Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019103.1 Corchorus olitorius cultivar O-4 contig19136, 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: 8358
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:97 original size:16 final size:15
Alignment explanation
Indices: 57--99 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
47 TCGGGCTGCC
57 TCGGGTTCGGGTATT
1 TCGGGTTCGGGTATT
* *
72 TTGGGCTCGGGTAATT
1 TCGGGTTCGGGT-ATT
88 TCGGGTTCGGGT
1 TCGGGTTCGGGT
100 TCGGGACGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.07, C:0.14, G:0.42, T:0.37
Consensus pattern (15 bp):
TCGGGTTCGGGTATT
Found at i:2035 original size:764 final size:764
Alignment explanation
Indices: 718--2224 Score: 2802
Period size: 764 Copynumber: 2.0 Consensus size: 764
708 TTTTCTACAA
*
718 TTGTTATTGTTTATTGTTTGTTGATTTATGATTAGTCACCAAGTTAGGTTATTTGAATTCTTATG
1 TTGTTATTGTTTATTGTTTGTTGATTTATGATTAGTCACCAAGTTAGATTATTTGAATTCTTATG
783 TTTGTCTTCTCCTTAGATCATATATGCACCTAATTAATTACGTAATTAGTAAATCTTAGGCAAAA
66 TTTGTCTTCTCCTTAGATCATATATGCACCTAATTAATTACGTAATTAGTAAATCTTAGGCAAAA
848 CTATTACTTGATGAATCAAACTTTCACCATAATTTTACGAACAAGACTCTTAAGACTTAAAATTA
131 CTATTACTTGATGAATCAAACTTTCACCATAATTTTACGAACAAGACTCTTAAGACTTAAAATTA
*
913 TGGAGGCATTTGTCAAAATTTGAGATCACATTCCTTTTTTAGACAGTAATTATTTTACTTAGTGT
196 TGGAGGCATTTGTCAAAATTTGAGATCACATTCCTTTTTTAGACAATAATTATTTTACTTAGTGT
*
978 AAGCTTATAATAATAAATGATTTGTTTACAAAAAAAGTTCAAATTATCAATTTATGTAAATATCA
261 AAGCTTATAATAATAAATGATTTGTGTACAAAAAAAGTTCAAATTATCAATTTATGTAAATATCA
*
1043 CTTAAACCAATCAAACACTTAATTAAATCTTTGCTAATTACTTCTCAATTACTAATCCACCACCT
326 CTTAAACCAATCAAACACTTAATTAAATCTTTGCTAATCACTTCTCAATTACTAATCCACCACCT
1108 CGCCTATCCCATCAACTCTTTGAACTTTTCTTGCATCAATAGGTTCTTAATTACTACTACTATTT
391 CGCCTATCCCATCAACTCTTTGAACTTTTCTTGCATCAATAGGTTCTTAATTACTACTACTATTT
1173 TGGATAAAGCAAAACCATATAGTATACAATAGATTAATAGAACTAAGCTTAATTTTTCTCCTAAT
456 TGGATAAAGCAAAACCATATAGTATACAATAGATTAATAGAACTAAGCTTAATTTTTCTCCTAAT
*
1238 TAGCTAGGCTTTAAACAAAAAAAAAGGGGATAGCACCCGAGTTGTTAGCACAACTGGTAGGTGCA
521 TAGCTAGGCTTTAAACAAAAAAAAAGAGGATAGCACCCGAGTTGTTAGCACAACTGGTAGGTGCA
* * * * ** *
1303 CTGTGTCTGGACCGTGAGGTCCTGGTTTTTAGTCTCACGGAATGTGAGTTTAGTTTGTAATTTGT
586 CCGTGCCTGGACCATGAGGTCCTGGGTTCAAGTCTCACGGAATGCGAGTTTAGTTTGTAATTTGT
*
1368 TTATTTGTGTATTTAGTAGGTAGATGGTTTATTTATGGTAGTTTCTTAGTTTGAGTTGATTTCTC
651 TTATTTCTGTATTTAGTAGGTAGATGGTTTATTTATGGTAGTTTCTTAGTTTGAGTTGATTTCTC
1433 ATTTAGATGTTTGGGCATATAGAGATTTCACATGTACTCACTCAACCAT
716 ATTTAGATGTTTGGGCATATAGAGATTTCACATGTACTCACTCAACCAT
1482 TTGTTATTGTTTATTGTTTGTTGATTTATGATTAGTCACCAAGTTAGATTATTTGAATTCTTATG
1 TTGTTATTGTTTATTGTTTGTTGATTTATGATTAGTCACCAAGTTAGATTATTTGAATTCTTATG
1547 TTTGTCTTCTCCTTAGATCATATATGCACCTAATTAATTACGTAATTAGTAAATCTTAGGCAAAA
