Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018406.1 Corchorus olitorius cultivar O-4 contig18439, 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: 50076
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:2815 original size:29 final size:29
Alignment explanation
Indices: 2783--2840 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2773 GTCTAGTTTC
2783 TTTTTTCATATGATTTATAGAAGATCATG
1 TTTTTTCATATGATTTATAGAAGATCATG
2812 TTTTTTCATATGATTTATAGAAGATCATG
1 TTTTTTCATATGATTTATAGAAGATCATG
2841 CTACTTAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (29 bp):
TTTTTTCATATGATTTATAGAAGATCATG
Found at i:6521 original size:33 final size:33
Alignment explanation
Indices: 6475--6608 Score: 162
Period size: 33 Copynumber: 4.1 Consensus size: 33
6465 GCGGAGGCAT
* * *
6475 CCTCAGGGGGCGCCTCCCACCGTGGCGGTGAGTC
1 CCTCGGGGGGCGCCACCCACCGTGGCGGGGAG-C
6509 CC-CGGGGGGCGCCACCCACCGTGGCGGGGAGC
1 CCTCGGGGGGCGCCACCCACCGTGGCGGGGAGC
*
6541 CCTCGGGGGGCGCCACCCACCGTGGCGGGGCGC
1 CCTCGGGGGGCGCCACCCACCGTGGCGGGGAGC
** * * **
6574 CCTTTGGGGACGCCATCCACCGTGATGGGGAGC
1 CCTCGGGGGGCGCCACCCACCGTGGCGGGGAGC
6607 CC
1 CC
6609 CCTGGGGACG
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
32 3 0.03
33 83 0.94
34 2 0.02
ACGTcount: A:0.10, C:0.39, G:0.41, T:0.10
Consensus pattern (33 bp):
CCTCGGGGGGCGCCACCCACCGTGGCGGGGAGC
Found at i:14558 original size:42 final size:42
Alignment explanation
Indices: 14499--14611 Score: 217
Period size: 42 Copynumber: 2.7 Consensus size: 42
14489 CAGATTCAGC
14499 AATCTTCTCAACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
1 AATCTTCTCAACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
*
14541 AATCTTTTCAACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
1 AATCTTCTCAACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
14583 AATCTTCTCAACAACTGGAAGGGGCTGCT
1 AATCTTCTCAACAACTGGAAGGGGCTGCT
14612 TATCTGCATT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (42 bp):
AATCTTCTCAACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
Found at i:17791 original size:3 final size:3
Alignment explanation
Indices: 17785--17810 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17775 AATCAAATGC
17785 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
17811 GCTAGTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43087 original size:108 final size:106
Alignment explanation
Indices: 42865--43066 Score: 264
Period size: 108 Copynumber: 1.9 Consensus size: 106
42855 TTTTTCTAAC
* ** * *
42865 CCTTAAAATAAAATTTTAATTTTAATTTGGATTAAACTTAGTGAATTAGTTATATATTTTATTTC
1 CCTTAAAATAAAAATAAAATTTTAATTTGGACTAAACTTAGTGAATTAGTTATATATTTCATTTC
* * *
42930 TAAAACCCTATAATAATAATATTATTAATTATGGAAATTAA
66 TAAAACCCTATAATAATAAAACTATTAATTATGCAAATTAA
* *
42971 CCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTCATT
1 CCTTAAAATAAAAATAAAATTTTAATTT-GGACTAAACTTAGTG-AATTAGTTATATATTTCATT
*
43036 TCTAAAACTCTATAATAA-AAAACCT-TTAATT
64 TCTAAAACCCTATAATAATAAAA-CTATTAATT
43067 TCATAATTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
106 25 0.30
107 22 0.27
108 36 0.43
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (106 bp):
CCTTAAAATAAAAATAAAATTTTAATTTGGACTAAACTTAGTGAATTAGTTATATATTTCATTTC
TAAAACCCTATAATAATAAAACTATTAATTATGCAAATTAA
Found at i:43858 original size:26 final size:26
Alignment explanation
Indices: 43822--43873 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
43812 CCCTACATGA
*
43822 GTGTAAAATTAAATATGTAGTTTTAG
1 GTGTAAAATTAAATAGGTAGTTTTAG
