Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024137.1 Corchorus olitorius cultivar O-4 contig24170, 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: 27543
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:918 original size:2 final size:2
Alignment explanation
Indices: 911--946 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
901 TGTGGCCGGT
911 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
947 GTGTAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9109 original size:38 final size:38
Alignment explanation
Indices: 9054--9159 Score: 160
Period size: 38 Copynumber: 2.8 Consensus size: 38
9044 CTTTAATGAT
*
9054 TGAAAT-TTTTTTCTTTGAGTCTAACATGAAATTATAG
1 TGAAATGTTTTTTATTTGAGTCTAACATGAAATTATAG
9091 TGAAATGTTTTTTATTTGAGTCTAACATGAAATTATAG
1 TGAAATGTTTTTTATTTGAGTCTAACATGAAATTATAG
** * *
9129 TGAAATGGCTTTTATTTGAATCTAATATGAA
1 TGAAATGTTTTTTATTTGAGTCTAACATGAA
9160 TTTGCTTCTT
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
37 6 0.10
38 57 0.90
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (38 bp):
TGAAATGTTTTTTATTTGAGTCTAACATGAAATTATAG
Found at i:21053 original size:9 final size:9
Alignment explanation
Indices: 21038--21102 Score: 69
Period size: 9 Copynumber: 6.9 Consensus size: 9
21028 CAGAAATATG
21038 CAAAAAAAGA
1 CAAAAAAA-A
*
21048 AAAAAAAACGA
1 CAAAAAAA--A
21059 CAAAAAAAA
1 CAAAAAAAA
*
21068 CAACAAAAA
1 CAAAAAAAA
21077 CAAAAAAAA
1 CAAAAAAAA
21086 -ACAAAAAAA
1 CA-AAAAAAA
21095 CAAAAAAA
1 CAAAAAAA
21103 GTGAAAATTG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
8 1 0.02
9 30 0.62
10 8 0.17
11 9 0.19
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:21054 original size:10 final size:10
Alignment explanation
Indices: 21039--21102 Score: 71
Period size: 10 Copynumber: 6.5 Consensus size: 10
21029 AGAAATATGC
*
21039 AAAAAAAGAA
1 AAAAAAACAA
21049 AAAAAAACGACA
1 AAAAAAAC-A-A
21061 AAAAAAAC-A
1 AAAAAAACAA
*
21070 ACAAAAACAA
1 AAAAAAACAA
21080 AAAAAAAC--
1 AAAAAAACAA
21088 AAAAAAACAA
1 AAAAAAACAA
21098 AAAAA
1 AAAAA
21103 GTGAAAATTG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
8 8 0.17
9 8 0.17
10 20 0.43
11 1 0.02
12 9 0.20
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:21063 original size:12 final size:12
Alignment explanation
Indices: 21039--21076 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
21029 AGAAATATGC
21039 AAAAAAA-GA-A
1 AAAAAAACGACA
21049 AAAAAAACGACA
1 AAAAAAACGACA
*
21061 AAAAAAACAACA
1 AAAAAAACGACA
21073 AAAA
1 AAAA
21077 CAAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 16 0.64
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (12 bp):
AAAAAAACGACA
Found at i:21079 original size:18 final size:17
Alignment explanation
Indices: 21058--21102 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 17
21048 AAAAAAAACG
21058 ACAAAAAAAACAACAAAA
1 ACAAAAAAAACAA-AAAA
21076 ACAAAAAAAAACAAAAAA
1 AC-AAAAAAAACAAAAAA
21094 ACAAAAAAA
1 ACAAAAAAA
21103 GTGAAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.27
18 8 0.31
19 11 0.42
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (17 bp):
ACAAAAAAAACAAAAAA
Found at i:21109 original size:18 final size:18
Alignment explanation
Indices: 21038--21102 Score: 87
Period size: 18 Copynumber: 3.4 Consensus size: 18
21028 CAGAAATATG
21038 CAAAAAAAGAA-AAAAAAA
1 CAAAAAAA-AACAAAAAAA
21056 CGACAAAAAAAACAACAAAAA
1 C-A-AAAAAAAACAA-AAAAA
21077 CAAAAAAAAACAAAAAAA
1 CAAAAAAAAACAAAAAAA
21095 CAAAAAAA
1 CAAAAAAA
21103 GTGAAAATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
18 14 0.33
19 14 0.33
20 9 0.21
21 6 0.14
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (18 bp):
CAAAAAAAAACAAAAAAA
Found at i:21124 original size:19 final size:20
Alignment explanation
Indices: 21100--21141 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
21090 AAAAACAAAA
