Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021499.1 Corchorus olitorius cultivar O-4 contig21532, 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: 20544
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Found at i:99 original size:28 final size:28
Alignment explanation
Indices: 67--663 Score: 358
Period size: 28 Copynumber: 21.4 Consensus size: 28
57 TTGTCTTCGA
67 GAGCGTACTACCTCTTCGCGATCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
95 GAGCGTACTACCGCTTCGCGGTCGTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
123 GAGCGTACCACCGCTTCGCGGTCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
151 GAGCGTACTACCGCTTCGCGCTCTCTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
179 GAGCGTACTACCTCTTTGCGATCCTTGA
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * * * *
207 GAGTGTACTACCACCTCGAGAGCTTGGAGG
1 GAGCGTACTACCTCTTCGCGATCTT--TGG
* * * ** * *
237 GGGCATTCTACCAATTCGTGAGCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
265 G-GCATACTACCGCTTCGCGGTCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
** * *
292 GAGCGTACTACGCAT-TT-TTG-TCTTCGA
1 GAGCGTACTAC-C-TCTTCGCGATCTTTGG
319 GAGCGTACTACCTCTTCGCGATCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
347 GAGCGTACTACCTCTTTGCGATCCTTGA
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* *
375 GAGCGTACTA-CTGCTTCGCGGTCGTTGG
1 GAGCGTACTACCT-CTTCGCGATCTTTGG
* *
403 GAGCGTACTA-CTGCTTCACGCTCTTTGG
1 GAGCGTACTACCT-CTTCGCGATCTTTGG
* * *
431 GAGCGTACTACCGCTTCACGCTCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * *
459 GAGCGTACTACCACCTCGAGAGC-TTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
486 AGGGCGTACTACCAT-TTCGTGAACTTT-G
1 -GAGCGTACTACC-TCTTCGCGATCTTTGG
* * * * *
514 AAGCGTACTACCACTTTGCGATCCTTGA
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * *
542 GAGCGTACTACCACCTCGGGAGC-TTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
569 AGGGAGTACTACCAT-TTCGCGAACTTT-G
1 -GAGCGTACTACC-TCTTCGCGATCTTTGG
* * * *
597 AAGCGTACTACCACTTCGAGAGC-TTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * *
624 AGGGTGTACTACCAT-TTCGCGAACTTTAG
1 -GAGCGTACTACC-TCTTCGCGATCTTTGG
*
653 GAGCGTTCTAC
1 GAGCGTACTAC
664 GCCTTAGGAT
Statistics
Matches: 441, Mismatches: 105, Indels: 46
0.74 0.18 0.08
Matches are distributed among these distances:
25 1 0.00
26 5 0.01
27 82 0.19
28 323 0.73
29 11 0.02
30 19 0.04
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (28 bp):
GAGCGTACTACCTCTTCGCGATCTTTGG
Found at i:602 original size:55 final size:56
Alignment explanation
Indices: 518--663 Score: 199
Period size: 55 Copynumber: 2.6 Consensus size: 56
508 ACTTTGAAGC
* * *
518 GTACTACCACTTT-GCGATCCTTGAGAGCGTACTACCACCTCGGGAGCTTGGAGGGA
1 GTACTACCA-TTTCGCGAACTTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGA
* *
574 GTACTACCATTTCGCGAACTTTGA-AGCGTACTACCACTTCGAGAGCTTGGAGGGT
1 GTACTACCATTTCGCGAACTTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGA
*
629 GTACTACCATTTCGCGAACTTT-AGGAGCGTTCTAC
1 GTACTACCATTTCGCGAACTTTGA-GAGCGTACTAC
664 GCCTTAGGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
54 1 0.01
55 53 0.65
56 27 0.33
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (56 bp):
GTACTACCATTTCGCGAACTTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGA
Found at i:637 original size:83 final size:83
Alignment explanation
Indices: 180--617 Score: 285
Period size: 83 Copynumber: 5.2 Consensus size: 83
170 GCTCTCTGGG
* * * * * *
180 AGCGTACTACCTCTTTGCGATCCTTGAGAGTGTACTACCACCTCGAGAGCTTGGAGGGGGCATTC
1 AGCGTACTACCACTTCGAGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGAG--TAC
* * * *
245 TACCAATTCGTGAGCTTTGG
64 TACCATTTCGCGAACTTTGA
* * * * * * * * *** * * * *
265 GGCATACTACCGCTTCGCGGTCTTTGGGAGCGTACTACGCA-TTTTTG-TCTTCGAGAGCGTACT
