Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021683.1 Corchorus olitorius cultivar O-4 contig21716, 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: 23477
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:599 original size:88 final size:88
Alignment explanation
Indices: 491--667 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
481 TTCAACTCAA
491 TCAAAATTCATCAAAGTCCCAACTAATATAACAACTATAGAGGGAAATTGATATTAAAAAAATAT
1 TCAAAATTCATCAAAGTCCCAACTAATATAACAACTATAGAGGGAAATTGATATTAAAAAAATAT
556 ACACAAAATTGGGATGCCAATTG
66 ACACAAAATTGGGATGCCAATTG
579 TCAAAATTCATCAAAGTCCCAACTAATATAACAACTATAGAGGGAAATTGATATTAAAAAAATAT
1 TCAAAATTCATCAAAGTCCCAACTAATATAACAACTATAGAGGGAAATTGATATTAAAAAAATAT
644 ACACAAAATTGGGATGCCAATTG
66 ACACAAAATTGGGATGCCAATTG
667 T
1 T
668 ATCTGGAATG
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.25
Consensus pattern (88 bp):
TCAAAATTCATCAAAGTCCCAACTAATATAACAACTATAGAGGGAAATTGATATTAAAAAAATAT
ACACAAAATTGGGATGCCAATTG
Found at i:2887 original size:42 final size:42
Alignment explanation
Indices: 2828--2912 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
2818 TTTAGACCAG
2828 TTTTATTGTAATTTCACTTCTCCTAATTATTGTTTCTTATAA
1 TTTTATTGTAATTTCACTTCTCCTAATTATTGTTTCTTATAA
2870 TTTTATTGTAATTTCACTTCTCCTAATTATTGTTTCTTATAA
1 TTTTATTGTAATTTCACTTCTCCTAATTATTGTTTCTTATAA
2912 T
1 T
2913 ATATATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.14, G:0.05, T:0.58
Consensus pattern (42 bp):
TTTTATTGTAATTTCACTTCTCCTAATTATTGTTTCTTATAA
Found at i:3836 original size:12 final size:12
Alignment explanation
Indices: 3821--3909 Score: 62
Period size: 12 Copynumber: 7.7 Consensus size: 12
3811 TATAAATATT
3821 TTATATATATAA
1 TTATATATATAA
**
3833 TTATATAT-TTG
1 TTATATATATAA
*
3844 TTTTATA-ATTAA
1 TTATATATA-TAA
*
3856 TTTTATATATAA
1 TTATATATATAA
3868 -TATA-ACTATAA
1 TTATATA-TATAA
* **
3879 -TATATATTTTG
1 TTATATATATAA
3890 TTATATATATAA
1 TTATATATATAA
3902 TTATATAT
1 TTATATAT
3910 TTTGTTTTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
10 1 0.02
11 21 0.36
12 36 0.61
13 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (12 bp):
TTATATATATAA
Found at i:3888 original size:29 final size:29
Alignment explanation
Indices: 3847--3956 Score: 79
Period size: 29 Copynumber: 3.8 Consensus size: 29
3837 ATATTTGTTT
3847 TATAAT-TA-ATTTTATATATA-ATATAA
1 TATAATATATATTTTATATATATATATAA
*
3873 CTATAATATATATTTTGT-TATATATATAA
1 -TATAATATATATTTTATATATATATATAA
* * *
3902 T-TATATATTTTGTTTTATAATTTATATATAA
1 TATA-ATA-TATATTTTAT-ATATATATATAA
3933 TATAATTATAATATATTTA-ATATA
1 TATAA-TAT-ATAT-TTTATATATA
3957 AAATCCATTC
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
27 8 0.12
28 10 0.16
29 19 0.30
31 17 0.27
32 6 0.09
33 4 0.06
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.54
Consensus pattern (29 bp):
TATAATATATATTTTATATATATATATAA
Found at i:3937 original size:65 final size:69
Alignment explanation
Indices: 3821--3948 Score: 203
Period size: 65 Copynumber: 1.9 Consensus size: 69
3811 TATAAATATT
3821 TTATATATATAATTATATATTTGTTTTATAATTAATTTTATATATAATATAACTATAATATATAT
1 TTATATATATAATTATATATTTGTTTTATAATTAATTTTATATATAATATAACTATAATATATAT
3886 TTTG
66 TTTG
*
3890 TTATATATATAATTATATATTT-TGTTT-T-A-TAA-TTTATATATAATATAATTATAATATAT
