Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010386.1 Corchorus olitorius cultivar O-4 contig10418, 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: 19038
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:2901 original size:96 final size:92
Alignment explanation
Indices: 2771--2950 Score: 315
Period size: 96 Copynumber: 1.9 Consensus size: 92
2761 CGAATGCGCT
2771 ATGAAAGTGACATATATATCTGATGAAATATCCCCCAACACATGCCCCTTAACCTATCTCCTTGA
1 ATGAAAGTGACATATATATCTGATGAAATATCCCCCAACACATGCCCCTTAACCTATCTCCTTGA
2836 AATTTCCTACCCTTCAATTTTGCACAA
66 AATTTCCTACCCTTCAATTTTGCACAA
*
2863 ATGAAAGTGAATATATATATCTGATTATGAAATATCCCCCAACACATGCCCCTTAACCTATCTCC
1 ATGAAAGTG-ACATATATATCTG---ATGAAATATCCCCCAACACATGCCCCTTAACCTATCTCC
2928 TTGAAATTTCCTACCCTTCAATT
62 TTGAAATTTCCTACCCTTCAATT
2951 AAGAGATCAG
Statistics
Matches: 83, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
92 9 0.11
93 12 0.14
96 62 0.75
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.32
Consensus pattern (92 bp):
ATGAAAGTGACATATATATCTGATGAAATATCCCCCAACACATGCCCCTTAACCTATCTCCTTGA
AATTTCCTACCCTTCAATTTTGCACAA
Found at i:7985 original size:329 final size:329
Alignment explanation
Indices: 6554--8152 Score: 1441
Period size: 333 Copynumber: 4.8 Consensus size: 329
6544 TTCATCATAG
* * *
6554 TTTTTGGCTAAAAACGCGTTTCGGGACCTCGACTTATTTTTGCATGACTTTTTG-CGCCGAGACT
1 TTTTTGGCTAAAAACGCGTTCCGGG-CC-CGACTTAGTTTTGCATGA-TTTTTGACGCCAAGACT
* **
6618 CCTTGAAATATCTATATTGATCTAATGAAATCTCAGCCACA-TTGAATTTAAGGATTTGTTTTTA
63 CCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTTG-ATTTAAGGATTTGTTTTTA
* * * *
6682 CGAACATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAAATATGAAAAACGATAT
127 CGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAATAGGAAAAACGATAT
* * * *
6747 TAAAAGCGTGAAAAG-TCCTCCAATCTTTTTGACGTTGAATTATATATATTTTATGATTTTTTTG
191 TAAAAGCGTGAAAAGCT-CTTCAATCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTTTG
* * *
6811 GCTAAAAATTAAGGAAAAATATTTCAGATCAATTTTTGCAAAATTTTAGCCGAAATCGTG--T-A
255 GCTAAAAATTGAGGAAAAATATTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAA
*
6873 CCAATCACGGTTT
320 TCAATCAC-G--T
* * * ** *
6886 TTTTTGGGCTAAAAACGCATTTCGGTACCTCGGGTCAGTTTTGCATGATTTTTTGTA-G-CAAGA
1 TTTTT-GGCTAAAAACGCGTTCCGG-GCC-CGACTTAGTTTTGCATGA-TTTTTG-ACGCCAAGA
* * *
6949 CTCCTTAAAATATCTATATTCATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTT
61 CTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTTGATTTAAGGATTTGTTTTT
* * * * * *
7014 ACGAGTATTTGAATCATGTTTCGATTTAATTAAAAATTAATTTGAAAACAATAGGGAAAGCGATA
126 ACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAA-AATAGGAAAAACGATA
* * * * *
7079 TTAGAAGCGTGAGAAGCCCTTCAATCCTTTT-AGCGTTGAATTATATATTTTTTATGAGTATTGT
190 TTAAAAGCGTGAAAAGCTCTTCAATCTTTTTGA-CGTTGAATTATATATTTTTTATGAGTATTTT
