Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014938.1 Corchorus olitorius cultivar O-4 contig14971, 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: 132544
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:17113 original size:3 final size:3
Alignment explanation
Indices: 17105--17144 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
17095 TATCATTTTG
17105 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
17145 TATAAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:35525 original size:18 final size:18
Alignment explanation
Indices: 35492--35527 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35482 AATTACTTCT
**
35492 CAACAACAACTGCAGCAA
1 CAACAACAACAACAGCAA
35510 CAACAACAACAACAGCAA
1 CAACAACAACAACAGCAA
35528 GCCGTTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.33, G:0.08, T:0.03
Consensus pattern (18 bp):
CAACAACAACAACAGCAA
Found at i:43249 original size:57 final size:57
Alignment explanation
Indices: 43156--43349 Score: 316
Period size: 57 Copynumber: 3.4 Consensus size: 57
43146 AATAGCTGAA
* *
43156 AATTACTTTCAGGAGGAGGGTAATTGGCAGGCTGTTGATAAGTGGAAGGGACCTGGG
1 AATTGCTTTCAGGAGGAGGGTAATGGGCAGGCTGTTGATAAGTGGAAGGGACCTGGG
43213 AATTGCTTTCAGGAGGAGGGTAATGGGCAGGCTGTTGATAAGTGGAAGGGACCTGGG
1 AATTGCTTTCAGGAGGAGGGTAATGGGCAGGCTGTTGATAAGTGGAAGGGACCTGGG
* * * *
43270 AATTGCTTTCAGGAGGAGGGTAATGGGCAGGCGGTTGATAAGTGGAGGGGGCTTGGG
1 AATTGCTTTCAGGAGGAGGGTAATGGGCAGGCTGTTGATAAGTGGAAGGGACCTGGG
* *
43327 AATTGCTTTCAGGGGGTGGGTAA
1 AATTGCTTTCAGGAGGAGGGTAA
43350 GGCACATGTG
Statistics
Matches: 129, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 129 1.00
ACGTcount: A:0.24, C:0.10, G:0.42, T:0.24
Consensus pattern (57 bp):
AATTGCTTTCAGGAGGAGGGTAATGGGCAGGCTGTTGATAAGTGGAAGGGACCTGGG
Found at i:50802 original size:12 final size:12
Alignment explanation
Indices: 50785--50810 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
50775 TTTGTCTTGT
50785 TGGTTCTGATTC
1 TGGTTCTGATTC
50797 TGGTTCTGATTC
1 TGGTTCTGATTC
50809 TG
1 TG
50811 ATCATCTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.27, T:0.50
Consensus pattern (12 bp):
TGGTTCTGATTC
Found at i:50811 original size:18 final size:16
Alignment explanation
Indices: 50783--50834 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 16
50773 AATTTGTCTT
*
50783 GTTGGTTCTGATTCTG
1 GTTGATTCTGATTCTG
*
50799 GTTCTGATTCTGATCATCTT
1 G-T-TGATTCTGAT--TCTG
50819 GTTGATTCTGATTCTG
1 GTTGATTCTGATTCTG
50835 ATCATCTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
16 4 0.14
17 1 0.03
18 19 0.66
19 1 0.03
20 4 0.14
ACGTcount: A:0.12, C:0.15, G:0.23, T:0.50
Consensus pattern (16 bp):
GTTGATTCTGATTCTG
Found at i:50832 original size:24 final size:24
Alignment explanation
Indices: 50800--50854 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
50790 CTGATTCTGG
50800 TTCTGATTCTGATCATCTTGTTGA
1 TTCTGATTCTGATCATCTTGTTGA
*
50824 TTCTGATTCTGATCATCTTGTTGT
1 TTCTGATTCTGATCATCTTGTTGA
50848 TTCTGAT
1 TTCTGAT
50855 CATAATTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.15, C:0.16, G:0.16, T:0.53
Consensus pattern (24 bp):
TTCTGATTCTGATCATCTTGTTGA
Found at i:51379 original size:17 final size:19
Alignment explanation
Indices: 51347--51381 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
51337 TGTTTAAATA
51347 AATTGAAAATTAAATTAAT
1 AATTGAAAATTAAATTAAT
51366 AATT-AAAA-TAAATTAA
1 AATTGAAAATTAAATTAA
51382 CACCGTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
AATTGAAAATTAAATTAAT
Found at i:52155 original size:78 final size:78
Alignment explanation
Indices: 52025--52183 Score: 273
Period size: 78 Copynumber: 2.0 Consensus size: 78
52015 TTTCTAGTTG
* * *
52025 AAATAGTTAAATGGTAAACTGAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGAGT
1 AAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGAGT
52090 TTTTAGTTGAGTA
66 TTTTAGTTGAGTA
* *
52103 AAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAGTTAAATAAAAATAGAGT
1 AAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGAGT
52168 TTTTAGTTGAGTA
66 TTTTAGTTGAGTA
52181 AAA
