Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007290.1 Corchorus capsularis cultivar CVL-1 contig07311, 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: 18156
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:8075 original size:26 final size:26
Alignment explanation
Indices: 8046--8095 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
8036 TTCAGTATGA
8046 TTAAGGAAAGTTAA-GAAAAGTAAGTC
1 TTAAGGAAA-TTAAGGAAAAGTAAGTC
* *
8072 TTAATGAAATTAAGGAAAATTAAG
1 TTAAGGAAATTAAGGAAAAGTAAG
8096 AAAAATCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.52, C:0.02, G:0.20, T:0.26
Consensus pattern (26 bp):
TTAAGGAAATTAAGGAAAAGTAAGTC
Found at i:8280 original size:37 final size:36
Alignment explanation
Indices: 8239--8446 Score: 170
Period size: 37 Copynumber: 5.6 Consensus size: 36
8229 GTCAAGGTAG
* *
8239 TTAATCCAGGGTAATTAAGTAAAAGCAGTCAAAGAAC
1 TTAATTCATGGTAATTAAGTAAAAGCAGT-AAAGAAC
* * *
8276 TTAATTCAT-ATAAATTAGGTAAAAACAGAAGTCAAA-AGAC
1 TTAATTCATGGT-AATTAAGT--AAA-AGCAGT-AAAGA-AC
* * * *
8316 TTAATTCATGGCAATTAAGTAAAAACGGTAAGAGGAC
1 TTAATTCATGGTAATTAAGTAAAAGCAGTAA-AGAAC
* * *
8353 TTAATTCATAGTAATTAAGTAAAAGCAGTTATAGGAC
1 TTAATTCATGGTAATTAAGTAAAAGCAG-TAAAGAAC
* *
8390 TTATTTCAGGGTAATTAAGTAAAAGCAGT-AAGATGAC
1 TTAATTCATGGTAATTAAGTAAAAGCAGTAAAGA--AC
8427 TTAATTCATGGTAATTAAGT
1 TTAATTCATGGTAATTAAGT
8447 GAAGATAAGC
Statistics
Matches: 136, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
35 2 0.01
36 4 0.03
37 94 0.69
38 5 0.04
39 4 0.03
40 27 0.20
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (36 bp):
TTAATTCATGGTAATTAAGTAAAAGCAGTAAAGAAC
Found at i:8332 original size:40 final size:40
Alignment explanation
Indices: 8265--8376 Score: 117
Period size: 40 Copynumber: 2.9 Consensus size: 40
8255 AAGTAAAAGC
* *
8265 AGTCAAAGAACTTAATTCATATAAATTAGGTAAAAACAGA
1 AGTCAAAGAACTTAATTCATAGAAATTAAGTAAAAACAGA
* *
8305 AGTCAAA-AGACTTAATTCATGGCAATTAAGTAAAAAC-G-
1 AGTCAAAGA-ACTTAATTCATAGAAATTAAGTAAAAACAGA
* *
8343 -GT-AAGAGGACTTAATTCATAGTAATTAAGTAAAA
1 AGTCAA-AGAACTTAATTCATAGAAATTAAGTAAAA
8377 GCAGTTATAG
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
36 2 0.03
37 27 0.44
39 2 0.03
40 31 0.50
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (40 bp):
AGTCAAAGAACTTAATTCATAGAAATTAAGTAAAAACAGA
Found at i:8421 original size:74 final size:76
Alignment explanation
Indices: 8239--8446 Score: 235
Period size: 74 Copynumber: 2.8 Consensus size: 76
8229 GTCAAGGTAG
* * *
8239 TTAATCCAGGGTAATTAAGTAAAAGCAGTCAA-AGAACTTAATTCATA-TAAATTAGGTAAAAAC
1 TTAATTCAGGGTAATTAAGTAAAAGCAGT-AAGAGGACTTAATTCATAGT-AATTAAGT-AAAAC
8302 AGAAGTCAAAAGAC
63 AGAAGTCAAAAGAC
* * * * *
8316 TTAATTCATGGCAATTAAGTAAAAACGGTAAGAGGACTTAATTCATAGTAATTAAGT-AAA-AGC
1 TTAATTCAGGGTAATTAAGTAAAAGCAGTAAGAGGACTTAATTCATAGTAATTAAGTAAAACAGA
* * *
8379 AGTTATAGGAC
66 AGTCAAAAGAC
* * *
8390 TTATTTCAGGGTAATTAAGTAAAAGCAGTAAGATGACTTAATTCATGGTAATTAAGT
1 TTAATTCAGGGTAATTAAGTAAAAGCAGTAAGAGGACTTAATTCATAGTAATTAAGT
8447 GAAGATAAGC
Statistics
Matches: 111, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
74 60 0.54
75 3 0.03
76 2 0.02
77 45 0.41
78 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (76 bp):
