Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019378.1 Corchorus olitorius cultivar O-4 contig19411, 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: 17812
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1731 original size:22 final size:22
Alignment explanation
Indices: 1679--1908 Score: 155
Period size: 22 Copynumber: 10.5 Consensus size: 22
1669 TAAGGAGTAC
* *
1679 CAAAATTTGATAGA-AAGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
1700 C-AAATCTCATAGAGTGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * *
1721 CGAAATTTCATAAAGATCAGATTAT
1 CAAAATTTCAT--AGA-GAGGTTAT
*
1746 CAAAATTT-ATA-AGAAGATTAT
1 CAAAATTTCATAGAG-AGGTTAT
* * ***
1767 CAAAATTTTATAGTGTTATTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
1789 CAAAATTTCAAAGCGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * *
1811 CAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGA-GAGGTTAT
* * *
1833 CAAAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAGAGAGGTTAT
*
1855 CAAAATTTTATAGAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
1877 TAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
*
1899 CAAATTTTCA
1 CAAAATTTCA
1909 AAATGTGATT
Statistics
Matches: 161, Mismatches: 38, Indels: 19
0.74 0.17 0.09
Matches are distributed among these distances:
20 10 0.06
21 23 0.14
22 109 0.68
23 2 0.01
24 5 0.03
25 12 0.07
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGGTTAT
Found at i:1832 original size:44 final size:45
Alignment explanation
Indices: 1696--1932 Score: 202
Period size: 44 Copynumber: 5.4 Consensus size: 45
1686 TGATAGAAAG
* * * *
1696 TTATC-AAATCTCAT-AGAGTGGTTATCGAAATTTCATAAAGATCAGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATG-T--GA
* * * *
1742 TTATCAAAATTT-ATAAGA-AGATTATCAAAATTTTATAGTGTTA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* *
1785 TTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * * *
1829 TTATCAAAATTTCAT-AGAGGGGTCAACAAAATTTTATAGA-GAGG
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATA-ATGTGA
* * *
1873 TTATTAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
*
1917 TTACCAAAATTTCATA
1 TTATCAAAATTTCATA
1933 GTGGTATTTT
Statistics
Matches: 150, Mismatches: 33, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
43 17 0.11
44 99 0.66
45 3 0.02
46 23 0.15
47 8 0.05
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (45 bp):
TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
Found at i:1882 original size:88 final size:88
Alignment explanation
Indices: 1767--1933 Score: 228
Period size: 88 Copynumber: 1.9 Consensus size: 88
1757 AGAAGATTAT
* ** * *
1767 CAAAATTTTATAGTGTTATTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTTATAGAGAGATTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGATT
*
1831 ATCAAAATTTCATAGAGGGGTCAA
65 ACCAAAATTTCATAGAGGGGTCAA
* * * *
1855 CAAAATTTTATAGAGAGGTTATTAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
1920 CCAAAATTTCATAG
66 CCAAAATTTCATAG
1934 TGGTATTTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
88 66 0.97
89 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (88 bp):
CAAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CCAAAATTTCATAGAGGGGTCAA
Found at i:2066 original size:22 final size:22
Alignment explanation
Indices: 1985--2594 Score: 210
Period size: 22 Copynumber: 28.0 Consensus size: 22
1975 ACCAAATTAG
* * *
1985 GAAGGTTATTAAACTTTTATTAT
1 GAAGGTTATCAAAATTTCA-TAT
*
2008 GAA-GTTATCAAAATTT--TAG
1 GAAGGTTATCAAAATTTCATAT
* *
2027 GCAGGATATCAAAATTTCATAT
1 GAAGGTTATCAAAATTTCATAT
2049 GAAGGTTATCAAAATTTCATAGT
1 GAAGGTTATCAAAATTTCATA-T
** *
2072 TTA-GTTTTCAAAATTTCATA-
1 GAAGGTTATCAAAATTTCATAT
2092 GAAGGGTTATCAAAATTTCATA-
1 GAA-GGTTATCAAAATTTCATAT
* * * *
2114 GTATGTAGATCAAAATTTCATAG
1 GAAGGT-TATCAAAATTTCATAT
* * *
2137 GGAGATTAACAAAATTTCATAAT
1 GAAGGTTATCAAAATTTCAT-AT
** *
2160 G-AGGTTATCAAAAAGTCATAG
1 GAAGGTTATCAAAATTTCATAT
*
2181 GGAGGTTATCAAAA--T--T-T
1 GAAGGTTATCAAAATTTCATAT
* * *
2198 GTA-GTTATCAAGATTTCATAA
1 GAAGGTTATCAAAATTTCATAT
* * * *
2219 GGAGATTATCAAAATTTTATAG
1 GAAGGTTATCAAAATTTCATAT
* * *
2241 GGAGGTTCATCAAAATTTTATAG
1 GAAGGTT-ATCAAAATTTCATAT
*
2264 GAAGATTTATCAAAATTTCATA-
1 GAAG-GTTATCAAAATTTCATAT
* * *
2286 GCGAGATTATCACAATTTCATAGT
1 G-AAGGTTATCAAAATTTCATA-T
* *