1 AAA
52184 CTATAAATCT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.50, C:0.01, G:0.14, T:0.35
Consensus pattern (78 bp):
AAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGAGT
TTTTAGTTGAGTA
Found at i:69113 original size:33 final size:33
Alignment explanation
Indices: 69071--69135 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
69061 GGTCAAGGGA
69071 AATCCTCAAAATTATTTAATACTTACTACTAAG
1 AATCCTCAAAATTATTTAATACTTACTACTAAG
* *
69104 AATCCTCAAAGTTATTTAATACTTATTACTAA
1 AATCCTCAAAATTATTTAATACTTACTACTAA
69136 ATAAACAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (33 bp):
AATCCTCAAAATTATTTAATACTTACTACTAAG
Found at i:86428 original size:3 final size:3
Alignment explanation
Indices: 86420--86475 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
86410 TAAATACTAG
86420 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
86468 TAA TAA TA
1 TAA TAA TA
86476 TGAATTTGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:91102 original size:14 final size:15
Alignment explanation
Indices: 91083--91114 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
91073 AGCTTATTTG
91083 CTTAATTA-ATCTTT
1 CTTAATTATATCTTT
91097 CTTAATTATATCTTT
1 CTTAATTATATCTTT
91112 CTT
1 CTT
91115 TCCCAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (15 bp):
CTTAATTATATCTTT
Found at i:92527 original size:10 final size:10
Alignment explanation
Indices: 92514--92538 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
92504 CGGATAATAA
92514 GAAAAGAAAG
1 GAAAAGAAAG
92524 GAAAAGAAAG
1 GAAAAGAAAG
92534 GAAAA
1 GAAAA
92539 CGAATAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
GAAAAGAAAG
Found at i:113055 original size:37 final size:37
Alignment explanation
Indices: 113004--113079 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
112994 TGCCTCGAAT
* * *
113004 CAATTACATGAGAAATACTAGTATTAAAATTCAAGGC
1 CAATCACATGAGAAATACTACTATTAAAATTCAAAGC
*
113041 CAATCACATGAGAAATACTACTATTAATATTCAAAGC
1 CAATCACATGAGAAATACTACTATTAAAATTCAAAGC
113078 CA
1 CA
113080 GGGGGCCAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (37 bp):
CAATCACATGAGAAATACTACTATTAAAATTCAAAGC
Found at i:113584 original size:9 final size:9
Alignment explanation
Indices: 113570--113606 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
113560 CTAAGACCTT
113570 TTTTTTTTC
1 TTTTTTTTC
113579 TTTTTTTTC
1 TTTTTTTTC
113588 --TTTTTTC
1 TTTTTTTTC
*
113595 TTTTTTCTC
1 TTTTTTTTC
113604 TTT
1 TTT
113607 CGGTTGGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
7 7 0.28
9 18 0.72
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:113593 original size:16 final size:16
Alignment explanation
Indices: 113568--113606 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
113558 GGCTAAGACC
113568 TTTT-TTTTTTCTTTT
1 TTTTCTTTTTTCTTTT
113583 TTTTCTTTTTTCTTTT
1 TTTTCTTTTTTCTTTT
*
113599 TTCTCTTT
1 TTTTCTTT
113607 CGGTTGGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTCTTTTTTCTTTT
Found at i:119244 original size:13 final size:14
Alignment explanation
Indices: 119210--119242 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
119200 GGCTGTAGCA
119210 TGATTT-TGAAAATC
1 TGATTTGTG-AAATC
119224 TGATTTGTGAAATC
1 TGATTTGTGAAATC
119238 TGATT
1 TGATT
119243 GTTATATGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (14 bp):
TGATTTGTGAAATC
Found at i:123913 original size:17 final size:17
Alignment explanation
Indices: 123891--123927 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
123881 TTATATTGTC
*
123891 CTTATTTAGTCTGGTTT
1 CTTATTCAGTCTGGTTT
123908 CTTATTCAGTCTGGTTT
1 CTTATTCAGTCTGGTTT
123925 CTT
1 CTT
123928 GCCCTGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (17 bp):
CTTATTCAGTCTGGTTT
Found at i:129404 original size:33 final size:33
Alignment explanation
Indices: 129364--129513 Score: 237
Period size: 33 Copynumber: 4.4 Consensus size: 33
129354 AACTCCAAAG
129364 TTTAGTAGGGTCATCTGTGTCATCTAGTCCGGT
1 TTTAGTAGGGTCATCTGTGTCATCTAGTCCGGT
*
129397 TTTAGTAGGGTCATATGTGTCATCTAGTCCGGT
1 TTTAGTAGGGTCATCTGTGTCATCTAGTCCGGT
