Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018932.1 Corchorus olitorius cultivar O-4 contig18965, 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: 35389
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5977 original size:31 final size:31
Alignment explanation
Indices: 5927--6012 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 31
5917 GTGTCCGACG
* * *
5927 ATGGCATGCCACGTGTACCAAAAAGCGACAT
1 ATGGCACGCCATGTGTACCAAAAAGCGACAC
* * *
5958 GTGGCACGCCATGTATACCAAAAAGTGACAC
1 ATGGCACGCCATGTGTACCAAAAAGCGACAC
**
5989 ATATCACGCCATGTGTACCAAAAA
1 ATGGCACGCCATGTGTACCAAAAA
6013 AGTGATCATG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (31 bp):
ATGGCACGCCATGTGTACCAAAAAGCGACAC
Found at i:6031 original size:21 final size:20
Alignment explanation
Indices: 5998--6037 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5988 CATATCACGC
5998 CATGTGTACCAAAAAAGTGAT
1 CATGTGTACC-AAAAAGTGAT
**
6019 CATGTGTTTCAAAAAGTGA
1 CATGTGTACCAAAAAGTGA
6038 CACGTGTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (20 bp):
CATGTGTACCAAAAAGTGAT
Found at i:12493 original size:25 final size:25
Alignment explanation
Indices: 12454--12512 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
12444 ACCCTCAACC
* *
12454 AAACTCAATCAAAAT-CGCAAGAACA
1 AAACTCAAACAAAATCCCCAA-AACA
*
12479 AAACTCAAACGAAATCCCCAAAACA
1 AAACTCAAACAAAATCCCCAAAACA
*
12504 AAACCCAAA
1 AAACTCAAA
12513 TCAGCTTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.58, C:0.29, G:0.05, T:0.08
Consensus pattern (25 bp):
AAACTCAAACAAAATCCCCAAAACA
Found at i:15468 original size:31 final size:30
Alignment explanation
Indices: 15370--15476 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 30
15360 ATTGACACAG
* *
15370 GGCCCTTATTTGAGCATTTTCGGTAACGTTA
1 GGCCCTTATTTGAGCATTTT-GGAAACATTA
* ** * * **
15401 GGCCCTTATTTGACCAAATT-AAAAGATCG
1 GGCCCTTATTTGAGCATTTTGGAAACATTA
15430 GGCCCTTATTTGAGCATTTTGGCAAACATTA
1 GGCCCTTATTTGAGCATTTTGG-AAACATTA
15461 GGCCCTTATTTGAGCA
1 GGCCCTTATTTGAGCA
15477 ATTAGCCTTG
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
29 20 0.34
31 38 0.66
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (30 bp):
GGCCCTTATTTGAGCATTTTGGAAACATTA
Found at i:15577 original size:24 final size:24
Alignment explanation
Indices: 15528--15574 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
15518 ATCTCTTATG
15528 TTTTTCTTTTGAACAAAATAATCC
1 TTTTTCTTTTGAACAAAATAATCC
* *
15552 TTTTT-TTTTGGACAAATTAATCC
1 TTTTTCTTTTGAACAAAATAATCC
15575 CTTACGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (24 bp):
TTTTTCTTTTGAACAAAATAATCC
Found at i:15852 original size:32 final size:32
Alignment explanation
Indices: 15798--15861 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
15788 GCCCTTTGCG
* *
15798 TCAGGGGGCAAATTGTCTTTGAATTTGGAAGT
1 TCAGGGGGCAAACTGTCTTTGAATTTGCAAGT
*
15830 TCAGGAGGGCTAACTGTC-TTGAATTTGCAAGT
1 TCAGG-GGGCAAACTGTCTTTGAATTTGCAAGT
15862 CTAGGGTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.33
Consensus pattern (32 bp):
TCAGGGGGCAAACTGTCTTTGAATTTGCAAGT
Found at i:25732 original size:6 final size:6
Alignment explanation
