Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021896.1 Corchorus olitorius cultivar O-4 contig21929, 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: 41441
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1708 original size:57 final size:57
Alignment explanation
Indices: 1503--1709 Score: 240
Period size: 57 Copynumber: 3.6 Consensus size: 57
1493 ATAAAAAACC
* * * **
1503 AAAATGACCAAAATGCCCCCTGGATACGCAGAGGTGACCAAAATGCCCCTGAATTGTGCA
1 AAAATGACCAAAATG-CCCTTGGATTCACA-AAATGACCAAAATGCCCCTGAA-TGTGCA
* * *
1563 AAAATGATCAAAATGCCCTTGGATATGC-GAAAATGACCAAAATGCTCCTGAATGTGCA
1 AAAATGACCAAAATGCCCTTGGAT-T-CACAAAATGACCAAAATGCCCCTGAATGTGCA
* *
1621 AAAATGACCAAAATGCCCTTGAATTTACAAAATGACCAAAATGCCCCT-AGATGTGCA
1 AAAATGACCAAAATGCCCTTGGATTCACAAAATGACCAAAATGCCCCTGA-ATGTGCA
1678 AAAATGACCAAAATG-CCTCTGGATTCACAAAA
1 AAAATGACCAAAATGCCCT-TGGATTCACAAAA
1710 GGTCAATTAA
Statistics
Matches: 128, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
56 4 0.03
57 53 0.41
58 28 0.22
59 27 0.21
60 15 0.12
61 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (57 bp):
AAAATGACCAAAATGCCCTTGGATTCACAAAATGACCAAAATGCCCCTGAATGTGCA
Found at i:1709 original size:29 final size:28
Alignment explanation
Indices: 1503--1702 Score: 186
Period size: 29 Copynumber: 6.9 Consensus size: 28
1493 ATAAAAAACC
*
1503 AAAATGACCAAAATGCCCCCTGGATACGCA
1 AAAATGACCAAAATG-CCCCTGGAT-TGCA
* ** *
1533 GAGGTGACCAAAATGCCCCTGAATTGTGCA
1 AAAATGACCAAAATGCCCCTGGA-T-TGCA
* * *
1563 AAAATGATCAAAATGCCCTTGGATATGCG
1 AAAATGACCAAAATGCCCCTGGAT-TGCA
* *
1592 AAAATGACCAAAATGCTCCTGAATGTGCA
1 AAAATGACCAAAATGCCCCTGGAT-TGCA
* * *
1621 AAAATGACCAAAATGCCCTTGAATT-TA
1 AAAATGACCAAAATGCCCCTGGATTGCA
*
1648 CAAAATGACCAAAATGCCCCTAGATGTGCA
1 -AAAATGACCAAAATGCCCCTGGAT-TGCA
*
1678 AAAATGACCAAAATGCCTCTGGATT
1 AAAATGACCAAAATGCCCCTGGATT
1703 CACAAAAGGT
Statistics
Matches: 137, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
27 1 0.01
28 23 0.17
29 79 0.58
30 34 0.25
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGGATTGCA
Found at i:7454 original size:13 final size:13
Alignment explanation
Indices: 7436--7461 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7426 CATTCGGAAG
7436 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
7449 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
7462 CTTGGCCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:9218 original size:35 final size:35
Alignment explanation
Indices: 9172--9664 Score: 484
Period size: 35 Copynumber: 13.9 Consensus size: 35
9162 CCAAGTGACT
* * * *
9172 CAGGGCGGTCTTTCTTCAATTCATTTCAGTTGACC
1 CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATC
* * * * * *
9207 CAGGGTGGTCTTTATCCAATTTATTTCAGTTGACC
1 CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATC
* * * * *
9242 CAAGGTGGTCCTTATTCAGTTTATTTCAGTTGATC
1 CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATC
* *
9277 CATGGCGATCTTTCTTTAGTTTATTTCAGTTGATC
1 CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATC
* * *
9312 CAGGGCGATCTTTCCTTCAATTTATTTCAGCTGACC
1 CAGGGCGATCTTT-CTTCAGTTTATTTCAGTTGATC
* * *
9348 CAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGATT
1 CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATC
* * *
9383 TAGGACGATCTCTTCTTCAGTTTATTTCAATTGATC
1 CAGGGCGATCT-TTCTTCAGTTTATTTCAGTTGATC
* * *
9419 CTGGGCGATCTTGCCTTCA-TTTCATTTCAGTTGACC
1 CAGGGCGATCTT-TCTTCAGTTT-ATTTCAGTTGATC
* * * * *
9455 CAAGGTGGTCCTTATTCAGTTTATTTCAGTTGATC
1 CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATC
* * *
9490 CAGGGCGATCTTTCTTTAGCTTATTTCAATTGATC
1 CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATC
* *
9525 CAGGGCGATCTTTCCTTCAATTTATTTCAGCTGATC
1 CAGGGCGATCTTT-CTTCAGTTTATTTCAGTTGATC
* *
9561 CAGGGTGATCTTTCTTTAGTTTATTTCAGTTGATC
1 CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATC
* * * *
9596 CAGAGTGATCTTTTCTGCAGTCTATTTCAGTTGATC
1 CAGGGCGATC-TTTCTTCAGTTTATTTCAGTTGATC
* * * *
9632 CAGAGTGATCTTTCTTTAGTTTGTTTCAGTTGA
1 CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGA
9665 CCCAATTTAA
Statistics
Matches: 380, Mismatches: 71, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
35 234 0.62
36 146 0.38
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (35 bp):
CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATC
Found at i:9360 original size:71 final size:70
Alignment explanation
Indices: 9172--9664 Score: 502
Period size: 71 Copynumber: 7.0 Consensus size: 70
9162 CCAAGTGACT
* * * * * * ** *
9172 CAGGGCGGTCTTTCTTCAATTCATTTCAGTTGACCCAGGGTGGTCTTTATCCAATTTATTTCAGT
1 CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTCTTTAGTTTATTTCAGT
*
9237 TGACC
66 TGATC
* * * * * * *
9242 CAAGGTGGTCCTTATTCAGTTTATTTCAGTTGATCCATGGCGATCTTTCTTTAGTTTATTTCAGT
1 CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTCTTTAGTTTATTTCAGT
9307 TGATC
66 TGATC
* * * * *
9312 CAGGGCGATCTTTCCTTCAATTTATTTCAGCTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAG
1 CAGGGCGATCTTT-CTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTCTTTAGTTTATTTCAG
*
9377 TTGATT
65 TTGATC
* * * * * * *
9383 TAGGACGATCTCTTCTTCAGTTTATTTCAATTGATCCTGGGCGATCTTGCCTTCA-TTTCATTTC
1 CAGGGCGATCT-TTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTT-TCTTTAGTTT-ATTTC
*
9447 AGTTGACC
63 AGTTGATC
* * * * * * * *
9455 CAAGGTGGTCCTTATTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTCTTTAGCTTATTTCAAT
1 CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTCTTTAGTTTATTTCAGT
9520 TGATC
66 TGATC
* *
9525 CAGGGCGATCTTTCCTTCAATTTATTTCAGCTGATCCAGGGTGATCTTTCTTTAGTTTATTTCAG
1 CAGGGCGATCTTT-CTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTCTTTAGTTTATTTCAG
9590 TTGATC
65 TTGATC
* * * * * *
9596 CAGAGTGATCTTTTCTGCAGTCTATTTCAGTTGATCCAGAGTGATCTTTCTTTAGTTTGTTTCAG
1 CAGGGCGATC-TTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTCTTTAGTTTATTTCAG
9661 TTGA
65 TTGA
9665 CCCAATTTAA
Statistics
Matches: 344, Mismatches: 72, Indels: 13
0.80 0.17 0.03
Matches are distributed among these distances:
70 88 0.26
71 230 0.67
72 26 0.08
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (70 bp):
CAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTCTTTAGTTTATTTCAGT
TGATC
Found at i:9624 original size:213 final size:212
Alignment explanation
Indices: 9225--9669 Score: 678
Period size: 213 Copynumber: 2.1 Consensus size: 212
9215 TCTTTATCCA
*
9225 ATTTATTTCAGTTGACCCAAGGTGGTCCTTATTCAGTTTATTTCAGTTGATCCATGGCGATCTTT
1 ATTTATTTCAGTTGACCCAAGGTGGTCCTTATTCAGTTTATTTCAGTTGATCCAGGGCGATCTTT
* *
9290 CTTTAGTTTATTTCAGTTGATCCAGGGCGATCTTTCCTTCAATTTATTTCAGCTGACCCAGGGTG
66 CTTTAGCTTATTTCAATTGATCCAGGGCGATCTTTCCTTCAATTTATTTCAGCTGACCCAGGGTG
* ** * *
9355 GTCTTTCTTCAGTTTATTTCAGTTGATTTAGGACGATCTCTTCTTCAGTTTATTTCAATTGATCC
131 ATCTTTCTTCAGTTTATTTCAGTTGATCCAGGACGATCTCTTCTGCAGTCTATTTCAATTGATCC
9420 TGGGCGATCTTGCCTTC
196 TGGGCGATCTTGCCTTC
9437 ATTTCATTTCAGTTGACCCAAGGTGGTCCTTATTCAGTTTATTTCAGTTGATCCAGGGCGATCTT
1 ATTT-ATTTCAGTTGACCCAAGGTGGTCCTTATTCAGTTTATTTCAGTTGATCCAGGGCGATCTT
*
9502 TCTTTAGCTTATTTCAATTGATCCAGGGCGATCTTTCCTTCAATTTATTTCAGCTGATCCAGGGT
65 TCTTTAGCTTATTTCAATTGATCCAGGGCGATCTTTCCTTCAATTTATTTCAGCTGACCCAGGGT
* * * *
9567 GATCTTTCTTTAGTTTATTTCAGTTGATCCA-GAGTGATCTTTTCTGCAGTCTATTTCAGTTGAT
130 GATCTTTCTTCAGTTTATTTCAGTTGATCCAGGA-CGATCTCTTCTGCAGTCTATTTCAATTGAT
* * * * *
9631 CCAGAGTGATCTT-TCTTT
194 CCTGGGCGATCTTGCCTTC
*
9649 AGTTTGTTTCAGTTGACCCAA
1 A-TTTATTTCAGTTGACCCAA
9670 TTTAAATGTC
Statistics
Matches: 211, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
212 25 0.12
213 186 0.88
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (212 bp):
ATTTATTTCAGTTGACCCAAGGTGGTCCTTATTCAGTTTATTTCAGTTGATCCAGGGCGATCTTT
CTTTAGCTTATTTCAATTGATCCAGGGCGATCTTTCCTTCAATTTATTTCAGCTGACCCAGGGTG
ATCTTTCTTCAGTTTATTTCAGTTGATCCAGGACGATCTCTTCTGCAGTCTATTTCAATTGATCC
TGGGCGATCTTGCCTTC
Found at i:10462 original size:38 final size:38
Alignment explanation
Indices: 10413--10501 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 38
10403 TATTTTCAAT