* * *
7143 GGCTAAAAATTGA-GAAAAATATTT-TGGATCAATTTTTGCAAAATTTAAGCCGAAATCTTGTAC
254 GGCTAAAAATTGAGGAAAAATATTTCTGG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAT
* * ***
7206 CATCATGGTCTTTTTT
318 AATCA--ATC--ACGT
* * * ** * * *
7222 TTTTTGTAATACTAAAAACGCGTTGCGGGGTCCTGTGTAAGTTTTGCATGATTTTTGGCGCCAAA
1 TTTTTG----GCTAAAAACGCGTT-CCGGG-CCCGACTTAGTTTTGCATGATTTTTGACGCCAAG
* * *
7287 ACTTCTTAAAATATATCTATATTCATCTAACCAAATGTCAGCCACA-TTGTATTTAAGGATTTAG
60 ACTCCTT-GAA-ATATCTATATTCATCTAACCAAATCTCAGCCACATTTG-ATTTAAGGATTT-G
* * * *
7351 --TTTACAAG--TTGCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAATAAAATAGGA
121 TTTTTACGAGCATT--TGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCG-AA-AAAATAGGA
* * *
7412 AAAATGATATTATAAGCGTGAAAAGGCT-TTCAAT-TATTTTGGCGTTGAATTATATATTTTTTA
181 AAAACGATATTAAAAGCGTGAAAA-GCTCTTCAATCT-TTTTGACGTTGAATTATATATTTTTTA
* * * * * * * *
7475 TGAATATTTTCGCTAGAAATTGAGGAAATATCTTTCGGGTCAACTTTTGCAAAATTTTAGCTGAA
244 TGAGTATTTTGGCTAAAAATTGAGGAAAAATATTTCTGGTCAATTTTTGCAAAATTTTAGCCGAA
* * *
7540 ATCGTATACTAA-CCATCACGG
309 ATCGTGTA-TAATCAATCACGT
* * * * ** *
7561 TTTTCGGCTAAAAATGCGTTCCGCGGTCCGACTGAGTTTTGCATGATTTTTGGTGCCAAGACTCT
1 TTTTTGGCTAAAAACGCGTTCCG-GGCCCGACTTAGTTTTGCATGATTTTTGACGCCAAGACTCC
*
7626 TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTTGATTTAAGAATTTGTTTTTACGA
65 TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTTGATTTAAGGATTTGTTTTTACGA
* * * * *
7691 GCATTTGAATCTTGTCTCGATTTAATTAGAAATTAATTCGGAAAAA-GGGAAAAACAATATTAGA
130 GCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGATATTAAA
* * * * * * *
7755 AGCGTTAAAAGCTCTTCAATCTTTTTTTATGTCGAATTATATATTTTTTATGAGTATTCTAGC-C
195 AGCGTGAAAAGCTCTTCAATC-TTTTTGACGTTGAATTATATATTTTTTATGAGTATTTTGGCTA
* * *
7819 AAAATTGAGGAAATATCTTTCTGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTATTAATCA
259 AAAATTGAGGAAAAATATTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-TAATCA
*
7884 ATCACGA
323 ATCACGT
* * * *
7891 TTTTTGGTTAAAGACGCCTTCCAGGGCCACGACTCTA-TTTTGCATGATTTTTTGACGCCGAGAC
1 TTTTTGGCTAAAAACGCGTTCC-GGGCC-CGACT-TAGTTTTGCATGA-TTTTTGACGCCAAGAC
* * * * **
7955 TCCTTGAATTATCT-T-TT-ATCTAATCAAATCTTAGTCACATTAAATTTAAGGATTTGTTTTTA
62 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTTGATTTAAGGATTTGTTTTTA
* ** * * * * * *
8017 TGTTCATCTGAATCTTGTTTCAATTTAATTATAAATTAATTCAAAAAAATATGAAAAACAATATT
127 CGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGATATT
* * * * * * * * *
8082 AAAAGCGTGAAAA-ATCCTCCAATCTTTTTGGCATTGAAGTATAAATATTTTATGATTATTTTTG
192 AAAAGCGTGAAAAGCT-CTTCAATCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTTTGG
*
8146 CCAAAAA
256 CTAAAAA
8153 AAATGAGAAA
Statistics
Matches: 1032, Mismatches: 179, Indels: 114
0.78 0.14 0.09
Matches are distributed among these distances:
328 3 0.00
329 196 0.19
330 101 0.10
331 21 0.02
332 124 0.12
333 255 0.25
334 37 0.04
335 20 0.02
336 6 0.01
337 2 0.00
338 9 0.01
339 41 0.04
340 43 0.04
341 49 0.05
342 79 0.08
343 43 0.04
344 3 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (329 bp):
TTTTTGGCTAAAAACGCGTTCCGGGCCCGACTTAGTTTTGCATGATTTTTGACGCCAAGACTCCT
TGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTTGATTTAAGGATTTGTTTTTACGAG
CATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGATATTAAAA
GCGTGAAAAGCTCTTCAATCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAA
AATTGAGGAAAAATATTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAATCAATC
ACGT
Found at i:8642 original size:2 final size:2
Alignment explanation
Indices: 8593--8624 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8583 AATCAAAGAA
8593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8625 TGGTGAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8684 original size:2 final size:2
Alignment explanation
Indices: 8677--8706 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8667 CTTTTATTAT
8677 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8707 CTAGTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8811 original size:22 final size:20
Alignment explanation
Indices: 8774--8955 Score: 71
Period size: 22 Copynumber: 8.4 Consensus size: 20
8764 TTTTTTTAAA
8774 TTTGATAATCACTATAAAAT
1 TTTGATAATCACTATAAAAT
*
8794 TTTGATAATTACACTATAAAGT
1 TTTGATAA-T-CACTATAAAAT
* *
8816 TTTTATGACGAT-ACTATAGAAT
1 TTTGAT-A--ATCACTATAAAAT
* * * *
8838 TTCGAGAACCTCTATATGAAAT
1 TTTGATAATCACTATA--AAAT
* *
8860 TTTGTTAACTTCCCTATAAAAT
1 TTTGATAA--TCACTATAAAAT
*
8882 TTTG-TCACACTCCCTATAAAAT
1 TTTGAT-A-A-TCACTATAAAAT
* * *
8904 TTTAATAATTACTTAATGAAAT
1 TTTGATAATCAC-T-ATAAAAT
* *
8926 TTTGATAACCACCCTATGAAAT
1 TTTGATAATCA--CTATAAAAT
8948 TTTGATAA
1 TTTGATAA
8956 CCTCCCAATG
Statistics
Matches: 122, Mismatches: 23, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
19 1 0.01
20 15 0.12
21 5 0.04
22 88 0.72
23 4 0.03
24 8 0.07
25 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (20 bp):
TTTGATAATCACTATAAAAT
Found at i:8956 original size:22 final size:22
Alignment explanation
Indices: 8852--9116 Score: 135
Period size: 22 Copynumber: 12.0 Consensus size: 22
8842 AGAACCTCTA
* *
8852 TATGAAATTTTGTTAACTTCCC
1 TATGAAATTTTGATAACCTCCC
* *
8874 TATAAAATTTTG-TCACACTCCC
1 TATGAAATTTTGATAAC-CTCCC
* * * * *
8896 TATAAAATTTTAATAA-TTACT
1 TATGAAATTTTGATAACCTCCC
*
8917 TAATGAAATTTTGATAACCACCC
1 T-ATGAAATTTTGATAACCTCCC
8940 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* * * * **
8962 AATGAAATGTTGGTAAGCGCACAT
1 TATGAAATTTTGATAA-C-CTCCC
*
8986 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTCCC
* * * * * * * **
9008 GATAAAATATAGGTAATCACAT