21100 AAAGTGAAAATTGAAAA-TG
1 AAAGTGAAAATTGAAAATTG
**
21119 AAAGTGGTAATTGAAAATTG
1 AAAGTGAAAATTGAAAATTG
21139 AAA
1 AAA
21142 AAGTATAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (20 bp):
AAAGTGAAAATTGAAAATTG
Found at i:22569 original size:146 final size:145
Alignment explanation
Indices: 22319--23024 Score: 907
Period size: 146 Copynumber: 4.9 Consensus size: 145
22309 CCATTTTGGT
* * * *
22319 AAGTTTTTCATCAAATTTGCGTTTAAATTT--TAAT--AAACCTTGCTCAAGGTTGAGTTTGCAT
1 AAGTTTTTAATCAAAGTTGCATTTAAATTTCAAAATAAAAACCTTGCTCAAGGTTGAGTTTGCAT
*
22380 TTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTTTGATAAATCCTCCGGGTA
66 TTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTA
*
22445 CCATTTCATTTCATC
131 TCATTTCATTTCATC
* *
22460 AAGTTTTTAATCAAAGTTGCATTTAAAATTCAAAATAAAAAACCTTGCTCAAGATTGAGTTTGCA
1 AAGTTTTTAATCAAAGTTGCATTTAAATTTCAAAAT-AAAAACCTTGCTCAAGGTTGAGTTTGCA
* ** *
22525 TTTGTAAGACCTCCGGGCACCATTTCAGATTCCTCCAGGTATTAATTCTGATAAATCCTCCGGGT
65 TTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGT
* * *
22590 ATCATATAATTTCCTC
130 ATCATTTCATTTCATC
*
22606 AAGTTTTTAATCAAAGTTGCATTTAAGTTTCAAAATCAAAAACCTTGCTCAAGGTTGAGTTTGCA
1 AAGTTTTTAATCAAAGTTGCATTTAAATTTCAAAAT-AAAAACCTTGCTCAAGGTTGAGTTTGCA
* * *
22671 TTTGTAAGTCCTCCGGACACCATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGT
65 TTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGT
22736 ATCATTTCATTTCATC
130 ATCATTTCATTTCATC
* * ** * * * * *
22752 AA-ATTTT--TCAAAGCTGTGTTTAAGTTCCAAAATCACAACCTTGCTCAAGGTCTCAATTCATA
1 AAGTTTTTAATCAAAGTTGCATTTAAATTTCAAAATAAAAACCTTGCTCAAGG------TT--GA
*
22814 ATTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCC
58 GTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCC
22879 TCCGGG--T-A--TCATTTCATC
123 TCCGGGTATCATTTCATTTCATC
* * * *
22897 AAGTTTTTAATCAAAGTTGCATTTAATTTTCAAAATCAAAACCTTGCTCAAGGTCGAGTGTGC-T
1 AAGTTTTTAATCAAAGTTGCATTTAAATTTCAAAATAAAAACCTTGCTCAAGGTTGAGTTTGCAT
* *
22961 TCTGTAAGACCTCCGGGTACAATTTCAGAAACCTCTGGGTATTAATTCTGATAAATCCTCCGGG
66 T-TGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGG
23025 CATTCCATAG
Statistics
Matches: 496, Mismatches: 52, Indels: 35
0.85 0.09 0.06
Matches are distributed among these distances:
139 2 0.00
140 65 0.13
141 26 0.05
142 16 0.03
143 25 0.05
145 16 0.03
146 237 0.48
147 1 0.00
148 40 0.08
150 68 0.14
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (145 bp):
AAGTTTTTAATCAAAGTTGCATTTAAATTTCAAAATAAAAACCTTGCTCAAGGTTGAGTTTGCAT
TTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTA
TCATTTCATTTCATC
Found at i:23206 original size:40 final size:40
Alignment explanation
Indices: 23156--23544 Score: 386
Period size: 40 Copynumber: 10.0 Consensus size: 40
23146 AAAATTATGT
23156 TCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTAC
1 TCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTAC
*
23196 TCAGGATCATTGCTTTATTAAATTAATTTCAGAATCCTAC
1 TCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTAC
*
23236 TCAGGATCATTGCTTTATCAAATTAATTTTAGAATCCTAC
1 TCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTAC
* *
23276 TCAGGATCACTGCTTTATCAAATTAATTTCAGAATCCTGC
1 TCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTAC
* *
23316 TCAGGATCTTTGCTTTATCAAATTAATTTCAGAATCCTGC
1 TCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTAC
* * *** * * * *
23356 TCAGGATCATTTCTTTAT-TAGCCACTTT--TACTCCTAT
1 TCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTAC
* * * * * *
23393 TCAGGATTATTTCTTCATC-AATCAATTTC--CATCCTAT
1 TCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTAC
* * * *
23430 TTAGGATCATTG-TTGTGTC-AA-TCATTTCAGAATCCTGC
1 TCAGGATCATTGCTT-TATCAAATTAATTTCAGAATCCTAC
* * * *
23468 TCAGGATTATTGCTTTATCAAATCAATTT--TAATCCTAT
1 TCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTAC
* * * * *
23506 TCAGGATCATTGCCTTATCAGATCAATTTTAAAATCCTA
