Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012093.1 Corchorus olitorius cultivar O-4 contig12126, 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: 55242
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1580 original size:22 final size:21
Alignment explanation
Indices: 1553--1593 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
1543 GTTTAGTCAG
1553 TTTTTTGAGTCAGTTCAGTTCT
1 TTTTTTGAGTCAGTT-AGTTCT
1575 TTTTTTGAGTCAGTTAGTT
1 TTTTTTGAGTCAGTTAGTT
1594 TGAGTCTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.15, C:0.10, G:0.20, T:0.56
Consensus pattern (21 bp):
TTTTTTGAGTCAGTTAGTTCT
Found at i:3058 original size:49 final size:49
Alignment explanation
Indices: 2986--3084 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
2976 CTAGGCTGAC
2986 TATTTGCAGGGTTAATACACTTGTTCGCTTTAACATGGAACTGGGCCAT
1 TATTTGCAGGGTTAATACACTTGTTCGCTTTAACATGGAACTGGGCCAT
3035 TATTTGCAGGGTTAATACACTTGTTCGCTTTAACATGGAACTGGGCCAT
1 TATTTGCAGGGTTAATACACTTGTTCGCTTTAACATGGAACTGGGCCAT
3084 T
1 T
3085 TGCTTCAGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (49 bp):
TATTTGCAGGGTTAATACACTTGTTCGCTTTAACATGGAACTGGGCCAT
Found at i:3851 original size:27 final size:28
Alignment explanation
Indices: 3821--3874 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
3811 TATTCATATA
3821 TTTTTATTTA-T-ATAACATTTTACATAG
1 TTTTTATTTAGTGAT-ACATTTTACATAG
* *
3848 TTTTTTTTTAGTGGTACATTTTACATA
1 TTTTTATTTAGTGATACATTTTACATA
3875 ACTAGTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 9 0.39
28 13 0.57
29 1 0.04
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.57
Consensus pattern (28 bp):
TTTTTATTTAGTGATACATTTTACATAG
Found at i:4005 original size:22 final size:22
Alignment explanation
Indices: 3980--4562 Score: 170
Period size: 22 Copynumber: 26.6 Consensus size: 22
3970 ATTACACTAT
*
3980 TTTTGATGACCTCCTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * *
4002 TTTTGGTAATCTTCTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * * *
4024 TTTTAATAACAATAC-TATGGAA
1 TTTTGATAAC-CTCCTTATGAAA
* * * **
4046 TATCGAGAACCTTTTTAT-AAA
1 TTTTGATAACCTCCTTATGAAA
** * *
4067 TTTTTTCTTAATCTTCTTAT-AAA
1 --TTTTGATAACCTCCTTATGAAA
* * * *
4090 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAACCTCCTTATGAAA
4112 TTTTGA-AGACCTCAC-TATGAAA
1 TTTTGATA-ACCTC-CTTATGAAA
** **
4134 TTTTGATAAATTCCGAATGAAA
1 TTTTGATAACCTCCTTATGAAA
* *
4156 TTTTGATAACCAACAC-TATGAGA
1 TTTTGATAACC-TC-CTTATGAAA
* * * *
4179 TGTTGATAACCTTCATATGATA
1 TTTTGATAACCTCCTTATGAAA
* * *
4201 TATTGATAACCACGTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * **
4223 ATTT-AAAACCCTCCAAATG-AA
1 TTTTGATAA-CCTCCTTATGAAA
* * *
4244 TTGTT-AGTAATCACAC-TCTGAAA
1 TT-TTGA-TAACCTC-CTTATGAAA
*
4267 TTTTGATAA-TTGCAC-TATGAAA
1 TTTTGATAACCT-C-CTTATGAAA
* * *
4289 TTGTAATAACCTCGC-AATGAAA
1 TTTTGATAACCTC-CTTATGAAA
* *
4311 TTTTAATAAACCTTCC-TATAAAA
1 TTTTGAT-AACC-TCCTTATGAAA
* *
4334 TTTTGATAAACCTCCATATAAAA
1 TTTTGAT-AACCTCCTTATGAAA
4357 TTTTGATAACCTCCTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
*
4379 TCTTT-ATAA----C-TA-CAAA
1 T-TTTGATAACCTCCTTATGAAA
* **
4395 TTTTGATAACCTCCCTATGATT
1 TTTTGATAACCTCCTTATGAAA
*
4417 TTTTGATAACCTCATTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * *
4439 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * * *
4461 TTTTGATCTACATAC-TATGCAA
1 TTTTGAT-AACCTCCTTATGAAA
4483 TTTTGATAACC-CTCTTATGAAA
1 TTTTGATAACCTC-CTTATGAAA
* * ****
4505 TTTCGA-AAACTAAACAGTGAAA
1 TTTTGATAACCTCCTTA-TGAAA
* * *
4527 TTTTGAGAACCTTCATATGAAA
1 TTTTGATAACCTCCTTATGAAA
*
4549 TTTTGATATCCTCC
1 TTTTGATAACCTCC
4563 CTGATTTTTT
Statistics
Matches: 409, Mismatches: 115, Indels: 74
0.68 0.19 0.12
Matches are distributed among these distances:
15 3 0.01
16 8 0.02
17 2 0.00
18 1 0.00
20 1 0.00
21 34 0.08
22 267 0.65
23 90 0.22
24 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TTTTGATAACCTCCTTATGAAA
Found at i:4334 original size:23 final size:23
Alignment explanation
Indices: 4308--4387 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
4298 CCTCGCAATG
*
4308 AAATTTTAATAAACCTTCC-TATA
1 AAATTTTGATAAACC-TCCATATA
4331 AAATTTTGATAAACCTCCATATA
1 AAATTTTGATAAACCTCCATATA
* *
4354 AAATTTTGAT-AACCTCCTTATG
1 AAATTTTGATAAACCTCCATATA
4376 AAATCTTT-ATAA
1 AAAT-TTTGATAA
4388 CTACAAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
22 19 0.37
23 32 0.63
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCATATA
Found at i:4713 original size:22 final size:23
Alignment explanation
Indices: 4656--4715 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
4646 GAAACACCAC
* *
4656 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAAGCACATT
*
4679 T-TGTAAA-TTTGATAAGCTC-TT
1 TATG-AAATTTTGATAAGCACATT
4700 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
4716 CCTTTCTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 6 0.19
22 21 0.68
23 4 0.13
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (23 bp):
TATGAAATTTTGATAAGCACATT
Found at i:4776 original size:22 final size:22
Alignment explanation
Indices: 4749--4893 Score: 86
Period size: 22 Copynumber: 6.5 Consensus size: 22
4739 CCCCTCTATA
4749 AAATTTTGATAATCACATTATG
1 AAATTTTGATAATCACATTATG
* * *
4771 TAATTTTGATAATCTCGCTT-TG
1 AAATTTTGATAATCAC-ATTATG
* *
4793 AAAGTTTGATAA-CAACACTATG
1 AAATTTTGATAATC-ACATTATG
* *
4815 AAATTTTGATAATCTTC-CTAT-
1 AAATTTTGATAATC-ACATTATG
* *
4836 AAATTTTGATAATCCGATCTTTGTG
1 AAATTTTGATAAT-C-A-CATTATG
*
4861 AAATTTCGATAATCAC-TCTATG
1 AAATTTTGATAATCACAT-TATG
*
4883 AGA-TTTGATAA
1 AAATTTTGATAA
4894 CCTTCTATCA
Statistics
Matches: 95, Mismatches: 19, Indels: 19
0.71 0.14 0.14
Matches are distributed among these distances:
21 23 0.24
22 51 0.54
23 6 0.06
24 3 0.03
25 12 0.13
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAATCACATTATG
Found at i:4819 original size:89 final size:89
Alignment explanation
Indices: 4655--4819 Score: 197
Period size: 89 Copynumber: 1.9 Consensus size: 89
4645 AGAAACACCA
* * * * * ***
4655 CTATGAAATTTTGGTAATCACATTTTGTAAATTTGATAAGCTCTTTATGAAATTTTGATAACCTT
1 CTATAAAATTTTGATAATCACATTATGTAAATTTGATAAGCTCCTTATGAAAGTTTGATAACAAC
* *
4720 TCTGTAAAATTGGGTCTCACCCCT
66 ACTATAAAATTGGGTCTCACCCCT
* *
4744 CTATAAAATTTTGATAATCACATTATGTAATTTTGATAATCTCGCTT-TGAAAGTTTGATAACAA
1 CTATAAAATTTTGATAATCACATTATGTAAATTTGATAAGCTC-CTTATGAAAGTTTGATAACAA
*
4808 CACTATGAAATT
65 CACTATAAAATT
4820 TTGATAATCT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
89 60 0.97
90 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (89 bp):
CTATAAAATTTTGATAATCACATTATGTAAATTTGATAAGCTCCTTATGAAAGTTTGATAACAAC
ACTATAAAATTGGGTCTCACCCCT
