Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021361.1 Corchorus olitorius cultivar O-4 contig21394, 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: 27183
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:4634 original size:19 final size:18
Alignment explanation
Indices: 4601--4636 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4591 TTGAGATAAT
4601 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
4619 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
4637 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:11280 original size:21 final size:21
Alignment explanation
Indices: 11255--11295 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
11245 AACGCAAGTA
11255 ATGAAATGAAACAAGTAACTT
1 ATGAAATGAAACAAGTAACTT
*
11276 ATGAAATGAGACAAGTAACT
1 ATGAAATGAAACAAGTAACT
11296 CAAACATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.17, T:0.22
Consensus pattern (21 bp):
ATGAAATGAAACAAGTAACTT
Found at i:11779 original size:36 final size:36
Alignment explanation
Indices: 11697--11789 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 36
11687 ACGAAATCTA
* * *
11697 AACAGAGACATAAACAAGTTTCTAAACGAAACATTG
1 AACAGAGACCTAAGCAGGTTTCTAAACGAAACATTG
* *
11733 AACAGAGACCTAAGCAGGTTTCTAAACGAAGCTTTG
1 AACAGAGACCTAAGCAGGTTTCTAAACGAAACATTG
**
11769 AACATTGACCTAAGCAGGTTT
1 AACAGAGACCTAAGCAGGTTT
11790 AATCAAACGA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (36 bp):
AACAGAGACCTAAGCAGGTTTCTAAACGAAACATTG
Found at i:11856 original size:39 final size:39
Alignment explanation
Indices: 11775--12188 Score: 254
Period size: 39 Copynumber: 10.9 Consensus size: 39
11765 TTTGAACATT
* * * * * * *
11775 GACCTAAGCAGGTTTAATCAAA-CGAGATTCTAAGCGGG
1 GACCTAAGCAGGTTTACTTAAATAGAAACTCTAAGCAGA
* * *
11813 GACCTAAGCAGGTTTTCTTAAATAGAAATTCTAAGCACA
1 GACCTAAGCAGGTTTACTTAAATAGAAACTCTAAGCAGA
* *
11852 GACCTAAGCAGGTTTACCT-AATCA-AAGCTCTAAGCAGA
1 GACCTAAGCAGGTTTACTTAAAT-AGAAACTCTAAGCAGA
* * * * *
11890 GATCCTAAACGGGTTTTCTTAAAT-GAAAATTCTAAGTAGA
1 GA-CCTAAGCAGGTTTACTTAAATAG-AAACTCTAAGCAGA
* * * **
11930 GAGCTGAGCAGGTTTTCTTAAGCA-AAACTCTAAGCAGA
1 GACCTAAGCAGGTTTACTTAAATAGAAACTCTAAGCAGA
* *
11968 GACCTAAGCAGGTTTGA-TTAAA-CGAAGCTCTAAGCAGA
1 GACCTAAGCAGGTTT-ACTTAAATAGAAACTCTAAGCAGA
* * * * *
12006 GGCCTAAGCAGGTTTACTGAAATGGAAATTCTAAAC-GA
1 GACCTAAGCAGGTTTACTTAAATAGAAACTCTAAGCAGA
* * * *
12044 GGACCTAAGCAGGTTGGA-TTGAA-CGAAGCTCTAAGCAGA
1 -GACCTAAGCAGGTT-TACTTAAATAGAAACTCTAAGCAGA
*
12083 GATCCTAAGCAGGTTTACTTAAA-CG--A----AA-CAGA
1 GA-CCTAAGCAGGTTTACTTAAATAGAAACTCTAAGCAGA
* ** * * *
12115 GACCTAAGCAGGTTAACTTAAACGGAAATTCTAAACATA
1 GACCTAAGCAGGTTTACTTAAATAGAAACTCTAAGCAGA
* *
12154 GACCTAAGCAGGTTTACTTGAAT-GAAACCCTAAGC
1 GACCTAAGCAGGTTTACTTAAATAGAAACTCTAAGC
12189 CAAGAGAAAC
Statistics
Matches: 292, Mismatches: 60, Indels: 48
0.73 0.15 0.12
Matches are distributed among these distances:
31 19 0.07
32 7 0.02
33 2 0.01
34 1 0.00
37 1 0.00
38 120 0.41
39 125 0.43
40 17 0.06
