Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020178.1 Corchorus olitorius cultivar O-4 contig20211, 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: 80533
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2194 original size:35 final size:35
Alignment explanation
Indices: 2139--2207 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
2129 TTAGTTGAAT
* * *
2139 ATTTATCATCTCTTATTATTTTGAAGTATTTTAAC
1 ATTTATCACCTCTTATTATTTTCAAGGATTTTAAC
*
2174 ATTTTTCACCTCTTATTATTTTCAAGGATTTTAA
1 ATTTATCACCTCTTATTATTTTCAAGGATTTTAA
2208 AAGAGATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.06, T:0.54
Consensus pattern (35 bp):
ATTTATCACCTCTTATTATTTTCAAGGATTTTAAC
Found at i:10873 original size:18 final size:18
Alignment explanation
Indices: 10850--10898 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
10840 CCCGAAAAAG
10850 GAAAAAGACATAAGGAA-A
1 GAAAAAGACA-AAGGAAGA
*
10868 GAAAAAGAGAAAGGAAGA
1 GAAAAAGACAAAGGAAGA
* *
10886 GGAAAAGAAAAAG
1 GAAAAAGACAAAG
10899 AAAAAGAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.67, C:0.02, G:0.29, T:0.02
Consensus pattern (18 bp):
GAAAAAGACAAAGGAAGA
Found at i:10880 original size:24 final size:23
Alignment explanation
Indices: 10843--10913 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
10833 GGCCTGGCCC
10843 GAAAAAGGAAAAAGACATAAGG-AAA
1 GAAAAA-GAAAAAGA-A-AAGGAAAA
* *
10868 GAAAAAGAGAAAGGAAGAGGAAAA
1 GAAAAAGA-AAAAGAAAAGGAAAA
*
10892 GAAAAAGAAAAAGAGAA-GAAAA
1 GAAAAAGAAAAAGAAAAGGAAAA
10914 TAGGAATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 5 0.13
23 9 0.23
24 14 0.36
25 11 0.28
ACGTcount: A:0.70, C:0.01, G:0.27, T:0.01
Consensus pattern (23 bp):
GAAAAAGAAAAAGAAAAGGAAAA
Found at i:21765 original size:21 final size:21
Alignment explanation
Indices: 21728--21771 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
21718 TGATCATTGT
* *
21728 AATTTCATTTTTATAAATAAA
1 AATTACATTTTTATAAAAAAA
21749 AATTACATTTTCT-TAAAAAAA
1 AATTACATTTT-TATAAAAAAA
21770 AA
1 AA
21772 ACTATTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTACATTTTTATAAAAAAA
Found at i:23034 original size:17 final size:17
Alignment explanation
Indices: 22987--23038 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 17
22977 ATATAGCTAC
22987 AAATTCTCATGAAATT-
1 AAATTCTCATGAAATTA
*
23003 -ATTTCTCA--AAA--A
1 AAATTCTCATGAAATTA
23015 AAATTCTCATGAAATTA
1 AAATTCTCATGAAATTA
23032 AAATTCT
1 AAATTCT
23039 ATATAGGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
13 10 0.36
15 10 0.36
17 8 0.29
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (17 bp):
AAATTCTCATGAAATTA
Found at i:28096 original size:3 final size:3
Alignment explanation
Indices: 28088--28141 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
28078 ATTAGTTCTT
28088 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
28136 ATA ATA
1 ATA ATA
28142 CTTAATTTTG
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:28371 original size:31 final size:32
Alignment explanation
Indices: 28329--28409 Score: 146
Period size: 32 Copynumber: 2.6 Consensus size: 32
28319 GAGACGGAAT
28329 AAACTCAATATCCAACATATTGCC-AAAAAAA
1 AAACTCAATATCCAACATATTGCCAAAAAAAA
*
28360 AAATTCAATATCCAACATATTGCCAAAAAAAA
1 AAACTCAATATCCAACATATTGCCAAAAAAAA
28392 AAACTCAATATCCAACAT
1 AAACTCAATATCCAACAT
28410 TTGAGTTTAG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 23 0.49
32 24 0.51
ACGTcount: A:0.54, C:0.22, G:0.02, T:0.21
Consensus pattern (32 bp):
AAACTCAATATCCAACATATTGCCAAAAAAAA
Found at i:41897 original size:2 final size:2
Alignment explanation
Indices: 41890--41915 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41880 AATCTATACA
41890 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
41916 TTTAAAAGAA
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):
AT
Found at i:45769 original size:4 final size:4
Alignment explanation
Indices: 45762--45815 Score: 108
Period size: 4 Copynumber: 13.5 Consensus size: 4
45752 TTTTTACCTA
45762 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
45810 AAAG AA
1 AAAG AA
