Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016508.1 Corchorus olitorius cultivar O-4 contig16541, 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: 66458
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3580 original size:25 final size:25
Alignment explanation
Indices: 3552--3601 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3542 ATGTAGCAAA
*
3552 ACTCCACTCAAGTAGTGGTGGCACC
1 ACTCCACTCAAGTAGTGGTAGCACC
3577 ACTCCACTCAAGTAGTGGTAGCACC
1 ACTCCACTCAAGTAGTGGTAGCACC
3602 GGTCTTGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.32, G:0.22, T:0.20
Consensus pattern (25 bp):
ACTCCACTCAAGTAGTGGTAGCACC
Found at i:3765 original size:70 final size:70
Alignment explanation
Indices: 3652--3862 Score: 361
Period size: 70 Copynumber: 3.0 Consensus size: 70
3642 TCATGGTGGA
*
3652 CCAAATTTCGACTCAATTTTTCGGGCTGTATAGCAAAACTCAATTCAGTTTCAACAGATCCTGAT
1 CCAAATTTCGACTCAATTTTTCGGGCTGTATAGCAAAACTCAATTCAGTTTCAACAGATCCTGAA
3717 GAGAC
66 GAGAC
*
3722 CCAAATTTCGACTCAATTTTTCGGGCTGTATAACAAAACTCAATTCAGTTTCAACAGATCCT-AA
1 CCAAATTTCGACTCAATTTTTCGGGCTGTATAGCAAAACTCAATTCAGTTTCAACAGATCCTGAA
*
3786 GTTGAC
66 G-AGAC
* *
3792 CCAAATTTCGACTCAATTTTTCGAGCTGTATAGCAAAACTCAATTCAGTTTCAACAGATCCTGAG
1 CCAAATTTCGACTCAATTTTTCGGGCTGTATAGCAAAACTCAATTCAGTTTCAACAGATCCTGAA
3857 GAGAC
66 GAGAC
3862 C
1 C
3863 TGAATAGTAA
Statistics
Matches: 132, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
69 2 0.02
70 128 0.97
71 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (70 bp):
CCAAATTTCGACTCAATTTTTCGGGCTGTATAGCAAAACTCAATTCAGTTTCAACAGATCCTGAA
GAGAC
Found at i:14358 original size:22 final size:21
Alignment explanation
Indices: 14333--14412 Score: 88
Period size: 22 Copynumber: 3.7 Consensus size: 21
14323 AGATCATTAT
14333 TCATTATGAAATTTGGATAACC
1 TCATTATGAAATTTGG-TAACC
*
14355 TCATTATAAAATTTTGGTAACC
1 TCATTATGAAA-TTTGGTAACC
* * *
14377 TCCTTATTAAATGTTGGTAATC
1 TCATTATGAAAT-TTGGTAACC
*
14399 ACATTATGAAATTT
1 TCATTATGAAATTT
14413 TGATAACCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
21 3 0.06
22 41 0.84
23 5 0.10
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.41
Consensus pattern (21 bp):
TCATTATGAAATTTGGTAACC
Found at i:17648 original size:27 final size:28
Alignment explanation
Indices: 17618--17672 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
17608 AATTAAGGAT
17618 GTGGATAATT-AAAAAGAAACA-AGAGAA
1 GTGGATAATTAAAAAAG-AACAGAGAGAA
17645 GTGGATAATTAAAAAAGAACAGAGAGAA
1 GTGGATAATTAAAAAAGAACAGAGAGAA
17673 TATTAAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.58, C:0.04, G:0.24, T:0.15
Consensus pattern (28 bp):
GTGGATAATTAAAAAAGAACAGAGAGAA
Found at i:24555 original size:17 final size:17
Alignment explanation
Indices: 24533--24567 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
24523 ACCCGAGGCA
*
24533 ACCCGAGCCCGATCCCG
1 ACCCGAGCCCGAACCCG
24550 ACCCGAGCCCGAACCCG
1 ACCCGAGCCCGAACCCG
24567 A
1 A
24568 AATAATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.51, G:0.23, T:0.03
Consensus pattern (17 bp):
ACCCGAGCCCGAACCCG
Found at i:25069 original size:31 final size:30
Alignment explanation
Indices: 24998--25069 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 30
24988 GTCTATCAGC
*
