Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019817.1 Corchorus olitorius cultivar O-4 contig19850, 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: 28101
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5581 original size:14 final size:14
Alignment explanation
Indices: 5562--5592 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5552 ATATAAGCAA
5562 ATAAGAGATATTTT
1 ATAAGAGATATTTT
5576 ATAAGAGATATTTT
1 ATAAGAGATATTTT
5590 ATA
1 ATA
5593 TGGATACAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (14 bp):
ATAAGAGATATTTT
Found at i:15975 original size:11 final size:11
Alignment explanation
Indices: 15959--15983 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15949 CCATTAGTTT
15959 CTTGAGAGCAA
1 CTTGAGAGCAA
15970 CTTGAGAGCAA
1 CTTGAGAGCAA
15981 CTT
1 CTT
15984 TTCATGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (11 bp):
CTTGAGAGCAA
Found at i:18881 original size:33 final size:33
Alignment explanation
Indices: 18836--18902 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
18826 TTTATGTATA
18836 TTATTTTATTTTTCTGGACAAACTCGAAAATGT
1 TTATTTTATTTTTCTGGACAAACTCGAAAATGT
* *
18869 TTATTTCT-TTTTTTTGTACAAACTCGAAAATGT
1 TTATTT-TATTTTTCTGGACAAACTCGAAAATGT
18902 T
1 T
18903 GTAGAACTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.49
Consensus pattern (33 bp):
TTATTTTATTTTTCTGGACAAACTCGAAAATGT
Found at i:21276 original size:6 final size:6
Alignment explanation
Indices: 21265--21291 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
21255 AATCCAAATG
21265 CTTAAT CTTAAT CTTAAT CTTAAT CTT
1 CTTAAT CTTAAT CTTAAT CTTAAT CTT
21292 TTTGTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTAAT
Found at i:21630 original size:137 final size:136
Alignment explanation
Indices: 21352--21796 Score: 503
Period size: 137 Copynumber: 3.2 Consensus size: 136
21342 ATGACGAGAT
* * * *
21352 TGACCCTTCGACCGAAAGGGTATTCTTGG-AAATGA-AAAATACTAAACTCAAAAGCGAAAATGA
1 TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAGAAAATACTAAACTCAAATGC-AAAAAGA
* * *
21415 AGAAACTGACCCTTTC-ACC-AAATGGGCAATTTTTGGAAG-AAAG-ACTAAA-TTTAGATGCAA
65 AGAAAATGACCC-TTCGACCGAAA-GGG-TATTTTTGGAAGAAAAGTACTAAACTTGA-ATGCAA
*
21475 AAATATGAAAAAA
126 AAAGATG--AAAA
* **
21488 CTGACCCTTTGACCGAAAGGGTATTTTTGGAAAAAGAGAAAATACTAAACTTGAATGCAAAAAGA
1 -TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAGAAAATACTAAACTCAAATGCAAAAAGA
* * *
21553 TGAAAATAACTCTTCGACCGAAAGGGTA-TTTTGGAAGGACAAAGTACTAAACTTGAATGCAAAA
65 AGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAA-GA-AAAGTACTAAACTTGAATGCAAAA
21617 AGATGAAAA
128 AGATGAAAA
* * * *
21626 TGACCCTTCGATCGAAAGGATATTTTTGGAAAAAGAGAAAATACTAAACTCAAATGCAAAGAGAC
1 TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAGAAAATACTAAACTCAAATGCAAAAAGAA
*
21691 GAAAATGACCCTTCGACCGAAA-GGTATTTTTGGGAAAAGAGAAAATACTAAACTTGAATGCAAA
66 GAAAATGACCCTTCGACCGAAAGGGTATTTTT-GG--AAGA-AAAGTACTAAACTTGAATGCAAA
*
21755 AAGACGAAAA
127 AAGATGAAAA
* *
21765 TGACCATTCGATCGAAAGGGTATTTTTGGAAA
1 TGACCCTTCGACCGAAAGGGTATTTTTGGAAA
