Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013518.1 Corchorus olitorius cultivar O-4 contig13551, 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: 56290
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:12412 original size:49 final size:48
Alignment explanation
Indices: 12348--12471 Score: 149
Period size: 49 Copynumber: 2.5 Consensus size: 48
12338 TTACATTTCC
* * *
12348 TGCACCTTTTTCTCAATTTTTACAACAAAATTTAATCTTTAATTTTCTT
1 TGCA-CTTTTTCTCAATTTTTACAACAAAATTAAATATTTAATTTTCAT
** *
12397 TGCATCTTTTTCTCAATTTTTATGACAAAATTAAATATTTACTTTTCAT
1 TGCA-CTTTTTCTCAATTTTTACAACAAAATTAAATATTTAATTTTCAT
*
12446 TGCACTTTTTATCAACTTTTTGACAA
1 TGCACTTTTTCTCAA-TTTTT-ACAA
12472 AATTGATTGG
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 10 0.16
49 51 0.81
50 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.50
Consensus pattern (48 bp):
TGCACTTTTTCTCAATTTTTACAACAAAATTAAATATTTAATTTTCAT
Found at i:14184 original size:33 final size:33
Alignment explanation
Indices: 14065--14362 Score: 188
Period size: 33 Copynumber: 9.0 Consensus size: 33
14055 TACTACTTAA
* * * *
14065 CCTGCTTATAGTGGCTTCTTCCCTGCTACTTGG
1 CCTGCTTAAAGGGGCATCATCCCTGCTACTTGG
* *
14098 GCTGCTTAAAGGGGCATCATCCCTGCTGCTTGG
1 CCTGCTTAAAGGGGCATCATCCCTGCTACTTGG
*
14131 GCTGCTTAAAGGGGCATCATCCCTGCTACTTGG
1 CCTGCTTAAAGGGGCATCATCCCTGCTACTTGG
** * * * * *
14164 CCTGCTTATCGAGGCCTCATCCATGCAACTTAG
1 CCTGCTTAAAGGGGCATCATCCCTGCTACTTGG
* ** * * * *
14197 CCTGCTCATTGGGGCATGATCCATACTACCTGG
1 CCTGCTTAAAGGGGCATCATCCCTGCTACTTGG
** * * * *
14230 CCTGC-TATTCGGAGCATCACCCCTACTATTTGG
1 CCTGCTTA-AAGGGGCATCATCCCTGCTACTTGG
* *
14263 CCTGCTTAACA-GGGCATCATCCCTTCTCCTTGG
1 CCTGCTTAA-AGGGGCATCATCCCTGCTACTTGG
* * * ** * *
14296 CCAG-ATAATTGGCTCATCATCCCTACTACCTGG
1 CCTGCTTAA-AGGGGCATCATCCCTGCTACTTGG
* ** *
14329 CCTGCGTACTGGGGCATCATCCCTACTACTTGG
1 CCTGCTTAAAGGGGCATCATCCCTGCTACTTGG
14362 C
1 C
14363 ATATCATCTT
Statistics
Matches: 206, Mismatches: 54, Indels: 10
0.76 0.20 0.04
Matches are distributed among these distances:
32 4 0.02
33 198 0.96
34 4 0.02
ACGTcount: A:0.17, C:0.32, G:0.22, T:0.29
Consensus pattern (33 bp):
CCTGCTTAAAGGGGCATCATCCCTGCTACTTGG
Found at i:20149 original size:6 final size:6
Alignment explanation
Indices: 20138--20167 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
20128 CTTGCTTCTA
20138 TATTTT TATTTT TATTTT TATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT
20168 GAGTGGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:21240 original size:12 final size:12
Alignment explanation
Indices: 21223--21250 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
21213 CCCCACCACC
21223 TTTTTTCCTTTT
1 TTTTTTCCTTTT
21235 TTTTTTCCTTTT
1 TTTTTTCCTTTT
21247 TTTT
1 TTTT
21251 CCCTCTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTCCTTTT
Found at i:22052 original size:2 final size:2
Alignment explanation
Indices: 22045--22085 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
22035 ATATGTAGTT
*
22045 TA TA TA TA TA TA TA TG TA GTA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
22086 GTCTTTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22059 original size:21 final size:21
Alignment explanation
Indices: 22035--22080 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
22025 GTTTCAAATA
*
22035 ATATGTAGTTTATATATATAT
1 ATATGTAGTATATATATATAT
22056 ATATGTAGTATATATATATAT
1 ATATGTAGTATATATATATAT
22077 ATAT
1 ATAT
22081 ATATAGTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (21 bp):
ATATGTAGTATATATATATAT
Found at i:24233 original size:14 final size:13
Alignment explanation
Indices: 24214--24252 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
24204 AAATTGTAAA
24214 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
24227 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
24241 ATTTAAAAAATT
1 ATTTAAAAAATT
24253 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:24408 original size:124 final size:114
Alignment explanation
Indices: 24238--24475 Score: 341
Period size: 116 Copynumber: 2.0 Consensus size: 114