Indices: 25721--25760 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
25711 CCACAGTAAA
25721 TATATC TATATC TATATC TATATC TATATC TATA-C TATAT
1 TATATC TATATC TATATC TATATC TATATC TATATC TATAT
25761 ATAAAAGTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:26816 original size:20 final size:20
Alignment explanation
Indices: 26779--26817 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
26769 TACTATTATT
26779 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
26799 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
26818 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:27046 original size:22 final size:21
Alignment explanation
Indices: 26994--27208 Score: 115
Period size: 22 Copynumber: 9.7 Consensus size: 21
26984 CTGTATGGTA
* *
26994 ATCAAAATTTTATAAGATGGTT
1 ATCAAAATTTCATAGGA-GGTT
* *
27016 ATTATAATTTCATGAGGAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* *
27038 ATCAAAATTCCATAGTGTGGTT
1 ATCAAAATTTCATAG-GAGGTT
* * *
27060 ACCAAAATCTCATATGGAAGTT
1 ATCAAAATTTCATA-GGAGGTT
* *
27082 ATAAAAATTTCATGGGAAGGTT
1 ATCAAAATTTCATAGG-AGGTT
*
27104 ATCAAAATTTCATAGTGTGGTT
1 ATCAAAATTTCATAG-GAGGTT
* * * *
27126 ACCAAACTTTTATAGAATTGGGTT
1 ATCAAAATTTCATAGGA---GGTT
** *
27150 ATTTAAATTTCTTAGGAAGGTT
1 ATCAAAATTTCATAGG-AGGTT
** *
27172 ATTGAAATTTCATAGTGTGGTT
1 ATCAAAATTTCATAG-GAGGTT
* *
27194 ATCACAATTTTATAG
1 ATCAAAATTTCATAG
27209 AAATGTTATC
Statistics
Matches: 143, Mismatches: 40, Indels: 20
0.70 0.20 0.10
Matches are distributed among these distances:
21 4 0.03
22 119 0.83
23 6 0.04
24 13 0.09
25 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.39
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAGGTT
Found at i:27325 original size:22 final size:22
Alignment explanation
Indices: 27226--27641 Score: 134
Period size: 22 Copynumber: 18.6 Consensus size: 22
27216 ATCAAAGAAA
* *
27226 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGGGAGG
*
27248 TTAT-AAGAATTTCATA-GTATGG
1 TTATCAA-AATTTCATAGGGA-GG
* * * *
27270 TTAACAAAATTTCATATGAAGA
1 TTATCAAAATTTCATAGGGAGG
* *
27292 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGGGAGG
* *
27314 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGGGAGG
** * *
27336 TTATCAAAATTTTTTTAGTGTGG
1 TTATCAAAA-TTTCATAGGGAGG
* *
27359 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAGGGAGG
* **
27381 TTATAAAAGTCTCAATTTCATTAGGA-G
1 TTAT-CAA-----AATTTCATAGGGAGG
* * *
27408 -TACCAAAATTTGAT-GGAAGG
1 TTATCAAAATTTCATAGGGAGG
*** * * * *
27428 TTATTTTAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGGGAGG
* * *
27450 TTATCGAAATTTCATAGAGATCGAA
1 TTATCAAAATTTCATAGGGA--G-G
* *
27475 TTATCAAAATTT-ATAGGAAGA
1 TTATCAAAATTTCATAGGGAGG
* **
27496 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGGGAGG
**
27518 TTATCAAAATTTC-TAATCGAGG
1 TTATCAAAATTTCAT-AGGGAGG
* * * *
27540 TTATCAAAATTACAAAATTGTA--
1 TTATCAAAATTTC-ATA-GGGAGG
27562 TTATCAAAATTTCATAGAGG-GG
1 TTATCAAAATTTCATAG-GGAGG
* * * *
27584 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGGGAGG
** *
27606 TTATCAAAATTTCATAAAGATG
1 TTATCAAAATTTCATAGGGAGG
*
