Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016048.1 Corchorus capsularis cultivar CVL-1 contig16069, 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: 63408
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:179 original size:23 final size:23
Alignment explanation
Indices: 149--195 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
139 GTGGGTCTGT
*
149 CCCACCTAATAATTTGTTGAAGA
1 CCCACCTAATAATTTCTTGAAGA
172 CCCACCTAATAATTTCTTGAAGA
1 CCCACCTAATAATTTCTTGAAGA
195 C
1 C
196 AAGGGGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.30
Consensus pattern (23 bp):
CCCACCTAATAATTTCTTGAAGA
Found at i:14313 original size:16 final size:16
Alignment explanation
Indices: 14292--14325 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
14282 AAAGGAGCTA
14292 AATTGGAGCTATTTAG
1 AATTGGAGCTATTTAG
**
14308 AATTGGTTCTATTTAG
1 AATTGGAGCTATTTAG
14324 AA
1 AA
14326 CAAGTTGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (16 bp):
AATTGGAGCTATTTAG
Found at i:18793 original size:2 final size:2
Alignment explanation
Indices: 18786--18814 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18776 CTAATTGTGC
18786 AT 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 AT A
18815 GTCTCCTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24709 original size:2 final size:2
Alignment explanation
Indices: 24702--24735 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
24692 TTTCCCTCAA
*
24702 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24736 TTGGTTAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27973 original size:18 final size:18
Alignment explanation
Indices: 27946--27984 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
27936 TCTTGAATAA
* *
27946 AAACATAATTCAATTAAT
1 AAACAAAATTAAATTAAT
27964 AAACAAAATTAAATTAAT
1 AAACAAAATTAAATTAAT
27982 AAA
1 AAA
27985 AAAGAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (18 bp):
AAACAAAATTAAATTAAT
Found at i:29175 original size:23 final size:24
Alignment explanation
Indices: 29145--29190 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
29135 TCCTCTAGCA
29145 TTTTGTCTGTCTCG-TTTTTTTTC
1 TTTTGTCTGTCTCGCTTTTTTTTC
*
29168 TTTTGTCTTTCTCGCTTTTTTTT
1 TTTTGTCTGTCTCGCTTTTTTTT
29191 TCCTGGTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.00, C:0.17, G:0.11, T:0.72
Consensus pattern (24 bp):
TTTTGTCTGTCTCGCTTTTTTTTC
Found at i:29834 original size:4 final size:4
Alignment explanation
Indices: 29825--29873 Score: 71
Period size: 4 Copynumber: 11.5 Consensus size: 4
29815 CATGCGCCCC
29825 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTGTAA TTTAA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-T-A TTT-A TTTA TT
29874 AATTGTAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 33 0.77
5 7 0.16
6 3 0.07
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:30534 original size:16 final size:17
Alignment explanation
Indices: 30501--30535 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
30491 TATAATAAAC
30501 AAAACATTTAGAAAATT
1 AAAACATTTAGAAAATT
30518 AAAACATTTAG-AAATT
1 AAAACATTTAGAAAATT
30534 AA
1 AA
30536 CTATTGACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
AAAACATTTAGAAAATT
Found at i:32423 original size:69 final size:71
Alignment explanation
Indices: 32300--32442 Score: 218
Period size: 69 Copynumber: 2.0 Consensus size: 71
32290 GATGACGATG
* *
32300 AAATTTTTTTCTAAAGGTTGCTCTCAAGCACTAAATTCTTATAGATGTGTATCCTTCTTTTCATG
1 AAATTTTTTTCTAAAGGTTGCTCTCAA-CAC-AAATCCTTATAGATGTGTATCCTTCTTTTCATA
32365 ACAATGCA
64 ACAATGCA
* *
32373 AAATTTTTTTCTAAAGGTTGCTCTCAA-AC-ACTCCTTATAGATGTGTATCCTTCTTTTCTTAAC
1 AAATTTTTTTCTAAAGGTTGCTCTCAACACAAATCCTTATAGATGTGTATCCTTCTTTTCATAAC
32436 AATGCA
66 AATGCA
32442 A
1 A
32443 TTTTAGTTTC
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
69 37 0.56
71 2 0.03
73 27 0.41
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (71 bp):
AAATTTTTTTCTAAAGGTTGCTCTCAACACAAATCCTTATAGATGTGTATCCTTCTTTTCATAAC
AATGCA
Found at i:33338 original size:175 final size:174
Alignment explanation
Indices: 33041--33371 Score: 547
Period size: 175 Copynumber: 1.9 Consensus size: 174
33031 CTAAATTAAC
* *
33041 TCCATTTAATGAAAAATATATATATTCTATAACGTTACAAAATCAAACATATAATGATTGAAATA
1 TCCATTTAATGAAAAATATATATAATCTATAACGATACAAAATCAAACATATAATGATTGAAATA