TTAATTCAGGGTAATTAAGTAAAAGCAGTAAGAGGACTTAATTCATAGTAATTAAGTAAAACAGA
AGTCAAAAGAC
Found at i:8676 original size:39 final size:38
Alignment explanation
Indices: 8475--9111 Score: 588
Period size: 39 Copynumber: 16.7 Consensus size: 38
8465 AATTGTAGAG
8475 GAAGGAAATTAGGTAAAGAAAAGACT-AGCTTAATTTC--
1 GAAGGAAATTAGGTAAAG-AAAGACTGA-CTTAATTTCAA
* *
8512 -AAGGAAATTAAGTAAA-AAAGACTGCCTTAATTTCAA
1 GAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAA
* *
8548 GAAAGGAAATTGGGTAAAAAGAAGACTGACTTAATTTC--
1 G-AAGGAAATTAGGTAAAGA-AAGACTGACTTAATTTCAA
* *
8586 -AAGGAAATTAGGTAAAAAGAATACTTG-CTTAATTTC--
1 GAAGGAAATTAGGTAAAGA-AAGAC-TGACTTAATTTCAA
8622 -AAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAA
1 GAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAA
* * * *
8659 GAAAGGAAATTAAGTAAAAAGAAGATTGGCTTAATTTC--
1 G-AAGGAAATTAGGTAAAGA-AAGACTGACTTAATTTCAA
* * *
8697 -AAGGAAATTAGGT-AA-AAAGACAGGCTTAATTTCAG
1 GAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAA
8732 GAAAGGAAATTAGGTAAAGAGAAGACTG-CTTAATTTC--
1 G-AAGGAAATTAGGTAAAGA-AAGACTGACTTAATTTCAA
* *
8769 -AAGGAAATTAGGTAAAAAGAAGACTGGCTTAATTTCAA
1 GAAGGAAATTAGGTAAAGA-AAGACTGACTTAATTTCAA
* *
8807 GGAAGGAAATTAGGTAAAAAAAGACTG-CTTAGTTTCAA
1 -GAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAA
* *
8845 GGAAGGAAATTAGGCAAAGAAAGACTGACTTAAGTTCAA
1 -GAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAA
*
8884 GGAAGGAAATTAGGTAAAGAAAGACTGAGGCACAGACTTAATTTCAG
1 -GAAGGAAATTAGGTAAAGAAAGACT--------GACTTAATTTCAA
* *
8931 GAAAGGAAATTAGGTAAAAAGAAGACTGGCTTAATTTC--
1 G-AAGGAAATTAGGTAAAGA-AAGACTGACTTAATTTCAA
** *
8969 -AAGGAAATTAGGTAAAGGTAGACTGGCTTAATTTCAA
1 GAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAA
* *
9006 GGAAGGAAATTAGGTAAAAAAAGACT-AGCTTTATTTCAA
1 -GAAGGAAATTAGGTAAAGAAAGACTGA-CTTAATTTCAA
*
9045 GGAAGGAAATTAGGCAAAGAAAGACTGACTTAATTTCAA
1 -GAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAA
9084 GAAAGGAAATTAGGTAAAGAAAGACTGA
1 G-AAGGAAATTAGGTAAAGAAAGACTGA
9112 GGCACATGCT
Statistics
Matches: 516, Mismatches: 40, Indels: 86
0.80 0.06 0.13
Matches are distributed among these distances:
33 15 0.03
34 19 0.04
35 56 0.11
36 100 0.19
37 15 0.03
38 52 0.10
39 158 0.31
40 66 0.13
46 1 0.00
47 28 0.05
48 6 0.01
ACGTcount: A:0.46, C:0.08, G:0.22, T:0.23
Consensus pattern (38 bp):
GAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAA
Found at i:9102 original size:200 final size:198
Alignment explanation
Indices: 8473--9142 Score: 853
Period size: 200 Copynumber: 3.5 Consensus size: 198
8463 TTAATTGTAG
* *
8473 AGGAAGGAAATTAGGTAAAGAAAAGACT-AGCTTAATTTC---AAGGAAATTAAGTAAA-AAAGA
1 AGGAAGGAAATTAGGCAAAG-AAAGACTGA-CTTAATTTCAAGAAGGAAATTAGGTAAAGAAAGA
* * *
8533 CT---G--C--CTTAATTTCAAGAAAGGAAATTGGGTAAAAAGAAGACTGACTTAATTTCAAGGA
64 CTGAGGCACAGCTTAATTTCAGGAAAGGAAATTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGA
* * * *
8591 AATTAGGTAAAAAGAATACTTGCTTAATTTC----AAGGAAATTAGGTAAAGAAAGACTGACTTA
129 AATTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGAAGGAAATTAGGTAAAAAAAGACTG-CTTT
8652 ATTTCA
193 ATTTCA
* * * * * *
8658 AGAAAGGAAATTAAGTAAAAAGAAGATTGGCTTAATTTC---AAGGAAATTAGGT-AA-AAAGAC
