTTT
1 TTTTCTTCTTCTTTTT
28299 TT
1 TT
28301 GAGTGCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTCTTCTTCTTTTT
Found at i:39588 original size:17 final size:17
Alignment explanation
Indices: 39568--39614 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 17
39558 TAAAGGGGAT
39568 AATAAT-ATAAGTAATGA
1 AATAATAATAAG-AATGA
39585 AATAATAATAAGAATGA
1 AATAATAATAAGAATGA
39602 AATGAGATAATAA
1 AAT-A-ATAATAA
39615 AGGATAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 14 0.52
18 6 0.22
19 7 0.26
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (17 bp):
AATAATAATAAGAATGA
Found at i:41777 original size:19 final size:18
Alignment explanation
Indices: 41749--41785 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
41739 AGTGCTTCAA
*
41749 CTTTCTTTTTTTTCTTTT
1 CTTTCTTTTTCTTCTTTT
41767 CTTTGCTTTTTCTTCTTTT
1 CTTT-CTTTTTCTTCTTTT
41786 TGAGTCCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (18 bp):
CTTTCTTTTTCTTCTTTT
Found at i:46629 original size:6 final size:6
Alignment explanation
Indices: 46615--46649 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
46605 TGTAGGAGTC
*
46615 TTTTCT TTTTGT TTTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
46650 GTTGCTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:46644 original size:13 final size:12
Alignment explanation
Indices: 46615--46649 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
46605 TGTAGGAGTC
*
46615 TTTTCTTTTTGT
1 TTTTCTTTTTCT
46627 TTTTCTTCTTTCT
1 TTTTCTT-TTTCT
46640 TTTTCTTTTT
1 TTTTCTTTTT
46650 GTTGCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:46878 original size:15 final size:15
Alignment explanation
Indices: 46855--46887 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
46845 TAAAGAAAGG
46855 GAATAGAAATGGAAA
1 GAATAGAAATGGAAA
*
46870 GAATTGAAATGGAAA
1 GAATAGAAATGGAAA
46885 GAA
1 GAA
46888 ATGTTATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (15 bp):
GAATAGAAATGGAAA
Found at i:51430 original size:14 final size:14
Alignment explanation
Indices: 51411--51457 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
51401 TGTTATGAAT
51411 TTCTTTTTCTTTTC
1 TTCTTTTTCTTTTC
*
51425 TTCTTTTTCTTCTTT
1 TTCTTTTTCTT-TTC
51440 TTCTTCTTTTCTTTTC
1 TTC-T-TTTTCTTTTC
51456 TT
1 TT
51458 TTTGCACTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 11 0.39
15 5 0.18
16 5 0.18
17 7 0.25
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTCTTTTTCTTTTC
Found at i:51434 original size:9 final size:9
Alignment explanation
Indices: 51420--51460 Score: 64
Period size: 9 Copynumber: 4.4 Consensus size: 9
51410 TTTCTTTTTC
51420 TTTTCTTCT
1 TTTTCTTCT
51429 TTTTCTTCT
1 TTTTCTTCT
51438 TTTTCTTCT
1 TTTTCTTCT
*
51447 TTTCTTTTCT
1 TTT-TCTTCT
51457 TTTT
1 TTTT
51461 GCACTCCAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 22 0.73
10 8 0.27
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:51439 original size:23 final size:23
Alignment explanation
Indices: 51411--51454 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
51401 TGTTATGAAT
51411 TTCTTTTTCTT-TTCTTCTTTTTC
1 TTCTTTTTCTTCTT-TTCTTTTTC
51434 TTCTTTTTCTTCTTTTCTTTT
1 TTCTTTTTCTTCTTTTCTTTT
51455 CTTTTTGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
TTCTTTTTCTTCTTTTCTTTTTC
Found at i:51851 original size:35 final size:36
Alignment explanation
Indices: 51812--51895 Score: 127
Period size: 35 Copynumber: 2.4 Consensus size: 36
51802 AAATGGAATT
* **
51812 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATAGAAGA
51847 TGGTGATGATATAGGCGTGATAATGGTGATAGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATAGAAGA
51883 TGGTGATGA-ATAG
1 TGGTGATGATATAG
51896 ATTGTATCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
35 25 0.56
36 20 0.44
ACGTcount: A:0.30, C:0.04, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATAGAAGA
Found at i:53446 original size:20 final size:20
Alignment explanation
Indices: 53410--53453 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
53400 ATGGTCTTAA
*
53410 GAAATGAATATATAATAAAG
1 GAAATGAATATAAAATAAAG
*
53430 GAAATGAA-ATAAAAATAAAT
1 GAAATGAATAT-AAAATAAAG
53450 GAAA
1 GAAA
53454 GAGAGATGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (20 bp):
GAAATGAATATAAAATAAAG
Found at i:53900 original size:19 final size:20
Alignment explanation
Indices: 53858--53909 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
53848 GAAACCCCTT
*
53858 TGAAAATACATGATTTTTTGA
1 TGAAAATACATGA-TTTTTAA
53879 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
53898 TGAAGATACATG
1 TGAAAATACATG
53910 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:57228 original size:19 final size:18
Alignment explanation
Indices: 57188--57234 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
57178 TTTGAATTAT
*
57188 TTTTCTTTTCTTTTCTTC
1 TTTTCTTTTCTTTTCTTA
57206 TTTTCTTCTTCTTTT-TGTA
1 TTTTCTT-TTCTTTTCT-TA
57225 TTTTTCTTTT
1 -TTTTCTTTT
57235 TGCACTCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTCTTTTCTTTTCTTA
Found at i:57983 original size:19 final size:20
Alignment explanation
Indices: 57941--57992 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
57931 GAAACCCCTT
*
57941 TGAAAATACATGATTTTTTGA
1 TGAAAATACATGA-TTTTTAA
57962 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
57981 TGAAGATACATG
1 TGAAAATACATG
57993 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:80785 original size:19 final size:20
Alignment explanation
Indices: 80761--80800 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
80751 TATCTTTTAT
80761 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
80780 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
80800 T
1 T
80801 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Done.