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.23
Consensus pattern (39 bp):
GACCTAAGCAGGTTTACTTAAATAGAAACTCTAAGCAGA
Found at i:11931 original size:40 final size:38
Alignment explanation
Indices: 11801--12058 Score: 169
Period size: 38 Copynumber: 6.7 Consensus size: 38
11791 ATCAAACGAG
* * *
11801 ATTCTAAGCGGGGACCTAAGCAGGTTTTCTTAAATAGAA
1 ATTCTAAGCAGAGACCTAAACAGGTTTTCTTAAATA-AA
* * * *
11840 ATTCTAAGCACAGACCTAAGCAGGTTTACCT-AATCAAA
1 ATTCTAAGCAGAGACCTAAACAGGTTTTCTTAAAT-AAA
** *
11878 GCTCTAAGCAGAGATCCTAAACGGGTTTTCTTAAATGAAA
1 ATTCTAAGCAGAGA-CCTAAACAGGTTTTCTTAAAT-AAA
* * * * **
11918 ATTCTAAGTAGAGAGCTGAGCAGGTTTTCTTAAGCAAA
1 ATTCTAAGCAGAGACCTAAACAGGTTTTCTTAAATAAA
* * ** **
11956 ACTCTAAGCAGAGACCTAAGCAGGTTTGATTAAACGAA
1 ATTCTAAGCAGAGACCTAAACAGGTTTTCTTAAATAAA
** * * * * *
11994 GCTCTAAGCAGAGGCCTAAGCAGGTTTACTGAAATGGAA
1 ATTCTAAGCAGAGACCTAAACAGGTTTTCTTAAAT-AAA
* *
12033 ATTCTAAAC-GAGGACCTAAGCAGGTT
1 ATTCTAAGCAGA-GACCTAAACAGGTT
12059 GGATTGAACG
Statistics
Matches: 174, Mismatches: 40, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
38 80 0.46
39 77 0.44
40 17 0.10
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (38 bp):
ATTCTAAGCAGAGACCTAAACAGGTTTTCTTAAATAAA
Found at i:12039 original size:77 final size:75
Alignment explanation
Indices: 11693--12171 Score: 270
Period size: 77 Copynumber: 6.4 Consensus size: 75
11683 CTGAACGAAA
* * * * *
11693 TCTAAACAGAGACATAAACAAGTTT-CTAAACGAAACAT-TGAA-CAGAGACCTAAGCAGGTTT-
1 TCTAAGCAGAGACCTAAGCAGGTTTACTAAAGGAAAC-TCT-AAGCAGAGACCTAAGCAGGTTTG
*
11754 -CTAAACGAAGC
64 ATTAAACGAAGC
* ** * * * * * * *
11765 TTTGAA-CATTGACCTAAGCAGGTTTAATCAAACGAGATTCTAAGCGGGGACCTAAGCAGGTTTT
1 TCT-AAGCAGAGACCTAAGCAGGTTTACT-AAAGGAAACTCTAAGCAGAGACCTAAGCAGGTTTG
* * **
11829 CTTAAATAGAAAT
64 ATTAAA-CGAAGC
* ** * *
11842 TCTAAGCACAGACCTAAGCAGGTTTACCT-AATCAAAGCTCTAAGCAGAGATCCTAAACGGGTTT
1 TCTAAGCAGAGACCTAAGCAGGTTTA-CTAAAGGAAA-CTCTAAGCAGAGA-CCTAAGCAGGTTT
** * **
11906 TCTTAAATGAAAAT
63 GATTAAACG-AAGC
* * * * * *
11920 TCTAAGTAGAGAGCTGAGCAGGTTTTCTTAAGCAAAACTCTAAGCAGAGACCTAAGCAGGTTTGA
1 TCTAAGCAGAGACCTAAGCAGGTTTACTAAAG-GAAACTCTAAGCAGAGACCTAAGCAGGTTTGA
11985 TTAAACGAAGC
65 TTAAACGAAGC
* * * *
11996 TCTAAGCAGAGGCCTAAGCAGGTTTACTGAAATGGAAATTCTAAAC-GAGGACCTAAGCAGGTTG
1 TCTAAGCAGAGACCTAAGCAGGTTTACT-AAA-GGAAACTCTAAGCAGA-GACCTAAGCAGGTTT
*
12060 GATTGAACGAAGC
63 GATTAAACGAAGC
* *
12073 TCTAAGCAGAGATCCTAAGCAGGTTTACTTAAACG--A----AA-CAGAGACCTAAGCAGG-TTA
1 TCTAAGCAGAGA-CCTAAGCAGGTTTAC-TAAAGGAAACTCTAAGCAGAGACCTAAGCAGGTTTG
**
12130 ACTTAAACGGAAAT
64 A-TTAAAC-GAAGC
* *
12144 TCTAAACATAGACCTAAGCAGGTTTACT
1 TCTAAGCAGAGACCTAAGCAGGTTTACT
12172 TGAATGAAAC
Statistics
Matches: 322, Mismatches: 62, Indels: 49
0.74 0.14 0.11
Matches are distributed among these distances:
69 3 0.01
70 33 0.10
71 17 0.05
72 16 0.05
73 6 0.02
74 25 0.08
75 1 0.00
76 37 0.11
77 102 0.32
78 78 0.24
79 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (75 bp):
TCTAAGCAGAGACCTAAGCAGGTTTACTAAAGGAAACTCTAAGCAGAGACCTAAGCAGGTTTGAT
