Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018344.1 Corchorus olitorius cultivar O-4 contig18377, 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: 33333
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:7065 original size:7 final size:8
Alignment explanation
Indices: 7021--7062 Score: 77
Period size: 8 Copynumber: 5.4 Consensus size: 8
7011 GAAAAAGATT
7021 AAAAC-AA
1 AAAACAAA
7028 AAAACAAA
1 AAAACAAA
7036 AAAACAAA
1 AAAACAAA
7044 AAAACAAA
1 AAAACAAA
7052 AAAACAAA
1 AAAACAAA
7060 AAA
1 AAA
7063 CAATAGAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 5 0.15
8 29 0.85
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAACAAA
Found at i:7691 original size:33 final size:32
Alignment explanation
Indices: 7649--7751 Score: 145
Period size: 33 Copynumber: 3.1 Consensus size: 32
7639 CCTCTTTTTC
*
7649 AGCCGTGACAGAGGGTTCAGTGTCCACTTCCAT
1 AGCCGTGACAG-GGGTTCAGTCTCCACTTCCAT
7682 AGCCGTGACAGGGGTTACAGTCTCCACTTCCAT
1 AGCCGTGACAGGGGTT-CAGTCTCCACTTCCAT
*
7715 AGCC-TCGACAGGGGGTACAGTCTCCACTTCCAT
1 AGCCGT-GACA-GGGGTTCAGTCTCCACTTCCAT
7748 AGCC
1 AGCC
7752 ATGGATTCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
32 6 0.09
33 54 0.83
34 5 0.08
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.22
Consensus pattern (32 bp):
AGCCGTGACAGGGGTTCAGTCTCCACTTCCAT
Found at i:7900 original size:33 final size:33
Alignment explanation
Indices: 7872--8442 Score: 247
Period size: 33 Copynumber: 17.3 Consensus size: 33
7862 TAAGGTCATT
*
7872 GGATTAGTTGGAGTTTCCTCATGCAAGGTGGTG
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* *
7905 GGGTCAGATGGAGTTTCCTCATGCAAGGTGGTG
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * **
7938 GGATCAGTTGTAGTTTCCTCA-CCCAGAGAAGTG
1 GGATCAGTTGGAGTTTCCTCATGCAAG-GTGGTG
*** * **
7971 GGATCAGTTGGAGTTTCCTCGCCCAAAGTGGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * ** *
8004 GAATCATTTGGAGTTTCCTCACCCAATGTTGG-G
1 GGATCAGTTGGAGTTTCCTCATGCAA-GGTGGTG
*
8037 GGATCAGTTGGAGTTTCCT--TGCTCAATGTTGG-G
1 GGATCAGTTGGAGTTTCCTCATG--CAA-GGTGGTG
* * * **
8070 GGATCAGTTGTAGCTTCCTCATGCAAGGTTGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * **
8103 GGAACTGTTGCAGCTTCCTCATGCAAAAT--TG
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * **
8134 CAGATTCGGTTGTAGTTTCCTCATGCAAGGTTGCA
1 -GGA-TCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * ** * **
8169 GGAACTGTTGTAGCTTCCTCATGCAAAATTGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * **
8202 GGTTCGGTTGTAGTTTCCTCATGCAAGGTTGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * **
8235 GGTTCAGTTGTAGTTTCCTCGTGCAAGGTTGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * **
8268 GGTTCAGTTGTAGTTTCCTCTTGCAAGGTTGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * ** * **
8301 GGTTCAGTTGTAGTTTCCTCGTGTGAGGTTGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * **
8334 GGTTCAGTTGTAGTTTCCTCGTGCAAGGTTGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * **
8367 GGTTCAGTTGTAGTTTCCTCGTGCAAGGTTGCC
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * *
8400 GGTTCAGTTGCAGTTTCCTCATGCAAGGTTGTG
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
8433 GGATCAGTTG
1 GGATCAGTTG
8443 TCGCTTCCAC
Statistics
Matches: 451, Mismatches: 75, Indels: 24
0.82 0.14 0.04
Matches are distributed among these distances:
32 8 0.02
33 433 0.96
34 8 0.02
35 2 0.00
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.33
Consensus pattern (33 bp):
GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
Found at i:8440 original size:66 final size:66
Alignment explanation
Indices: 7877--8443 Score: 512
Period size: 66 Copynumber: 8.6 Consensus size: 66
7867 TCATTGGATT
* * ** * * * * * ** *
7877 AGTTGGAGTTTCCTCATGCAAGGTGGTGGGGTCAGATGGAGTTTCCTCATGCAAGGTGGTGGGAT
1 AGTTGTAGTTTCCTCATGCAAGGTTGCAGGATCAGTTGTAGTTTCCTCGTGCAAGGTTGCAGGTT
7942 C
66 C
** * ** * *
7943 AGTTGTAGTTTCCTCACCCAGAGAAG-TG--GGATCAGTTGGAGTTTCCTCGCCCAAAGTGGCAG
1 AGTTGTAGTTTCCTCATGCA-AG--GTTGCAGGATCAGTTGTAGTTTCCTCGTGCAAGGTTGCAG
**
8005 AATC
63 GTTC
* * ** * ** * * * ** *
8009 ATTTGGAGTTTCCTCACCCAATGTTGGGGGATCAGTTGGAGTTTCCTTGCT-CAATGTTGGGGGA
1 AGTTGTAGTTTCCTCATGCAAGGTTGCAGGATCAGTTGTAGTTTCCTCG-TGCAAGGTTGCAGGT
8073 TC
65 TC
* * * * * * ** *
8075 AGTTGTAGCTTCCTCATGCAAGGTTGCAGGAACTGTTGCAGCTTCCTCATGCAAAATTGCAGATT
1 AGTTGTAGTTTCCTCATGCAAGGTTGCAGGATCAGTTGTAGTTTCCTCGTGCAAGGTTGCAGGTT
8140 C
66 C
* * * * * **
8141 GGTTGTAGTTTCCTCATGCAAGGTTGCAGGAACTGTTGTAGCTTCCTCATGCAAAATTGCAGGTT
1 AGTTGTAGTTTCCTCATGCAAGGTTGCAGGATCAGTTGTAGTTTCCTCGTGCAAGGTTGCAGGTT
8206 C
66 C
* *
8207 GGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGTAGTTTCCTCGTGCAAGGTTGCAGGTT
1 AGTTGTAGTTTCCTCATGCAAGGTTGCAGGATCAGTTGTAGTTTCCTCGTGCAAGGTTGCAGGTT
8272 C
66 C
* * **
8273 AGTTGTAGTTTCCTCTTGCAAGGTTGCAGGTTCAGTTGTAGTTTCCTCGTGTGAGGTTGCAGGTT
1 AGTTGTAGTTTCCTCATGCAAGGTTGCAGGATCAGTTGTAGTTTCCTCGTGCAAGGTTGCAGGTT
8338 C
66 C
* * *
8339 AGTTGTAGTTTCCTCGTGCAAGGTTGCAGGTTCAGTTGTAGTTTCCTCGTGCAAGGTTGCCGGTT
1 AGTTGTAGTTTCCTCATGCAAGGTTGCAGGATCAGTTGTAGTTTCCTCGTGCAAGGTTGCAGGTT
8404 C
66 C
* **
8405 AGTTGCAGTTTCCTCATGCAAGGTTGTGGGATCAGTTGT
1 AGTTGTAGTTTCCTCATGCAAGGTTGCAGGATCAGTTGT
8444 CGCTTCCACA
Statistics
Matches: 426, Mismatches: 67, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
63 1 0.00
64 2 0.00
65 2 0.00
66 417 0.98
67 2 0.00
68 1 0.00
69 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.33
Consensus pattern (66 bp):
AGTTGTAGTTTCCTCATGCAAGGTTGCAGGATCAGTTGTAGTTTCCTCGTGCAAGGTTGCAGGTT
C
Found at i:8440 original size:99 final size:99
Alignment explanation
Indices: 7872--8443 Score: 497
Period size: 99 Copynumber: 5.8 Consensus size: 99
7862 TAAGGTCATT
* * * ** * * * * *
7872 GGATTAGTTGGAGTTTCCTCATGCAAGGTGGTGGGGTCAGATGGAGTTTCCTCATGCAAGGTGGT
1 GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGCAGTTTCCTCATGCAAGGTTGC
***
7937 GGGATCAGTTGTAGTTTCCTCACCCAGAGAAG-TG--
66 GGGATCAGTTGTAGTTTCCTCGTGCA-AG--GTTGCA
* *** * * ** * * ** * *
7971 GGATCAGTTGGAGTTTCCTCGCCCAAAGTGGCAGAATCATTTGGAGTTTCCTCACCCAATGTTGG
1 GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGCAGTTTCCTCATGCAAGGTTGC
