Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016434.1 Corchorus olitorius cultivar O-4 contig16467, 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: 64646
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1514 original size:31 final size:31
Alignment explanation
Indices: 1422--1506 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
1412 TTTACGTGAC
1422 AATGCCACGTGGCATGGCCACATTGGACCAA
1 AATGCCACGTGGCATGGCCACATTGGACCAA
1453 AATGCCACGTGGCATGGCCACATTGGACCAA
1 AATGCCACGTGGCATGGCCACATTGGACCAA
* *
1484 AATGCCACGTGGCAAGGCTACAT
1 AATGCCACGTGGCATGGCCACAT
1507 CAGACCAAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.16
Consensus pattern (31 bp):
AATGCCACGTGGCATGGCCACATTGGACCAA
Found at i:16932 original size:15 final size:15
Alignment explanation
Indices: 16912--16941 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16902 AGCTTGAGAT
16912 AGAAGATGAAGATGA
1 AGAAGATGAAGATGA
*
16927 AGAAGATGATGATGA
1 AGAAGATGAAGATGA
16942 TGAGGATGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (15 bp):
AGAAGATGAAGATGA
Found at i:16937 original size:3 final size:3
Alignment explanation
Indices: 16916--17004 Score: 52
Period size: 3 Copynumber: 29.7 Consensus size: 3
16906 TGAGATAGAA
* * * * * * * *
16916 GAT GAA GAT GAA GAA GAT GAT GAT GAT GAG GAT GAG GAC GAA GAT GAG
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * * * * *
16964 GAG GAA GAG GAT GAG GAT GAG GAT GAT GAT GAG GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
17005 AGAAGAAACA
Statistics
Matches: 66, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.39, C:0.01, G:0.43, T:0.17
Consensus pattern (3 bp):
GAT
Found at i:16973 original size:27 final size:27
Alignment explanation
Indices: 16928--16989 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
16918 TGAAGATGAA
* * *
16928 GAAGATGATGATGATGAGGATGAGGAC
1 GAAGATGAGGAGGAAGAGGATGAGGAC
*
16955 GAAGATGAGGAGGAAGAGGATGAGGAT
1 GAAGATGAGGAGGAAGAGGATGAGGAC
*
16982 GAGGATGA
1 GAAGATGA
16990 TGATGAGGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.39, C:0.02, G:0.45, T:0.15
Consensus pattern (27 bp):
GAAGATGAGGAGGAAGAGGATGAGGAC
Found at i:23709 original size:15 final size:17
Alignment explanation
Indices: 23681--23717 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
23671 AGTTTCTCTG
*
23681 TTTTTCTTCTAAATAT-
1 TTTTTATTCTAAATATC
23697 TTTTTATTC-AAATATC
1 TTTTTATTCTAAATATC
23713 TTTTT
1 TTTTT
23718 CTTTAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTATTCTAAATATC
Found at i:25425 original size:31 final size:31
Alignment explanation
Indices: 25390--25487 Score: 124
Period size: 31 Copynumber: 3.2 Consensus size: 31
25380 CGAGGCATGC
* * *
25390 CACGTGTCACTTTTCGATACACATGGCGTGA
1 CACGTGTCGCTTTTTGGTACACATGGCGTGA
* * *
25421 CACGTGTCGCTTTTTGGTACACGTAGCGTGT
1 CACGTGTCGCTTTTTGGTACACATGGCGTGA
* *
25452 CACGTGTCGCTTTTTGGTACACATGGCATGC
1 CACGTGTCGCTTTTTGGTACACATGGCGTGA
25483 CACGT
1 CACGT
25488 CGGACACCGT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.32
Consensus pattern (31 bp):
CACGTGTCGCTTTTTGGTACACATGGCGTGA
Found at i:26483 original size:17 final size:17
Alignment explanation
Indices: 26461--26500 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
26451 TCAGCCCCGT
*
26461 AGATCACTAGTGAT-CTA
1 AGATCACCAGTGATGC-A
26478 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
26495 AGATCA
1 AGATCA
26501 TCGGTAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:27611 original size:16 final size:16
Alignment explanation
Indices: 27590--27624 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
27580 ACAAATTACA
27590 AACAAACTCACAAAAT
1 AACAAACTCACAAAAT
27606 AACAAACTCACAAAAT
1 AACAAACTCACAAAAT
27622 AAC
1 AAC
27625 TACATACCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.63, C:0.26, G:0.00, T:0.11
