Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013672.1 Corchorus olitorius cultivar O-4 contig13705, 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: 30076
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:7568 original size:38 final size:39
Alignment explanation
Indices: 7511--7620 Score: 145
Period size: 38 Copynumber: 2.9 Consensus size: 39
7501 GGCTGTGCAT
* * * * *
7511 AGTGGACCCATACCACAGGGGGTTAAATTG-TTGGTAGG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG
7549 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG
*
7588 AGTGAACCCGTGCCTCAGGGGGTT-AACTG-TTGG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGG
7621 CTAGATTTCG
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
37 4 0.06
38 31 0.48
39 30 0.46
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.24
Consensus pattern (39 bp):
AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG
Found at i:7597 original size:39 final size:38
Alignment explanation
Indices: 7526--7620 Score: 147
Period size: 39 Copynumber: 2.5 Consensus size: 38
7516 ACCCATACCA
* * *
7526 CAGGGGGTTAAATTGTTGGTAGGAGTGGACCCGTGCCT
1 CAGGGGGTTAAACTGTTGGTAAGAGTGAACCCGTGCCT
7564 CAGGGGGTTAAACTGATTGGTAAGAGTGAACCCGTGCCT
1 CAGGGGGTTAAACTG-TTGGTAAGAGTGAACCCGTGCCT
7603 CAGGGGGTT-AACTGTTGG
1 CAGGGGGTTAAACTGTTGG
7621 CTAGATTTCG
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
37 4 0.08
38 19 0.36
39 30 0.57
ACGTcount: A:0.21, C:0.16, G:0.38, T:0.25
Consensus pattern (38 bp):
CAGGGGGTTAAACTGTTGGTAAGAGTGAACCCGTGCCT
Found at i:7662 original size:6 final size:6
Alignment explanation
Indices: 7651--7676 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7641 CGTTAACGGA
7651 TGATTG TGATTG TGATTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TG
7677 GTGCATCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:14387 original size:935 final size:930
Alignment explanation
Indices: 12579--14435 Score: 2650
Period size: 935 Copynumber: 2.0 Consensus size: 930
12569 TGATGTGCTC
* * * *
12579 AGGGCTTATCATGGACATGAAGATGGCAATGGAGATCATGGAAAGGATGAGCATGGAGTACGAGG
1 AGGGCTTATCATGGACATGAAGATGACAATGGAGAGCATGGAAAGGATGAGCAAGGAGTACAAGG
** *
12644 AAGCATGGAGAAGCATGAAGATGATGGAGATATCCTTGAGCATGTTCCAAGCACCAAGAAAATGC
66 AAGCATGGAGAAGCATGAAGAACATGGAGATATCCTTGAGCATATTCCAAGCACCAAGAAAATGC
*
12709 CATTTGATCCGTTAAAGATGCCTATCGGTCCAAGACAAGAGCAAGAGCTACAAGATTCAAGGATG
131 CATTTGATCCATTAAAGATGCCTATCGGTCCAAGACAAGAGCAAGAGCTACAAGATTCAAGGATG
