Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016622.1 Corchorus olitorius cultivar O-4 contig16655, 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: 11781
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Found at i:647 original size:9 final size:9
Alignment explanation
Indices: 629--666 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
619 TTAATTCATT
629 TAATTT-CA
1 TAATTTCCA
637 TAATTTCCA
1 TAATTTCCA
*
646 TAATTTCCT
1 TAATTTCCA
655 TAATTTCCA
1 TAATTTCCA
664 TAA
1 TAA
667 GTAATTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 6 0.22
9 21 0.78
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.47
Consensus pattern (9 bp):
TAATTTCCA
Found at i:2740 original size:14 final size:13
Alignment explanation
Indices: 2697--2743 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2687 TTTCCTTTAG
2697 TTTTGTTTTTAT-T
1 TTTTGTTTTT-TGT
* *
2710 TTTCGTATTTTGT
1 TTTTGTTTTTTGT
2723 TTTTGTTTTTGTGT
1 TTTTGTTTTT-TGT
2737 TTTTGTT
1 TTTTGTT
2744 AATTTTGCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 1 0.04
13 17 0.61
14 10 0.36
ACGTcount: A:0.04, C:0.02, G:0.15, T:0.79
Consensus pattern (13 bp):
TTTTGTTTTTTGT
Found at i:2743 original size:6 final size:6
Alignment explanation
Indices: 2697--2739 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
2687 TTTCCTTTAG
*
2697 TTTTGT TTTTAT TTTTCGT ATTTTGT TTTTGT TTTTGT GTTTT
1 TTTTGT TTTTGT TTTT-GT -TTTTGT TTTTGT TTTTGT -TTTT
2740 TGTTAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 21 0.66
7 7 0.22
8 4 0.12
ACGTcount: A:0.05, C:0.02, G:0.14, T:0.79
Consensus pattern (6 bp):
TTTTGT
Found at i:7849 original size:22 final size:21
Alignment explanation
Indices: 7819--7896 Score: 84
Period size: 22 Copynumber: 3.6 Consensus size: 21
7809 TCTTTTTATG
*
7819 GTTATCAAAATTTAATAGTGTA
1 GTTATCAAAATTTTATAGT-TA
* *
7841 GTTACCAAAGTTTTATAGTTA
1 GTTATCAAAATTTTATAGTTA
*
7862 GATTATCAAAATTTTATAGTATG
1 G-TTATCAAAATTTTATAGT-TA
*
7885 GTTATCTAAATT
1 GTTATCAAAATT
7897 CCATAGTGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 3 0.06
22 42 0.89
23 2 0.04
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (21 bp):
GTTATCAAAATTTTATAGTTA
Found at i:7903 original size:44 final size:44
Alignment explanation
Indices: 7820--7903 Score: 98
Period size: 44 Copynumber: 1.9 Consensus size: 44
7810 CTTTTTATGG
* **
7820 TTATCAAAATTTAATAGTGTAGTTACCAAAGTTTTATAGTTAGA
1 TTATCAAAATTTAATAGTATAGTTACCAAAGTTCCATAGTTAGA
* * *
7864 TTATCAAAATTTTATAGTATGGTTATCTAAA-TTCCATAGT
1 TTATCAAAATTTAATAGTATAGTTA-CCAAAGTTCCATAGT
7904 GTGGGTACCG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
44 29 0.88
45 4 0.12
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (44 bp):
TTATCAAAATTTAATAGTATAGTTACCAAAGTTCCATAGTTAGA
Found at i:7966 original size:22 final size:20
Alignment explanation
Indices: 7931--8144 Score: 119
Period size: 22 Copynumber: 9.8 Consensus size: 20
7921 ATAAGGATTT
*
7931 TTATCAAAACTTCATAATGCCG
1 TTATCAAAATTTCATAATG--G
* *
7953 TTACCAAAATTTCATAGTGG
1 TTATCAAAATTTCATAATGG
7973 TTATCAAAATTTCATAA-GG
1 TTATCAAAATTTCATAATGG
*
7992 CATTTATCAAAATTTCATAGTGTG
1 ---TTATCAAAATTTCATAATG-G
*
8016 ATTAGCAAAATTTCATAGGATGG
1 -TTATCAAAATTTCATA--ATGG
*
8039 TTATCAAAATTTCATAGTGCAG
1 TTATCAAAATTTCATAATG--G
* *