43848 GTGTAAAATTAAATAGGTAGTTTTAG
1 GTGTAAAATTAAATAGGTAGTTTTAG
43874 CTATTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.40
Consensus pattern (26 bp):
GTGTAAAATTAAATAGGTAGTTTTAG
Found at i:45297 original size:65 final size:64
Alignment explanation
Indices: 45199--45489 Score: 284
Period size: 66 Copynumber: 4.5 Consensus size: 64
45189 GAGAAATTGA
* * * * * *
45199 ACCTTTC-ACCCAAGGATCATTTTTGGAAGACAAACCTAAACTTAGATG-CAAAAAGACGAAATT
1 ACCTTTCGACCGAAGGAT-ATTTTTGGAAAACAAACCT-AACTTAGATGTGAAAAATATGAAACT
45262 G
64 G
* *
45263 ACCTTTCGACCGAGAGGATATTTTGGGAAAACAAAACCTAACCTAGATGTGAAAAATATGAAACT
1 ACCTTTCGACCGA-AGGATATTTTTGGAAAAC-AAACCTAACTTAGATGTGAAAAATATGAAACT
45328 G
64 G
* * **
45329 ACCCTTCGACCGAAAGGGTATTTTTGGAAAACAAAATTGAACTTAGATGTGAAAAATATGAAACT
1 ACCTTTCGACCG-AAGGATATTTTTGGAAAACAAACCT-AACTTAGATGTGAAAAATATGAAACT
45394 G
64 G
* * * ** *
45395 ACCATTCGACCGGAATGG-TATTTATGGAAAGCAAAATTGAACTTAAATGTGAAAAATATGAAAC
1 ACCTTTCGACC-GAA-GGATATTTTTGGAAAACAAACCT-AACTTAGATGTGAAAAATATGAAAC
45459 TG
63 TG
* *
45461 ACCCTTCGACCGGAAGGGTA-TTTTGGAAA
1 ACCTTTCGACC-GAAGGATATTTTTGGAAA
45490 GTAGAATAAA
Statistics
Matches: 198, Mismatches: 20, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
64 7 0.04
65 38 0.19
66 149 0.75
67 4 0.02
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (64 bp):
ACCTTTCGACCGAAGGATATTTTTGGAAAACAAACCTAACTTAGATGTGAAAAATATGAAACTG
Found at i:45671 original size:67 final size:66
Alignment explanation
Indices: 45234--46024 Score: 643
Period size: 67 Copynumber: 11.9 Consensus size: 66
45224 GAAGACAAAC
* * * * * * **
45234 CTAAACTT-AGATGCAAAAAGACGAAATTGACCTTTCGACCGAGAGGATATTTTGGGAAAACAAA
1 CTAAACTTGA-ATGTAAAAAGAC-AAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAA
*
45298 A-C
64 ATA
* * * * **
45300 CTAACCTAG-ATGTGAAAAATATGAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAAACAAA
1 CTAAACTTGAATGT-AAAAAGA-CAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAA
45364 AT-
64 ATA
* * * * * * *
45366 -TGAACTT-AGATGTGAAAAATATGAAACTGACCATTCGACCGGAATGGTATTTATGGAAA-GCA
1 CTAAACTTGA-ATGT-AAAAAGA-CAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATG-A
45428 AAAT-
62 AAATA
* * * * * * *
45432 -TGAACTTAAATGTGAAAAATATGAAACTGACCCTTCGACCGGAAGGGTA-TTTTGGAAA-GTAG
1 CTAAACTTGAATGT-AAAAAGA-CAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAA
45494 A-A
64 ATA
** * * *
45496 -TAAAC-TGAAATGCGGAAATGATGAAACTGACCCTTTC-ACCGAAAGGGTATTTTTGGAAATCA
1 CTAAACTTG-AATG-TAAAAAGA-CAAACTGACCC-TTCGACCGAAAGGGTATTTTTGGAAATGA
45558 AAAGTA
62 AAA-TA
* * * * * *
45564 CTGAACTTGAATGCAAAAAGACAAAACCGACCCTTCGACCGGAAGGGAATTTTTGGAAATCAAAA
1 CTAAACTTGAATGTAAAAAGAC-AAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAA
45629 TA
65 TA
* * * *
45631 CTAAATTTGAATGCAAAAAGACAAGACTGACCTTTTGACCGAAAGGGTATTTTTGGAAATGAAAA
1 CTAAACTTGAATGTAAAAAGACAA-ACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATG-AAA
45696 ATA
64 ATA
* * * *
45699 CTAAACTTGAATGTAAAAAGATGAAATTAACCCTTCGACTGAAAGGGTATTTTTGGAAATGAAAA
1 CTAAACTTGAATGTAAAAAGA-CAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAA
45764 TA
65 TA
* *
45766 CTGAACTTGAATGTAAAAAGACGAATCTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAA
1 CTAAACTTGAATGTAAAAAGAC-AAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAA
45831 TA
65 TA
*
45833 CTAAACTTGAATGTAAAAAGACAAGACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAA
1 CTAAACTTGAATGTAAAAAGACAA-ACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAA
45898 TA
65 TA