* * *
10413 CCTGGTTTAGGATCATTGCTTTATTGGTTTATTGCGAC
1 CCTGGTTTAGGATCATTGCTTTATCGGTTCATTGCAAC
* *
10451 CCTGGTTTAGGATCATTGCTTTATCGGTTCATTTCAAT
1 CCTGGTTTAGGATCATTGCTTTATCGGTTCATTGCAAC
10489 CCTGGTTTAGGAT
1 CCTGGTTTAGGAT
10502 ATTTGCTCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (38 bp):
CCTGGTTTAGGATCATTGCTTTATCGGTTCATTGCAAC
Found at i:10508 original size:38 final size:34
Alignment explanation
Indices: 10406--10753 Score: 241
Period size: 30 Copynumber: 10.8 Consensus size: 34
10396 ATCAGTTTAT
**
10406 TTTCAATCCTGGTTTAGGATCATTGCTTTATTGGTTTA
1 TTTCAATCCTGGTTTAGGATCATTGCTTTA----TCCA
* * *
10444 TTGCGACCCTGGTTTAGGATCATTGCTTTATCGGTTCA
1 TTTCAATCCTGGTTTAGGATCATTGCTTTATC----CA
10482 TTTCAATCCTGGTTTAGGAT-ATTTGC----TCCA
1 TTTCAATCCTGGTTTAGGATCA-TTGCTTTATCCA
* *
10512 TTTCAATCCTGGTTTAGGATCTTTACTTTATCCA
1 TTTCAATCCTGGTTTAGGATCATTGCTTTATCCA
* *
10546 TTTCAATCCTGGTTCAGGATCATTACTTTA--C-
1 TTTCAATCCTGGTTTAGGATCATTGCTTTATCCA
*
10577 TTT-AATCCTGGTTGAGGATCATTGCTTTAT---
1 TTTCAATCCTGGTTTAGGATCATTGCTTTATCCA
* * *
10607 TTT-AGTCCTGGTTTAGGATCATCGTTTTAT-C-
1 TTTCAATCCTGGTTTAGGATCATTGCTTTATCCA
* *
10638 -TT-AATCCTAGTTTAAGATCATTG-TTT-T--A
1 TTTCAATCCTGGTTTAGGATCATTGCTTTATCCA
* *
10666 TTTTAATCCTGGTTGAGGATCATTGCTTTAT-C-
1 TTTCAATCCTGGTTTAGGATCATTGCTTTATCCA
* *
10698 -TT-AATTCTGATTTAGGATCATTGCTTTAT---
1 TTTCAATCCTGGTTTAGGATCATTGCTTTATCCA
10727 TTT-AATCCTGGTTTAGGATCATTGCTT
1 TTTCAATCCTGGTTTAGGATCATTGCTT
10754 CGTCAGTTAA
Statistics
Matches: 261, Mismatches: 30, Indels: 46
0.77 0.09 0.14
Matches are distributed among these distances:
28 1 0.00
29 5 0.02
30 160 0.61
31 8 0.03
32 2 0.01
34 35 0.13
37 1 0.00
38 49 0.19
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (34 bp):
TTTCAATCCTGGTTTAGGATCATTGCTTTATCCA
Found at i:10750 original size:30 final size:30
Alignment explanation
Indices: 10481--10753 Score: 305
Period size: 30 Copynumber: 9.0 Consensus size: 30
10471 TTATCGGTTC
* **
10481 ATTTCAATCCTGGTTTAGGAT-ATTTGCTCC
1 ATTTTAATCCTGGTTTAGGATCA-TTGCTTT
* * *
10511 ATTTCAATCCTGGTTTAGGATCTTTACTTT
1 ATTTTAATCCTGGTTTAGGATCATTGCTTT
* *
10541 ATCCATTTCAATCCTGGTTCAGGATCATTACTTT
1 AT---TTT-AATCCTGGTTTAGGATCATTGCTTT
* *
10575 ACTTTAATCCTGGTTGAGGATCATTGCTTT
1 ATTTTAATCCTGGTTTAGGATCATTGCTTT
* * *
10605 ATTTTAGTCCTGGTTTAGGATCATCGTTTT
1 ATTTTAATCCTGGTTTAGGATCATTGCTTT
* * * *
10635 ATCTTAATCCTAGTTTAAGATCATTGTTTT
1 ATTTTAATCCTGGTTTAGGATCATTGCTTT
*
10665 ATTTTAATCCTGGTTGAGGATCATTGCTTT
1 ATTTTAATCCTGGTTTAGGATCATTGCTTT
* * *
10695 ATCTTAATTCTGATTTAGGATCATTGCTTT
1 ATTTTAATCCTGGTTTAGGATCATTGCTTT
10725 ATTTTAATCCTGGTTTAGGATCATTGCTT
1 ATTTTAATCCTGGTTTAGGATCATTGCTT
10754 CGTCAGTTAA