24228 ATTTAAGAAA
*
24238 TATATTTAAAAAATTCTAATATATAAGTTTTTAAAATAAAATAGTAAAAAGGTAAAAATAAAATA
1 TATATTTAAAAAATTCTAATATATAAGTTTTTAAAATAAAATAGTAAAAAGGTAAAAAT----CA
24303 GGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACT
62 --TA-AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACT
* * *
24360 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATCATA
1 TATATTTAAAAAATTCT-A-ATATATAAGTTTTTAAAATAAAATAGTAAAAAGGTAAAAATCATA
*
24425 AAGATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACT
64 AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACT
24476 ATAAAAGTTT
Statistics
Matches: 109, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
116 48 0.44
117 2 0.02
118 2 0.02
120 1 0.01
122 17 0.16
123 1 0.01
124 38 0.35
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (114 bp):
TATATTTAAAAAATTCTAATATATAAGTTTTTAAAATAAAATAGTAAAAAGGTAAAAATCATAAA
GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACT
Found at i:27307 original size:32 final size:32
Alignment explanation
Indices: 27251--27330 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
27241 AGAAAACATG
27251 AAAAAGAGTTAAAAG-TTTTTTTTTTTGAAAA
1 AAAAAGAGTTAAAAGTTTTTTTTTTTTGAAAA
*
27282 AAAAAGAGTTAAAAGTTTTTTTTTTTTGAAAG
1 AAAAAGAGTTAAAAGTTTTTTTTTTTTGAAAA
27314 AAAAAGAGTTAAAAGTT
1 AAAAAGAGTTAAAAGTT
27331 CAACTCAAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 15 0.32
32 32 0.68
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (32 bp):
AAAAAGAGTTAAAAGTTTTTTTTTTTTGAAAA
Found at i:30324 original size:15 final size:16
Alignment explanation
Indices: 30306--30339 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30296 ATTTGATTGA
*
30306 GAAAAA-TTATTTTAT
1 GAAAAATTTATTTCAT
30321 GAAAAATTTATTTCAT
1 GAAAAATTTATTTCAT
30337 GAA
1 GAA
30340 TGAAATAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (16 bp):
GAAAAATTTATTTCAT
Found at i:31807 original size:36 final size:36
Alignment explanation
Indices: 31760--32042 Score: 435
Period size: 36 Copynumber: 7.9 Consensus size: 36
31750 TAAGCTCAAA
* * *
31760 TAATTGAGTAAAATCAATAAAAGACTTAATTCAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
*
31796 TAATTAAGTAAAATCAGTCAAAGGCTTAATTCAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
*
31832 TAATTAAGTAAAATCAGTCAAAGACTTAAGTCAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
* * *
31868 TAAATAAGTAAAATCAG-CATAGACTTAATTCAAGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
* *
31903 TAATTAAGTAAAATCAG-CAGAGACTTAATTAAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
*
31938 TTATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
* *
31974 TAATTAAGTAAAATCAGTCAAAGACTTGATTCGGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
32010 TAATTAAGTAAAATCAGTCAAAGACTTAATTCA
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCA
32043 ATCTTAGAAA
Statistics
Matches: 224, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
35 62 0.28
36 162 0.72
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.28
Consensus pattern (36 bp):
TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
Found at i:33049 original size:35 final size:35
Alignment explanation
Indices: 33010--33135 Score: 184
Period size: 35 Copynumber: 3.6 Consensus size: 35
33000 TTCGTTTATT
33010 GTAAGCAACTTAATTCAGGGTAATTAAGTAAGTGA
1 GTAAGCAACTTAATTCAGGGTAATTAAGTAAGTGA
* * *
33045 GTAAGAAACTTAATTTAGGGTAATTAAGTAAGTCA
1 GTAAGCAACTTAATTCAGGGTAATTAAGTAAGTGA
*
33080 GTAAGCAACTTAGTT-ATGGGTAATTAAGTAAGTCG-
1 GTAAGCAACTTAATTCA-GGGTAATTAAGTAAGT-GA
33115 GTAAGCAACTTAATTCAGGGT
1 GTAAGCAACTTAATTCAGGGT
33136 CGACGAAAGA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
34 1 0.01
35 79 0.98
36 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (35 bp):
GTAAGCAACTTAATTCAGGGTAATTAAGTAAGTGA
Found at i:34978 original size:20 final size:20
Alignment explanation
Indices: 34934--34979 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
34924 TCAAGGAAAC
34934 AACCCGTTGAAACCCGGTGT
1 AACCCGTTGAAACCCGGTGT
*
34954 GACCCGTTGAAACCCGGAT-T
1 AACCCGTTGAAACCCGG-TGT
34974 AACCCG
1 AACCCG
