Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018055.1 Corchorus olitorius cultivar O-4 contig18088, 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: 44187
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:14 original size:3 final size:3
Alignment explanation
Indices: 7--165 Score: 279
Period size: 3 Copynumber: 53.3 Consensus size: 3
1 TGTTAC
7 TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52 TAT TAT TAT TA- TAT TAT TAT TATT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
96 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
144 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
166 GTTAGAACTA
Statistics
Matches: 151, Mismatches: 0, Indels: 10
0.94 0.00 0.06
Matches are distributed among these distances:
2 6 0.04
3 139 0.92
4 6 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3985 original size:29 final size:29
Alignment explanation
Indices: 3952--4017 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
3942 TTTGTTTATT
* **
3952 GTGGTTGATTAAGTGCGGGTTGTGCACTC
1 GTGGTTGATCAAGTGCGGGTTGAACACTC
* *
3981 GTGGTTAATCAAGTGCGGGTTGAACACTT
1 GTGGTTGATCAAGTGCGGGTTGAACACTC
4010 GTGGTTGA
1 GTGGTTGA
4018 AGCTTTGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.18, C:0.12, G:0.36, T:0.33
Consensus pattern (29 bp):
GTGGTTGATCAAGTGCGGGTTGAACACTC
Found at i:4031 original size:14 final size:14
Alignment explanation
Indices: 4014--4044 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4004 ACACTTGTGG
*
4014 TTGAAGCTTTGGGT
1 TTGAAGCTTTGAGT
4028 TTGAAGCTTTGAGT
1 TTGAAGCTTTGAGT
4042 TTG
1 TTG
4045 TAAAAAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.32, T:0.45
Consensus pattern (14 bp):
TTGAAGCTTTGAGT
Found at i:5891 original size:42 final size:42
Alignment explanation
Indices: 5843--5932 Score: 180
Period size: 42 Copynumber: 2.1 Consensus size: 42
5833 AAAGAATACT
5843 CTTGAGGATGCATTAAAGCATGCAACATAGGAAAAAGAGAAA
1 CTTGAGGATGCATTAAAGCATGCAACATAGGAAAAAGAGAAA
5885 CTTGAGGATGCATTAAAGCATGCAACATAGGAAAAAGAGAAA
1 CTTGAGGATGCATTAAAGCATGCAACATAGGAAAAAGAGAAA
5927 CTTGAG
1 CTTGAG
5933 CATGACTTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.46, C:0.12, G:0.24, T:0.18
Consensus pattern (42 bp):
CTTGAGGATGCATTAAAGCATGCAACATAGGAAAAAGAGAAA
Found at i:23654 original size:27 final size:27
Alignment explanation
Indices: 23613--23704 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 27
23603 ATACTTGAAG
* * *
23613 TGACCAAAATGCCCCTGGATGTGCAAA
1 TGACCAAAATACCCCTGGACGAGCAAA
*
23640 TGACCAAAATACCCCTGGACGCGCAAA
1 TGACCAAAATACCCCTGGACGAGCAAA
* * * *
23667 TGACGAAAATGCCTCTGGACAAGCAAA
1 TGACCAAAATACCCCTGGACGAGCAAA
23694 TGACCAAAATA
1 TGACCAAAATA
23705 AGAAGGAAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (27 bp):
TGACCAAAATACCCCTGGACGAGCAAA
Found at i:25837 original size:36 final size:37
Alignment explanation
Indices: 25785--25856 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
25775 CTGGAAGATG
**
25785 GTTTCTTAGAGGA-TTTTAAAAGTACATCGGAAGACA
1 GTTTCTTAGAAAATTTTTAAAAGTACATCGGAAGACA
* **
25821 GTTTCTTAGAAAATTTTTAAGAGTGGATCGGAAGAC
1 GTTTCTTAGAAAATTTTTAAAAGTACATCGGAAGAC
25857 GATCTAGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 11 0.37
37 19 0.63
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.32
Consensus pattern (37 bp):
GTTTCTTAGAAAATTTTTAAAAGTACATCGGAAGACA
Found at i:26248 original size:27 final size:27
Alignment explanation
Indices: 26210--26271 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
26200 AAATTGTTAT
* * *
26210 TCAGAAATGGTTTGGAAGATGATCTCA
1 TCAGAAATGGTTCGAAAGACGATCTCA
26237 TCAGAAATGGTTCGAAAGACGATCTCA