1 TTATATATATAATTATATATTTGT-TTTATAATTAATTTTATATATAATATAACTATAATATAT
3949 TTAATATAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
65 26 0.46
66 3 0.05
67 1 0.02
68 2 0.04
69 25 0.44
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (69 bp):
TTATATATATAATTATATATTTGTTTTATAATTAATTTTATATATAATATAACTATAATATATAT
TTTG
Found at i:3940 original size:36 final size:36
Alignment explanation
Indices: 3804--3942 Score: 128
Period size: 36 Copynumber: 3.9 Consensus size: 36
3794 CGGTCAATAG
3804 TTTT-TTTTATAAATATT-TTATATATATAATTATATA
1 TTTTGTTTTAT-AAT-TTATTATATATATAATTATATA
* *
3840 -TTTGTTTTATAATTAATTTTATATATAA-TATA-A
1 TTTTGTTTTATAATTTATTATATATATAATTATATA
* * ** * * *
3873 CTATAATATATATTTTGTTATATATATAATTATATA
1 TTTTGTTTTATAATTTATTATATATATAATTATATA
3909 TTTTGTTTTATAATTTA-TATATAATATAATTATA
1 TTTTGTTTTATAATTTATTATAT-ATATAATTATA
3943 ATATATTTAA
Statistics
Matches: 80, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
33 1 0.01
34 25 0.31
35 26 0.32
36 28 0.35
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.58
Consensus pattern (36 bp):
TTTTGTTTTATAATTTATTATATATATAATTATATA
Found at i:5612 original size:46 final size:47
Alignment explanation
Indices: 5559--5651 Score: 152
Period size: 49 Copynumber: 2.0 Consensus size: 47
5549 CATTACCTAA
*
5559 ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATAT
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATAT
5605 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAT
5652 TAATTGTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
46 6 0.14
49 37 0.86
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (47 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATAT
Found at i:8412 original size:37 final size:37
Alignment explanation
Indices: 8325--8414 Score: 144
Period size: 37 Copynumber: 2.4 Consensus size: 37
8315 ACAAATCAAA
* *
8325 TCAAGCCCAATGCTTTCAACTATCAAATTTTCAACTC
1 TCAAGCCCAGTGCTTTCAACTATCAAACTTTCAACTC
*
8362 TCAAGCCTAGTGCTTTCAACTATCAAACTTTCAACTC
1 TCAAGCCCAGTGCTTTCAACTATCAAACTTTCAACTC
*
8399 TCAAGCCCCGTGCTTT
1 TCAAGCCCAGTGCTTT
8415 TACTCTCATT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (37 bp):
TCAAGCCCAGTGCTTTCAACTATCAAACTTTCAACTC
Found at i:8759 original size:23 final size:23
Alignment explanation
Indices: 8732--8784 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
8722 GGCTATGTCA
*
8732 GGTTCGGTCTCGGGTTGGGTTAG
1 GGTTCGGACTCGGGTTGGGTTAG
*
8755 GGTTCGGACTCGGGTTGGGTTCG
1 GGTTCGGACTCGGGTTGGGTTAG
*
8778 GGCTCGG
1 GGTTCGG
8785 GTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.04, C:0.17, G:0.49, T:0.30
Consensus pattern (23 bp):
GGTTCGGACTCGGGTTGGGTTAG
Found at i:9144 original size:31 final size:31
Alignment explanation
Indices: 9099--9180 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
9089 AAAACAAATT
* *
9099 AAGCATTAAATTAAATAAATCATTAAAATGA
1 AAGCCTTAAATTAAACAAATCATTAAAATGA
*
9130 AAGCCTTGAATTAAACAAATCATTAAAATGA
1 AAGCCTTAAATTAAACAAATCATTAAAATGA
*
9161 AAGCTTTAAATTAAACAAAT
1 AAGCCTTAAATTAAACAAAT
9181 TAAAAGCTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (31 bp):
AAGCCTTAAATTAAACAAATCATTAAAATGA
Found at i:10654 original size:71 final size:71
Alignment explanation
Indices: 10552--10720 Score: 311
Period size: 71 Copynumber: 2.4 Consensus size: 71
