Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015290.1 Corchorus olitorius cultivar O-4 contig15323, 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: 36561
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:16 original size:2 final size:2
Alignment explanation
Indices: 5--53 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
1 TGTG
5 TA TA GTA 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 TA TA TA
48 TA TA TA
1 TA TA TA
54 AAAGTTAGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:192 original size:41 final size:43
Alignment explanation
Indices: 124--324 Score: 225
Period size: 41 Copynumber: 4.7 Consensus size: 43
114 AGAGAATTGT
*
124 CCCTATGTTATAAATGTGTTT-ATGGACTTT-GATATAGA-TGC
1 CCCTGTGTTATAAATGTGTTTGA-GGACTTTAGATATAGAGTGC
* *
165 CTCTGTGTTATAAATGTGTTTGAGGACTTTGGA-ATAGAGGTGC
1 CCCTGTGTTATAAATGTGTTTGAGGACTTTAGATATAGA-GTGC
* * *
208 CCCTGTGTTATAAATGTGCTTGGGGACTTTAG-TATGGA-TGC
1 CCCTGTGTTATAAATGTGTTTGAGGACTTTAGATATAGAGTGC
* * * *
249 CTCTGTGTTATAAATGTGTTTGAGGACTTTAGAGAGAGAATTGC
1 CCCTGTGTTATAAATGTGTTTGAGGACTTTAGATATAG-AGTGC
* *
293 CCCTATGTTATAAATGTGTTTGGGGACTTTAG
1 CCCTGTGTTATAAATGTGTTTGAGGACTTTAG
325 GGAGGGAGAA
Statistics
Matches: 136, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
41 63 0.46
42 5 0.04
43 36 0.26
44 32 0.24
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.38
Consensus pattern (43 bp):
CCCTGTGTTATAAATGTGTTTGAGGACTTTAGATATAGAGTGC
Found at i:235 original size:84 final size:85
Alignment explanation
Indices: 112--324 Score: 304
Period size: 84 Copynumber: 2.5 Consensus size: 85
102 TCTTTGCCAT
* * **
112 AGAGAGAATTGTCCCTATGTTATAAATGTGTTTATGGACTTT-GATATAGATGCCTCTGTGTTAT
1 AGAGAGAAGTGCCCCTATGTTATAAATGTGTTTGGGGACTTTAG-TATAGATGCCTCTGTGTTAT
*
176 AAATGTGTTTGAGGACTTTGG
65 AAATGTGTTTGAGGACTTTAG
* * * * *
197 A-ATAGAGGTGCCCCTGTGTTATAAATGTGCTTGGGGACTTTAGTATGGATGCCTCTGTGTTATA
1 AGAGAGAAGTGCCCCTATGTTATAAATGTGTTTGGGGACTTTAGTATAGATGCCTCTGTGTTATA
261 AATGTGTTTGAGGACTTTAG
66 AATGTGTTTGAGGACTTTAG
*
281 AGAGAGAATTGCCCCTATGTTATAAATGTGTTTGGGGACTTTAG
1 AGAGAGAAGTGCCCCTATGTTATAAATGTGTTTGGGGACTTTAG
325 GGAGGGAGAA
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
84 72 0.65
85 39 0.35
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.38
Consensus pattern (85 bp):
AGAGAGAAGTGCCCCTATGTTATAAATGTGTTTGGGGACTTTAGTATAGATGCCTCTGTGTTATA
AATGTGTTTGAGGACTTTAG
Found at i:1817 original size:11 final size:11
Alignment explanation
Indices: 1801--1835 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
1791 TAATCATTAT
1801 CGTGTCTGACA
1 CGTGTCTGACA
1812 CGTGTCTGACA
1 CGTGTCTGACA
*
1823 CGTTTCTGACA
1 CGTGTCTGACA
1834 CG
1 CG
1836 AGACATGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.29
Consensus pattern (11 bp):
CGTGTCTGACA
Found at i:5575 original size:30 final size:30
Alignment explanation
Indices: 5541--5604 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
5531 CTCTTACGGA
5541 GTGTGAGTTTTCTTTGTAATTTATTTGTTT
1 GTGTGAGTTTTCTTTGTAATTTATTTGTTT
5571 GTGTGAGTTTTCTTTGTAATTTATTTGTTT
1 GTGTGAGTTTTCTTTGTAATTTATTTGTTT
5601 GTGT
1 GTGT
5605 ATTTAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.12, C:0.03, G:0.22, T:0.62
Consensus pattern (30 bp):
GTGTGAGTTTTCTTTGTAATTTATTTGTTT
Found at i:7330 original size:2 final size:2
Alignment explanation
Indices: 7323--7356 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
7313 TGTATCATAC
*
7323 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7357 GTAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7978 original size:2 final size:2
Alignment explanation
Indices: 7967--7998 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