1 AGGAAGGAAATTAGGCAAAGA-AAGACTGACTTAATTTCAAGAAGGAAATTAGGTAAAGAAAGAC
*
8718 --A-G----GCTTAATTTCAGGAAAGGAAATTAGGTAAAGAGAAGACT-GCTTAATTTCAAGGAA
65 TGAGGCACAGCTTAATTTCAGGAAAGGAAATTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGAA
8775 ATTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGAAGGAAATTAGGTAAAAAAAGACTGC-TTAG
130 ATTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGAAGGAAATTAGGTAAAAAAAGACTGCTTTA-
8839 TTTCA
194 TTTCA
*
8844 AGGAAGGAAATTAGGCAAAGAAAGACTGACTTAAGTTCAAGGAAGGAAATTAGGTAAAGAAAGAC
1 AGGAAGGAAATTAGGCAAAGAAAGACTGACTTAATTTCAA-GAAGGAAATTAGGTAAAGAAAGAC
8909 TGAGGCACAGACTTAATTTCAGGAAAGGAAATTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGA
65 TGAGGCACAG-CTTAATTTCAGGAAAGGAAATTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGA
* *
8974 AATTAGGT-AAAGGTAGACTGGCTTAATTTCAAGGAAGGAAATTAGGTAAAAAAAGACTAGCTTT
129 AATTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGAAGGAAATTAGGTAAAAAAAGACT-GCTTT
9038 ATTTCA
193 ATTTCA
9044 AGGAAGGAAATTAGGCAAAGAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAGAC
1 AGGAAGGAAATTAGGCAAAGAAAGACTGACTTAATTTCAAG-AAGGAAATTAGGTAAAGAAAGAC
*
9109 TGAGGCACATGCTTAATTTCAGGGAAGGAAATTA
65 TGAGGCACA-GCTTAATTTCAGGAAAGGAAATTA
9143 AGTAGAATAA
Statistics
Matches: 431, Mismatches: 26, Indels: 41
0.87 0.05 0.08
Matches are distributed among these distances:
183 43 0.10
184 45 0.10
185 59 0.14
186 23 0.05
187 24 0.06
189 13 0.03
190 2 0.00
191 6 0.01
193 1 0.00
194 1 0.00
198 1 0.00
199 86 0.20
200 123 0.29
201 4 0.01
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (198 bp):
AGGAAGGAAATTAGGCAAAGAAAGACTGACTTAATTTCAAGAAGGAAATTAGGTAAAGAAAGACT
GAGGCACAGCTTAATTTCAGGAAAGGAAATTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGAAA
TTAGGTAAAAAGAAGACTGGCTTAATTTCAAGGAAGGAAATTAGGTAAAAAAAGACTGCTTTATT
TCA
Found at i:10558 original size:16 final size:16
Alignment explanation
Indices: 10526--10578 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
10516 GAACCCGAAT
*
10526 CCGAAAAAGCTCA-AAC
1 CCGAAAAA-ATCAGAAC
10542 CCGAAAAAATCAGAAC
1 CCGAAAAAATCAGAAC
* * *
10558 CCCAAAAAACCCGAAC
1 CCGAAAAAATCAGAAC
10574 CCGAA
1 CCGAA
10579 TTCGAATCCG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 3 0.10
16 28 0.90
ACGTcount: A:0.51, C:0.34, G:0.11, T:0.04
Consensus pattern (16 bp):
CCGAAAAAATCAGAAC
Found at i:10920 original size:29 final size:29
Alignment explanation
Indices: 10848--10928 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
10838 CCGGCTAAAT
* *
10848 GCTCAATTTTGTCCTAAACCTTTCACGGTCT
1 GCTCAATTTGGTCCTAAACCTTTCAC-G-CG
* *
10879 GCTCGATTTGGTCCTAAACCTTCTGAC-CG
1 GCTCAATTTGGTCCTAAACCTT-TCACGCG
10908 GCTCAATTTGGTCCTAAACCT
1 GCTCAATTTGGTCCTAAACCT
10929 ACGCGATTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
29 21 0.48
31 20 0.45
32 3 0.07
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.35
Consensus pattern (29 bp):
GCTCAATTTGGTCCTAAACCTTTCACGCG
Found at i:11762 original size:21 final size:21
Alignment explanation
Indices: 11737--11779 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
11727 TAACATAATG
11737 TTATAAAGAGACAAATAATCT