66 TTTGTCTTCTCCTTAGATCATATATGCACCTAATTAATTACGTAATTAGTAAATCTTAGGCAAAA
* *
1612 CTATTACTTGATGAATCAAACTTTCACCATAATTTTACGTACAAGACTCTTACGACTTAAAATTA
131 CTATTACTTGATGAATCAAACTTTCACCATAATTTTACGAACAAGACTCTTAAGACTTAAAATTA
*
1677 TGGAGGCATTTGTCAAAATTTGGGATCACATTCCTTTTTTAGACAATAATTATTTTACTTAGTGT
196 TGGAGGCATTTGTCAAAATTTGAGATCACATTCCTTTTTTAGACAATAATTATTTTACTTAGTGT
1742 AAGCTTATAATAATAAATGATTTGTGTA-AAAAAAAGTTCAAATTATCAATTTATGTAAATATCA
261 AAGCTTATAATAATAAATGATTTGTGTACAAAAAAAGTTCAAATTATCAATTTATGTAAATATCA
**
1806 CTTAAATTAATCAAACACTTAATTAAATCTTTGCTAATCACTTCTCAATTACTAATCCACCACCT
326 CTTAAACCAATCAAACACTTAATTAAATCTTTGCTAATCACTTCTCAATTACTAATCCACCACCT
1871 CGCCTATCCCATCAACTCTTTGAACTTTTCTTGCATCAATAGGTTCTTAATTACTACTACTATTT
391 CGCCTATCCCATCAACTCTTTGAACTTTTCTTGCATCAATAGGTTCTTAATTACTACTACTATTT
1936 TGGATAAAGCAAAACCATATAGTATACAATAGATTAATAGAACTAAGCTTAATTTTTTCTCCTAA
456 TGGATAAAGCAAAACCATATAGTATACAATAGATTAATAGAACTAAGCTTAA-TTTTTCTCCTAA
2001 TTAGCTAGGCTTTAAACAAACAAAAAA-AGGATAGCACCCGAGTTGTTAGCACAACTGGTAGGTG
520 TTAGCTAGGCTTTAAACAAA-AAAAAAGAGGATAGCACCCGAGTTGTTAGCACAACTGGTAGGTG
*
2065 CACCGTGCCTGGATCATGAGGTCCTGGGTTCAAGTCTCACGGAATGCGAGTTTAGTTTGTAATTT
584 CACCGTGCCTGGACCATGAGGTCCTGGGTTCAAGTCTCACGGAATGCGAGTTTAGTTTGTAATTT
*
2130 GTTTATTTCTGTATTTGGTAGGTAGATGGTTTATTTATGGTAGTTTCTTAGTTTGAGTTGATTTC
649 GTTTATTTCTGTATTTAGTAGGTAGATGGTTTATTTATGGTAGTTTCTTAGTTTGAGTTGATTTC
2195 TCATTTAGATGTTTGGGCATATAGAGATTT
714 TCATTTAGATGTTTGGGCATATAGAGATTT
2225 ATTCTGATTG
Statistics
Matches: 721, Mismatches: 20, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
763 215 0.30
764 500 0.69
765 6 0.01
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (764 bp):
TTGTTATTGTTTATTGTTTGTTGATTTATGATTAGTCACCAAGTTAGATTATTTGAATTCTTATG
TTTGTCTTCTCCTTAGATCATATATGCACCTAATTAATTACGTAATTAGTAAATCTTAGGCAAAA
CTATTACTTGATGAATCAAACTTTCACCATAATTTTACGAACAAGACTCTTAAGACTTAAAATTA
TGGAGGCATTTGTCAAAATTTGAGATCACATTCCTTTTTTAGACAATAATTATTTTACTTAGTGT
AAGCTTATAATAATAAATGATTTGTGTACAAAAAAAGTTCAAATTATCAATTTATGTAAATATCA
CTTAAACCAATCAAACACTTAATTAAATCTTTGCTAATCACTTCTCAATTACTAATCCACCACCT
CGCCTATCCCATCAACTCTTTGAACTTTTCTTGCATCAATAGGTTCTTAATTACTACTACTATTT
TGGATAAAGCAAAACCATATAGTATACAATAGATTAATAGAACTAAGCTTAATTTTTCTCCTAAT
TAGCTAGGCTTTAAACAAAAAAAAAGAGGATAGCACCCGAGTTGTTAGCACAACTGGTAGGTGCA
CCGTGCCTGGACCATGAGGTCCTGGGTTCAAGTCTCACGGAATGCGAGTTTAGTTTGTAATTTGT
TTATTTCTGTATTTAGTAGGTAGATGGTTTATTTATGGTAGTTTCTTAGTTTGAGTTGATTTCTC
ATTTAGATGTTTGGGCATATAGAGATTTCACATGTACTCACTCAACCAT
Found at i:7599 original size:26 final size:27
Alignment explanation
Indices: 7547--7613 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
7537 CAGACTCTGG
* *
7547 ATTTTGAGTTTCGAACATGACATGCAA
1 ATTTTGAGTTTTGAACATGAAATGCAA
7574 ATTTTGAGTTTTGAA-ATGAAATGCAA