10542 TATGGAACTA
*
10552 AGCTATTATTTGGCTTCTAAGTTCTTCAGATCGAGCATTTTTTTTATTGTCACGTGAACTTTATG
1 AGCTATCATTTGGCTTCTAAGTTCTTCAGATCGAGCATTTTTTTTATTGTCACGTGAACTTTATG
10617 ATATGG
66 ATATGG
* *
10623 AGCTATCATTTGGCTTCTAAGTTCTTTAGATCGAGCTTTTTTTTTATTGTCACGTGAACTTTATG
1 AGCTATCATTTGGCTTCTAAGTTCTTCAGATCGAGCATTTTTTTTATTGTCACGTGAACTTTATG
10688 ATATGG
66 ATATGG
10694 AGCTATCATTTGGCTTCTAAGTTCTTC
1 AGCTATCATTTGGCTTCTAAGTTCTTC
10721 TAACCATTTG
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 94 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (71 bp):
AGCTATCATTTGGCTTCTAAGTTCTTCAGATCGAGCATTTTTTTTATTGTCACGTGAACTTTATG
ATATGG
Found at i:10697 original size:38 final size:38
Alignment explanation
Indices: 10584--10697 Score: 87
Period size: 38 Copynumber: 3.1 Consensus size: 38
10574 TCTTCAGATC
*
10584 GAGCATTTTTTTTATTGTCACGTGAACTTTATGATATG
1 GAGCTTTTTTTTTATTGTCACGTGAACTTTATGATATG
* ** *** * * *
10622 GAGCTATCATTTGGCT-TCTAAGT--TCTTTA-G--ATC
1 GAGCTTTTTTTTTATTGTC-ACGTGAACTTTATGATATG
10655 GAGCTTTTTTTTTATTGTCACGTGAACTTTATGATATG
1 GAGCTTTTTTTTTATTGTCACGTGAACTTTATGATATG
10693 GAGCT
1 GAGCT
10698 ATCATTTGGC
Statistics
Matches: 50, Mismatches: 19, Indels: 14
0.60 0.23 0.17
Matches are distributed among these distances:
33 15 0.30
34 2 0.04
35 6 0.12
36 6 0.12
37 2 0.04
38 19 0.38
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (38 bp):
GAGCTTTTTTTTTATTGTCACGTGAACTTTATGATATG
Found at i:10874 original size:16 final size:16
Alignment explanation
Indices: 10849--10882 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
10839 ATGACTTTGC
10849 TCAGAATTGAAATTGT
1 TCAGAATTGAAATTGT
*
10865 TCAGACTTGAAATTGT
1 TCAGAATTGAAATTGT
10881 TC
1 TC
10883 TCTCACGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (16 bp):
TCAGAATTGAAATTGT
Found at i:13113 original size:45 final size:45
Alignment explanation
Indices: 13058--13154 Score: 160
Period size: 45 Copynumber: 2.2 Consensus size: 45
13048 AGTGCATTAC
*
13058 CTAA-ATTCTACTCCTCCATCTCTAGGGAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCCATCTCTAGAGAATTCATCAAAATAAAG
* *
13102 CTAATATTCTACTCCTCCATCTCTATATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCCATCTCTAGAGAATTCATCAAAATAAAG
13147 CTAATATT
1 CTAATATT
13155 AATTGTTGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 4 0.08
45 45 0.92
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (45 bp):
CTAATATTCTACTCCTCCATCTCTAGAGAATTCATCAAAATAAAG
Found at i:15123 original size:15 final size:15
Alignment explanation
Indices: 15080--15124 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
15070 TATCATCCAT
*
15080 AATATATCCTTCAAA
1 AATATATCCTTAAAA
*
15095 AATAAATCCTTTAAAA
1 AATATATCC-TTAAAA
*
15111 AATATATTCTTAAA
1 AATATATCCTTAAA
15125 TATCATTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATATCCTTAAAA
Found at i:20258 original size:21 final size:20
Alignment explanation
Indices: 20234--20281 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
20224 ATCGATTTCA
*
20234 AAATAAAGCAGATGATAAAGT
1 AAATAAAGAAGATGATAAA-T
*
20255 AAATAAGGAAGATGATAAAT
1 AAATAAAGAAGATGATAAAT
*
20275 AGATAAA
1 AAATAAA
20282 CGCATACAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.60, C:0.02, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATAAAGAAGATGATAAAT
Done.