* * * * *
12774 CACTCATGGGTCTTGTTTGAAGTCATCTGGATGATATGAAAGTCATTGATGCACAATTGAAGAGC
196 CACTCATAGGCCTTGTTCGAAGTCATCTAGAAGATATGAAAGTCATTGATGCACAATTGAAGAGC
* *
12839 TTTGGTGATGATTTGAGTAAGCATTCATCCATTGATTCCAAGATTATCACCTTACTTGCAATCGA
261 TTTGGTGATGATTTGAGCAAGCATTCATCCATTGATTCCAAGATCATCACCTTACTTGCAATCGA
* *
12904 TCTGCATTAGAGCTTGAATGTATTATTTTGGCTATTATAAGGCCTTAGATTAGCTTATCTTTATG
326 TATGCATTAGAGCTTGAATGTATTATTTCGGCTATTATAAGGCCTTAGATTAGCTTATCTTTATG
* *
12969 TTTAGATGACATTAGGATCGGGCTTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGTATTGTT
391 TTTAGATGACATTAGGATCGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCATTGTT
**
13034 ATTTATTTTTCCTTTTTGGACTTGGATTAGGCTATTTCCTTGTCCTTTCCAATATGATTGCCGCC
456 ATTTATTTTTCCTAGTTGGACTTGGATTAGGCTATTTCCTTGTCCTTT-C-ATATGATTGCCGCC
* * ** * *
13099 CAAGACATGTATGAAACACCTATAGGGCTTATTTTTCTTATTTTGGGTCGACCCCTTTGCCTATA
519 CAAGACATGTATGAAACACCCATAGGGCTTAATTAGCTGATATT--GTCGACCCCTTTGCCTATA
* *
13164 TAAGGGCATCGACCCGCCTCTTGTAATCAAGTTAAGTTTTTCAATCAAAGAGAGTTCTTTTGAGA
582 TAAGGGCATCGACACGCCTCTTGTAAACAAGTTAAGTTTTTCAATCAAAGAGAGTTCTTTTGAGA
*
13229 ATTTCGCTTCATTGTTCTAGTTTGAGCATACTTAGGATCTCTTCAATCTTGAAGAGTCCTAGTAA
647 ATTTAGCTTCATTGTTCTAGTTTGAGCATACTTAGGATCTCTTCAATCTTGAAGAGTCCTAGTAA
*
13294 ACAATTAGATAGTGATTATCTAGTTGTGTTTCTTGTGATCTTAGGTTGTCAATTGCAGGTCTAAT
712 ACAATTAGATAGTGATTATCTAGTTGTGTTTCATGTGATCTTAGGTTGTCAATTGCAGGTCTAAT
*
13359 TGATCATCTAGGGCCGACGAAAGAAGATTGGATCTTTGGGAAGACTGTCAAGTTCATCAAGTCTA
777 TGATCATCTAGGGCCGACGAAAGAAGATTGGATCTTTGGGAAGACTATCAAGTTCATCAAGTCTA
* *
13424 GAAGTTGGAGTTTCAAGTAGATCTTTGGAAGAATTCAATGGTAGATTTGAATCTATCACAACTAG
842 GAAGTTGGAGTTTCAAGTAGATCTTTGGAAGAATTCAAGGGTAGATTTGAATCCATCACAACTAG
13489 ATTCATATCAATAATGATGCACCA
907 ATTCATATCAATAATGATGCACCA
* * *
13513 AGGGCTTATCATGGACTTGAAGATGACAATGGAGAGCATGGAAAGGATGATCAAGG-GCTGCAAG
1 AGGGCTTATCATGGACATGAAGATGACAATGGAGAGCATGGAAAGGATGAGCAAGGAG-TACAAG
* ** **
13577 GAAGCATGGAGATGCATGAAGAACATGGAGATATTGTTGAGCATATTCCAAGCACCAAGAAGTTG
65 GAAGCATGGAGAAGCATGAAGAACATGGAGATATCCTTGAGCATATTCCAAGCACCAAGAAAATG
* * * *
13642 CCATTTGATCCATTAAATATGCCTATTGGTCCAATGACTAGAGCAAGAGCTA-AGAGGTTCAAGG
130 CCATTTGATCCATTAAAGATGCCTATCGGTCCAA-GACAAGAGCAAGAGCTACA-AGATTCAAGG
* **
13706 ATGCACTCATAGGCCTTGTTCGAAGTCATCTAGAAGATATGAAGGTCATTGATGTGCAATTGAAG
193 ATGCACTCATAGGCCTTGTTCGAAGTCATCTAGAAGATATGAAAGTCATTGATGCACAATTGAAG
*
13771 AGTTTTGGTGATGATTTGAGCAAGCATTCATCCATTGATTCCAAGATCATCACCTTACTTGCAAT