1 ATTTTGAGTTTTGAACATGAAATGCAA
*
7600 ATTTTGAATTTTGA
1 ATTTTGAGTTTTGA
7614 CTTTTGAGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 23 0.62
27 14 0.38
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.40
Consensus pattern (27 bp):
ATTTTGAGTTTTGAACATGAAATGCAA
Found at i:7671 original size:43 final size:43
Alignment explanation
Indices: 7590--7671 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
7580 AGTTTTGAAA
* * *
7590 TGAAATGCAAATTTTGAATTTTGACTTTTGAGGAATGAAATGT
1 TGAAATGCAAATTTTGAAATTTGAATTTTGAGCAATGAAATGT
** *
7633 TGAAATGCAGGTTTTGAAATTTGAATTTTGAGCCATGAA
1 TGAAATGCAAATTTTGAAATTTGAATTTTGAGCAATGAA
7672 TTTTGAGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (43 bp):
TGAAATGCAAATTTTGAAATTTGAATTTTGAGCAATGAAATGT
Found at i:7750 original size:7 final size:7
Alignment explanation
Indices: 7672--7747 Score: 143
Period size: 7 Copynumber: 10.9 Consensus size: 7
7662 GAGCCATGAA
7672 TTTTGAG
1 TTTTGAG
7679 TTTTGAG
1 TTTTGAG
7686 TTTTGAG
1 TTTTGAG
7693 TTTTGAG
1 TTTTGAG
7700 TTTTGAG
1 TTTTGAG
7707 TTTTGAG
1 TTTTGAG
7714 TTTTGAG
1 TTTTGAG
7721 TTTTGAG
1 TTTTGAG
7728 TTTTGAG
1 TTTTGAG
*
7735 TTTTGAA
1 TTTTGAG
7742 TTTTGA
1 TTTTGA
7748 ATTGCCTATT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
7 68 1.00
ACGTcount: A:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (7 bp):
TTTTGAG
Found at i:7946 original size:33 final size:33
Alignment explanation
Indices: 7904--7981 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
7894 AGAAACTGTG
* * *
7904 GATTTTGAACTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
7937 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
7970 AATTTTGAACTT
1 GATTTTGAACTT
7982 CCTAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:8079 original size:56 final size:55
Alignment explanation
Indices: 8019--8351 Score: 185
Period size: 55 Copynumber: 6.0 Consensus size: 55
8009 AATTCAACCT
* * *
8019 TGATCATGGAAATATTTCTTGGAACGACCGCACTGGATCAA-TTTAGAGATCAACTC
1 TGATCATCGAAA-ACTTCTTGGAACGACCACACTGGATCAACTTTA-AGATCAACTC
* *
8075 TGATCATCGTAAACTTCTTGGAATGACCACACTGGATCAACTTTAAGATCAACT-
1 TGATCATCGAAAACTTCTTGGAACGACCACACTGGATCAACTTTAAGATCAACTC
** * * * ** *
8129 TAGATTTTTGAAAACTTCTATGGAA-GACCACACAGGGTCGTC-TGAAGATCAACT-
1 T-GATCATCGAAAACTTCT-TGGAACGACCACACTGGATCAACTTTAAGATCAACTC
* * *
8183 TAGATC-TCTGAAAACTTCTAT-GAAAGACCACACTGGGTCATC-TTAAGATCAACT-
1 T-GATCATC-GAAAACTTCT-TGGAACGACCACACTGGATCAACTTTAAGATCAACTC
* * *
8237 TAGATC-TCTGAAAACTTCTATGAAAGACCAC-ACCGGCACTGGGTCATC-TTAAGATCAACT-
1 T-GATCATC-GAAAACTTCT-TG---GA--ACGACC-ACACTGGATCAACTTTAAGATCAACTC
* *
8297 TAAATC-TCTGAAAACTTCTAT-GAAAGACCTACACTGGATCAAC-TTAAGATCAACT
1 T-GATCATC-GAAAACTTCT-TGGAACGACC-ACACTGGATCAACTTTAAGATCAACT
8352 TTCTAGA