8061 GT-TCTAAAACTTCATAGGGAT-G
1 TTATC-AAAATTTCATA---ATGG
*
8083 TTATCAAAATTTCATAGAGTGC
1 TTATCAAAATTTCATA-A-TGG
**
8105 TTATCAAAATTTTACAGGATCAGG
1 TTATCAAAA-TTT-CATAAT--GG
8129 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
8145 GAAAGGTATC
Statistics
Matches: 150, Mismatches: 22, Indels: 40
0.71 0.10 0.19
Matches are distributed among these distances:
19 2 0.01
20 20 0.13
21 3 0.02
22 98 0.65
23 11 0.07
24 15 0.10
25 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (20 bp):
TTATCAAAATTTCATAATGG
Found at i:7981 original size:42 final size:43
Alignment explanation
Indices: 7931--8116 Score: 164
Period size: 44 Copynumber: 4.3 Consensus size: 43
7921 ATAAGGATTT
* *
7931 TTATCAAAACTTCATAATGCCGTTACCAAAATTTCATAGTG-G-
1 TTATCAAAATTTCATAATG-CGTTATCAAAATTTCATAGTGTGA
* *
7973 TTATCAAAATTTCATAAGGCATTTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCATAATGC-GTTATCAAAATTTCATAGTGTGA
* * *
8017 TTAGCAAAATTTCATAGGATG-GTTATCAAAATTTCATAGTGCAGG
1 TTATCAAAATTTCATA--ATGCGTTATCAAAATTTCATAGTG-TGA
* * ** * * *
8062 TTCT-AAAACTTCATAGGGATGTTATCAAAATTTCATAGAGTGC
1 TTATCAAAATTTCATAATG-CGTTATCAAAATTTCATAGTGTGA
8105 TTATCAAAATTT
1 TTATCAAAATTT
8117 TACAGGATCA
Statistics
Matches: 116, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
41 1 0.01
42 36 0.31
43 5 0.04
44 69 0.59
45 3 0.03
46 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (43 bp):
TTATCAAAATTTCATAATGCGTTATCAAAATTTCATAGTGTGA
Found at i:8043 original size:44 final size:42
Alignment explanation
Indices: 7952--8145 Score: 196
Period size: 44 Copynumber: 4.4 Consensus size: 42
7942 TCATAATGCC
*
7952 GTTACCAAAATTTCATAGTG-GTTATCAAAATTTCATAAGGCAT
1 GTTATCAAAATTTCATAGTGTGTTATCAAAATTTCAT-AGG-AT
*
7995 -TTATCAAAATTTCATAGTGTGATTAGCAAAATTTCATAGGAT
1 GTTATCAAAATTTCATAGTGTG-TTATCAAAATTTCATAGGAT
* * *
8037 GGTTATCAAAATTTCATAGTGCAGGT-TCTAAAACTTCATAGGGAT
1 -GTTATCAAAATTTCATAGTG-TGTTATC-AAAATTTCATA-GGAT
* * *
8082 GTTATCAAAATTTCATAGAGTGCTTATCAAAATTTTACAGGAT
1 GTTATCAAAATTTCATAGTGTG-TTATCAAAATTTCATAGGAT
8125 CAGGTTATCAAAATTTCATAG
1 ---GTTATCAAAATTTCATAG
8146 AAAGGTATCA
Statistics
Matches: 127, Mismatches: 12, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
42 20 0.16
43 10 0.08
44 72 0.57
45 7 0.06
46 18 0.14
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (42 bp):
GTTATCAAAATTTCATAGTGTGTTATCAAAATTTCATAGGAT
Found at i:8075 original size:66 final size:65
Alignment explanation
Indices: 7931--8116 Score: 200
Period size: 66 Copynumber: 2.8 Consensus size: 65
7921 ATAAGGATTT
** ** * *
7931 TTATCAAAACTTCATAATGCCGTTACCAAAATTTCATAG-TGGTTATCAAAATTTCATAAGGCAT
1 TTATCAAAACTTCATAGGGATGTTAGCAAAATTTCATAGATGGTTATCAAAATTTCATAAGGCAG
* *
7995 TTATCAAAATTTCATAGTG-TGATTAGCAAAATTTCATAGGATGGTTATCAAAATTTCAT-AGTG
1 TTATCAAAACTTCATAGGGATG-TTAGCAAAATTTCATA-GATGGTTATCAAAATTTCATAAG-G
8058 CAG
63 CAG
* * *
8061 GT-TCTAAAACTTCATAGGGATGTTATCAAAATTTCATAGAGTGCTTATCAAAATTT
1 TTATC-AAAACTTCATAGGGATGTTAGCAAAATTTCATAGA-TGGTTATCAAAATTT
8117 TACAGGATCA
Statistics
Matches: 105, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 32 0.30
65 7 0.07
66 63 0.60
67 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (65 bp):
TTATCAAAACTTCATAGGGATGTTAGCAAAATTTCATAGATGGTTATCAAAATTTCATAAGGCAG
Found at i:8200 original size:22 final size:22
