Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013027.1 Corchorus olitorius cultivar O-4 contig13060, 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: 30426
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3982 original size:6 final size:6
Alignment explanation
Indices: 3971--4002 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3961 CAGGCTGCAC
3971 CACAAT CACAAT CACAAT CACAAT CACAAT CA
1 CACAAT CACAAT CACAAT CACAAT CACAAT CA
4003 TCCGTTAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:4085 original size:38 final size:38
Alignment explanation
Indices: 4032--4167 Score: 175
Period size: 38 Copynumber: 3.6 Consensus size: 38
4022 TCGAGTCTAG
*
4032 CCAACAG-TTAACCCCCTGAGGCATGGGTACACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCATGGGTCCACTCTTA
* *
4069 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCCTA
1 CCAACAGTTTAACCCCCTGAGGCATGGGTCCACTCTTA
* * * * *
4107 CCAACAATTTAACCCCGTGTGGTATGAGTCCACTCTTTA
1 CCAACAGTTTAACCCCCTGAGGCATGGGTCCACTC-TTA
*
4146 CCATCAGTTTAACCCCCTGAGG
1 CCAACAGTTTAACCCCCTGAGG
4168 TACGGTTCCA
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
37 7 0.08
38 56 0.67
39 20 0.24
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.24
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCATGGGTCCACTCTTA
Found at i:4325 original size:22 final size:22
Alignment explanation
Indices: 4282--4325 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4272 CTCGATCCGA
* *
4282 TTTTAAGAAAACAACAATACTT
1 TTTTAAAAAAACAACAACACTT
4304 TTTTAAAAACAACAA-AACACTT
1 TTTTAAAAA-AACAACAACACTT
4326 CAAATCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (22 bp):
TTTTAAAAAAACAACAACACTT
Found at i:4517 original size:10 final size:10
Alignment explanation
Indices: 4493--4539 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
4483 CTTCTCTCTA
*
4493 GAGTGTG-AA
1 GAGTGTGTAT
4502 GAGTGTGTAT
1 GAGTGTGTAT
* *
4512 GAGTGTGAAG
1 GAGTGTGTAT
*
4522 GAGTCTGTAT
1 GAGTGTGTAT
4532 GAGTGTGT
1 GAGTGTGT
4540 GGAGAGAGAG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.23, C:0.02, G:0.43, T:0.32
Consensus pattern (10 bp):
GAGTGTGTAT
Found at i:4517 original size:19 final size:20
Alignment explanation
Indices: 4493--4538 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
4483 CTTCTCTCTA
*
4493 GAGTGTGAA-GAGTGTGTAT
1 GAGTGTGAAGGAGTCTGTAT
4512 GAGTGTGAAGGAGTCTGTAT
1 GAGTGTGAAGGAGTCTGTAT
4532 GAGTGTG
1 GAGTGTG
4539 TGGAGAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.24, C:0.02, G:0.43, T:0.30
Consensus pattern (20 bp):
GAGTGTGAAGGAGTCTGTAT
Found at i:6505 original size:27 final size:27
Alignment explanation
Indices: 6417--6492 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
6407 TGAATATGCG
6417 AATG-CCAAAATGCCCCTAGGTGCAAA
1 AATGACCAAAATGCCCCTAGGTGCAAA
* **
6443 AATGACCAAAATGCCCATAGGTGTGAA
1 AATGACCAAAATGCCCCTAGGTGCAAA
6470 AATGACCAAAATGCCCCTAGGTG
1 AATGACCAAAATGCCCCTAGGTG
6493 ACCCTAATGC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 4 0.09
27 41 0.91
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (27 bp):