27628 TTATCAAATTTTCA
1 TTATCAAAATTTCA
27642 AAATGTGATT
Statistics
Matches: 289, Mismatches: 77, Indels: 56
0.68 0.18 0.13
Matches are distributed among these distances:
19 2 0.01
20 8 0.03
21 30 0.10
22 186 0.64
23 28 0.10
24 8 0.03
25 14 0.05
26 2 0.01
27 1 0.00
28 10 0.03
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGG
Found at i:27358 original size:23 final size:23
Alignment explanation
Indices: 27312--27374 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
27302 TTCATGGGGA
27312 GGTTATCAAAA-TTTCATAGTGT
1 GGTTATCAAAATTTTCATAGTGT
**
27334 GGTTATCAAAATTTTTTTAGTGT
1 GGTTATCAAAATTTTCATAGTGT
27357 GGTTATCAAAA-TTTCATA
1 GGTTATCAAAATTTTCATA
27375 TGAAGGTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 16 0.44
23 20 0.56
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (23 bp):
GGTTATCAAAATTTTCATAGTGT
Found at i:27498 original size:21 final size:23
Alignment explanation
Indices: 27448--27668 Score: 86
Period size: 22 Copynumber: 9.9 Consensus size: 23
27438 CTCATAGAGT
* * *
27448 GATTATCGAAATTTCATAGAGATC
1 GATTATCAAAATTTCATAGTGA-A
27472 GAATTATCAAAATTT-ATAG-GAA
1 G-ATTATCAAAATTTCATAGTGAA
**
27494 GATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAGTGAA
*
27517 G-TTATCAAAATTTC-TAATCG-A
1 GATTATCAAAATTTCATAGT-GAA
* * * *
27538 GGTTATCAAAATTACAAAATTG--
1 GATTATCAAAATTTC-ATAGTGAA
* * *
27560 TATTATCAAAATTTCATAGAG-G
1 GATTATCAAAATTTCATAGTGAA
* * * * *
27582 GGTCAACAAAATTTTATAGAG-A
1 GATTATCAAAATTTCATAGTGAA
* ** *
27604 GGTTATCAAAATTTCATAAAGAT
1 GATTATCAAAATTTCATAGTGAA
* * * *
27627 G-TTATCAAATTTTCAAAATG-T
1 GATTATCAAAATTTCATAGTGAA
*
27648 GATTACCAAAATTTCATAGTG
1 GATTATCAAAATTTCATAGTG
27669 GTATTTCTAG
Statistics
Matches: 154, Mismatches: 33, Indels: 22
0.74 0.16 0.11
Matches are distributed among these distances:
21 22 0.14
22 107 0.69
23 6 0.04
24 7 0.05
25 12 0.08
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (23 bp):
GATTATCAAAATTTCATAGTGAA
Found at i:27632 original size:66 final size:65
Alignment explanation
Indices: 27475--27641 Score: 155
Period size: 66 Copynumber: 2.5 Consensus size: 65
27465 AGAGATCGAA
* ** * * **
27475 TTATCAAAATTT-ATAGGAAGA-TTATCAAAATTTCATAGTGTTGTTATCAAAATTTCTAATCGA
1 TTATCAAAATTTCATA--AAGATTTATCAAAATTTCATAGAGGGGTCAACAAAATTTCTAAGAGA
27538 GG
64 GG
*
27540 TTATCAAAATTACA-AAATTG-TATTATCAAAATTTCATAGAGGGGTCAACAAAATTT-TATAGA
1 TTATCAAAATTTCATAAA--GAT-TTATCAAAATTTCATAGAGGGGTCAACAAAATTTCTA-AGA
27602 GAGG
62 GAGG
*
27606 TTATCAAAATTTCATAAAGATGTTATCAAATTTTCA
1 TTATCAAAATTTCATAAAGAT-TTATCAAAATTTCA
27642 AAATGTGATT
Statistics
Matches: 83, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
63 2 0.02
65 16 0.19
66 62 0.75
67 3 0.04
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.37
Consensus pattern (65 bp):
TTATCAAAATTTCATAAAGATTTATCAAAATTTCATAGAGGGGTCAACAAAATTTCTAAGAGAGG
Found at i:27796 original size:22 final size:22
Alignment explanation
Indices: 27752--28225 Score: 118
Period size: 22 Copynumber: 21.8 Consensus size: 22
27742 CGGAGTAATT
* *
27752 AAAATTTCA-A-GGAGGATATC
1 AAAATTTCATATGAAGGTTATC
*
27772 AAAATTTCTTATGAAGGTTATC