24998 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGA-TTTAATTT
*
25029 TAATT-ATTTGTTTAATTTAATG-TTTAATTT
1 T-TTTAATTTGTTTAATTTAA-GATTTAATTT
25059 GTTTTAATTTG
1 -TTTTAATTTG
25070 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 9 0.26
31 22 0.65
32 3 0.09
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.62
Consensus pattern (30 bp):
TTTTAATTTGTTTAATTTAAGATTTAATTT
Found at i:25490 original size:17 final size:17
Alignment explanation
Indices: 25469--25512 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
25459 AAAATCAAAC
*
25469 TCGAACCCGATCCGAG-
1 TCGAACCCGACCCGAGA
*
25485 TCCGAACCCTACCCGAGA
1 T-CGAACCCGACCCGAGA
25503 TCGAACCCGA
1 TCGAACCCGA
25513 AAATACCCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 21 0.91
18 1 0.04
ACGTcount: A:0.27, C:0.41, G:0.20, T:0.11
Consensus pattern (17 bp):
TCGAACCCGACCCGAGA
Found at i:25525 original size:16 final size:16
Alignment explanation
Indices: 25504--25594 Score: 71
Period size: 16 Copynumber: 5.8 Consensus size: 16
25494 TACCCGAGAT
25504 CGAACCCGAAAATACC
1 CGAACCCGAAAATACC
*
25520 CGAACCCG-ATATAACC
1 CGAACCCGAAAAT-ACC
**
25536 CGAGTCCGAAAATACC
1 CGAACCCGAAAATACC
* **
25552 CGAATCC-AACTTAACC
1 CGAACCCGAAAAT-ACC
* *
25568 CGAACCCGAAAAAACT
1 CGAACCCGAAAATACC
25584 CGAACCC-AAAA
1 CGAACCCGAAAA
25595 CCGCCCAATT
Statistics
Matches: 59, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
15 10 0.17
16 44 0.75
17 5 0.08
ACGTcount: A:0.43, C:0.35, G:0.12, T:0.10
Consensus pattern (16 bp):
CGAACCCGAAAATACC
Found at i:25548 original size:32 final size:32
Alignment explanation
Indices: 25504--25592 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
25494 TACCCGAGAT
*
25504 CGAACCCGAAAATACCCGAACCCGA-TATAACC
1 CGAACCCGAAAATACCCGAACCCAACT-TAACC
** *
25536 CGAGTCCGAAAATACCCGAATCCAACTTAACC
1 CGAACCCGAAAATACCCGAACCCAACTTAACC
* *
25568 CGAACCCGAAAAAACTCGAACCCAA
1 CGAACCCGAAAATACCCGAACCCAA
25593 AACCGCCCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 46 0.98
33 1 0.02
ACGTcount: A:0.42, C:0.36, G:0.12, T:0.10
Consensus pattern (32 bp):
CGAACCCGAAAATACCCGAACCCAACTTAACC
Found at i:49667 original size:45 final size:45
Alignment explanation
Indices: 49597--49686 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
49587 CCTCTCTTAC
*
49597 TTTTATTTTTCATTTCTTAACTGAATTTTCTTAAAATAATTTATA
1 TTTTATTTTTCATTTATTAACTGAATTTTCTTAAAATAATTTATA
*
49642 TTTTATTTTTCATTTATTAATTGAATTTTCTTAAAATAATTTATA
1 TTTTATTTTTCATTTATTAACTGAATTTTCTTAAAATAATTTATA
49687 AAATAACGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (45 bp):
TTTTATTTTTCATTTATTAACTGAATTTTCTTAAAATAATTTATA
Found at i:66456 original size:33 final size:33
Alignment explanation
Indices: 66358--66458 Score: 141
Period size: 33 Copynumber: 3.1 Consensus size: 33
66348 AAATAACTGG
* * *
66358 TGCCGCCCTCCTAGGACGGCACTGACCATGG-CG
1 TGCCGCCCTCCTTGGGCGGCA-TGACCATGGTCA
66391 TGCCGCCCTCCTTGGGCGGCATGACCATGGTCA
1 TGCCGCCCTCCTTGGGCGGCATGACCATGGTCA
* *
66424 TGCCTCCCTCCTTGGGTGGCATGACCATGGTCA
1 TGCCGCCCTCCTTGGGCGGCATGACCATGGTCA
66457 TG
1 TG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 9 0.15
33 53 0.85
ACGTcount: A:0.13, C:0.36, G:0.30, T:0.22
Consensus pattern (33 bp):
TGCCGCCCTCCTTGGGCGGCATGACCATGGTCA
Done.