Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023307.1 Corchorus olitorius cultivar O-4 contig23340, 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: 36676
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:2235 original size:40 final size:39
Alignment explanation
Indices: 2159--2237 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
2149 GAGAGATTAC
* * * *
2159 AATTCTAGATAATTAAGGGGGTAGGAGTTATTATAACAT
1 AATTCTAAATAATAAAGGGGATAGGAGTTATCATAACAT
*
2198 AATTCTAAATAATCAAAGGGGATAGGATTTATCATAACAT
1 AATTCTAAATAAT-AAAGGGGATAGGAGTTATCATAACAT
2238 TTATGTGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 12 0.35
40 22 0.65
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.32
Consensus pattern (39 bp):
AATTCTAAATAATAAAGGGGATAGGAGTTATCATAACAT
Found at i:2440 original size:2 final size:2
Alignment explanation
Indices: 2433--2462 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2423 TACTATTTAG
2433 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
2463 GTTAAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23640 original size:19 final size:19
Alignment explanation
Indices: 23597--23637 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
23587 CTCATATGAC
**
23597 AAAGAAACAGTAGCAGAAG
1 AAAGAAACAGTAAAAGAAG
23616 AAAGAAACAAGTAAAAGAAG
1 AAAGAAAC-AGTAAAAGAAG
23636 AA
1 AA
23638 GAAGAGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.66, C:0.07, G:0.22, T:0.05
Consensus pattern (19 bp):
AAAGAAACAGTAAAAGAAG
Found at i:25649 original size:17 final size:17
Alignment explanation
Indices: 25629--25664 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25619 ATTTTCTTAT
* *
25629 TTTCTTCTTTTTTCCTC
1 TTTCTTCTTCTTCCCTC
25646 TTTCTTCTTCTTCCCTC
1 TTTCTTCTTCTTCCCTC
25663 TT
1 TT
25665 AGACCGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTCTTCTTCTTCCCTC
Found at i:31936 original size:14 final size:11
Alignment explanation
Indices: 31903--31927 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31893 GTTTATACTA
31903 AAATATTAATC
1 AAATATTAATC
31914 AAATATTAATC
1 AAATATTAATC
31925 AAA
1 AAA
31928 GTATATTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATATTAATC
Found at i:32888 original size:5 final size:6
Alignment explanation
Indices: 32874--32908 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
32864 ACGTTATTAC
32874 AAAATA AAAATA AAAATA AAAAT- AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
32909 GGGAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:32891 original size:12 final size:12
Alignment explanation
Indices: 32874--32908 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
32864 ACGTTATTAC
32874 AAAATAAAAATA
1 AAAATAAAAATA
32886 AAAATAAAAAT-
1 AAAATAAAAATA
32897 AAAATAAAAATA
1 AAAATAAAAATA
32909 GGGAAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAATAAAAATA
Found at i:33710 original size:3 final size:3
Alignment explanation
Indices: 33695--33736 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
33685 AGTATATACT
* *
33695 TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
33737 AAGTTATCCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:34083 original size:2 final size:2
Alignment explanation
Indices: 34076--34102 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34066 AATCTAGTGA
34076 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 A
34103 AATAAAAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36297 original size:16 final size:16
Alignment explanation
Indices: 36276--36310 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
36266 ACAATTCAGA
36276 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
36292 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
36308 AAG
1 AAG
36311 TATTTTCAGA
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:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:36463 original size:41 final size:41
Alignment explanation
Indices: 36406--36629 Score: 304
Period size: 41 Copynumber: 5.4 Consensus size: 41
36396 TTTTCGTTTG
36406 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
36447 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
** *
36488 TTCAAGATTGAGTCATCGAGACTCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
36529 TTCAAGAACAAGTCATCGAGACCCTTGAATCGAATTATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
* * * * *
36573 TTCAAGACCAAGTCGTCAAGACCCTTGAATTAGATTGTCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
36614 TTCAAGACCAAGTCAT
1 TTCAAGATCAAGTCAT
36630 TCGACCTTGA
Statistics
Matches: 165, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
41 127 0.77
42 2 0.01
43 1 0.01
44 35 0.21
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.29
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:36654 original size:126 final size:122
Alignment explanation
Indices: 36406--36646 Score: 297
Period size: 126 Copynumber: 2.0 Consensus size: 122
36396 TTTTCGTTTG
* * *** *
36406 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGATTGAGTCATCGAGACCC
1 TTCAAGAACAAGTCATCGAGACCCTTGAATGAAATTATCAATTCAAGACCAAGTCATCAAGACCC
*** * *
36471 TTGAATTAAATTATCAATTCAAGATTGAGTCATCGAGACTCTTGAATTAAATTATCAA
66 TTGAATTAAATTATCAATTCAAGACCAAGTCATC-AGACTCTTGAATCAAATAATCAA
*
36529 TTCAAGAACAAGTCATCGAGACCCTTGAATCGAATTATTATCAATTCAAGACCAAGTCGTCAAGA
1 TTCAAGAACAAGTCATCGAGACCCTTGAAT-GAA--ATTATCAATTCAAGACCAAGTCATCAAGA
* *
36594 CCCTTGAATTAGATTGTCAATTCAAGACCAAGTCATTC-GAC-CTTGAATCAAAT
63 CCCTTGAATTAAATTATCAATTCAAGACCAAGTCA-TCAGACTCTTGAATCAAAT
36647 CAAATCAAAC
Statistics
Matches: 101, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
123 29 0.29
124 13 0.13
125 3 0.03
126 54 0.53
127 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (122 bp):
TTCAAGAACAAGTCATCGAGACCCTTGAATGAAATTATCAATTCAAGACCAAGTCATCAAGACCC
TTGAATTAAATTATCAATTCAAGACCAAGTCATCAGACTCTTGAATCAAATAATCAA
Done.