129430 TTTAGTAGGGTCATCTGTGTCATCTAGTCCGGT
1 TTTAGTAGGGTCATCTGTGTCATCTAGTCCGGT
* *
129463 TTTAGTAGGGTCATTTGCATCATCTATCTAGTCCGGT
1 TTTAGTAGGGTCATCTG--T-GTC-ATCTAGTCCGGT
129500 TTTAGTAGGGTCAT
1 TTTAGTAGGGTCAT
129514 TTGCATCATA
Statistics
Matches: 109, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
33 80 0.73
35 1 0.01
36 2 0.02
37 26 0.24
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (33 bp):
TTTAGTAGGGTCATCTGTGTCATCTAGTCCGGT
Found at i:129592 original size:26 final size:26
Alignment explanation
Indices: 129556--130069 Score: 715
Period size: 26 Copynumber: 19.8 Consensus size: 26
129546 CTTTATCATG
*
129556 TAGTTACATATTCAGTAGGGCCCATA
1 TAGTTGCATATTCAGTAGGGCCCATA
129582 TAGTTGCATATTCAGTAGGGCCCATA
1 TAGTTGCATATTCAGTAGGGCCCATA
129608 TAGTTGCATATTCAGTAGGGCCCATA
1 TAGTTGCATATTCAGTAGGGCCCATA
**
129634 TAGTTGCATATTCAGTAGGGGACATA
1 TAGTTGCATATTCAGTAGGGCCCATA
129660 TAGTTGCATATTCAGTAGGGCCCATA
1 TAGTTGCATATTCAGTAGGGCCCATA
*
129686 TAGTTGCATATTTAGTAGGGCCCATA
1 TAGTTGCATATTCAGTAGGGCCCATA
**
129712 TAGTTGCATATTCAGTAGGGGACATA
1 TAGTTGCATATTCAGTAGGGCCCATA
129738 TAGTTGCATATTCAGTAGGGCCCATA
1 TAGTTGCATATTCAGTAGGGCCCATA
*
129764 TAGTTGCATATTCAGTAGGGCTCATA
1 TAGTTGCATATTCAGTAGGGCCCATA
129790 TAGTTGCATATTCAGTAGGGCCCATA
1 TAGTTGCATATTCAGTAGGGCCCATA
**
129816 TAGTTGCATATTCAGTAGGGGACATA
1 TAGTTGCATATTCAGTAGGGCCCATA
* **
129842 TAGTTGCATATTTAGTAGGGGACATA
1 TAGTTGCATATTCAGTAGGGCCCATA
* * **
129868 TAGCTGCATATTAAGTAGGGGACATA
1 TAGTTGCATATTCAGTAGGGCCCATA
*
129894 TAGTTGCATATTCAGTTGGGCCCATA
1 TAGTTGCATATTCAGTAGGGCCCATA
* **
129920 TAGATGCATATTCAGTAGGGGACATA
1 TAGTTGCATATTCAGTAGGGCCCATA
* ** * *
129946 TAGTTGTATATTTTGTTGGGCTCATA
1 TAGTTGCATATTCAGTAGGGCCCATA
* **
129972 TAGTTGCATATTCATTAGGGTTCATA
1 TAGTTGCATATTCAGTAGGGCCCATA
* **
129998 TAGTTGCATATTCATTAGGGTTCATA
1 TAGTTGCATATTCAGTAGGGCCCATA
*
130024 TAGTTGCATATTCAGTATGGG-ACATA
1 TAGTTGCATATTCAGTA-GGGCCCATA
*
130050 TAGTTCCATATTCAGTAGGG
1 TAGTTGCATATTCAGTAGGG
130070 GTCATCTGCA
Statistics
Matches: 444, Mismatches: 43, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
25 3 0.01
26 438 0.99
27 3 0.01
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (26 bp):
TAGTTGCATATTCAGTAGGGCCCATA
Found at i:132082 original size:62 final size:62
Alignment explanation
Indices: 132001--132282 Score: 519
Period size: 62 Copynumber: 4.5 Consensus size: 62
131991 TGAAGGCACG
*
132001 ACAGACACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
132063 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
*
132125 ACAGGCACGGAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
* *
132187 GCAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTTCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
*
132249 GCAGGCACGAAGGTACACGAGAAGACAGAGGAAG
1 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAG
132283 ACAGACATGA
Statistics
Matches: 215, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 215 1.00
ACGTcount: A:0.36, C:0.22, G:0.39, T:0.04
Consensus pattern (62 bp):
ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
Found at i:132300 original size:34 final size:34
Alignment explanation
Indices: 132254--132343 Score: 162
Period size: 34 Copynumber: 2.6 Consensus size: 34
132244 GGCCAGCAGG
132254 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
*
132288 CATGAAGGTACACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
*
132322 CACGAAGATACACGAGAAGACA
1 CACGAAGGTACACGAGAAGACA
132344 CAGTGGTACT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.48, C:0.18, G:0.30, T:0.04
Consensus pattern (34 bp):
CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
Found at i:132450 original size:2 final size:2
Alignment explanation
Indices: 132445--132544 Score: 200
Period size: 2 Copynumber: 50.0 Consensus size: 2
132435 ACAGAAACAC
132445 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
132487 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
132529 AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 98 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.