45816 GGCCTTGATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:62307 original size:56 final size:56
Alignment explanation
Indices: 62217--62330 Score: 203
Period size: 56 Copynumber: 2.0 Consensus size: 56
62207 TATCTGTTTC
*
62217 CTTTCACAGCATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACAGCATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
62273 CTTTCACA-CAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
1 CTTTCACAGC-ATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
62329 CT
1 CT
62331 ACAAAATAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
55 1 0.02
56 55 0.98
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (56 bp):
CTTTCACAGCATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
Found at i:62452 original size:16 final size:16
Alignment explanation
Indices: 62431--62468 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
62421 ATTGTTTGAT
62431 AAGTATGAGATTTCGA
1 AAGTATGAGATTTCGA
62447 AAGTATGAGATTTCGA
1 AAGTATGAGATTTCGA
62463 AAGTAT
1 AAGTAT
62469 CATGATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (16 bp):
AAGTATGAGATTTCGA
Found at i:63032 original size:42 final size:42
Alignment explanation
Indices: 62973--63053 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
62963 TAAGGATCAG
62973 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
63015 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
63054 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:63783 original size:3 final size:3
Alignment explanation
Indices: 63775--63878 Score: 190
Period size: 3 Copynumber: 34.7 Consensus size: 3
63765 ATCGATCCAC
* *
63775 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
63823 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
63871 TTA TTA TT
1 TTA TTA TT
63879 TTCTTAAATT
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 97 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:69790 original size:30 final size:30
Alignment explanation
Indices: 69726--69794 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
69716 TAATTTTGTA
69726 CAATTTT-GACATTTTGTCCCCCTAAACTT
1 CAATTTTGGACATTTTGTCCCCCTAAACTT
* *
69755 TAATTTTGGACATTTTGT-CCCTTAAACTCT
1 CAATTTTGGACATTTTGTCCCCCTAAACT-T
69785 CAA-TTTGGAC
1 CAATTTTGGAC
69795 CCTTTTTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (30 bp):
CAATTTTGGACATTTTGTCCCCCTAAACTT
Found at i:70495 original size:53 final size:53
Alignment explanation
Indices: 70437--70655 Score: 257
Period size: 53 Copynumber: 4.2 Consensus size: 53
70427 TGGTGAGAAC
* * *
70437 TTTGAAAAACTGA-CTAAATTGAATACTTTGAAAATTGATGGGAACTTTCCCGA
1 TTTGAAAAA-TGAGCTAGATTGAATACTTTGAAAACTGATGGGAACTTTCCCAA
* *
70490 CTTGAAAAA-GAGCTAGATTGAATATTTTTGAAAACTGATGGGAACTTTCCCAA
1 TTTGAAAAATGAGCTAGATTGAATA-CTTTGAAAACTGATGGGAACTTTCCCAA
** * *
70543 TTTGAAAAAAAAGCTAGATTGAATGCTTTGTAAACTGATGGGAACTTT-CCAA
1 TTTGAAAAATGAGCTAGATTGAATACTTTGAAAACTGATGGGAACTTTCCCAA
*** * * *
70595 -AAAAAAAAGGAGCTAGATTGAATATTTTGAAAACTGGTGGGAACTTTCCCAA
1 TTTGAAAAATGAGCTAGATTGAATACTTTGAAAACTGATGGGAACTTTCCCAA
70647 TTTGAAAAA
1 TTTGAAAAA
70656 CTTAAATTGA
Statistics
Matches: 139, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
51 40 0.29
52 19 0.14
53 67 0.48
54 13 0.09
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (53 bp):
TTTGAAAAATGAGCTAGATTGAATACTTTGAAAACTGATGGGAACTTTCCCAA
Found at i:79406 original size:21 final size:24
Alignment explanation
Indices: 79377--79427 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
79367 TTTTGAACTC
79377 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
79400 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
79423 ATTAT
1 ATTAT
79428 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:79422 original size:25 final size:25
Alignment explanation
Indices: 79377--79425 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
79367 TTTTGAACTC
*
79377 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
79402 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
79426 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Done.