1 AAAATTTCATATGAAGGTTATC
** *
27794 AAAATTTCATAGTTTA-GTTTTC
1 AAAATTTCATA-TGAAGGTTATC
* *
27816 AAAATTTCATAAGAGGGTTATC
1 AAAATTTCATATGAAGGTTATC
* * * *
27838 AAAATCTCATA-GTATGTAGATC
1 AAAATTTCATATGAAGGT-TATC
* * * * *
27860 AAAATTTTATAGGGAGATTAAC
1 AAAATTTCATATGAAGGTTATC
* *
27882 AAATTTTCATAATG-AGATTATC
1 AAAATTTCAT-ATGAAGGTTATC
*
27904 AAACA-TTCATAGGGAA-GTTATC
1 AAA-ATTTCATA-TGAAGGTTATC
*
27926 AAAA--T--T-TGTA-GTTATC
1 AAAATTTCATATGAAGGTTATC
* * *
27942 AAGATTTCATAAGGAGGTTATC
1 AAAATTTCATATGAAGGTTATC
* * *
27964 AAAATTTTATAGGCAGGTTTATC
1 AAAATTTCATATGAAGG-TTATC
*
27987 AAAATTTCATA-GCGAGGTTATC
1 AAAATTTCATATG-AAGGTTATC
* * * * ***
28009 ACATTTTTATATTATTATTATC
1 AAAATTTCATATGAAGGTTATC
*
28031 AAAATTTCAGAGTGTAA--TTA-C
1 AAAATTTCATA-TG-AAGGTTATC
* * *
28052 TAACAA-TTCATATGGAGGTTTTT
1 -AA-AATTTCATATGAAGGTTATC
* * *
28075 AAATTTTCATAACG-TGGTTATC
1 AAAATTTCAT-ATGAAGGTTATC
* * *
28097 AATATATCATATGCAGGTTATC
1 AAAATTTCATATGAAGGTTATC
* * ** *
28119 AACATCTCATAGTGTTGGTCATC
1 AAAATTTCATA-TGAAGGTTATC
28142 AAAATTTCAT-TGGGAA-GTTATC
1 AAAATTTCATAT--GAAGGTTATC
28164 AAAATTTCATGATG-AGGTCT-TC
1 AAAATTTCAT-ATGAAGGT-TATC
*
28186 AAAATTCCTCA-A-GGAGGTTAAT-
1 AAAATT--TCATATGAAGGTT-ATC
*
28208 AAAATTTCATAAGAAGGT
1 AAAATTTCATATGAAGGT
28226 AAAAGAAATT
Statistics
Matches: 330, Mismatches: 81, Indels: 84
0.67 0.16 0.17
Matches are distributed among these distances:
16 11 0.03
18 2 0.01
20 14 0.04
21 19 0.06
22 229 0.69
23 50 0.15
24 5 0.02
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
AAAATTTCATATGAAGGTTATC
Found at i:27989 original size:23 final size:22
Alignment explanation
Indices: 27752--28009 Score: 123
Period size: 22 Copynumber: 12.0 Consensus size: 22
27742 CGGAGTAATT
*
27752 AAAATTTCA-AGG-AGGATATC
1 AAAATTTCATAGGCAGGTTATC
* * *
27772 AAAATTTCTTATGAAGGTTATC
1 AAAATTTCATAGGCAGGTTATC
** *
27794 AAAATTTCATAGTTTA-GTTTTC
1 AAAATTTCATAG-GCAGGTTATC
*
27816 AAAATTTCATAAG-AGGGTTATC
1 AAAATTTCATAGGCA-GGTTATC
* * * *
27838 AAAATCTCATA-GTATGTAGATC
1 AAAATTTCATAGGCAGGT-TATC
* * * *
27860 AAAATTTTATAGGGAGATTAAC
1 AAAATTTCATAGGCAGGTTATC
* * *
27882 AAATTTTCATAATG-AGATTATC
1 AAAATTTCAT-AGGCAGGTTATC
* *
27904 AAACA-TTCATAGGGAAGTTATC
1 AAA-ATTTCATAGGCAGGTTATC
*
27926 AAAA-TT--T--GTA-GTTATC
1 AAAATTTCATAGGCAGGTTATC
*
27942 AAGATTTCATAAGG-AGGTTATC
1 AAAATTTCAT-AGGCAGGTTATC
*
27964 AAAATTTTATAGGCAGGTTTATC
1 AAAATTTCATAGGCAGG-TTATC
27987 AAAATTTCATA-GCGAGGTTATC
1 AAAATTTCATAGGC-AGGTTATC
28009 A
1 A
28010 CATTTTTATA
Statistics
Matches: 183, Mismatches: 34, Indels: 40
0.71 0.13 0.16
Matches are distributed among these distances:
16 9 0.05
17 4 0.02
19 2 0.01
20 9 0.05
21 14 0.08
22 121 0.66
23 24 0.13
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAGGCAGGTTATC
Found at i:35001 original size:15 final size:16
Alignment explanation
Indices: 34981--35018 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
34971 CGTTCAAATG
34981 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
34996 TCGGGTCAATTCTGGGT
1 TCGGGTCAATT-TGGGT
35013 T-GGGTC
1 TCGGGTC
35019 GTTTTCGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Done.