Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017083.1 Corchorus olitorius cultivar O-4 contig17116, 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: 34136
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Found at i:1510 original size:20 final size:21
Alignment explanation
Indices: 1474--1514 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1464 CAACAGATTC
1474 GTGCAAAGGTTGCTTCTCCAA
1 GTGCAAAGGTTGCTTCTCCAA
*
1495 GTGCAAA-GTTGGTTCTCCAA
1 GTGCAAAGGTTGCTTCTCCAA
1515 CATCATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
GTGCAAAGGTTGCTTCTCCAA
Found at i:4316 original size:24 final size:24
Alignment explanation
Indices: 4287--4336 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
4277 AGCAGCGTCT
4287 TCCTCCAATTGTTCTGCTTGCTCC
1 TCCTCCAATTGTTCTGCTTGCTCC
*
4311 TCCTCCAATTGTTTTGCTTGCTCC
1 TCCTCCAATTGTTCTGCTTGCTCC
4335 TC
1 TC
4337 TGCCTCTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.36, G:0.12, T:0.44
Consensus pattern (24 bp):
TCCTCCAATTGTTCTGCTTGCTCC
Found at i:4530 original size:61 final size:61
Alignment explanation
Indices: 4407--4531 Score: 205
Period size: 61 Copynumber: 2.0 Consensus size: 61
4397 TCTAATGGTG
* * * * *
4407 TTATTTTCTATATTTGTTAATACTTTAATGTGACGACAATTTAATGGGAAAATATTTTTTT
1 TTATTTTCTATATCTGTTAATACTCTAATGTGACGACAATTTAATGGGAAAAGAATTCTTT
4468 TTATTTTCTATATCTGTTAATACTCTAATGTGACGACAATTTAATGGGAAAAGAATTCTTT
1 TTATTTTCTATATCTGTTAATACTCTAATGTGACGACAATTTAATGGGAAAAGAATTCTTT
4529 TTA
1 TTA
4532 CCAGAAAGGG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (61 bp):
TTATTTTCTATATCTGTTAATACTCTAATGTGACGACAATTTAATGGGAAAAGAATTCTTT
Found at i:9541 original size:1 final size:1
Alignment explanation
Indices: 9535--9570 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
9525 GACAAGCGGT
9535 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9571 CCTTGGTCGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20759 original size:16 final size:16
Alignment explanation
Indices: 20740--20781 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
20730 TGAAACTGAT
*
20740 AAAACCTGAACCCGAA
1 AAAACCCGAACCCGAA
*
20756 AAAACCCGAACCTGAA
1 AAAACCCGAACCCGAA
20772 AAAACCCGAA
1 AAAACCCGAA
20782 TTCAATACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.52, C:0.31, G:0.12, T:0.05
Consensus pattern (16 bp):
AAAACCCGAACCCGAA
Found at i:20998 original size:32 final size:32
Alignment explanation
Indices: 20960--21054 Score: 138
Period size: 32 Copynumber: 3.0 Consensus size: 32
20950 AAACCCAGCC
* *
20960 CGAACCCGAATTAACCTGACCCAAAATTGAC-
1 CGAACCCGAATCAACCTGACCCAAAATTAACT
*
20991 CGGAACCCGAATCAACCTGACCCAAATTTAACT
1 C-GAACCCGAATCAACCTGACCCAAAATTAACT
*
21024 CGAACCCGAATCAACCTGACCCAAATTTAAC
1 CGAACCCGAATCAACCTGACCCAAAATTAAC
21055 CCGACCTGAC
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
31 1 0.02
32 57 0.97
33 1 0.02
ACGTcount: A:0.38, C:0.34, G:0.12, T:0.17
Consensus pattern (32 bp):
CGAACCCGAATCAACCTGACCCAAAATTAACT
Found at i:21060 original size:16 final size:16
Alignment explanation
Indices: 21004--21060 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
20994 AACCCGAATC
*
21004 AACCTGACCCAAATTT
1 AACCCGACCCAAATTT
* * *
21020 AACTCGAACCCGAA-TC
1 AACCCG-ACCCAAATTT
*
21036 AACCTGACCCAAATTT
1 AACCCGACCCAAATTT