* * * **
8036 GGGATCAGTTGGAGTTTCCTTGCT-CAATGTTGGG
66 GGGATCAGTTGTAGTTTCCTCG-TGCAAGGTTGCA
* ** * * **
8070 GGATCAGTTGTAGCTTCCTCATGCAAGGTTGCAGGAACTGTTGCAGCTTCCTCATGCAAAATTGC
1 GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGCAGTTTCCTCATGCAAGGTTGC
* * *
8135 -AGATTCGGTTGTAGTTTCCTCATGCAAGGTTGCA
66 GGGA-TCAGTTGTAGTTTCCTCGTGCAAGGTTGCA
* * * ** * *
8169 GGAACTGTTGTAGCTTCCTCATGCAAAATTGCAGGTTCGGTTGTAGTTTCCTCATGCAAGGTTGC
1 GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGCAGTTTCCTCATGCAAGGTTGC
* *
8234 AGGTTCAGTTGTAGTTTCCTCGTGCAAGGTTGCA
66 GGGATCAGTTGTAGTTTCCTCGTGCAAGGTTGCA
* * * * **
8268 GGTTCAGTTGTAGTTTCCTCTTGCAAGGTTGCAGGTTCAGTTGTAGTTTCCTCGTGTGAGGTTGC
1 GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGCAGTTTCCTCATGCAAGGTTGC
* *
8333 AGGTTCAGTTGTAGTTTCCTCGTGCAAGGTTGCA
66 GGGATCAGTTGTAGTTTCCTCGTGCAAGGTTGCA
* * * *
8367 GGTTCAGTTGTAGTTTCCTCGTGCAAGGTTGCCGGTTCAGTTGCAGTTTCCTCATGCAAGGTTGT
1 GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGCAGTTTCCTCATGCAAGGTTGC
8432 GGGATCAGTTGT
66 GGGATCAGTTGT
8444 CGCTTCCACA
Statistics
Matches: 384, Mismatches: 82, Indels: 14
0.80 0.17 0.03
Matches are distributed among these distances:
96 1 0.00
97 2 0.01
98 4 0.01
99 376 0.98
100 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.33
Consensus pattern (99 bp):
GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGCAGTTTCCTCATGCAAGGTTGC
GGGATCAGTTGTAGTTTCCTCGTGCAAGGTTGCA
Found at i:8642 original size:33 final size:33
Alignment explanation
Indices: 8605--8680 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
8595 ACAGAATAGG
*
8605 TAGGAGTTTCTTCAGCCAAGGTTGTGGAAATGC
1 TAGGAGTTTCTTCAGCCAAGGTTGCGGAAATGC
*
8638 TAGGAGTTTCTTCAGCCAAGGTTGCGGGAATGC
1 TAGGAGTTTCTTCAGCCAAGGTTGCGGAAATGC
8671 TAGGAGTTTC
1 TAGGAGTTTC
8681 AGCACTCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (33 bp):
TAGGAGTTTCTTCAGCCAAGGTTGCGGAAATGC
Found at i:8691 original size:33 final size:33
Alignment explanation
Indices: 8605--8702 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 33
8595 ACAGAATAGG
** *
8605 TAGGAGTTTCTTCAGCCAAGGTTGTGGAAATGC
1 TAGGAGTTTCAGCAGCCAAGGTTGTGGGAATGC
** *
8638 TAGGAGTTTCTTCAGCCAAGGTTGCGGGAATGC
1 TAGGAGTTTCAGCAGCCAAGGTTGTGGGAATGC
*
8671 TAGGAGTTTCAGCA-CTCAAGGCTGTGGGAATG
1 TAGGAGTTTCAGCAGC-CAAGGTTGTGGGAATG
8703 GTTGAAGTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 1 0.02
33 57 0.98
ACGTcount: A:0.23, C:0.16, G:0.33, T:0.28
Consensus pattern (33 bp):
TAGGAGTTTCAGCAGCCAAGGTTGTGGGAATGC
Found at i:18908 original size:21 final size:20
Alignment explanation
Indices: 18882--18928 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
18872 ATCGAAAAGG
18882 AAAAAAAAAT-CAAGGACCTT
1 AAAAAAAAATGCAAGG-CCTT
18902 AAAAAAAAATGCAAGGCCTT
1 AAAAAAAAATGCAAGGCCTT
18922 AAAAAAA
1 AAAAAAA
18929 TAATAAGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.64, C:0.13, G:0.11, T:0.13
Consensus pattern (20 bp):
AAAAAAAAATGCAAGGCCTT
Found at i:22703 original size:65 final size:65
Alignment explanation