Found at i:5044 original size:22 final size:21
Alignment explanation
Indices: 4985--5044 Score: 50
Period size: 22 Copynumber: 2.7 Consensus size: 21
4975 GTAACATCCT
*
4985 TATGAAATTTTGTTAACCACAC
1 TATG-AATTTTGATAACCACAC
* *
5007 TATGGAATTCTT-ATAACCTCGC
1 TAT-GAATT-TTGATAACCACAC
5029 TATGACATTTTGATAA
1 TATGA-ATTTTGATAA
5045 TCTCTTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 4 0.13
22 24 0.77
23 3 0.10
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
TATGAATTTTGATAACCACAC
Found at i:5163 original size:22 final size:22
Alignment explanation
Indices: 5062--5284 Score: 132
Period size: 22 Copynumber: 10.0 Consensus size: 22
5052 GATAACCTTT
* * *
5062 CTATAAAATTGTGATAACTACA
1 CTATGAAATTTTGATAACCACA
** *
5084 CTATGAAATTTCAATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
* * **
5106 CTAAGAAATTTTAATAACCTGATT
1 CTATGAAATTTTGATAACC--ACA
* * *
5130 CTCTAAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
5152 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
* *
5174 CCATGACATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
5197 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* * *
5218 TTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* * *
5239 CTCATGAAATTATAATAACCATA
1 CT-ATGAAATTTTGATAACCACA
*
5262 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
5284 C
1 C
5285 AGAGACAAGA
Statistics
Matches: 149, Mismatches: 41, Indels: 22
0.70 0.19 0.10
Matches are distributed among these distances:
20 1 0.01
21 3 0.02
22 127 0.85
23 3 0.02
24 15 0.10
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:5257 original size:66 final size:66
Alignment explanation
Indices: 5067--5284 Score: 199
Period size: 66 Copynumber: 3.3 Consensus size: 66
5057 CCTTTCTATA
* * * ** * * * **
5067 AAATTGTGATAACTACACTATGAAATTTCAATAACCTTCCTAAGAAATTTTAATAACCTGATTCT
1 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTATAATAACCACA-T-T
* *
5132 CTA
64 ATG
* * *
5135 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGACATTTTGATAACTTC-CA-T
1 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTATAATAAC--CACATT
5198 ATG
64 ATG
* * *
5201 AAATTTTGGTAACCACATTATGGAATTTTGATAACC-TCCTCATGAAATTATAATAACCATATTA
1 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-CATGAAATTATAATAACCACATTA
5265 TG
65 TG
*
5267 AAATTTTGATAACCACAC
1 AAATTTTGGTAACCACAC
5285 AGAGACAAGA
Statistics
Matches: 125, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
64 1 0.01
65 4 0.03
66 70 0.56
68 48 0.38
69 1 0.01
70 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (66 bp):
AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTATAATAACCACATTAT
G
Found at i:7102 original size:2 final size:2
Alignment explanation
Indices: 7095--7121 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7085 CATAGATTAC
7095 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
7122 CACTTCTATA
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:8635 original size:19 final size:18
Alignment explanation
Indices: 8611--8646 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8601 TGAAGACTTA
8611 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
8630 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
8647 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:17258 original size:16 final size:16
Alignment explanation