258 AGCTTTGGTGATGATTTGAGCAAGCATTCATCCATTGATTCCAAGATCATCACCTTACTTGCAAT
13836 CGATATG-ACTTAGAGCTTGAATGTATTATTTCGGCTATTATAAGGCCTTATTCTATCTTAGATT
323 CGATATGCA-TTAGAGCTTGAATGTATTATTTCGGCTATTATAAGG-------C---CTTAGATT
*
13900 AGCTTATCTTTATGTTTAGATGACATTAGGATTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTT
377 AGCTTATCTTTATGTTTAGATGACATTAGGATCGGGCCTTGTTTGACTAAGTCCAATCCTTGTTT
*
13965 AATTATGCCTTGTTATTTATTTTTCCTAGTTGGACTTGGATTA-G-T-TTTCCTTGT-CTTT-AT
442 AATTATGCATTGTTATTTATTTTTCCTAGTTGGACTTGGATTAGGCTATTTCCTTGTCCTTTCAT
* * ** * * ** * * * *
14025 -T-TTTG-GGCTTGTAAGGCTTG-AT-AGCCGCCCATATGTCTTTAGGATTAGGTGA-ATT-TCG
507 ATGATTGCCGC--CCAAGACATGTATGAAACACCCATAGGGC-TTA--ATTAGCTGATATTGTCG
***** * ** *
14083 TTTTTTTATGCCTATATTAGGGGGTC-A-ATGCCTCTTGTAAACACAAGTTAAGTTTTTCAATCA
567 ACCCCTT-TGCCTATATAAGGGCATCGACACGCCTCTTGT-AA-ACAAGTTAAGTTTTTCAATCA
*
14146 AAGAGAGTTCTTTTTAGAATTTAGCTTCATTGTTCTAGTTTGAGCATACTTAGGATCTCTTCAAT
629 AAGAGAGTTCTTTTGAGAATTTAGCTTCATTGTTCTAGTTTGAGCATACTTAGGATCTCTTCAAT
*
14211 CTTGTAGAGTCCTAGTAAACAATTAGATAGTGATTATCTAGTTGTGTTTCATGTGATCTTAGGTT
694 CTTGAAGAGTCCTAGTAAACAATTAGATAGTGATTATCTAGTTGTGTTTCATGTGATCTTAGGTT
14276 GTCAATTGCAGGTCTAATTGATCATCTAGGGCCGACGAAAGAAGATTGGATCTTTGGGAAGACTA
759 GTCAATTGCAGGTCTAATTGATCATCTAGGGCCGACGAAAGAAGATTGGATCTTTGGGAAGACTA
* * *
14341 TTAAGTTCATCAAGTCTAGAAGTTGGAGTTTCAAGTAGATCTTTGGAGGAATTCAAGGGTAGTTT
824 TCAAGTTCATCAAGTCTAGAAGTTGGAGTTTCAAGTAGATCTTTGGAAGAATTCAAGGGTAGATT
*
14406 TTAATCCATCACAACTAGATTCATATCAAT
889 TGAATCCATCACAACTAGATTCATATCAAT
14436 TGGTATTCAG
Statistics
Matches: 822, Mismatches: 79, Indels: 43
0.87 0.08 0.05
Matches are distributed among these distances:
933 10 0.01
934 153 0.19
935 510 0.62
936 8 0.01
937 9 0.01
938 6 0.01
941 4 0.00
942 10 0.01
943 1 0.00
944 1 0.00
945 110 0.13
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (930 bp):
AGGGCTTATCATGGACATGAAGATGACAATGGAGAGCATGGAAAGGATGAGCAAGGAGTACAAGG
AAGCATGGAGAAGCATGAAGAACATGGAGATATCCTTGAGCATATTCCAAGCACCAAGAAAATGC
CATTTGATCCATTAAAGATGCCTATCGGTCCAAGACAAGAGCAAGAGCTACAAGATTCAAGGATG
CACTCATAGGCCTTGTTCGAAGTCATCTAGAAGATATGAAAGTCATTGATGCACAATTGAAGAGC
TTTGGTGATGATTTGAGCAAGCATTCATCCATTGATTCCAAGATCATCACCTTACTTGCAATCGA
TATGCATTAGAGCTTGAATGTATTATTTCGGCTATTATAAGGCCTTAGATTAGCTTATCTTTATG
TTTAGATGACATTAGGATCGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCATTGTT
ATTTATTTTTCCTAGTTGGACTTGGATTAGGCTATTTCCTTGTCCTTTCATATGATTGCCGCCCA
AGACATGTATGAAACACCCATAGGGCTTAATTAGCTGATATTGTCGACCCCTTTGCCTATATAAG
