Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023260.1 Corchorus olitorius cultivar O-4 contig23293, 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: 35062
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2359 original size:22 final size:22
Alignment explanation
Indices: 2332--2455 Score: 124
Period size: 22 Copynumber: 5.6 Consensus size: 22
2322 TATAAGTAGA
*
2332 TTATCAAATTTTCACATTGAGG
1 TTATCAAATTTTCACAGTGAGG
* * *
2354 TTATCAAAATTTCATAGTGTGG
1 TTATCAAATTTTCACAGTGAGG
* * *
2376 TTACCAAAATTTCACAGTGTGG
1 TTATCAAATTTTCACAGTGAGG
* *
2398 TTATCAAATTTTCATAGGGAGG
1 TTATCAAATTTTCACAGTGAGG
* * *
2420 TTATCGAAA-TTCCAAAATGAGG
1 TTATC-AAATTTTCACAGTGAGG
2442 TTATCAAATTTTCA
1 TTATCAAATTTTCA
2456 AATTAATGTT
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
21 3 0.04
22 78 0.93
23 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (22 bp):
TTATCAAATTTTCACAGTGAGG
Found at i:2391 original size:44 final size:44
Alignment explanation
Indices: 2336--2455 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 44
2326 AGTAGATTAT
* * * * *
2336 CAAATTTTCACATTGAGGTTATCAAAATTTCATAGTGTGGTTAC
1 CAAAATTTCACAATGAGGTTATCAAATTTTCATAGGGAGGTTAC
* * *
2380 CAAAATTTCACAGTGTGGTTATCAAATTTTCATAGGGAGGTTAT
1 CAAAATTTCACAATGAGGTTATCAAATTTTCATAGGGAGGTTAC
* * *
2424 CGAAATTCCAAAATGAGGTTATCAAATTTTCA
1 CAAAATTTCACAATGAGGTTATCAAATTTTCA
2456 AATTAATGTT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 64 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (44 bp):
CAAAATTTCACAATGAGGTTATCAAATTTTCATAGGGAGGTTAC
Found at i:2444 original size:66 final size:66
Alignment explanation
Indices: 2332--2455 Score: 158
Period size: 66 Copynumber: 1.9 Consensus size: 66
2322 TATAAGTAGA
** * * * *
2332 TTATCAAATTTTCACATTGAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCACAGTGTG
1 TTATCAAATTTTCACAGGGAGGTTATCAAAATTCCAAAATGAGGTTACCAAAATTTCACAGTGTG
2397 G
66 G
* * * *
2398 TTATCAAATTTTCATAGGGAGGTTATCGAAATTCCAAAATGAGGTTATCAAATTTTCA
1 TTATCAAATTTTCACAGGGAGGTTATCAAAATTCCAAAATGAGGTTACCAAAATTTCA
2456 AATTAATGTT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 48 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (66 bp):
TTATCAAATTTTCACAGGGAGGTTATCAAAATTCCAAAATGAGGTTACCAAAATTTCACAGTGTG
G
Found at i:4796 original size:2 final size:2
Alignment explanation
Indices: 4791--4818 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4781 ACATATATTG
4791 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4819 TAGGCTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5906 original size:99 final size:98
Alignment explanation
Indices: 5800--6373 Score: 648
Period size: 99 Copynumber: 5.8 Consensus size: 98
5790 CTCCTTTTGC
* * *
5800 TGAATCTTTATATAGAGAATCGTATCCATCATCAGCATATTGAGAATCATCATTTATACCTTTGT
1 TGAATCTTCATATAGAGAATCATATCCATCATCAGCATATTGAGAATCATCATTTACACCTTTGT
*
5865 TTTTTGGAGCATTATCATGACCTCTAGAATTTTT
66 TATTTGGAGCATTATCATGACCTCTAG-ATTTTT
* * *
5899 CGTATCTTTACTATATAGAGAATCATATCCATCATCAGCATACTGAGAATCATCATTTACACCTT
1 TGAATC-TT-C-ATATAGAGAATCATATCCATCATCAGCATATTGAGAATCATCATTTACACCTT
*
5964 TGTTATTTGG-GTCATTATCATGAGCTCTAGATTCTTT
63 TGTTATTTGGAG-CATTATCATGACCTCTAGATT-TTT
* * * *
6001 TGAATCTTTATATAAAGAATCATATCTATCATCAGCATATTG-GTAATCATCGTTTACACCTTTG
1 TGAATCTTCATATAGAGAATCATATCCATCATCAGCATATTGAG-AATCATCATTTACACCTTTG
* * * *