34980 GTGACCCGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.17
Consensus pattern (20 bp):
AACCCGTTGAAACCCGGTGT
Found at i:45566 original size:21 final size:21
Alignment explanation
Indices: 45527--45566 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
45517 CAAGCACCAA
*
45527 AAAGATGCCATTTGATCCATT
1 AAAGATGCCAATTGATCCATT
* *
45548 AAAGATGGCAATTGGTCCA
1 AAAGATGCCAATTGATCCA
45567 ATGACTAGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (21 bp):
AAAGATGCCAATTGATCCATT
Found at i:47755 original size:36 final size:35
Alignment explanation
Indices: 47689--47934 Score: 343
Period size: 35 Copynumber: 7.0 Consensus size: 35
47679 ATCAATGTGA
* *
47689 AGATCAACTCTGATCATCGAAAACTTCTTGAAATA
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
47724 AGATCAACTTTGATCATAAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCAT-CAAAAACTTCTTGAAATG
* * *
47760 AAATCAACTCTGACCATAAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCAT-CAAAAACTTCTTGAAATG
* *
47796 AGATCAACTCTGATCGA-CAAAAACTTCTTAAAAGG
1 AGATCAACTCTGATC-ATCAAAAACTTCTTGAAATG
47831 AGATCAACTCTGATCAT-AAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
47865 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
47900 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
47935 CGACCGCACT
Statistics
Matches: 190, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
34 33 0.17
35 95 0.50
36 61 0.32
37 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (35 bp):
AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
Found at i:47768 original size:19 final size:19
Alignment explanation
Indices: 47746--47804 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
47736 ATCATAAAAA
47746 AACTTCTTGAAATGAAATC
1 AACTTCTTGAAATGAAATC
* **
47765 AAC-TC-TGACCAT-AAAAA
1 AACTTCTTGA-AATGAAATC
*
47782 AACTTCTTGAAATGAGATC
1 AACTTCTTGAAATGAAATC
47801 AACT
1 AACT
47805 CTGATCGACA
Statistics
Matches: 29, Mismatches: 7, Indels: 8
0.66 0.16 0.18
Matches are distributed among these distances:
17 9 0.31
18 8 0.28
19 12 0.41
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (19 bp):
AACTTCTTGAAATGAAATC
Found at i:47877 original size:69 final size:69
Alignment explanation
Indices: 47689--47934 Score: 323
Period size: 69 Copynumber: 3.5 Consensus size: 69
47679 ATCAATGTGA
** * * *
47689 AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTTTGATCATAAAAAAACTTCTT
1 AGATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATC--ACAAAAACTTCTT
*
47754 GAAATG
64 GAAACG
* *
47760 AAATCAACTCTGACCATAAAAAAACTTCTTGAAATGAGATCAACTCTGATCGACAAAAACTTCTT
1 AGATCAACTCTGATCAT-AAAAAACTTCTTGAAATGAGATCAACTCTGATC-ACAAAAACTTCTT
* *
47825 AAAAGG
64 GAAACG
*
47831 AGATCAACTCTGATCAT-AAAAACTTCTTGAAATGAGATCAACTCTGATCATCGAAAACTTCTTG
1 AGATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCA-CAAAAACTTCTTG
47895 AAACG
65 AAACG
**
47900 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATAAAAAACTTCTTGAAATG
47935 CGACCGCACT
Statistics
Matches: 156, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
68 1 0.01
69 64 0.41
70 16 0.10
71 46 0.29
72 29 0.19
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (69 bp):
AGATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCACAAAAACTTCTTGA
AACG
Found at i:47996 original size:56 final size:55
Alignment explanation
Indices: 47901--48074 Score: 242
Period size: 56 Copynumber: 3.1 Consensus size: 55
47891 CTTGAAACGA
* ** *
47901 GATCAACTCTGATCA-TCGAAAACTTCTTGAAATGCGACCGCACTGGATCATCTGAG
1 GATCAACTCTAATCATTAAAAAACTTCTTGGAAT--GACCGCACTGGATCATCTGAG
47957 GATCAACTCTAATCATTAAAAAAACTTCTTGGAATGACCGCACTGGATCATCTGAG
1 GATCAACTCTAATCATT-AAAAAACTTCTTGGAATGACCGCACTGGATCATCTGAG
* * *
48013 GATCAACTCTAATCCTTAAAAAACTTCTTGGAATGACCGCATTGGATCATTTTGAG
1 GATCAACTCTAATCATTAAAAAACTTCTTGGAATGACCGCACTGGATCA-TCTGAG
48069 GATCAA
1 GATCAA
48075 AAGACCGCAC
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
55 31 0.29
56 62 0.57
57 1 0.01
58 14 0.13
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (55 bp):
GATCAACTCTAATCATTAAAAAACTTCTTGGAATGACCGCACTGGATCATCTGAG
Done.