Indices: 17237--17273 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
17227 ATATAAAAAA
17237 TTCAAAAGT-TCATGTC
1 TTCAAAAGTCT-ATGTC
17253 TTC-AAAGTCTATGTC
1 TTCAAAAGTCTATGTC
17268 TTCAAA
1 TTCAAA
17274 GCCCATGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (16 bp):
TTCAAAAGTCTATGTC
Found at i:17266 original size:15 final size:15
Alignment explanation
Indices: 17248--17292 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
17238 TCAAAAGTTC
17248 ATGTCTTCAAAGTCT
1 ATGTCTTCAAAGTCT
* *
17263 ATGTCTTCAAAGCCC
1 ATGTCTTCAAAGTCT
*
17278 ATGTCTTTAAAGTCT
1 ATGTCTTCAAAGTCT
17293 TTGCGATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (15 bp):
ATGTCTTCAAAGTCT
Found at i:32516 original size:14 final size:14
Alignment explanation
Indices: 32497--32525 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
32487 TTATTGCTTG
32497 AATAATTGAGTCAT
1 AATAATTGAGTCAT
32511 AATAATTGAGTCAT
1 AATAATTGAGTCAT
32525 A
1 A
32526 TGCTAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (14 bp):
AATAATTGAGTCAT
Found at i:35568 original size:19 final size:18
Alignment explanation
Indices: 35532--35572 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
35522 TGAAATTTAT
35532 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
*
35550 TAATTATTT-TTCAA-AA
1 TAATTATTTATTAAATAA
35566 TAATTAT
1 TAATTAT
35573 CATTAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.41
17 4 0.18
18 9 0.41
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:41168 original size:2 final size:2
Alignment explanation
Indices: 41161--41186 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41151 AAATACGGCC
41161 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
41187 AAAGTTAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42355 original size:18 final size:19
Alignment explanation
Indices: 42332--42376 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
42322 TGAAACTTAT
42332 TAATTATTTATTAG-ATAA
1 TAATTATTTATTAGAATAA
* *
42350 TAATTATTTTTTTGAATAA
1 TAATTATTTATTAGAATAA
42369 TAATTATT
1 TAATTATT
42377 AATATTCCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
TAATTATTTATTAGAATAA
Found at i:53249 original size:30 final size:30
Alignment explanation
Indices: 53215--53280 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
53205 GCTGGGGAGT
* * *
53215 GTGTATAACATGCACTGATGTGGATGACAC
1 GTGTATAACAGGCACTGACGTGGACGACAC
*
53245 GTGTATAACAGGCACTGACGTGGACGGCAC
1 GTGTATAACAGGCACTGACGTGGACGACAC
53275 GTGTAT
1 GTGTAT
53281 GCCCACATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (30 bp):
GTGTATAACAGGCACTGACGTGGACGACAC
Found at i:53458 original size:18 final size:18
Alignment explanation
Indices: 53437--53473 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
53427 TTAAAAACAC
**
53437 CAAGAACATTCAAAATTG
1 CAAGAACATGAAAAATTG
53455 CAAGAACATGAAAAATTG
1 CAAGAACATGAAAAATTG
53473 C
1 C
53474 CAAAAATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (18 bp):
CAAGAACATGAAAAATTG
Found at i:55019 original size:14 final size:14
Alignment explanation
Indices: 55002--55031 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54992 AAAAAATATC
55002 AAAAAAATAATAAA
1 AAAAAAATAATAAA
*
55016 AAAATAATAATAAA
1 AAAAAAATAATAAA
55030 AA
1 AA
55032 TTTCGACCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAAAATAATAAA
Done.