* * * * *
33106 GAATTTATAGAATGAAACTGTCTCATATTTAAATGATTGTAATTATTATTTTTAAATTCAAAATG
66 GAATTTATAGAATGAAACTGCCTAATATTTAAATGATTGTAATTAGTATTATTAAATTCAAAACG
33171 TTA-AAAAAAATGAATTAAAGTATATAATGAATTAAAGAAGAAT
131 TTACAAAAAAATGAATTAAAGTATATAATGAATTAAAGAAGAAT
*
33214 TCCATTTAATGAAAAACATATATATAATCTATTACGATACAAAATCAAACATATAATGATTGAAA
1 TCCATTTAATG-AAAA-ATATATATAATCTATAACGATACAAAATCAAACATATAATGATTGAAA
*
33279 TAGAATTTATAGAATGAAACTGCCTAATATTTAAATTATTGTAATTAGTATTATTAAATTCAAAA
64 TAGAATTTATAGAATGAAACTGCCTAATATTTAAATGATTGTAATTAGTATTATTAAATTCAAAA
*
33344 CGTTACGAAAAAATGAATTAAAGTATAT
129 CGTTACAAAAAAATGAATTAAAGTATAT
33372 TAAATATGAT
Statistics
Matches: 145, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
173 11 0.08
174 4 0.03
175 109 0.75
176 21 0.14
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.35
Consensus pattern (174 bp):
TCCATTTAATGAAAAATATATATAATCTATAACGATACAAAATCAAACATATAATGATTGAAATA
GAATTTATAGAATGAAACTGCCTAATATTTAAATGATTGTAATTAGTATTATTAAATTCAAAACG
TTACAAAAAAATGAATTAAAGTATATAATGAATTAAAGAAGAAT
Found at i:37477 original size:39 final size:39
Alignment explanation
Indices: 37420--37568 Score: 241
Period size: 39 Copynumber: 3.9 Consensus size: 39
37410 CACAATCTAG
37420 CCAA-CAG-TTAACCCCCTGAGACACGGGTCCACTCTTA
1 CCAATCAGTTTAACCCCCTGAGACACGGGTCCACTCTTA
*
37457 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAATCAGTTTAACCCCCTGAGACACGGGTCCACTCTTA
*
37496 CCAATCAATTTAACCCCCTGAGACACGGGTCCACTCTTA
1 CCAATCAGTTTAACCCCCTGAGACACGGGTCCACTCTTA
* *
37535 CC-ATCAGTTTAACCCCCTGAGGCGCGGGTCCACT
1 CCAATCAGTTTAACCCCCTGAGACACGGGTCCACT
37569 ATGCACAGCC
Statistics
Matches: 104, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
37 4 0.04
38 32 0.31
39 68 0.65
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.21
Consensus pattern (39 bp):
CCAATCAGTTTAACCCCCTGAGACACGGGTCCACTCTTA
Found at i:40203 original size:42 final size:42
Alignment explanation
Indices: 40156--40244 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
40146 ACGGAGGGAG
* *
40156 TATTAGCTTTATTTTGATAAATTATCTAGAGATGGAGTAGAA
1 TATTAGCTTTATTTTGATAAATTACCTAGAGATGAAGTAGAA
* *
40198 TATTAGTTTTATTTTGATGAATTACCTAGAGATGAAGTAGAA
1 TATTAGCTTTATTTTGATAAATTACCTAGAGATGAAGTAGAA
40240 T-TTAG
1 TATTAG
40245 GTAATACACT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 4 0.09
42 39 0.91
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (42 bp):
TATTAGCTTTATTTTGATAAATTACCTAGAGATGAAGTAGAA
Found at i:50472 original size:16 final size:17
Alignment explanation
Indices: 50446--50480 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
50436 TCCCTCTCAT
50446 AGTACCTAGGTAGTATG
1 AGTACCTAGGTAGTATG
50463 AGTA-CTAGGTAGTATG
1 AGTACCTAGGTAGTATG
50479 AG
1 AG
50481 GTAATAGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (17 bp):
AGTACCTAGGTAGTATG
Found at i:57746 original size:6 final size:6
Alignment explanation
Indices: 57735--57766 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
57725 AAAGCAAAGC
57735 AAATCT AAATCT AAATCT AAATCT AAATCT AA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AA
57767 GGCAAATTAA
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:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:58700 original size:10 final size:10
Alignment explanation
Indices: 58685--58709 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
58675 GAGGACTCTA
58685 GAATTTTCTG
1 GAATTTTCTG
58695 GAATTTTCTG
1 GAATTTTCTG
58705 GAATT
1 GAATT
58710 GAGCAGGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:62450 original size:63 final size:63
Alignment explanation
Indices: 62351--62533 Score: 339
Period size: 63 Copynumber: 2.9 Consensus size: 63
62341 TGCTCAAAAA
*
62351 AAATTTACTTTAAATTCTTGATAGTTTATTCTAATCCAAAATCATTCCCGCAGCAAATGTGTC
1 AAATTTACTTTAAATTCTTGATAGTTTCTTCTAATCCAAAATCATTCCCGCAGCAAATGTGTC
*
62414 AAATTTACTTTAAATTCTTGATAATTTCTTCTAATCCAAAATCATTCCCGCAGCAAATGTGTC
1 AAATTTACTTTAAATTCTTGATAGTTTCTTCTAATCCAAAATCATTCCCGCAGCAAATGTGTC
*
62477 AAATTTACTTTAAATTCTTGATAGTTTCTTCTAATCCAAAATCATTCCCGCAACAAA
1 AAATTTACTTTAAATTCTTGATAGTTTCTTCTAATCCAAAATCATTCCCGCAGCAAA
62534 GTGCGGGTAA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 116 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (63 bp):
AAATTTACTTTAAATTCTTGATAGTTTCTTCTAATCCAAAATCATTCCCGCAGCAAATGTGTC
Done.