Consensus pattern (16 bp):
AACAAACTCACAAAAT
Found at i:31674 original size:3 final size:3
Alignment explanation
Indices: 31666--31758 Score: 159
Period size: 3 Copynumber: 30.3 Consensus size: 3
31656 CACACCTGAG
31666 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAGA GAGA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GA-A GAA GAA GAA
*
31713 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
31759 GAAACCAGCT
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
3 80 0.92
4 7 0.08
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:32176 original size:15 final size:15
Alignment explanation
Indices: 32160--32208 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
32150 TGCAGATTTC
*
32160 TTTTTTCCTTTTTTC
1 TTTTTTCCTTTTTTA
*
32175 TTTTTTCTTTTTTTA
1 TTTTTTCCTTTTTTA
* *
32190 ATTTGTCCTTTTTTA
1 TTTTTTCCTTTTTTA
32205 TTTT
1 TTTT
32209 CTTTCGTATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.06, C:0.12, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTTCCTTTTTTA
Found at i:32188 original size:8 final size:7
Alignment explanation
Indices: 32156--32187 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
32146 GGAATGCAGA
32156 TTTCTTT
1 TTTCTTT
32163 TTTCCTTT
1 TTT-CTTT
32171 TTTCTTT
1 TTTCTTT
32178 TTTCTTT
1 TTTCTTT
32185 TTT
1 TTT
32188 TAATTTGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTCTTT
Found at i:33545 original size:3 final size:3
Alignment explanation
Indices: 33532--33592 Score: 113
Period size: 3 Copynumber: 20.0 Consensus size: 3
33522 TATCCAAATA
33532 TAT TGAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
33578 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
33593 GTAAGAAATG
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:33809 original size:6 final size:6
Alignment explanation
Indices: 33798--33825 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
33788 CTAATGAATC
33798 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
33826 TCATTTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:36064 original size:2 final size:2
Alignment explanation
Indices: 36057--36085 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36047 ATTATAAGCA
36057 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36086 GCTAGATTCG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53076 original size:81 final size:81
Alignment explanation
Indices: 52941--53104 Score: 256
Period size: 81 Copynumber: 2.0 Consensus size: 81
52931 ATTAGATAGT
* * *
52941 TCCTTCAAATACTCTGATGAAGAAGGCATGAAGGATTCCAGGGTCCTAACAGAGTCTTTGATTAC
1 TCCTTCAAATACTCTGAAGAAGAAGGCATGAAGGACTCCAGGGTCCTAACAGAGTCTTTGACTAC
*
53006 TATGTTTTGGGTGGTA
66 TATGTCTTGGGTGGTA
* ** *
53022 TCCTTCATATACTCTGAAGAAGAAGGCATGGGGGACTCCGGGGTCCTAACAGAGTCTTTGACTAC
1 TCCTTCAAATACTCTGAAGAAGAAGGCATGAAGGACTCCAGGGTCCTAACAGAGTCTTTGACTAC
53087 TATGTCTTGGGTGGTA
66 TATGTCTTGGGTGGTA
53103 TC
1 TC
53105 AGTTTTGACA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (81 bp):
TCCTTCAAATACTCTGAAGAAGAAGGCATGAAGGACTCCAGGGTCCTAACAGAGTCTTTGACTAC
TATGTCTTGGGTGGTA
Found at i:60862 original size:2 final size:2
Alignment explanation
Indices: 60855--60892 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
60845 GTTGAGCAGA
60855 AT 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 AT
60893 TGTAGTGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62500 original size:17 final size:17
Alignment explanation
Indices: 62478--62510 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
62468 CTTGATCATC
62478 AAAAGTTGCTATATATA
1 AAAAGTTGCTATATATA
62495 AAAAGTTGCTATATAT
1 AAAAGTTGCTATATAT
62511 CAGCAACTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (17 bp):
AAAAGTTGCTATATATA
Done.