AATGACCAAAATGCCCCTAGGTGCAAA
Found at i:7020 original size:18 final size:19
Alignment explanation
Indices: 6997--7034 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
6987 ATGCATGCTC
*
6997 TGCATGGAGGC-ATGGAGA
1 TGCATGGAGACAATGGAGA
7015 TGCATGGAGACAATGGAGA
1 TGCATGGAGACAATGGAGA
7034 T
1 T
7035 AACAATGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.32, C:0.11, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACAATGGAGA
Found at i:9992 original size:30 final size:30
Alignment explanation
Indices: 9932--9994 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
9922 TCTTCAAGGG
* *
9932 GGAGGGAATGATGCGCCCAGGGCTGATCAT
1 GGAGGGAATGATGCGCCAAGGACTGATCAT
9962 GGAGGGAATGATGCGCCAAGGACTTG-TCAT
1 GGAGGGAATGATGCGCCAAGGAC-TGATCAT
9992 GGA
1 GGA
9995 CTTGAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.25, C:0.17, G:0.40, T:0.17
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAGGACTGATCAT
Found at i:10061 original size:18 final size:19
Alignment explanation
Indices: 10038--10075 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
10028 GTGCATGGGC
*
10038 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
10056 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
10075 T
1 T
10076 AACGATGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:11278 original size:16 final size:17
Alignment explanation
Indices: 11259--11294 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
11249 TTTCACACAC
11259 TTTCTG-TTTCTTTTTT
1 TTTCTGTTTTCTTTTTT
11275 TTTCTGTTTTCTTTTTT
1 TTTCTGTTTTCTTTTTT
11292 TTT
1 TTT
11295 TAAAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTCTGTTTTCTTTTTT
Found at i:12827 original size:31 final size:31
Alignment explanation
Indices: 12757--12866 Score: 118
Period size: 31 Copynumber: 3.6 Consensus size: 31
12747 TTTGCTGCCC
* * **
12757 CAAGCAACTAAGGATATAACG-TTACAA-AC
1 CAAGCAATTAAGGATATAACGTTTTCAATTT
* *
12786 CAAGCAATTAAGGACT-TAATGTTTTCGATTT
1 CAAGCAATTAAGGA-TATAACGTTTTCAATTT
*
12817 CAAGTAATTAAGGATATAACGTTTTCAATTT
1 CAAGCAATTAAGGATATAACGTTTTCAATTT
*
12848 CAAGCATTTAAGGATATAA
1 CAAGCAATTAAGGATATAA
12867 TCAGTTAGGG
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
29 17 0.26
30 6 0.09
31 43 0.65
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCAATTT
Found at i:15101 original size:37 final size:37
Alignment explanation
Indices: 14984--15211 Score: 297
Period size: 37 Copynumber: 6.2 Consensus size: 37
14974 AGAAGCTAAA
* * *
14984 ACTTGATGGGAACTTTCCCAATTATGAAATCTTTGAAA
1 ACTTGATGGGAACTTTCCCAATT-TGAAAACTATGAAG
*
15022 ACTTGATGGAAACTTTCCCAATTTTGAAAACTTTAT-AA-
1 ACTTGATGGGAACTTTCCCAA-TTTGAAAAC--TATGAAG
*
15060 ACTTGATGGGAACTTTCCCAATTAGAAAACTATGAAG
1 ACTTGATGGGAACTTTCCCAATTTGAAAACTATGAAG
*
15097 ACTTGATGGGAACTTTCCCAATTTG-AAAC--CGAAG
1 ACTTGATGGGAACTTTCCCAATTTGAAAACTATGAAG
* *
15131 ACTTGATGGGAAC-TTCCCAATTTGAAAACAATAAAG
1 ACTTGATGGGAACTTTCCCAATTTGAAAACTATGAAG
*
15167 ACTTGATGGGAACTTTCCCAATTTGAAAATTATGAAG
1 ACTTGATGGGAACTTTCCCAATTTGAAAACTATGAAG
15204 ACTTGATG
1 ACTTGATG
15212 AAAACCATGA
Statistics