21052 AACCCGACC
1 AACCCGACC
21061 TGACTCAAGC
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
15 6 0.20
16 18 0.60
17 6 0.20
ACGTcount: A:0.37, C:0.37, G:0.09, T:0.18
Consensus pattern (16 bp):
AACCCGACCCAAATTT
Found at i:21554 original size:56 final size:56
Alignment explanation
Indices: 21464--21577 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
21454 TATCTGTTTC
*
21464 CTTTCACACAATAAATATTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
*
21520 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
21576 CT
1 CT
21578 ACAAAATAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.39
Consensus pattern (56 bp):
CTTTCACACAATAAATATTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
Found at i:21671 original size:21 final size:21
Alignment explanation
Indices: 21647--21713 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
21637 AAGGATCAGG
21647 ATTTGAGCTGAGTATTTCTTA
1 ATTTGAGCTGAGTATTTCTTA
** * *
21668 ATTT-A-CAAAGAATTTTCTATG
1 ATTTGAGCTGAGTA-TTTCT-TA
*
21689 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGCTGAGTATTTCTTA
21710 ATTT
1 ATTT
21714 ACAGAGAATT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
19 4 0.12
20 6 0.18
21 14 0.42
22 6 0.18
23 3 0.09
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.49
Consensus pattern (21 bp):
ATTTGAGCTGAGTATTTCTTA
Found at i:21705 original size:42 final size:42
Alignment explanation
Indices: 21646--21726 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
21636 TAAGGATCAG
21646 GATTTGAGCTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGCTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
* *
21688 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGCTGAGTATTTCTTAATTTACAAAGAATTTTC
21727 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.46
Consensus pattern (42 bp):
GATTTGAGCTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:24216 original size:135 final size:133
Alignment explanation
Indices: 24070--24320 Score: 400
Period size: 136 Copynumber: 1.9 Consensus size: 133
24060 ATTGTTTAAA
24070 CTTTTATAGTTTTACTCAACTAAAAACTCTA-TTTTTATTTAATTAAATCTAATATCCTTATAAC
1 CTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAAC
* * *
24134 TATTAAATT-TTTTACCATTTTACTATTTTAATTAAAAAAAACTTA-TATATATTAGAATTTTTT
66 TATT---TTATTTTACCATTCTAATAATTTAATT-AAAAAAACTTAGT-TATATTAGAATTTTTT
24197 TAAATATG
126 TAAATATG
*
24205 CTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAGC
1 CTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAAC
24270 TATTTTATTTTACCATTCTAATAATTTAATTAAAAAAACTTAGTTATATTA
66 TATTTTATTTTACCATTCTAATAATTTAATTAAAAAAACTTAGTTATATTA
24321 ATTTTTAAAA
Statistics
Matches: 109, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
133 20 0.18
134 22 0.20
135 31 0.28
136 36 0.33
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (133 bp):
CTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAAC
TATTTTATTTTACCATTCTAATAATTTAATTAAAAAAACTTAGTTATATTAGAATTTTTTTAAAT
ATG
Found at i:24916 original size:15 final size:15
Alignment explanation
Indices: 24874--24916 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
24864 AATTTTCTCG
*
24874 GGTCATTCGGGTTCC
1 GGTCATTCGGGTTCA
24889 GGCTCA-TCTGGGTTCA
1 GG-TCATTC-GGGTTCA
24905 GGTCATTCGGGT
1 GGTCATTCGGGT