1 TATGAAATTTTGATAACCTCCC
* **
9030 TATGAAATTTTGATAAACATATC
1 TATGAAATTTTGAT-AACCTCCC
* *
9053 -ATGAAATTGTGAT-ACCTCAC
1 TATGAAATTTTGATAACCTCCC
*
9073 TATGAAAATTTT-ATAAACCTCTC
1 TATG-AAATTTTGAT-AACCTCCC
*
9096 TATAAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
9117 AGTTGAATCC
Statistics
Matches: 174, Mismatches: 57, Indels: 24
0.68 0.22 0.09
Matches are distributed among these distances:
20 4 0.02
21 11 0.06
22 125 0.72
23 19 0.11
24 15 0.09
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:8994 original size:46 final size:44
Alignment explanation
Indices: 8940--9045 Score: 140
Period size: 46 Copynumber: 2.4 Consensus size: 44
8930 ATAACCACCC
* * *
8940 TATGAAATTTTGATAACCTCCCAATGAAATGTTGGTAAGCGCACAT
1 TATGAAATTTTGATAACCTCCCAATAAAATATAGGTAA--GCACAT
* * *
8986 TATGAAATTTTGATAACCTTCCGATAAAATATAGGTAATCACAT
1 TATGAAATTTTGATAACCTCCCAATAAAATATAGGTAAGCACAT
9030 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
9046 ACATATCATG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 21 0.39
46 33 0.61
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCAATAAAATATAGGTAAGCACAT
Found at i:15969 original size:12 final size:12
Alignment explanation
Indices: 15952--15981 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
15942 AGCTTCGTTG
15952 ATTACTATGTTA
1 ATTACTATGTTA
15964 ATTACTATGTTA
1 ATTACTATGTTA
15976 ATTACT
1 ATTACT
15982 CAAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (12 bp):
ATTACTATGTTA
Found at i:16119 original size:13 final size:13
Alignment explanation
Indices: 16101--16125 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16091 AGCAATTTGC
16101 TAAAGCCTTTCCT
1 TAAAGCCTTTCCT
16114 TAAAGCCTTTCC
1 TAAAGCCTTTCC
16126 CTATTTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (13 bp):
TAAAGCCTTTCCT
Found at i:18476 original size:119 final size:119
Alignment explanation
Indices: 18265--18503 Score: 478
Period size: 119 Copynumber: 2.0 Consensus size: 119
18255 TTTGCTAGGT
18265 ACTGCCTTTATAATTACATTTGCCAATTGGTTCTCTGACTTAACAAATGGAAATTTAATGATCTT
1 ACTGCCTTTATAATTACATTTGCCAATTGGTTCTCTGACTTAACAAATGGAAATTTAATGATCTT
18330 CTCTTTCAGGTTCTGTTTTATGAATTGTTTGTCTACCTCCACATGCTTGATGTG
66 CTCTTTCAGGTTCTGTTTTATGAATTGTTTGTCTACCTCCACATGCTTGATGTG
18384 ACTGCCTTTATAATTACATTTGCCAATTGGTTCTCTGACTTAACAAATGGAAATTTAATGATCTT
1 ACTGCCTTTATAATTACATTTGCCAATTGGTTCTCTGACTTAACAAATGGAAATTTAATGATCTT
18449 CTCTTTCAGGTTCTGTTTTATGAATTGTTTGTCTACCTCCACATGCTTGATGTG
66 CTCTTTCAGGTTCTGTTTTATGAATTGTTTGTCTACCTCCACATGCTTGATGTG
18503 A
1 A
18504 TCATGTTGAA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 120 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (119 bp):
ACTGCCTTTATAATTACATTTGCCAATTGGTTCTCTGACTTAACAAATGGAAATTTAATGATCTT
CTCTTTCAGGTTCTGTTTTATGAATTGTTTGTCTACCTCCACATGCTTGATGTG
Done.