Statistics
Matches: 237, Mismatches: 27, Indels: 27
0.81 0.09 0.09
Matches are distributed among these distances:
53 4 0.02
54 77 0.32
55 85 0.36
56 21 0.09
58 2 0.01
59 3 0.01
60 45 0.19
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.28
Consensus pattern (55 bp):
TGATCATCGAAAACTTCTTGGAACGACCACACTGGATCAACTTTAAGATCAACTC
Found at i:8144 original size:55 final size:54
Alignment explanation
Indices: 8044--8352 Score: 336
Period size: 54 Copynumber: 5.6 Consensus size: 54
8034 TTCTTGGAAC
* * * *
8044 GACCGCACTGGATCAATTTAGAGATCAACTCT-GATCATC-GTAAACTTCT-TGGAAT
1 GACCACACTGGATCAACTTA-AGATCAACT-TAGATC-TCTGAAAACTTCTAT-GAAA
* * *
8099 GACCACACTGGATCAACTTTAAGATCAACTTAGATTTTTGAAAACTTCTATGGAA
1 GACCACACTGGATCAAC-TTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
* * ** *
8154 GACCACACAGGGTCGTCTGAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
1 GACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
* *
8208 GACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
1 GACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
* * *
8262 GACCACACCGGCACTGGGTCATCTTAAGATCAACTTAAATCTCTGAAAACTTCTATGAAA
1 GA-C-CA----CACTGGATCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
8322 GACCTACACTGGATCAACTTAAGATCAACTT
1 GACC-ACACTGGATCAACTTAAGATCAACTT
8353 TCTAGA
Statistics
Matches: 222, Mismatches: 21, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
54 88 0.40
55 75 0.34
56 6 0.03
58 1 0.00
59 2 0.01
60 50 0.23
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (54 bp):
GACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
Found at i:8323 original size:114 final size:108
Alignment explanation
Indices: 8085--8352 Score: 367
Period size: 114 Copynumber: 2.4 Consensus size: 108
8075 TGATCATCGT
* * *
8085 AAACTTCT-TGGAATGACCACACTGGATCAACTTTAAGATCAACTTAGATTTTTGAAAACTTCTA
1 AAACTTCTAT-GAAAGACCACACTGGATCAAC-TTAAGATCAACTTAGATCTCTGAAAACTTCTA
* * *
8149 TGGAAGACCACACAGGGTCGTCTGAAGATCAACTTAGATCTCTGA
64 TGAAAGACCACACAGGGTCATCTGAAGATCAACTTAAATCTCTGA
* *
8194 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATG
1 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATG
*
8259 AAAGACCACACCGGCACTGGGTCATCTTAAGATCAACTTAAATCTCTGA
66 AAAGACCACA----CA--GGGTCATCTGAAGATCAACTTAAATCTCTGA
8308 AAACTTCTATGAAAGACCTACACTGGATCAACTTAAGATCAACTT
1 AAACTTCTATGAAAGACC-ACACTGGATCAACTTAAGATCAACTT
8353 TCTAGA
Statistics
Matches: 140, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
108 41 0.29
109 26 0.19
110 1 0.01
112 2 0.01
114 46 0.33
115 24 0.17
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.27
Consensus pattern (108 bp):
AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATG
AAAGACCACACAGGGTCATCTGAAGATCAACTTAAATCTCTGA
Done.