21797 GACAAAGTTA
Statistics
Matches: 267, Mismatches: 28, Indels: 24
0.84 0.09 0.08
Matches are distributed among these distances:
136 12 0.04
137 114 0.43
138 31 0.12
139 87 0.33
140 20 0.07
141 3 0.01
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (136 bp):
TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAGAAAATACTAAACTCAAATGCAAAAAGAA
GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAGAAAAGTACTAAACTTGAATGCAAAAAGA
TGAAAA
Found at i:21754 original size:69 final size:70
Alignment explanation
Indices: 21352--21796 Score: 452
Period size: 70 Copynumber: 6.5 Consensus size: 70
21342 ATGACGAGAT
* * ** * *
21352 TGACCCTTCGACCGAAAGGGTATTCTTGG-AAATGA-AAAATACTAAACTCAAAAGCGAAAATGA
1 TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAGAAAATACTAAACTTGAATGC-AAAAAGA
* *
21415 AGAAAC
65 CGAAAA
* * *
21421 TGACCCTTTC-ACC-AAATGGGCAATTTTTGG----A-AG-AAAGACTAAA-TTTAGATGCAAAA
1 TGACCC-TTCGACCGAAA-GGG-TATTTTTGGAAAAAGAGAAAATACTAAACTTGA-ATGCAAAA
* *
21477 ATATGAAAAAA
62 AGACG--AAAA
*
21488 CTGACCCTTTGACCGAAAGGGTATTTTTGGAAAAAGAGAAAATACTAAACTTGAATGCAAAAAGA
1 -TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAGAAAATACTAAACTTGAATGCAAAAAGA
*
21553 TGAAAA
65 CGAAAA
* * * * * *
21559 TAACTCTTCGACCGAAAGGGTA-TTTTGG--AAGGACAAAGTACTAAACTTGAATGCAAAAAGAT
1 TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAGAAAATACTAAACTTGAATGCAAAAAGAC
21621 GAAAA
66 GAAAA
* * ** *
21626 TGACCCTTCGATCGAAAGGATATTTTTGGAAAAAGAGAAAATACTAAACTCAAATGCAAAGAGAC
1 TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAGAAAATACTAAACTTGAATGCAAAAAGAC
21691 GAAAA
66 GAAAA
*
21696 TGACCCTTCGACCGAAA-GGTATTTTTGGGAAAAGAGAAAATACTAAACTTGAATGCAAAAAGAC
1 TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAGAAAATACTAAACTTGAATGCAAAAAGAC
21760 GAAAA
66 GAAAA
* *
21765 TGACCATTCGATCGAAAGGGTATTTTTGGAAA
1 TGACCCTTCGACCGAAAGGGTATTTTTGGAAA
21797 GACAAAGTTA
Statistics
Matches: 313, Mismatches: 42, Indels: 41
0.79 0.11 0.10
Matches are distributed among these distances:
65 8 0.03
66 13 0.04
67 67 0.21
68 21 0.07
69 83 0.27
70 90 0.29
71 5 0.02
72 2 0.01
73 21 0.07
74 3 0.01
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (70 bp):
TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAGAAAATACTAAACTTGAATGCAAAAAGAC
GAAAA
Found at i:22822 original size:19 final size:18
Alignment explanation
Indices: 22798--22837 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
22788 TTGAAGATTT
*
22798 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
22817 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
22835 ATT
1 ATT
22838 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:26946 original size:8 final size:9
Alignment explanation
Indices: 26910--26947 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
26900 CCCAAATTAC
26910 TTATGGAAA
1 TTATGGAAA
*
26919 TTAAGGAAA
1 TTATGGAAA
26928 TTATGGAAA
1 TTATGGAAA
26937 TTAT-GAAA
1 TTATGGAAA
26945 TTA
1 TTA
26948 AATGAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (9 bp):
TTATGGAAA
Done.