1 TCAGAAATGGTTCGAAAGACGATCTCA
26264 TCAGAAAT
1 TCAGAAAT
26272 AGATTTGCCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.26
Consensus pattern (27 bp):
TCAGAAATGGTTCGAAAGACGATCTCA
Found at i:26323 original size:27 final size:27
Alignment explanation
Indices: 26281--26382 Score: 159
Period size: 27 Copynumber: 3.8 Consensus size: 27
26271 TAGATTTGCC
** *
26281 GAAATGGTTCAAAAGACGATCTCATCG
1 GAAATGGTTCGGAAGACGATCTCATCA
*
26308 GAAATGGTACGGAAGACGATCTCATCA
1 GAAATGGTTCGGAAGACGATCTCATCA
26335 GAAATGGTTCGGAAGACGATCTCATCA
1 GAAATGGTTCGGAAGACGATCTCATCA
*
26362 AAAATGGTTCGGAAGACGATC
1 GAAATGGTTCGGAAGACGATC
26383 CTTTTAAGAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (27 bp):
GAAATGGTTCGGAAGACGATCTCATCA
Found at i:26402 original size:27 final size:27
Alignment explanation
Indices: 26372--26457 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
26362 AAAATGGTTC
26372 GGAAGACGATCCTTTTAAGATTAAATT
1 GGAAGACGATCCTTTTAAGATTAAATT
* * * *
26399 GGAAGAC-A--GTTTGAAGGAGCT-GATT
1 GGAAGACGATCCTTTTAA-GA-TTAAATT
*
26424 TGAAGACGATCCTTTTAAGATTAAATT
1 GGAAGACGATCCTTTTAAGATTAAATT
26451 GGAAGAC
1 GGAAGAC
26458 AGTTTGAAGG
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
24 5 0.12
25 11 0.26
26 4 0.09
27 18 0.42
28 5 0.12
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.29
Consensus pattern (27 bp):
GGAAGACGATCCTTTTAAGATTAAATT
Found at i:26436 original size:52 final size:51
Alignment explanation
Indices: 26372--26541 Score: 209
Period size: 52 Copynumber: 3.3 Consensus size: 51
26362 AAAATGGTTC
*
26372 GGAAGACGATCCTTTTAAGATTAAATTGGAAGACAGTTTGAAGGAGCTGATT
1 GGAAGACGATCCTTTTAAGATTAAATTGGAAGACAGTTTGAAGGAG-TGATA
* * *
26424 TGAAGACGATCCTTTTAAGATTAAATTGGAAGACAGTTTGAAGGA-TAAGA
1 GGAAGACGATCCTTTTAAGATTAAATTGGAAGACAGTTTGAAGGAGTGATA
* * * * * * *
26474 GGAAGATGGTCCTCTAAAGATTGAATTGGAAGATAGTTTGAAGGAGTTGATC
1 GGAAGACGATCCTTTTAAGATTAAATTGGAAGACAGTTTGAAGGAG-TGATA
26526 GGAAGACGAT-CTTTTA
1 GGAAGACGATCCTTTTA
26542 TATTTGAATC
Statistics
Matches: 98, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
50 40 0.41
51 4 0.04
52 54 0.55
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (51 bp):
GGAAGACGATCCTTTTAAGATTAAATTGGAAGACAGTTTGAAGGAGTGATA
Found at i:26606 original size:42 final size:43
Alignment explanation
Indices: 26546--26634 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 43
26536 CTTTTATATT
*
26546 TGAATCAGATGACGCGGTGTAGCATCTTCAAG-TGGGATTCGG
1 TGAATCAGATGACGCGGTGTAGCATCTTCAAGATGGAATTCGG
*
26588 TGAATCAGATGACTCGGTGTAGCATCTTCAAGATTGGAATTCGG
1 TGAATCAGATGACGCGGTGTAGCATCTTCAAGA-TGGAATTCGG
26632 TGA
1 TGA
26635 GCTCGGTGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 31 0.72
44 12 0.28
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (43 bp):
TGAATCAGATGACGCGGTGTAGCATCTTCAAGATGGAATTCGG
Found at i:26858 original size:90 final size:89
Alignment explanation
Indices: 26612--26925 Score: 418
Period size: 89 Copynumber: 3.5 Consensus size: 89
26602 CGGTGTAGCA
*
26612 TCTTC-AAGATTGGAATTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGGCTGATTCGG
1 TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGGATGATTCGG
** *
26676 TGAATCAAGTTAATACGATGCATC
66 TGAATCAAGTTAATGTGGTGCATC
* * * * * * * *
26700 TCTTCAAAGATTGGAATTCGGTGAGCCCGGTGCAGCACATTTTGAAACAGTTGAGGACGATTCGG
1 TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGGATGATTCGG
26765 TGAATCAAGTTAATGTGGTGCATTAC
66 TGAATCAAGTTAATGTGGTGCA-T-C
* * * *
26791 TTTTTC-AAGATTGG-ACTCGATGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGGGTGATTCG
1 -TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGGATGATTCG
26854 GTGAATCAAGTTAATGTGGTGCATC
65 GTGAATCAAGTTAATGTGGTGCATC
* *
26879 TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCACATTTTCAAA
1 TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCAAATCTTCAAA
26926 CAAGCTGAAG
Statistics
Matches: 191, Mismatches: 29, Indels: 11
0.83 0.13 0.05
Matches are distributed among these distances:
87 4 0.02
88 14 0.07
89 98 0.51
90 62 0.32
91 9 0.05
92 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (89 bp):
TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGGATGATTCGG
TGAATCAAGTTAATGTGGTGCATC
Found at i:26942 original size:90 final size:88
Alignment explanation
Indices: 26612--26966 Score: 390
Period size: 89 Copynumber: 4.0 Consensus size: 88
26602 CGGTGTAGCA
* *
26612 TCTTCAAGATTGGAATTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGAT-CAGGCTGATTCGG
1 TCTTCAAGATTGGAATTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATGAAGAC-GATTCGG
* *
26676 TGAATCAAGTTAATACGATGCATC
65 TGAATCAAGTTAATGCGGTGCATC
* * * * * * *
26700 TCTTCAAAGATTGGAATTCGGTGAGCCCGGTGCAGCACATTTTGAAACAGTTGAGGACGATTCGG
1 TCTTC-AAGATTGGAATTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATGAAGACGATTCGG
*
26765 TGAATCAAGTTAATGTGGTGCATTAC
65 TGAATCAAGTTAATGCGGTGCA-T-C
* * * * * **
26791 TTTTTCAAGATTGG-ACTCGATGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGGGTGATTCGG
1 -TCTTCAAGATTGGAATTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATGAAGACGATTCGG
*
26855 TGAATCAAGTTAATGTGGTGCATC
65 TGAATCAAGTTAATGCGGTGCATC
* * * * *
26879 TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAAGCTGAAGACGATTCA
1 TCTTC-AAGATTGGAATTCGGTGAGCTCGGTGCAGCAAATCTTCAAA-TAGATGAAGACGATTCG
* *
26944 GTGAATTAAGTTACTGCGGTGCA
64 GTGAATCAAGTTAATGCGGTGCA
26967 GTATTTCCTC
Statistics
Matches: 220, Mismatches: 39, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
87 4 0.02
88 14 0.06
89 95 0.43
90 94 0.43
91 9 0.04
92 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (88 bp):
TCTTCAAGATTGGAATTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATGAAGACGATTCGGT
GAATCAAGTTAATGCGGTGCATC
Found at i:27728 original size:20 final size:20
Alignment explanation
Indices: 27703--27743 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
27693 GAAAATACAA
27703 GGCATTTGATTTACAAATTG
1 GGCATTTGATTTACAAATTG
*
27723 GGCATTTGATTTGCAAATTG
1 GGCATTTGATTTACAAATTG
27743 G
1 G
27744 TGCTCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (20 bp):
GGCATTTGATTTACAAATTG
Found at i:38978 original size:2 final size:2
Alignment explanation
Indices: 38967--39018 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
38957 AGAAAATCCT
38967 CA CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
39008 CA CA CA CA CA C
1 CA CA CA CA CA C
39019 TTGTTTACCA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:40521 original size:14 final size:15
Alignment explanation
Indices: 40502--40531 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40492 AACTAGGAAA
40502 AATAAAT-AACAAGG
1 AATAAATAAACAAGG
40516 AATAAATAAACAAGG
1 AATAAATAAACAAGG
40531 A
1 A
40532 TTGGACTTAG
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:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAAATAAACAAGG
Found at i:41581 original size:23 final size:23
Alignment explanation
Indices: 41549--41597 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
41539 CCACCATGGG
41549 CCATTATATTTTCTTTACTTGGT
1 CCATTATATTTTCTTTACTTGGT
*
41572 CCATTTTATTTTCTTTACTTGGT
1 CCATTATATTTTCTTTACTTGGT
41595 CCA
1 CCA
41598 GTTCTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.55
Consensus pattern (23 bp):
CCATTATATTTTCTTTACTTGGT
Done.