1 TCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTA
23545 TCATTTATAA
Statistics
Matches: 291, Mismatches: 48, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
36 7 0.02
37 46 0.16
38 50 0.17
39 9 0.03
40 179 0.62
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (40 bp):
TCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTAC
Found at i:23280 original size:120 final size:118
Alignment explanation
Indices: 23068--23544 Score: 459
Period size: 120 Copynumber: 4.1 Consensus size: 118
23058 TATCAATTTT
* * * ** * *
23068 AATCCTATTCATGATCATTGCTTTATT-AGTCGATTTCAAAATCCTGCTCAGGATCATTTCTTTT
1 AATCCTACTCAGGATCATTGCTTTATTAAATTAATTTCAGAATCCTGCTCAGGATCATTGC--TT
* * ** * *
23132 TATC-AGTCAATTATAAAATTATGTTCAGGATCATTGCTTTATCAAATTAATTTCAG
64 TATCAAATCAATT-T-TAATCCTATTCAGGATCATTGCTTTATCAAATCAATTTCAG
*
23188 AATCCTACTCAGGATCATTGCTTTATTAAATTAATTTCAGAATCCTACTCAGGATCATTGCTTTA
1 AATCCTACTCAGGATCATTGCTTTATTAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTA
* * * *
23253 TCAAATTAATTTTAGAATCCTACTCAGGATCACTGCTTTATCAAATTAATTTCAG
66 TCAAATCAATTTT--AATCCTATTCAGGATCATTGCTTTATCAAATCAATTTCAG
* * * *
23308 AATCCTGCTCAGGATCTTTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTTCTTTA
1 AATCCTACTCAGGATCATTGCTTTATTAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTA
* ** * * * * *
23373 T-TAGCCACTTTTACTCCTATTCAGGATTATTTCTTCATC-AATCAATTTC--
66 TCAAATCAATTTTAATCCTATTCAGGATCATTGCTTTATCAAATCAATTTCAG
* * * * * * *
23422 CATCCTATTTAGGATCATTG-TTGT-GTCAA-TCATTTCAGAATCCTGCTCAGGATTATTGCTTT
1 AATCCTACTCAGGATCATTGCTT-TATTAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTT
* * * *
23484 ATCAAATCAATTTTAATCCTATTCAGGATCATTGCCTTATCAGATCAATTTTAA
65 ATCAAATCAATTTTAATCCTATTCAGGATCATTGCTTTATCAAATCAATTTCAG
23538 AATCCTA
1 AATCCTA
23545 TCATTTATAA
Statistics
Matches: 292, Mismatches: 56, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
112 32 0.11
113 33 0.11
114 24 0.08
116 15 0.05
117 21 0.07
119 13 0.04
120 127 0.43
121 27 0.09
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.41
Consensus pattern (118 bp):
AATCCTACTCAGGATCATTGCTTTATTAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTA
TCAAATCAATTTTAATCCTATTCAGGATCATTGCTTTATCAAATCAATTTCAG
Found at i:23618 original size:40 final size:39
Alignment explanation
Indices: 23564--23696 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 39
23554 AATCCTTTTT
* * *
23564 AGGATTATTTCTTTACCAGTTAATATTCAGAATCCTACTC
1 AGGATCATTGCTTTACAAGTTAAT-TTCAGAATCCTACTC
* *
23604 AGGATCATTGCTTTATCAAATTATTTTC-GAAATCCTACTC
1 AGGATCATTGCTTTA-CAAGTTAATTTCAG-AATCCTACTC
** * *
23644 AGGATCATTGCTTTATTAGATTAATTTTAGAATCCTACTT
1 AGGATCATTGCTTTACAAG-TTAATTTCAGAATCCTACTC
23684 AGGATCATTGCTT
1 AGGATCATTGCTT
23697 GGTGAGTCAA
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
39 2 0.03
40 69 0.88
41 7 0.09
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (39 bp):
AGGATCATTGCTTTACAAGTTAATTTCAGAATCCTACTC
Found at i:25630 original size:24 final size:23
Alignment explanation
Indices: 25590--25653 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
25580 AAGAGGTACC
* *
25590 AAAAAATAGAGAGAAAA-ATTGAAG
1 AAAAAATACAGAAAAAAGATT--AG
*
25614 AAAAAATACAGAAAAAAGGGTTAG
1 AAAAAATACAGAAAAAA-GATTAG
25638 AAAAAATACAGAAAAA
1 AAAAAATACAGAAAAA
25654 GTAAAAACAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 33 0.94
26 2 0.06
ACGTcount: A:0.69, C:0.03, G:0.17, T:0.11
Consensus pattern (23 bp):
AAAAAATACAGAAAAAAGATTAG
Found at i:26777 original size:11 final size:11
Alignment explanation
Indices: 26761--26808 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
26751 GAAGTTCGTG
26761 TTTGAAGACCA
1 TTTGAAGACCA
**
26772 TTTGAAGATAA
1 TTTGAAGACCA
26783 TTTGAAGA-C-
1 TTTGAAGACCA
26792 -TTGAAGACCA
1 TTTGAAGACCA
26802 -TTGAAGA
1 TTTGAAGA
26809 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Done.