2310 G-TGAG-TATCAAAATTTCAGATT
1 GAAG-GTTATCAAAATTTCATA-T
* * *
2332 G-TGATTA-CTAACAA-ATCATAT
1 GAAGGTTATC-AA-AATTTCATAT
* * * *
2353 GAAGGTTTTTAAATTTTCATAAC
1 GAAGGTTATCAAAATTTCAT-AT
* * * *
2376 G-TGGTTATTAATATATCATAT
1 GAAGGTTATCAAAATTTCATAT
* * *
2397 GGAGGTTATCAACATCTCATAGT
1 GAAGGTTATCAAAATTTCATA-T
**
2420 GTTGGTTATCAAAATTTCAT-T
1 GAAGGTTATCAAAATTTCATAT
*
2441 GGGAA-GTTATCAAAATTTAATAGT
1 --GAAGGTTATCAAAATTTCATA-T
* * *
2465 G-AGGTCT-TCAAAATTCCTTAG
1 GAAGGT-TATCAAAATTTCATAT
* * *
2486 GGAGGTTAACAAAATTTCATAA
1 GAAGGTTATCAAAATTTCATAT
* * *
2508 GAAGGTT-TAAAAAATTTTATAA
1 GAAGGTTAT-CAAAATTTCATAT
* * * *
2530 AAAGGTTCTCGAAATTCCATA-
1 GAAGGTTATCAAAATTTCATAT
** * *
2551 GTATCGTTATTAAAATTTCATAG
1 G-AAGGTTATCAAAATTTCATAT
*
2574 GAAGATTATCAAAATTTCATA
1 GAAGGTTATCAAAATTTCATA
2595 AGGAGATTAT
Statistics
Matches: 440, Mismatches: 104, Indels: 87
0.70 0.16 0.14
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 2 0.00
19 4 0.01
20 15 0.03
21 16 0.04
22 320 0.73
23 68 0.15
24 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
GAAGGTTATCAAAATTTCATAT
Found at i:2192 original size:66 final size:65
Alignment explanation
Indices: 2033--2327 Score: 248
Period size: 66 Copynumber: 4.5 Consensus size: 65
2023 TTAGGCAGGA
* * * *
2033 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAGAAG-G
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAG-GTAGTTATCAAAATTTCATA-AAGAG
2097 GT
64 GT
* * * * * *
2099 TATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAG
1 TATCAAAATTTCATAGGGAGGT-TATCAAAATTTCATAGGTAG-TTATCAAAATTTCATAAAGAG
2163 GT
64 GT
** * * *
2165 TATCAAAAAGTCATAGGGAGGTTATCAAAA-TT--T--GTAGTTATCAAGATTTCATAAGGAGAT
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGTAGTTATCAAAATTTCATAAAGAGGT
* * * **
2225 TATCAAAATTTTATAGGGAGGTTCATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGA
1 TATCAAAATTTCATAGGGAGGTT-ATCAAAATTTCATAGGTAG--TTATCAAAATTTCATAAAGA
*
2290 GAT
63 GGT
*
2293 TATCACAATTTCATAGTGTGA-G-TATCAAAATTTCA
1 TATCAAAATTTCATAG-G-GAGGTTATCAAAATTTCA
2328 GATTGTGATT
Statistics
Matches: 187, Mismatches: 28, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
60 39 0.21
61 10 0.05
62 2 0.01
63 1 0.01
64 1 0.01
65 10 0.05
66 70 0.37
67 15 0.08
68 35 0.19
69 2 0.01
70 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (65 bp):
TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGTAGTTATCAAAATTTCATAAAGAGGT
Found at i:2601 original size:22 final size:22
Alignment explanation
Indices: 2557--2609 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
2547 CATAGTATCG
*
2557 TTATTAAAATTTCATAGGAAGA
1 TTATAAAAATTTCATAGGAAGA
*
2579 TTATCAAAATTTCATAAGG-AGA
1 TTATAAAAATTTCAT-AGGAAGA
2601 TTATAAAAA
1 TTATAAAAA
2610 GTAGTGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (22 bp):
TTATAAAAATTTCATAGGAAGA
Found at i:9967 original size:11 final size:12
Alignment explanation
Indices: 9950--9976 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9940 ATGTGATGCC
9950 AAAAAAAAAAAG
1 AAAAAAAAAAAG
9962 AAAAAAAAAAAG
1 AAAAAAAAAAAG
9974 AAA
1 AAA
9977 CCCATCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:11704 original size:13 final size:13
Alignment explanation
Indices: 11686--11714 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
11676 AAAATATATC
11686 ATAAGATAAAATT
1 ATAAGATAAAATT
11699 ATAAGATAAAATT
1 ATAAGATAAAATT
11712 ATA
1 ATA
11715 GAATGTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (13 bp):
ATAAGATAAAATT
Found at i:11807 original size:21 final size:21
Alignment explanation
Indices: 11781--11826 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
11771 GTATGTTTCC
11781 TTTTTTTATTCATCTTTTAGA
1 TTTTTTTATTCATCTTTTAGA
11802 TTTTTTTATTCATCTTTTAGA
1 TTTTTTTATTCATCTTTTAGA
11823 TTTT
1 TTTT
11827 ATAAGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTTTTATTCATCTTTTAGA
Found at i:17638 original size:31 final size:31
Alignment explanation
Indices: 17595--17659 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
17585 ATACTAATTA
* *
17595 ATAATAATAGGTCTCATACTACATATTATGC
1 ATAAGAATAGGTCTCATACTACATATTATAC
17626 ATAAGAATAGGTCTCATACTACATATTATAC
1 ATAAGAATAGGTCTCATACTACATATTATAC
17657 ATA
1 ATA
17660 TCCAATATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (31 bp):
ATAAGAATAGGTCTCATACTACATATTATAC
Done.