Alignment explanation
Indices: 8175--8239 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
8165 GTGTAAATAT
*
8175 CAAAATTTTATAGGAAGGTTAC
1 CAAAATTTTATAGGAAGGTTAA
** *
8197 CAAAATTTTATACTATGGTTAA
1 CAAAATTTTATAGGAAGGTTAA
* *
8219 CAAAATTTCATAGGGAGGTTA
1 CAAAATTTTATAGGAAGGTTA
8240 TTGAAATATC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (22 bp):
CAAAATTTTATAGGAAGGTTAA
Found at i:8424 original size:22 final size:21
Alignment explanation
Indices: 8391--8907 Score: 175
Period size: 22 Copynumber: 23.5 Consensus size: 21
8381 GGGGTAATAA
8391 AAAATTTCATAGTGAGATTATC
1 AAAATTTCATAGTGAG-TTATC
*
8413 AAAATTAT-ATAGAGATGTTATC
1 AAAATT-TCATAGTGA-GTTATC
* *
8435 AAAATTTCATAGTGAGGGTAAC
1 AAAATTTCATAGTGA-GTTATC
* * * *
8457 AAAATTTGAGAGTGTGGGT-TC
1 AAAATTTCATAGTG-AGTTATC
* * * *
8478 GAAATTTTATAGGGAGGTTAAC
1 AAAATTTCATAGTGA-GTTATC
*
8500 AAAATTTCATA-TGAATGTTATT
1 AAAATTTCATAGTG-A-GTTATC
**
8522 GTAATTTCACTATATAGTGTAGTTATC
1 AAAATTT--C---ATAGTG-AGTTATC
* * *
8549 AAAATTTCATAATGTGTATATA
1 AAAATTTCATAGTGAGT-TATC
* * **
8571 AAAATTTCATAGAGAAATTAAG
1 AAAATTTCATAGTG-AGTTATC
*
8593 AAAGTTTCATA-TGGAGGTTATC
1 AAAATTTCATAGT-GA-GTTATC
8615 AAAATTT-A-A-T-AGTTATC
1 AAAATTTCATAGTGAGTTATC
* * *
8632 AAAAGTTCACATGGTG-CTTATC
1 AAAA-TT-TCATAGTGAGTTATC
*
8654 AAAATTTTACA-AG-GAGGTAAATC
1 AAAA-TTT-CATAGTGA-GT-TATC
*
8677 AAAATTTCATAATGAGATTATC
1 AAAATTTCATAGTGAG-TTATC
*
8699 AAAATTCCATAAG-GAGGTTATC
1 AAAATTTCAT-AGTGA-GTTATC
* *
8721 ACAATTTCATAGTGTGCTTATC
1 AAAATTTCATAGTGAG-TTATC
*
8743 AAAATTTCATAG-GAATGCTATC
1 AAAATTTCATAGTG-A-GTTATC
* *
8765 AAAATTTCATAAG-GAGGCTAAC
1 AAAATTTCAT-AGTGA-GTTATC
* * *
8787 AAAATTTCATTGGGAAGTTAAC
1 AAAATTTCATAGTG-AGTTATC
*
8809 AAAATCTCATA-TGGAGGTTATC
1 AAAATTTCATAGT-GA-GTTATC
* * *
8831 GAAATTTTATACT-ATTGTTATC
1 AAAATTTCATAGTGA--GTTATC
*
8853 AAAATTTCATAGTGTGATTATC
1 AAAATTTCATAGTGAG-TTATC
* * *
8875 AAAATTTTATAGCGATGTTATT
1 AAAATTTCATAGTGA-GTTATC
8897 AAAATTTCATA
1 AAAATTTCATA
8908 TGATATAATT
Statistics
Matches: 367, Mismatches: 82, Indels: 92
0.68 0.15 0.17
Matches are distributed among these distances:
17 10 0.03
18 3 0.01
20 4 0.01
21 30 0.08
22 280 0.76
23 22 0.06
24 1 0.00
25 1 0.00
27 13 0.04
28 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
AAAATTTCATAGTGAGTTATC
Found at i:10301 original size:47 final size:46
Alignment explanation
Indices: 10240--10330 Score: 164
Period size: 47 Copynumber: 2.0 Consensus size: 46
10230 TTTAAGTCTT
10240 AAATTTTTTTTTCCTATAAGCATTTTTCGGATAAAGACATTTTTTG
1 AAATTTTTTTTTCCTATAAGCATTTTTCGGATAAAGACATTTTTTG
*
10286 AAATTTTTTATTTCCTATAAGCATTTTTCGGATAAAGGCATTTTT
1 AAATTTTTT-TTTCCTATAAGCATTTTTCGGATAAAGACATTTTT
10331 CGGATAAAGG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 9 0.21
47 34 0.79
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (46 bp):
AAATTTTTTTTTCCTATAAGCATTTTTCGGATAAAGACATTTTTTG
Found at i:10348 original size:18 final size:17
Alignment explanation
Indices: 10306--10347 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
10296 TTTCCTATAA
10306 GCATTTTTCGGATAAAG
1 GCATTTTTCGGATAAAG
10323 GCATTTTTCGGATAAAG
1 GCATTTTTCGGATAAAG
10340 GCATTTTT
1 GCATTTTT
10348 TGAATTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.40
Consensus pattern (17 bp):
GCATTTTTCGGATAAAG
Done.