Matches: 169, Mismatches: 12, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
33 11 0.07
34 21 0.12
35 3 0.02
36 22 0.13
37 60 0.36
38 46 0.27
39 4 0.02
40 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (37 bp):
ACTTGATGGGAACTTTCCCAATTTGAAAACTATGAAG
Found at i:15171 original size:70 final size:73
Alignment explanation
Indices: 14982--15194 Score: 281
Period size: 70 Copynumber: 2.9 Consensus size: 73
14972 AAAGAAGCTA
* * *
14982 AAACTTGATGGGAACTTTCCCAATTATGAAATCTTTGAAA-ACTTGATGGAAACTTTCCCAATTT
1 AAACTTGATGGGAACTTTCCCAATT-TGAAAACTAT-AAAGACTTGATGGGAACTTTCCCAA-TT
**
15046 TGAAAACTTTAT
63 TG-AAACTCGAT
* *
15058 AAACTTGATGGGAACTTTCCCAATTAGAAAACTATGAAGACTTGATGGGAACTTTCCCAATTTGA
1 AAACTTGATGGGAACTTTCCCAATTTGAAAACTATAAAGACTTGATGGGAACTTTCCCAATTTGA
15123 AAC-CGA-
66 AACTCGAT
* *
15129 AGACTTGATGGGAAC-TTCCCAATTTGAAAACAATAAAGACTTGATGGGAACTTTCCCAATTTGA
1 AAACTTGATGGGAACTTTCCCAATTTGAAAACTATAAAGACTTGATGGGAACTTTCCCAATTTGA
15193 AA
66 AA
15195 ATTATGAAGA
Statistics
Matches: 125, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
70 48 0.38
71 14 0.11
72 1 0.01
73 4 0.03
74 6 0.05
75 27 0.22
76 25 0.20
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (73 bp):
AAACTTGATGGGAACTTTCCCAATTTGAAAACTATAAAGACTTGATGGGAACTTTCCCAATTTGA
AACTCGAT
Found at i:15180 original size:107 final size:112
Alignment explanation
Indices: 14984--15211 Score: 333
Period size: 107 Copynumber: 2.1 Consensus size: 112
14974 AGAAGCTAAA
*
14984 ACTTGATGGGAACTTTCCCAATTATGAAATCTTTGAAAACTTGATGGAAACTTTCCCAATTTTGA
1 ACTTGATGGGAACTTTCCCAATTATGAAATC-TCGAAAACTTGATGGAAACTTTCCCAATTTTGA
**
15049 AAACTTTATAAACTTGATGGGAACTTTCCCAATTAGAAAACTATGAAG
65 AAACAATATAAACTTGATGGGAACTTTCCCAATTAGAAAACTATGAAG
* *
15097 ACTTGATGGGAACTTTCCCAATT-TGAAA-C-CGAAGACTTGATGGGAAC-TTCCCAA-TTTGAA
1 ACTTGATGGGAACTTTCCCAATTATGAAATCTCGAAAACTTGATGGAAACTTTCCCAATTTTGAA
* *
15157 AACAATA-AAGACTTGATGGGAACTTTCCCAATTTGAAAATTATGAAG
66 AACAATATAA-ACTTGATGGGAACTTTCCCAATTAGAAAACTATGAAG
15204 ACTTGATG
1 ACTTGATG
15212 AAAACCATGA
Statistics
Matches: 107, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
106 2 0.02
107 54 0.50
108 7 0.07
109 15 0.14
111 1 0.01
112 5 0.05
113 23 0.21
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (112 bp):
ACTTGATGGGAACTTTCCCAATTATGAAATCTCGAAAACTTGATGGAAACTTTCCCAATTTTGAA
AACAATATAAACTTGATGGGAACTTTCCCAATTAGAAAACTATGAAG
Found at i:27475 original size:14 final size:15
Alignment explanation
Indices: 27456--27485 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27446 CAATCAAAAC
27456 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
27470 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
27485 A
1 A
27486 TTAAAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:28015 original size:42 final size:42
Alignment explanation
Indices: 27964--28054 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
27954 GCCGGTCCTA
* * * *
27964 GCCGGGCATGTGGCTCGGATGAGGCTTGAGATGGCGGGCATG
1 GCCGGGCATGAGGCGCAGATGAGGCTTGAGATGCCGGGCATG
* * *
28006 GCCGGGCATGAGGCGCAGCTGAGGCTTGTGGTGCCGGGCATG