7957 CGTCTAAAGA
7967 TC TC -C TC TC TC TC TC TC TC TC TC TC TC -C TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
7999 ATAACAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:23174 original size:19 final size:19
Alignment explanation
Indices: 23154--23190 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
23144 AATTAATTAT
23154 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
23172 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
23191 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:23201 original size:19 final size:19
Alignment explanation
Indices: 23160--23201 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
23150 TTATTTTAAT
* * *
23160 ATTATATTTTTATTTATAT
1 ATTATATTTTTACTTAAAA
23179 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
23198 ATTA
1 ATTA
23202 CTCATAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:23490 original size:25 final size:22
Alignment explanation
Indices: 23461--23511 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 22
23451 ATAATACAAG
23461 TTAATTTTAATTTATTCATTTAATT
1 TTAATTTT-A-TTATT-ATTTAATT
23486 TTAA-TTTATTATTATTTAATT
1 TTAATTTTATTATTATTTAATT
*
23507 ATAAT
1 TTAAT
23512 AAAAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 11 0.46
22 5 0.21
23 1 0.04
24 3 0.12
25 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TTAATTTTATTATTATTTAATT
Found at i:24026 original size:2 final size:2
Alignment explanation
Indices: 24019--24044 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24009 AGGAAACTAC
24019 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
24045 ATTCAATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24200 original size:12 final size:12
Alignment explanation
Indices: 24183--24237 Score: 83
Period size: 12 Copynumber: 4.5 Consensus size: 12
24173 TTAATACAGG
* *
24183 TATCGATGGTTA
1 TATCGACGGATA
24195 TATCGAACGGATA
1 TATCG-ACGGATA
24208 TATCGACGGATA
1 TATCGACGGATA
24220 TATCGACGGATA
1 TATCGACGGATA
24232 TATCGA
1 TATCGA
24238 GGTATCGATG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
12 30 0.75
13 10 0.25
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:24211 original size:25 final size:24
Alignment explanation
Indices: 24183--24237 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
24173 TTAATACAGG
* *
24183 TATCGATGGTTATATCGAACGGATA
1 TATCGACGGATATATCG-ACGGATA
24208 TATCGACGGATATATCGACGGATA
1 TATCGACGGATATATCGACGGATA
24232 TATCGA
1 TATCGA
24238 GGTATCGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (24 bp):
TATCGACGGATATATCGACGGATA
Found at i:24525 original size:25 final size:26
Alignment explanation
Indices: 24472--24525 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
24462 ATACTAATTT
* **
24472 AATTATACATTTATTTTTTTTTGTGA
1 AATTATACATTTATTTTATTTTGCAA
24498 AATTATACATTTATTTTATTTT-CAA
1 AATTATACATTTATTTTATTTTGCAA
24523 AAT
1 AAT
24526 GATGGTTACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (26 bp):
AATTATACATTTATTTTATTTTGCAA
Found at i:25347 original size:3 final size:3
Alignment explanation
Indices: 25339--25374 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
25329 TCATTTCCCC
25339 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA- CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
25375 TTTGGTGAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:27902 original size:20 final size:19
Alignment explanation
Indices: 27878--27915 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
27868 TGCATATGAA
27878 AAAAAAAAGGTTTATGCAT
1 AAAAAAAAGGTTTATGCAT
27897 AAAAAAAAGGTTTATGCAT
1 AAAAAAAAGGTTTATGCAT
27916 GATGAAACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (19 bp):
