Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021184.1 Corchorus olitorius cultivar O-4 contig21217, 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: 9749
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:2652 original size:27 final size:27
Alignment explanation
Indices: 2610--2705 Score: 129
Period size: 27 Copynumber: 3.6 Consensus size: 27
2600 AAGTGAGCTT
2610 AAAATGACCAAAATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTGAATGTG
* *
2637 TAAATGACCAAGATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTGAATGTG
* * *
2664 AAAATGACAAAAATGCCCCTGGACGTG
1 AAAATGACCAAAATGCCCCTGAATGTG
* *
2691 CAAATGACAAAAATG
1 AAAATGACCAAAATG
2706 ACCTATATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGTG
Found at i:3129 original size:50 final size:50
Alignment explanation
Indices: 3057--3653 Score: 1023
Period size: 50 Copynumber: 11.9 Consensus size: 50
3047 CTATATGGAT
* *
3057 TTGATAGTTGACTCGTACGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
1 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
* *
3107 TTGATAATTGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCTACG
1 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
* *
3157 TTGATAATTGACTCGTATGGAAACGAATTTGGCTTGTAGAAAAGCCTATG
1 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
* * *
3207 TTGATAATTGACTCGTATGGAGACGAATTTGGCTTGTGGAAAAGCCCATG
1 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
3257 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
1 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
*
3307 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTG
1 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
*
3357 TTGATAATTGACTCGTAGGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
1 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
*
3407 TTGATAATTGACTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCCTATG
1 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
* * *
3457 TTCATAATTGACTCGTATGGAAACGAGTTTGGGCTTGTGGAAAAGCCTGTA
1 TTGATAATTGACTCGTATGGAAACGAGTTT-GGCTTGTGGAAAAGCCTATG
*
3508 TTGATAATTGATTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
1 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
3558 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
1 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
* *
3608 TTGATAATTGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCC
1 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
3654 AAAGCATTCG
Statistics
Matches: 516, Mismatches: 30, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
50 471 0.91
51 45 0.09
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (50 bp):
TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
Found at i:4366 original size:50 final size:48
Alignment explanation
Indices: 4275--4462 Score: 223
Period size: 50 Copynumber: 3.8 Consensus size: 48
4265 AAAATCGACC
* * * *
4275 TTTGGTCTTGGTCTCACAAATGGAGTGCAATCTTATTTTGAAATGCGAAT
1 TTTGATCTTGGACTCACAAATGGAATGCAAT-TTA-TTTGAAAAGCGAAT
*
4325 TTTGATCTTGGACTCACAAATGGAATGGAATTTCATATTGAAAAGCGAAT
1 TTTGATCTTGGACTCACAAATGGAATGCAATTT-AT-TTGAAAAGCGAAT
* * *
4375 TTTGATCTTGAACTCACAAATGCAAAAGCAATTTTACTTTGAAAAGCGAAT
1 TTTGATCTTGGACTCACAAATG-GAATGCAA-TTTA-TTTGAAAAGCGAAT
*
4426 TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATT
1 TTTGATCTTGGACTCACAAATGGAATGCAAT-TTATT
4463 GTAAATCTTC
Statistics
Matches: 119, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
49 6 0.05
50 70 0.59
51 39 0.33
52 4 0.03
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (48 bp):
TTTGATCTTGGACTCACAAATGGAATGCAATTTATTTGAAAAGCGAAT
Found at i:5085 original size:21 final size:21
Alignment explanation
Indices: 5061--5122 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
5051 TCTCTTTTGA
*
5061 TTTTGATTTGATTT-GATTTTT
1 TTTTGATTT-ATTTAAATTTTT
* *
5082 TTTTAATTTTTTTAAATTTTT
1 TTTTGATTTATTTAAATTTTT
* *
5103 TTATTGATTTTTTTGAATTT
1 TT-TTGATTTATTTAAATTT
5123 CCTAATGGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 3 0.09
21 16 0.47
22 15 0.44
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (21 bp):
TTTTGATTTATTTAAATTTTT
Found at i:5112 original size:22 final size:21
Alignment explanation
Indices: 5076--5122 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
5066 ATTTGATTTG
5076 ATTTTTTTTTAATTTTTTTAA
1 ATTTTTTTTTAATTTTTTTAA
* *
5097 ATTTTTTTATTGATTTTTTTGA
1 ATTTTTTT-TTAATTTTTTTAA
5119 ATTT
1 ATTT
5123 CCTAATGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.74
Consensus pattern (21 bp):
ATTTTTTTTTAATTTTTTTAA
Found at i:5509 original size:8 final size:8
Alignment explanation
Indices: 5490--5536 Score: 60
Period size: 9 Copynumber: 5.8 Consensus size: 8
5480 TTCCAAATGC
5490 TTTTTTCA
1 TTTTTTCA
5498 -TTTTTCA
1 TTTTTTCA
5505 TTTTTTTCA
1 -TTTTTTCA
5514 TTTTATTCA
1 TTTT-TTCA
*
5523 TTTATTCA
1 TTTTTTCA
5531 TTTTTT
1 TTTTTT
5537 TTTTATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 7 0.21
8 13 0.38
9 14 0.41
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:5546 original size:26 final size:25
Alignment explanation
Indices: 5490--5537 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
5480 TTCCAAATGC
5490 TTTT-TTCATTTTTCATTTTTTTCA
1 TTTTATTCATTTTTCATTTTTTTCA
5514 TTTTATTCATTTATTCATTTTTTT
1 TTTTATTCATTT-TTCATTTTTTT
5538 TTTATTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 4 0.18
25 7 0.32
26 11 0.50
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTATTCATTTTTCATTTTTTTCA
Found at i:6644 original size:42 final size:42
Alignment explanation
Indices: 6597--6680 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
6587 ATGTAGTAAT
*
6597 GAATGGATAATGCACGACCTATGCATGAACATATATACAAAG
1 GAATGGATAATGCACGACCGATGCATGAACATATATACAAAG
* ** *
6639 GAATGGATGATGCACGATGGATGTATGAACATATATACAAAG
1 GAATGGATAATGCACGACCGATGCATGAACATATATACAAAG
6681 ACATGGACGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.23
Consensus pattern (42 bp):
GAATGGATAATGCACGACCGATGCATGAACATATATACAAAG
Found at i:6687 original size:42 final size:42
Alignment explanation
Indices: 6621--6715 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
6611 CGACCTATGC
*
6621 ATGAACATATATACAAAGGAATGGATGATGCA-CGATGGATGT
1 ATGAACATATATACAAAGGAATGGACGATGCATCGA-GGATGT
*
6663 ATGAACATATATACAAA-GACATGGACGATGCATGGAGGATGT
1 ATGAACATATATACAAAGGA-ATGGACGATGCATCGAGGATGT
6705 ATG-ACATATAT
1 ATGAACATATAT
6716 CAATGGATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
41 10 0.20
42 37 0.76
43 2 0.04
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (42 bp):
ATGAACATATATACAAAGGAATGGACGATGCATCGAGGATGT
Done.