Statistics
Matches: 206, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
30 177 0.86
31 3 0.01
33 2 0.01
34 24 0.12
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (30 bp):
ATTTTAATCCTGGTTTAGGATCATTGCTTT
Found at i:11295 original size:27 final size:27
Alignment explanation
Indices: 11265--11340 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
11255 GCATTAGGGT
*
11265 CATCCAGGGGCATTTTAGTCATTTGCA
1 CATCCAGGGGCATTTTGGTCATTTGCA
*
11292 CATCCATGGGCATTTTGGTCATTTGCA
1 CATCCAGGGGCATTTTGGTCATTTGCA
*
11319 CATTCAGGGGCATTTTGGTCAT
1 CATCCAGGGGCATTTTGGTCAT
11341 ATCAAGTTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.36
Consensus pattern (27 bp):
CATCCAGGGGCATTTTGGTCATTTGCA
Found at i:12358 original size:21 final size:21
Alignment explanation
Indices: 12334--12397 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
12324 CCTTAGGCAA
12334 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGAGCTTGAAACCTT
*
12355 CTCCAATGAGCTTGCAACCTT
1 CTCCAATGAGCTTGAAACCTT
12376 CTCCAATGAGCTTGAAA-CTT
1 CTCCAATGAGCTTGAAACCTT
12396 CT
1 CT
12398 TTGTGAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 5 0.12
21 36 0.88
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.30
Consensus pattern (21 bp):
CTCCAATGAGCTTGAAACCTT
Found at i:17542 original size:31 final size:31
Alignment explanation
Indices: 17504--17566 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
17494 CCCACTGCCC
17504 CAAATAATTCTCCCATGGAGCTTGCAACCTT
1 CAAATAATTCTCCCATGGAGCTTGCAACCTT
17535 CAAATAATTCTCCCATGGAGCTTGCAACCTT
1 CAAATAATTCTCCCATGGAGCTTGCAACCTT
17566 C
1 C
17567 GACAATAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.29
Consensus pattern (31 bp):
CAAATAATTCTCCCATGGAGCTTGCAACCTT
Found at i:25103 original size:27 final size:28
Alignment explanation
Indices: 25073--25146 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
25063 AGTGGACTTA
* *
25073 AAATGGCCAAAATGTCCCTGA-ATGTGC
1 AAATGACCAAAATGCCCCTGAGATGTGC
*
25100 AAATGACTAAAATGCCCCT-AGATGTGC
1 AAATGACCAAAATGCCCCTGAGATGTGC
25127 AAATGACCAAAATGCCCCTG
1 AAATGACCAAAATGCCCCTG
25147 GTTGTCCCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
26 1 0.02
27 40 0.98
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGAGATGTGC
Found at i:35694 original size:21 final size:21
Alignment explanation
Indices: 35664--35703 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35654 CACCTGGGCG
35664 CCCATATGG-TTGCCTTGAGCA
1 CCCATATGGTTTG-CTTGAGCA
*
35685 CCCATGTGGTTTGCTTGAG
1 CCCATATGGTTTGCTTGAG
35704 AACCTAGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.33
Consensus pattern (21 bp):
CCCATATGGTTTGCTTGAGCA
Done.