24917 CTAGGGTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.09, C:0.23, G:0.35, T:0.33
Consensus pattern (15 bp):
GGTCATTCGGGTTCA
Found at i:27550 original size:19 final size:19
Alignment explanation
Indices: 27526--27562 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27516 CCACCATGAA
27526 GAGCACATTTCCTTGCCAG
1 GAGCACATTTCCTTGCCAG
* *
27545 GAGCACGTTTTCTTGCCA
1 GAGCACATTTCCTTGCCA
27563 AAATAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.30, G:0.22, T:0.30
Consensus pattern (19 bp):
GAGCACATTTCCTTGCCAG
Found at i:28148 original size:34 final size:34
Alignment explanation
Indices: 28105--28174 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
28095 GCAATTGTTC
28105 TTAATCTTCTGTGATTCTACGCTTTTTTGACTTT
1 TTAATCTTCTGTGATTCTACGCTTTTTTGACTTT
*
28139 TTAATCTTCTGTGATTCTACGTTTTTTTGACTTT
1 TTAATCTTCTGTGATTCTACGCTTTTTTGACTTT
28173 TT
1 TT
28175 GATGTGATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.14, C:0.16, G:0.11, T:0.59
Consensus pattern (34 bp):
TTAATCTTCTGTGATTCTACGCTTTTTTGACTTT
Found at i:30860 original size:35 final size:34
Alignment explanation
Indices: 30821--30994 Score: 177
Period size: 35 Copynumber: 4.9 Consensus size: 34
30811 TATGCAATTC
* *
30821 AATCAGTAGTCAACTTAATTCAGGGTAATTATGAA
1 AATCAGTAGT-AACTTAATTCAGGGTAATTAAGTA
* * * *
30856 AATCAAATAAGTAAATTAATTCAGGGTAAATAAGTG
1 AATC-AGT-AGTAACTTAATTCAGGGTAATTAAGTA
*
30892 AATCAGTAGTCAACTTAATTCAGGGCAATTAAGTA
1 AATCAGTAGT-AACTTAATTCAGGGTAATTAAGTA
* * * * *
30927 AGTCGGTCAATAACTTAATTTAAGGTAATTAAGTA
1 AATCAGT-AGTAACTTAATTCAGGGTAATTAAGTA
*
30962 AATCAGTAGTTAACTTAATTCAGAGTAATTAAG
1 AATCAGTAG-TAACTTAATTCAGGGTAATTAAG
30995 GGTCTGTTTG
Statistics
Matches: 111, Mismatches: 23, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
34 4 0.04
35 77 0.69
36 27 0.24
37 3 0.03
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.31
Consensus pattern (34 bp):
AATCAGTAGTAACTTAATTCAGGGTAATTAAGTA
Found at i:30977 original size:70 final size:71
Alignment explanation
Indices: 30821--30994 Score: 208
Period size: 70 Copynumber: 2.5 Consensus size: 71
30811 TATGCAATTC
* *
30821 AATCAGTAGTCAACTTAATTCAGGGTAATTATGAAAATCAAATAAGTAAATTAATTCAGGGTAAA
1 AATCAGTAGTCAACTTAATTCAGGGTAATTAAGAAAATCAAATAAGTAAATTAATTCAAGGTAAA
*
30886 TAAGTG
66 TAAGTA
* * * ** * *
30892 AATCAGTAGTCAACTTAATTCAGGGCAATTAAGTAAGTC-GGTCAA-TAACTTAATTTAAGGTAA
1 AATCAGTAGTCAACTTAATTCAGGGTAATTAAGAAAATCAAAT-AAGTAAATTAATTCAAGGTAA
*
30955 TTAAGTA
65 ATAAGTA
* *
30962 AATCAGTAGTTAACTTAATTCAGAGTAATTAAG
1 AATCAGTAGTCAACTTAATTCAGGGTAATTAAG
30995 GGTCTGTTTG
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
70 51 0.58
71 37 0.42
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.31
Consensus pattern (71 bp):
AATCAGTAGTCAACTTAATTCAGGGTAATTAAGAAAATCAAATAAGTAAATTAATTCAAGGTAAA
TAAGTA
Found at i:33927 original size:19 final size:19
Alignment explanation
Indices: 33891--33933 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
33881 ACAATTTATA
33891 TATATGTGTTAATTTTAATAT
1 TATATGTGTTAA-TTTAAT-T
*
33912 TATATGTTTTAA-TTAATT
1 TATATGTGTTAATTTAATT
33930 TATA
1 TATA
33934 ATAGGGAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 5 0.24
21 11 0.52
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (19 bp):
TATATGTGTTAATTTAATT
Done.