AAAAAAAAGGTTTATGCAT
Found at i:28708 original size:10 final size:10
Alignment explanation
Indices: 28693--28718 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28683 AATTGAATAT
28693 GGATATTTAC
1 GGATATTTAC
28703 GGATATTTAC
1 GGATATTTAC
28713 GGATAT
1 GGATAT
28719 ATCGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:28846 original size:12 final size:12
Alignment explanation
Indices: 28829--28867 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
28819 GTACAGATAT
28829 CGGATATATCGA
1 CGGATATATCGA
28841 CGGATATATCGA
1 CGGATATATCGA
28853 -GG---TATCGA
1 CGGATATATCGA
28861 CGGATAT
1 CGGATAT
28868 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:29280 original size:15 final size:15
Alignment explanation
Indices: 29260--29294 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
29250 TGGGCTTAAT
29260 TAAATTAAACAAGAG
1 TAAATTAAACAAGAG
29275 TAAATTAAACAAGAG
1 TAAATTAAACAAGAG
29290 TAAAT
1 TAAAT
29295 AAATCTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (15 bp):
TAAATTAAACAAGAG
Found at i:29358 original size:2 final size:2
Alignment explanation
Indices: 29351--29395 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
29341 TTCGGGAATT
*
29351 CA CA CA CA CA CA CA CA CA CA CA CA CA -A CA CA CA CA GA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
29392 CA CA
1 CA CA
29396 GATATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.47, G:0.02, T:0.00
Consensus pattern (2 bp):
CA
Found at i:29402 original size:2 final size:2
Alignment explanation
Indices: 29397--29432 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29387 ACACACACAG
29397 AT AT AT AT 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 AT AT AT AT
29433 CTAACCAAGT
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):
AT
Found at i:30225 original size:2 final size:2
Alignment explanation
Indices: 30218--30246 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30208 TAATATTTAG
30218 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30247 GTTATCGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32013 original size:30 final size:30
Alignment explanation
Indices: 31973--32037 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
31963 CATGAGGATA
* *
31973 AATCTTCATTTGATTTGAGGGAGTAGTTTG
1 AATCTCCATTTGATTTGAGAGAGTAGTTTG
32003 AATCTCCATTTGATTTGAGAGAGTAGTTTG
1 AATCTCCATTTGATTTGAGAGAGTAGTTTG
32033 AATCT
1 AATCT
32038 TCAAGAGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (30 bp):
AATCTCCATTTGATTTGAGAGAGTAGTTTG
Found at i:33835 original size:20 final size:18
Alignment explanation
Indices: 33811--33846 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
33801 TCGAATCATT
33811 ATATATATCCCAAGACTC
1 ATATATATCCCAAGACTC
33829 ATATATATCCCAAGACTC
1 ATATATATCCCAAGACTC
33847 CCGTAGTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.06, T:0.28
Consensus pattern (18 bp):
ATATATATCCCAAGACTC
Found at i:34019 original size:3 final size:3
Alignment explanation
Indices: 34011--34064 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
34001 GAATTTACAC
34011 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
34059 ATA ATA
1 ATA ATA
34065 TATTTAGGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:36412 original size:21 final size:21
Alignment explanation
Indices: 36386--36430 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
36376 AATTTGGGGA
*
36386 TTGCTAAATATCATCCCCTTT
1 TTGCTAAATATCACCCCCTTT
** *
36407 TTGCTAGTTATCGCCCCCTTT
1 TTGCTAAATATCACCCCCTTT
36428 TTG
1 TTG
36431 ACACTTTTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.29, G:0.11, T:0.44
Consensus pattern (21 bp):
TTGCTAAATATCACCCCCTTT
Done.