1 TTATAAAGAGACAAATAATCT
11758 TTATAAAGAGACAAATAATCT
1 TTATAAAGAGACAAATAATCT
11779 T
1 T
11780 GATTATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (21 bp):
TTATAAAGAGACAAATAATCT
Found at i:11792 original size:15 final size:15
Alignment explanation
Indices: 11772--11806 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
11762 AAAGAGACAA
11772 ATAATCTTGATTATT
1 ATAATCTTGATTATT
11787 ATAATCTTGATTATT
1 ATAATCTTGATTATT
11802 ATAAT
1 ATAAT
11807 AATTCAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (15 bp):
ATAATCTTGATTATT
Found at i:11830 original size:58 final size:58
Alignment explanation
Indices: 11766--11906 Score: 282
Period size: 58 Copynumber: 2.4 Consensus size: 58
11756 CTTTATAAAG
11766 AGACAAATAATCTTGATTATTATAATCTTGATTATTATAATAATTCAAAGTGGGGTAT
1 AGACAAATAATCTTGATTATTATAATCTTGATTATTATAATAATTCAAAGTGGGGTAT
11824 AGACAAATAATCTTGATTATTATAATCTTGATTATTATAATAATTCAAAGTGGGGTAT
1 AGACAAATAATCTTGATTATTATAATCTTGATTATTATAATAATTCAAAGTGGGGTAT
11882 AGACAAATAATCTTGATTATTATAA
1 AGACAAATAATCTTGATTATTATAA
11907 GTAACAGAAT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 83 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (58 bp):
AGACAAATAATCTTGATTATTATAATCTTGATTATTATAATAATTCAAAGTGGGGTAT
Found at i:11850 original size:15 final size:15
Alignment explanation
Indices: 11830--11864 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
11820 GTATAGACAA
11830 ATAATCTTGATTATT
1 ATAATCTTGATTATT
11845 ATAATCTTGATTATT
1 ATAATCTTGATTATT
11860 ATAAT
1 ATAAT
11865 AATTCAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (15 bp):
ATAATCTTGATTATT
Found at i:12603 original size:9 final size:9
Alignment explanation
Indices: 12589--12646 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
12579 TTGATAGATA
12589 ATGGAAATG
1 ATGGAAATG
12598 ATGGAAATG
1 ATGGAAATG
**
12607 GGGGAAATG
1 ATGGAAATG
*
12616 ATGGACATG
1 ATGGAAATG
* *
12625 CTGGACATG
1 ATGGAAATG
* *
12634 CTGGACATG
1 ATGGAAATG
12643 ATGG
1 ATGG
12647 CAACTTAGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.33, C:0.09, G:0.38, T:0.21
Consensus pattern (9 bp):
ATGGAAATG
Found at i:15041 original size:29 final size:29
Alignment explanation
Indices: 15003--15088 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 29
14993 GTTAAAAAAT
*
15003 TGAAAGGTTTAGGACCAAATTGAGC-CGG
1 TGAAAGGTTTAGGACCAAATTGAGCACCG
* * *
15031 TTAGAAGGTTTATGACCAAATCGAGCAGACCG
1 TGA-AAGGTTTAGGACCAAATTGAGC--ACCG
15063 TGAAAGGTTTAGGACCAAATTGAGCA
1 TGAAAGGTTTAGGACCAAATTGAGCA
15089 TTTAGCCCCC
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
28 2 0.04
29 21 0.45
31 20 0.43
32 4 0.09
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (29 bp):
TGAAAGGTTTAGGACCAAATTGAGCACCG
Found at i:15473 original size:16 final size:16
Alignment explanation
Indices: 15454--15490 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
15444 TTTTTTCAGA
*
15454 TTCGGGTTCGGTTTTT
1 TTCGGGTTCGGGTTTT
15470 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
*
15486 ATCGG
1 TTCGG
15491 ATTTTAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.03, C:0.14, G:0.35, T:0.49
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Done.