GGCATCGACACGCCTCTTGTAAACAAGTTAAGTTTTTCAATCAAAGAGAGTTCTTTTGAGAATTT
AGCTTCATTGTTCTAGTTTGAGCATACTTAGGATCTCTTCAATCTTGAAGAGTCCTAGTAAACAA
TTAGATAGTGATTATCTAGTTGTGTTTCATGTGATCTTAGGTTGTCAATTGCAGGTCTAATTGAT
CATCTAGGGCCGACGAAAGAAGATTGGATCTTTGGGAAGACTATCAAGTTCATCAAGTCTAGAAG
TTGGAGTTTCAAGTAGATCTTTGGAAGAATTCAAGGGTAGATTTGAATCCATCACAACTAGATTC
ATATCAATAATGATGCACCA
Found at i:14685 original size:10 final size:9
Alignment explanation
Indices: 14670--14703 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
14660 GGTTATATAG
14670 AAAAAAATCA
1 AAAAAAAT-A
14680 AAAAAAATAA
1 AAAAAAAT-A
14690 AAAAAAATA
1 AAAAAAATA
14699 AAAAA
1 AAAAA
14704 TAATTCAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 6 0.26
10 17 0.74
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAAAATA
Found at i:26839 original size:9 final size:9
Alignment explanation
Indices: 26827--26896 Score: 104
Period size: 9 Copynumber: 7.6 Consensus size: 9
26817 TCAATACATG
26827 CAAAATTTT
1 CAAAATTTT
26836 CAAAATTTT
1 CAAAATTTT
26845 CAAAATTTT
1 CAAAATTTT
*
26854 CAAAAAATTT
1 C-AAAATTTT
26864 CAAAATTTT
1 CAAAATTTT
*
26873 CAAAAAATTT
1 C-AAAATTTT
26883 CAAAATTTT
1 CAAAATTTT
26892 CAAAA
1 CAAAA
26897 AATTTATGGC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
9 39 0.71
10 16 0.29
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (9 bp):
CAAAATTTT
Found at i:26864 original size:19 final size:19
Alignment explanation
Indices: 26827--26901 Score: 134
Period size: 19 Copynumber: 4.0 Consensus size: 19
26817 TCAATACATG
*
26827 CAAAATTTTC-AAAATTTT
1 CAAAATTTTCAAAAAATTT
26845 CAAAATTTTCAAAAAATTT
1 CAAAATTTTCAAAAAATTT
26864 CAAAATTTTCAAAAAATTT
1 CAAAATTTTCAAAAAATTT
26883 CAAAATTTTCAAAAAATTT
1 CAAAATTTTCAAAAAATTT
26902 ATGGCATTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 10 0.18
19 45 0.82
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (19 bp):
CAAAATTTTCAAAAAATTT
Found at i:26864 original size:28 final size:28
Alignment explanation
Indices: 26828--26896 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
26818 CAATACATGC
*
26828 AAAATTTTCAAAATTTTCAAAATTTTCA
1 AAAAATTTCAAAATTTTCAAAATTTTCA
*
26856 AAAAATTTCAAAATTTTCAAAAAATTTC-
1 AAAAATTTCAAAATTTTC-AAAATTTTCA
*
26884 AAAATTTTCAAAA
1 AAAAATTTCAAAA
26897 AATTTATGGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 29 0.78
29 8 0.22
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (28 bp):
AAAAATTTCAAAATTTTCAAAATTTTCA
Done.