TAAACGAAGC
Found at i:12122 original size:31 final size:32
Alignment explanation
Indices: 12079--12138 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
12069 AAGCTCTAAG
*
12079 CAGAGATCCTAAGCAGGTTTACTTAAACGAAA
1 CAGAGATCCTAAGCAGGTTAACTTAAACGAAA
12111 CAGAGA-CCTAAGCAGGTTAACTTAAACG
1 CAGAGATCCTAAGCAGGTTAACTTAAACG
12139 GAAATTCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (32 bp):
CAGAGATCCTAAGCAGGTTAACTTAAACGAAA
Found at i:12175 original size:109 final size:111
Alignment explanation
Indices: 11957--12167 Score: 279
Period size: 109 Copynumber: 1.9 Consensus size: 111
11947 TTAAGCAAAA
* *
11957 CTCTAAGCAGAGACCTAAGCAGGTTTGATTAAACGAAGCTCTAAGCAGAGGCCTAAGCAGGTTTA
1 CTCTAAGCAGAGACCTAAGCAGGTTTGATTAAACGAA---C-AAGCAGAGACCTAAGCAGGTTAA
* *
12022 CTGAAATGGAAATTCTAAACGAGGACCTAAGCAGGTTGGATTGAACGAAG
62 CTGAAACGGAAATTCTAAACGAAGACCTAAGCAGGTTGGATTGAACGAAG
12072 CTCTAAGCAGAGATCCTAAGCAGGTTT-ACTTAAACG-A-AA-CAGAGACCTAAGCAGGTTAACT
1 CTCTAAGCAGAGA-CCTAAGCAGGTTTGA-TTAAACGAACAAGCAGAGACCTAAGCAGGTTAACT
*
12133 TAAACGGAAATTCTAAAC-ATAGACCTAAGCAGGTT
64 GAAACGGAAATTCTAAACGA-AGACCTAAGCAGGTT
12168 TACTTGAATG
Statistics
Matches: 88, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
108 1 0.01
109 50 0.57
110 2 0.02
115 15 0.17
116 20 0.23
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.21
Consensus pattern (111 bp):
CTCTAAGCAGAGACCTAAGCAGGTTTGATTAAACGAACAAGCAGAGACCTAAGCAGGTTAACTGA
AACGGAAATTCTAAACGAAGACCTAAGCAGGTTGGATTGAACGAAG
Found at i:14947 original size:2 final size:2
Alignment explanation
Indices: 14895--14928 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
14885 AGATAGCAAG
*
14895 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14929 GAAAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21792 original size:29 final size:28
Alignment explanation
Indices: 21748--21831 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 28
21738 TATTTTCTTC
*
21748 TTTGCGTTTTAGAAAAAAAAAATTGCGTT
1 TTTGCGTTTTAAAAAAAAAAAATT-CGTT
*
21777 TTTGCGTTTTAAAAAAAAATATATATTTGTT
1 TTTGCGTTTTAAAAAAAAA-A-A-ATTCGTT
*
21808 TCTGCGTTTTCAAAAAGAAAAAAA
1 TTTGCGTTTT-AAAAA-AAAAAAA
21832 AATATTTTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
29 18 0.38
30 2 0.04
31 14 0.30
32 9 0.19
33 4 0.09
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (28 bp):
TTTGCGTTTTAAAAAAAAAAAATTCGTT
Found at i:24927 original size:21 final size:21
Alignment explanation
Indices: 24883--24977 Score: 109
Period size: 21 Copynumber: 4.4 Consensus size: 21
24873 CCACTACCAA
* *
24883 GCCACAACCAGGCCATTCACCGT
1 GCCACCACC-GGCCATGC-CCGT
** *
24906 GCCACCACCGGTTAAGCCCGT
1 GCCACCACCGGCCATGCCCGT
24927 GCCACCACCGGCCATGCCCGT
1 GCCACCACCGGCCATGCCCGT
*
24948 GCCACCAACGGCCATGCCCGT
1 GCCACCACCGGCCATGCCCGT
*
24969 GCCATCACC
1 GCCACCACC
24978 ATTCCAAGCC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 49 0.80
22 4 0.07
23 8 0.13
ACGTcount: A:0.20, C:0.47, G:0.21, T:0.12
Consensus pattern (21 bp):
GCCACCACCGGCCATGCCCGT
Done.