Indices: 22617--22778 Score: 243
Period size: 65 Copynumber: 2.5 Consensus size: 65
22607 TATGTAATTG
* *
22617 AAAACGCATAAAAAGAGAATATTCGAATTATTCGAATTAATCCAACAATAGTGAGTCAATAATAA
1 AAAACGCATGAAAAGAGAATATTCGAATTATTCGAATTAATCCAACAATAGTGAGTCAACAATAA
* * * * * *
22682 AAAATGCGTGAAAAGAGAATATTCGAATGATTCGAGTTAATCCCACAATAGTGAGTTAACAATAA
1 AAAACGCATGAAAAGAGAATATTCGAATTATTCGAATTAATCCAACAATAGTGAGTCAACAATAA
*
22747 AAAACGCATGAAAGGAGAATATTCGAATTATT
1 AAAACGCATGAAAAGAGAATATTCGAATTATT
22779 ATAGAAGACA
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 85 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.25
Consensus pattern (65 bp):
AAAACGCATGAAAAGAGAATATTCGAATTATTCGAATTAATCCAACAATAGTGAGTCAACAATAA
Found at i:28913 original size:29 final size:33
Alignment explanation
Indices: 28871--28948 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
28861 GCCCCTGTTA
28871 AGAATTGTTGAGAT-TTTTTT-TTT-G-GCAAC
1 AGAATTGTTGAGATCTTTTTTCTTTGGCGCAAC
*
28900 AGAATTGTTGAGATCTTTTTTCTTTGGCGCCAC
1 AGAATTGTTGAGATCTTTTTTCTTTGGCGCAAC
28933 AGAATTGTTGAGATCT
1 AGAATTGTTGAGATCT
28949 AAATGGACCT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
29 14 0.32
30 6 0.14
31 3 0.07
32 1 0.02
33 20 0.45
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.44
Consensus pattern (33 bp):
AGAATTGTTGAGATCTTTTTTCTTTGGCGCAAC
Found at i:31605 original size:178 final size:177
Alignment explanation
Indices: 31294--31630 Score: 480
Period size: 178 Copynumber: 1.9 Consensus size: 177
31284 TTCCACCATA
* * * *
31294 AGCACAAATTATGTAATATTAAGCAGACCGTCTATTTCCGCTAACCAAAATAACTAATTCTTTGG
1 AGCACAAATTATATAATATTAAGCAGACCGTCTATTCCCGCTAACCAAAACAACAAATTCTTTGG
* **
31359 AAGTATTTTTATACCTTGAACATTAAATTTAGTTTTTGAGTCCTTCATGAAAGTTGTAGATCATG
66 AAGTATTTTTATACCTTGAACATTAAATTTAGTTTTCGAAACCTTCATGAAAGTTGTAGATCATG
*
31424 GAACAACCTTTCAAGAGACACTTGAATCATCTCAATCAAACATCTGG
131 GAACAACCTTTCAAGAGACACTTAAATCATCTCAATCAAACATCTGG
** * * *
31471 AGCA-AAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTTTG
1 AGCACAAA-TTATATAATATTAAGCAGACCGTCTATTCCCGCTAACCAAAACAACAAATTCTTTG
*
31535 GAAGTATTTTTGAT-TCTTGAAACATTAAATTTAGTTTTCGAAACCTTCATGAAAGTTGTAGATC
65 GAAGTATTTTT-ATACCTTG-AACATTAAATTTAGTTTTCGAAACCTTCATGAAAGTTGTAGATC
* * *
31599 ATGGAACAATCTTTGAATAGACACTTAAATCA
128 ATGGAACAACCTTTCAAGAGACACTTAAATCA
31631 CTTTAATCAG
Statistics
Matches: 140, Mismatches: 17, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
176 3 0.02
177 66 0.47
178 71 0.51
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (177 bp):
AGCACAAATTATATAATATTAAGCAGACCGTCTATTCCCGCTAACCAAAACAACAAATTCTTTGG
AAGTATTTTTATACCTTGAACATTAAATTTAGTTTTCGAAACCTTCATGAAAGTTGTAGATCATG
GAACAACCTTTCAAGAGACACTTAAATCATCTCAATCAAACATCTGG
Found at i:31876 original size:12 final size:12
Alignment explanation
Indices: 31859--31883 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31849 TATTCAGTAT
31859 TGTTTTTTATAA
1 TGTTTTTTATAA
31871 TGTTTTTTATAA
1 TGTTTTTTATAA
31883 T
1 T
31884 ATCATGCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TGTTTTTTATAA
Done.