Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012937.1 Corchorus olitorius cultivar O-4 contig12970, 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: 9403
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:4179 original size:17 final size:17
Alignment explanation
Indices: 4157--4209 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
4147 TAAAAAAAAT
4157 AAAAAATAAATCAATCA
1 AAAAAATAAATCAATCA
*
4174 AAAAAATAAAAT-AAT-T
1 AAAAAAT-AAATCAATCA
4190 AAAAAA-AAATCAAATCA
1 AAAAAATAAATC-AATCA
4207 AAA
1 AAA
4210 GAGAATGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 4 0.13
16 9 0.30
17 13 0.43
18 4 0.13
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAAATAAATCAATCA
Found at i:4195 original size:34 final size:33
Alignment explanation
Indices: 4113--4209 Score: 106
Period size: 33 Copynumber: 2.8 Consensus size: 33
4103 TTCAAAAAAG
* * *
4113 AAAAAAATCGAAAAAATCAATCAATCAAATCAATTA
1 AAAAAAAT--AAAAAATAAATCAATCAAA-AAAATA
4149 AAAAAAATAAAAAATAAATCAATCAAAAAAATA
1 AAAAAAATAAAAAATAAATCAATCAAAAAAATA
* *
4182 AAATAATTAAAAAA-AAATCAAATCAAAA
1 AAAAAAATAAAAAATAAATC-AATCAAAA
4210 GAGAATGGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 5 0.09
33 24 0.44
34 18 0.33
36 8 0.15
ACGTcount: A:0.72, C:0.09, G:0.01, T:0.18
Consensus pattern (33 bp):
AAAAAAATAAAAAATAAATCAATCAAAAAAATA
Found at i:6620 original size:50 final size:50
Alignment explanation
Indices: 6566--6715 Score: 219
Period size: 50 Copynumber: 3.0 Consensus size: 50
6556 AGTTTTATAA
* * * *
6566 TAAAATTGCTTTCCATTTATGAGTTCAAGATTAAAATTCGCTTTTTAAAG
1 TAAAATTGCTTTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
* *
6616 TAAAATTGCTTTCCATTTGTAAATCCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
** *
6666 TAGGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
6716 GGCATTTAAG
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
Found at i:7373 original size:50 final size:49
Alignment explanation
Indices: 7314--7457 Score: 209
Period size: 50 Copynumber: 2.9 Consensus size: 49
7304 CGAATGTTTT
* * *
7314 GGCTTTTCCATAAGTCAAACACGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTC-ATTATCAACATA
*
7364 GGCTTTTCCACAAGCCAAACTCGTTTCCATATGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTC-ATTATCAACATA
* *
7414 GGCTTTTCTACAAGCCGAACTCGTTTCCATACGAGTCATT-TCAA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCATTATCAA
7458 ACCTTGGTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
48 4 0.05
49 3 0.03
50 79 0.92
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31
Consensus pattern (49 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCATTATCAACATA
Found at i:7581 original size:51 final size:51
Alignment explanation
Indices: 7507--7714 Score: 375
Period size: 50 Copynumber: 4.1 Consensus size: 51
7497 GCATTACCTT
7507 TTTTAAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
7558 TTTTAAAGATTGAATTAGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
7609 TTTT-AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
7659 -TTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCCGAAGACGGTCC
1 TTTTAAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
7709 TTTTAA
1 TTTTAA
7715 TATTAGATTG
Statistics
Matches: 151, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
49 3 0.02
50 90 0.60
51 58 0.38
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.26
Consensus pattern (51 bp):
TTTTAAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:7638 original size:50 final size:50
Alignment explanation
Indices: 7507--7739 Score: 371
Period size: 50 Copynumber: 4.6 Consensus size: 50
7497 GCATTACCTT
7507 TTTTAAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTT-AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
7558 TTTTAAAGATTGAATTAGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTT-AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
7609 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
7659 TTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCCGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
7709 TTTTAATATT-AGATTGG-AGAACAATTCAAAG
1 TTTTAAGATTGA-ATTGGTAG-ACAGTTCAAAG
7740 AAATTGATCG
Statistics
Matches: 173, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
49 3 0.02
50 116 0.67
51 54 0.31
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:8043 original size:29 final size:29
Alignment explanation
Indices: 7982--8057 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
7972 AGGGTCACCC
* * *
7982 AGGGGCGTTTTTGGTCATTTTCAAAATCC
1 AGGGGCATTTTTGGTCATTTGCAAAATCA
** *
8011 AGGGGCATTTTTGGTCATTTGCGCATTCA
1 AGGGGCATTTTTGGTCATTTGCAAAATCA
8040 A-GGGCA-TTTTGGTCATTT
1 AGGGGCATTTTTGGTCATTT
8058 TAAGTTCACT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 12 0.29
28 5 0.12
29 24 0.59
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.39
Consensus pattern (29 bp):
AGGGGCATTTTTGGTCATTTGCAAAATCA
Found at i:8610 original size:19 final size:19
Alignment explanation
Indices: 8586--8627 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
8576 AAATACAGGT
8586 ACAAATATTCACCAAGTAC
1 ACAAATATTCACCAAGTAC
8605 ACAAATATTCACCAAGTAC
1 ACAAATATTCACCAAGTAC
8624 ACAA
1 ACAA
8628 GACCATAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.26, G:0.05, T:0.19
Consensus pattern (19 bp):
ACAAATATTCACCAAGTAC
Done.