** * *
45900 CT-ATGTCGAAATG-CAAAAGACGGAAA-TGACCCTTCGACCG-AAGGAGTA-TTTTGGAAATTT
1 CTAAACTTG-AATGTAAAAAGAC--AAACTGACCCTTCGACCGAAAGG-GTATTTTTGGAAA--T
*
45960 GAAAATG
60 GAAAATA
* * * *
45967 CTAAACTTAAATG-CAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTGGGAAA
1 CTAAACTTGAATGTAAAAAGAC-AAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAA
46025 AAAACTGATA
Statistics
Matches: 613, Mismatches: 77, Indels: 68
0.81 0.10 0.09
Matches are distributed among these distances:
63 1 0.00
64 37 0.06
65 41 0.07
66 181 0.30
67 228 0.37
68 113 0.18
69 10 0.02
70 2 0.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (66 bp):
CTAAACTTGAATGTAAAAAGACAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAAT
A
Found at i:45689 original size:135 final size:133
Alignment explanation
Indices: 45244--46024 Score: 670
Period size: 135 Copynumber: 5.9 Consensus size: 133
45234 CTAAACTTAG
* * * * * ** * * *
45244 ATGCAAAAAGACGAAATTGACCTTTCGACCGAGAGGATATTTTGGGAAAACAAAA-CCTAACCTA
1 ATGCAAAAAGACGAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTT
* * ** **
45308 G-ATGTGAAAAATATGAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAAACAAAAT--TGAA
66 GAATG-CAAAAAGACAAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAATACT-AA
*
45370 CTT-A
129 TTTGA
* * * * * * * *
45374 GATGTGAAAAATATGAAACTGACCATTCGACCGGAATGGTATTTATGGAAA-GCAAAAT--TGAA
1 -ATG-CAAAAAGACGAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATG-AAAATACTAAA
* * * ** * *
45436 CTTAAATGTGAAAAATATGAAACTGACCCTTCGACCGGAAGGGTA-TTTTGGAAA-GTAGAATA-
63 CTTGAATG-CAAAAAGACAAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATG-AAAATAC
*
45498 -AA-CTGAA
126 TAATTTG-A
* * * * *
45505 ATGCGGAAATGATGAAACTGACCCTTTC-ACCGAAAGGGTATTTTTGGAAATCAAAAGTACTGAA
1 ATGC-AAAAAGACGAAACTGACCC-TTCGACCGAAAGGGTATTTTTGGAAATGAAAA-TACTAAA
* * * *
45569 CTTGAATGCAAAAAGACAAAACCGACCCTTCGACCGGAAGGGAATTTTTGGAAATCAAAATACTA
63 CTTGAATGCAAAAAGACAAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAATACT-
45634 AATTTGA
127 AATTTGA
* *
45641 ATGCAAAAAGAC-AAGACTGACCTTTTGACCGAAAGGGTATTTTTGGAAATGAAAAATACTAAAC
1 ATGCAAAAAGACGAA-ACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATG-AAAATACTAAAC
* ** * * *
45705 TTGAATGTAAAAAGATGAAATTAACCCTTCGACTGAAAGGGTATTTTTGGAAATGAAAATACTGA
64 TTGAATGCAAAAAGACAAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAATACT-A
*
45770 ACTTGA
128 ATTTGA
* *
45776 ATGTAAAAAGACGAATCTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTT
1 ATGCAAAAAGACGAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTT
* * *
45841 GAATGTAAAAAGACAAGACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACT-ATG
66 GAATGCAAAAAGACAAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAT-
*
45905 TCGAA
130 TTG-A
*
45910 ATGC-AAAAGACGGAAA-TGACCCTTCGACCG-AAGGAGTA-TTTTGGAAATTTGAAAATGCTAA
1 ATGCAAAAAGAC-GAAACTGACCCTTCGACCGAAAGG-GTATTTTTGGAAA--TGAAAATACTAA
* *
45971 ACTTAAATGC-AAAAGACGAAAA-TGACCCTTCGACCGAAAGGGTATTTTGGGAAA
62 ACTTGAATGCAAAAAGAC-AAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAA
46025 AAAACTGATA
Statistics
Matches: 540, Mismatches: 79, Indels: 60
0.80 0.12 0.09
Matches are distributed among these distances:
129 1 0.00
130 43 0.08
131 25 0.05
132 122 0.23
133 88 0.16
134 101 0.19
135 145 0.27
136 13 0.02
137 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (133 bp):
ATGCAAAAAGACGAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTT
GAATGCAAAAAGACAAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAATACTAATT
TGA
Done.