1 GCCGGGCATGAGGCGCAGATGAGGCTTGAGATGCCGGGCATG
28048 GCCGGGC
1 GCCGGGC
28055 GTGATACTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.12, C:0.23, G:0.48, T:0.16
Consensus pattern (42 bp):
GCCGGGCATGAGGCGCAGATGAGGCTTGAGATGCCGGGCATG
Found at i:30379 original size:27 final size:27
Alignment explanation
Indices: 30325--30404 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
30315 TTTTTTTATG
* *
30325 ACGCAAAAACTCTTTTTTTTTA-GAAAA
1 ACGCAAAAACT-TTTTTTTTGACGCAAA
30352 ACGCAAAAACTTTTTTTTTGACGCAAA
1 ACGCAAAAACTTTTTTTTTGACGCAAA
*
30379 A-AC-AAAA-TTTTTTTTATGACGCAAA
1 ACGCAAAAACTTTTTTTT-TGACGCAAA
30404 A
1 A
30405 ATATTTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 8 0.17
25 14 0.29
26 10 0.21
27 16 0.33
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (27 bp):
ACGCAAAAACTTTTTTTTTGACGCAAA
Found at i:30385 original size:25 final size:26
Alignment explanation
Indices: 30308--30405 Score: 88
Period size: 25 Copynumber: 4.0 Consensus size: 26
30298 AAAACGCAGC
*
30308 CAAAATTTTTTTTTATGACGCAAAAA
1 CAAAACTTTTTTTTATGACGCAAAAA
*
30334 C---TCTTTTTTTT-T-A-G-AAAAA
1 CAAAACTTTTTTTTATGACGCAAAAA
30353 CGCAAAAACTTTTTTTT-TGACGCAAAAA
1 --C-AAAACTTTTTTTTATGACGCAAAAA
30381 CAAAA-TTTTTTTTATGACGCAAAAA
1 CAAAACTTTTTTTTATGACGCAAAAA
30406 TATTTTTTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 21
0.71 0.04 0.25
Matches are distributed among these distances:
19 5 0.08
20 1 0.02
21 2 0.03
22 1 0.02
23 8 0.14
24 8 0.14
25 25 0.42
26 3 0.05
27 1 0.02
28 5 0.08
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (26 bp):
CAAAACTTTTTTTTATGACGCAAAAA
Found at i:30390 original size:47 final size:45
Alignment explanation
Indices: 30309--30426 Score: 110
Period size: 47 Copynumber: 2.5 Consensus size: 45
30299 AAACGCAGCC
* ****
30309 AAAATTTTTTTTTATGACGCAAAAACTCTTTTTTTTTAGAAAAACGCA
1 AAAAATTTTTTTT-TGACGCAAAAACAAAATTTTTTT--AAAAACGCA
* * **
30357 AAAACTTTTTTTTTGACGCAAAAACAAAATTTTTTTTATGACGCA
1 AAAAATTTTTTTTTGACGCAAAAACAAAATTTTTTTAAAAACGCA
30402 AAAATATTTTTTTTTCGACGCAAAA
1 AAAA-ATTTTTTTTT-GACGCAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
45 10 0.17
46 9 0.15
47 28 0.47
48 12 0.20
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (45 bp):
AAAAATTTTTTTTTGACGCAAAAACAAAATTTTTTTAAAAACGCA
Found at i:30414 original size:25 final size:24
Alignment explanation
Indices: 30308--30426 Score: 83
Period size: 25 Copynumber: 5.0 Consensus size: 24
30298 AAAACGCAGC
30308 CAAAATTTTTTTTTATGACGCAAAAA
1 CAAAA-TTTTTTTT-TGACGCAAAAA
**
30334 C--TCTTTTTTTTT-A-G-AAAAA
1 CAAAATTTTTTTTTGACGCAAAAA
30353 CGCAAAAACTTTTTTTTTGACGCAAAAA
1 --C-AAAA-TTTTTTTTTGACGCAAAAA
30381 CAAAATTTTTTTTATGACGC--AAA
1 CAAAATTTTTTTT-TGACGCAAAAA
*
30404 -AATATTTTTTTTTCGACGCAAAA
1 CAAAATTTTTTTTT-GACGCAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 28
0.69 0.05 0.26
Matches are distributed among these distances:
19 5 0.07
20 1 0.01
21 3 0.04
22 17 0.23
23 11 0.15
24 10 0.13
25 19 0.25
26 3 0.04
27 1 0.01
28 5 0.07
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (24 bp):
CAAAATTTTTTTTTGACGCAAAAA
Done.