6065 TTACTTGGA--A-TATC-TCCATCTCTAGGTCCTTTAGT
65 TTATTTGGAGCATTATCAT-GACCTCTAGAT--TTT--T
* *
6100 TGAATCTTCATATAGAGAGTCATATCCATCATCAGCATATTGAGAATCATCATTTACACCCTTGT
1 TGAATCTTCATATAGAGAATCATATCCATCATCAGCATATTGAGAATCATCATTTACACCTTTGT
*
6165 TATTTGG-GTCATGATCATGACCTCTAGATTTTT
66 TATTTGGAG-CATTATCATGACCTCTAGATTTTT
* * *
6198 TCGAATCTTCATATAAAGAATCATATCCATCATCAGCATACTGAGAATCATCATTTACACATTTG
1 T-GAATCTTCATATAGAGAATCATATCCATCATCAGCATATTGAGAATCATCATTTACACCTTTG
* * * *
6263 TTACTTAGAGCATCT-CCAT---CTCTAGCTCCTTTAGT
65 TTATTTGGAGCAT-TATCATGACCTCTAGAT--TTT--T
* *
6298 TGAATCTTCATATAGAGAGTCATATCCATCATCAGCATATTGAGAATCATCGTTTACACCTTTGT
1 TGAATCTTCATATAGAGAATCATATCCATCATCAGCATATTGAGAATCATCATTTACACCTTTGT
6363 TATTTGGAGCA
66 TATTTGGAGCA
6374 CTTCTAAATA
Statistics
Matches: 403, Mismatches: 47, Indels: 50
0.81 0.09 0.10
Matches are distributed among these distances:
95 1 0.00
96 19 0.05
97 3 0.01
98 7 0.02
99 262 0.65
100 9 0.02
101 7 0.02
102 94 0.23
103 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (98 bp):
TGAATCTTCATATAGAGAATCATATCCATCATCAGCATATTGAGAATCATCATTTACACCTTTGT
TATTTGGAGCATTATCATGACCTCTAGATTTTT
Found at i:6155 original size:198 final size:198
Alignment explanation
Indices: 5911--6369 Score: 751
Period size: 198 Copynumber: 2.3 Consensus size: 198
5901 TATCTTTACT
* *
5911 ATATAGAGAATCATATCCATCATCAGCATACTGAGAATCATCATTTACACCTTTGTTATTTGGGT
1 ATATAGAGAGTCATATCCATCATCAGCATATTGAGAATCATCATTTACACCTTTGTTATTTGGGT
* * * *
5976 CATTATCATGAGCTCTAGATTCTTTT-GAATCTTTATATAAAGAATCATATCTATCATCAGCATA
66 CATGATCATGACCTCTAGATT-TTTTCGAATCTTCATATAAAGAATCATATCCATCATCAGCATA
* * * * * *
6040 TTG-GTAATCATCGTTTACACCTTTGTTACTTGGAATATCTCCATCTCTAGGTCCTTTAGTTGAA
130 CTGAG-AATCATCATTTACACATTTGTTACTTAGAACATCTCCATCTCTAGCTCCTTTAGTTGAA
6104 TCTTC
194 TCTTC
*
6109 ATATAGAGAGTCATATCCATCATCAGCATATTGAGAATCATCATTTACACCCTTGTTATTTGGGT
1 ATATAGAGAGTCATATCCATCATCAGCATATTGAGAATCATCATTTACACCTTTGTTATTTGGGT
6174 CATGATCATGACCTCTAGATTTTTTCGAATCTTCATATAAAGAATCATATCCATCATCAGCATAC
66 CATGATCATGACCTCTAGATTTTTTCGAATCTTCATATAAAGAATCATATCCATCATCAGCATAC
*
6239 TGAGAATCATCATTTACACATTTGTTACTTAGAGCATCTCCATCTCTAGCTCCTTTAGTTGAATC
131 TGAGAATCATCATTTACACATTTGTTACTTAGAACATCTCCATCTCTAGCTCCTTTAGTTGAATC
6304 TTC
196 TTC
*
6307 ATATAGAGAGTCATATCCATCATCAGCATATTGAGAATCATCGTTTACACCTTTGTTATTTGG
1 ATATAGAGAGTCATATCCATCATCAGCATATTGAGAATCATCATTTACACCTTTGTTATTTGG
6370 AGCACTTCTA
Statistics
Matches: 243, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
197 4 0.02
198 238 0.98
199 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (198 bp):
ATATAGAGAGTCATATCCATCATCAGCATATTGAGAATCATCATTTACACCTTTGTTATTTGGGT
CATGATCATGACCTCTAGATTTTTTCGAATCTTCATATAAAGAATCATATCCATCATCAGCATAC
TGAGAATCATCATTTACACATTTGTTACTTAGAACATCTCCATCTCTAGCTCCTTTAGTTGAATC
TTC
Found at i:8809 original size:13 final size:13
Alignment explanation
Indices: 8791--8864 Score: 82
Period size: 13 Copynumber: 5.8 Consensus size: 13
8781 AAACAAAAAT
8791 TGATTTCAGAATC
1 TGATTTCAGAATC
*
8804 TGATTTCAGAAAC
1 TGATTTCAGAATC
**
8817 TGAAATCAG-A-C
1 TGATTTCAGAATC
8828 TGATTTCAGAATC
1 TGATTTCAGAATC
8841 TGATTTCAGATAT-
1 TGATTTCAGA-ATC
*
8854 TGAATTCAGAA
1 TGATTTCAGAA
8865 ACTACAACCA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
11 8 0.15
12 3 0.06
13 39 0.75
14 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (13 bp):
TGATTTCAGAATC
Found at i:8849 original size:24 final size:25
Alignment explanation
Indices: 8791--8867 Score: 84
Period size: 24 Copynumber: 3.0 Consensus size: 25
8781 AAACAAAAAT
8791 TGATTTCAGAATCTGATTTCAGAAAC
1 TGATTTCAG-ATCTGATTTCAGAAAC
** *
8817 TGAAATCAGA-CTGATTTCAGAATC
1 TGATTTCAGATCTGATTTCAGAAAC
* *
8841 TGATTTCAGATATTGAATTCAGAAAC
1 TGATTTCAGAT-CTGATTTCAGAAAC
8867 T
1 T
8868 ACAACCAACA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
24 21 0.51
25 1 0.02
26 19 0.46
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (25 bp):
TGATTTCAGATCTGATTTCAGAAAC
Found at i:22493 original size:24 final size:24
Alignment explanation
Indices: 22447--22497 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
22437 CTTCAATTAC
*
22447 AAAATACCAAAAAACACACAAACCA
1 AAAATACCAAAAAACACA-AAAACA
**
22472 AAAATA-CAAAAAATGCAAAAACA
1 AAAATACCAAAAAACACAAAAACA
22495 AAA
1 AAA
22498 TACTCCTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 8 0.35
24 9 0.39
25 6 0.26
ACGTcount: A:0.73, C:0.20, G:0.02, T:0.06
Consensus pattern (24 bp):
AAAATACCAAAAAACACAAAAACA
Found at i:22832 original size:12 final size:12
Alignment explanation
Indices: 22815--22839 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22805 AATACAGTCC
22815 TCTCACCAAATA
1 TCTCACCAAATA
22827 TCTCACCAAATA
1 TCTCACCAAATA
22839 T
1 T
22840 AACCTTTTCG
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:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (12 bp):
TCTCACCAAATA
Found at i:26735 original size:7 final size:7
Alignment explanation
Indices: 26723--26803 Score: 51
Period size: 7 Copynumber: 11.6 Consensus size: 7
26713 AGGGATTTTA
26723 TTTTCTT
1 TTTTCTT
26730 TTTTC-T
1 TTTTCTT
26736 TTTTC-T
1 TTTTCTT
*
26742 TTTTC-G
1 TTTTCTT
26748 TTTTCTT
1 TTTTCTT
*
26755 TTTTGTT
1 TTTTCTT
* *
26762 TTTTGTA
1 TTTTCTT
*
26769 TTTTCTG
1 TTTTCTT
* *
26776 TCTTCTA
1 TTTTCTT
26783 TTTTCTAAT
1 TTTTCT--T
26792 TTTTCCTT
1 TTTT-CTT
26800 TTTT
1 TTTT
26804 TATTTGTGTT
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
6 17 0.28
7 32 0.53
8 5 0.08
9 4 0.07
10 2 0.03
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.77
Consensus pattern (7 bp):
TTTTCTT
Found at i:26764 original size:6 final size:6
Alignment explanation
Indices: 26723--26757 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
26713 AGGGATTTTA
*
26723 TTTTCTT TTTTCT TTTTCT TTTTCG TTTTCT TTTT
1 TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT TTTT
26758 TGTTTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:28038 original size:17 final size:19
Alignment explanation
Indices: 27998--28039 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
27988 AGATTATATT
*
27998 TAAAAATATTAATGAGTGA
1 TAAAAATAATAATGAGTGA
*
28017 AAAAAATAATAA-GA-TGA
1 TAAAAATAATAATGAGTGA
28034 TAAAAA
1 TAAAAA
28040 AATCAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 8 0.40
18 2 0.10
19 10 0.50
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (19 bp):
TAAAAATAATAATGAGTGA
Found at i:30421 original size:22 final size:22
Alignment explanation
Indices: 30381--30423 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
30371 AAAATGCAAT
* * *
30381 ATATAATATGATTTGATATTTG
1 ATATAATATAATGTCATATTTG
30403 ATATAATATAATGTCATATTT
1 ATATAATATAATGTCATATTT
30424 AAAAATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (22 bp):
ATATAATATAATGTCATATTTG
Done.