1 AGCGTACTACCACTTCGAGATCCTTGAGAGCGTACTAC-CACCTCGAGAGCTTGGAGGGAGTACT
* *
328 ACC-TCTTCGCGATCTTTGGG
65 ACCAT-TTCGCGAACTTT-GA
* * * ** * * * *
348 AGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACTGCTTCGCG-GTCGTTGG-GAGCGTAC
1 AGCGTACTACCACTTCGAGATCCTTGAGAGCGTACTACCACCTCGAGAG-C-TTGGAGGGAGTAC
*** * ** *
411 TACTGCTTCACGCTCTTTGGG
64 TACCATTTCGCGAACTTT-GA
* * * * *
432 AGCGTACTACCGCTTC-ACGCTCTTTGGGAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTACT
1 AGCGTACTACCACTTCGA-GATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGAGTACT
*
496 ACCATTTCGTGAACTTTGA
65 ACCATTTCGCGAACTTTGA
* * *
515 AGCGTACTACCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGGGAGCTTGGAGGGAGTACTA
1 AGCGTACTACCACTTCGAGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGAGTACTA
580 CCATTTCGCGAACTTTGA
66 CCATTTCGCGAACTTTGA
598 AGCGTACTACCACTTCGAGA
1 AGCGTACTACCACTTCGAGA
618 GCTTGGAGGG
Statistics
Matches: 274, Mismatches: 68, Indels: 24
0.75 0.19 0.07
Matches are distributed among these distances:
82 16 0.06
83 132 0.48
84 88 0.32
85 36 0.13
86 2 0.01
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (83 bp):
AGCGTACTACCACTTCGAGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGAGTACTA
CCATTTCGCGAACTTTGA
Found at i:1561 original size:57 final size:58
Alignment explanation
Indices: 1440--1570 Score: 156
Period size: 57 Copynumber: 2.3 Consensus size: 58
1430 TAGGTTGTAC
* * * * * * ** *
1440 GACCGTGGAATGCTCGTTTTTCTTTTTGCGCAAGTGGGGGATGCCCATTGGGTCGTGT
1 GACCGAGGGATGCTCGATTTTCTTATTGCACAAGTGGGGGATGCCCACTAAGTCATGT
**
1498 GACCGAGGGATGCTCGATTTTCTTATTGCATGAGT-GGGGATGCCCACTAAGTCATGT
1 GACCGAGGGATGCTCGATTTTCTTATTGCACAAGTGGGGGATGCCCACTAAGTCATGT
1555 GACCGAGGGATGCTCG
1 GACCGAGGGATGCTCG
1571 GTCGTTCTTG
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
57 34 0.55
58 28 0.45
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.30
Consensus pattern (58 bp):
GACCGAGGGATGCTCGATTTTCTTATTGCACAAGTGGGGGATGCCCACTAAGTCATGT
Found at i:7793 original size:16 final size:16
Alignment explanation
Indices: 7772--7803 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
7762 TCATGCGAGG
7772 AGATTATCTTCCAACT
1 AGATTATCTTCCAACT
7788 AGATTATCTTCCAACT
1 AGATTATCTTCCAACT
7804 TTCAAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (16 bp):
AGATTATCTTCCAACT
Found at i:9615 original size:55 final size:55
Alignment explanation
Indices: 9555--9728 Score: 124
Period size: 55 Copynumber: 3.1 Consensus size: 55
9545 CGAATGATCG
9555 CAAAAAAACTTAACATGATAGCTTTCAAAGTCTCCTTCAAACCCTAAGAAATGCA
1 CAAAAAAACTTAACATGATAGCTTTCAAAGTCTCCTTCAAACCCTAAGAAATGCA
** ** ** * * ** * *
9610 CAAAAAGCAGGTT--CATGATTTCTATGGAATACTCACCATATCAATTTCCGAATG--AT-CG
1 CAAAAA--AACTTAACATGATAGCT-TTCAA-AGTCTCC-T-TCAA-ACCCTAA-GAAATGCA
*
9668 CAAAAAACCTTAACATGATAGCTTTCAAAGTCTCCTTCAAACCCTAAGAAATGCA
1 CAAAAAAACTTAACATGATAGCTTTCAAAGTCTCCTTCAAACCCTAAGAAATGCA
9723 CAAAAA
1 CAAAAA
9729 GCCTCATCAA
Statistics
Matches: 82, Mismatches: 24, Indels: 26
0.62 0.18 0.20
Matches are distributed among these distances:
52 1 0.01
53 4 0.05
54 6 0.07
55 22 0.27
56 11 0.13
57 11 0.13
58 16 0.20
59 6 0.07
60 4 0.05
61 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (55 bp):
CAAAAAAACTTAACATGATAGCTTTCAAAGTCTCCTTCAAACCCTAAGAAATGCA
Found at i:9703 original size:113 final size:113
Alignment explanation
Indices: 9505--9730 Score: 418
Period size: 113 Copynumber: 2.0 Consensus size: 113
9495 GCTACTTCGG
*
9505 AGGTTCATGATTTCTATGGAATAACCACTATATCAATTTCCGAATGATCGCAAAAAAACTTAACA
1 AGGTTCATGATTTCTATGGAATAACCACCATATCAATTTCCGAATGATCGCAAAAAAACTTAACA
9570 TGATAGCTTTCAAAGTCTCCTTCAAACCCTAAGAAATGCACAAAAAGC
66 TGATAGCTTTCAAAGTCTCCTTCAAACCCTAAGAAATGCACAAAAAGC
*
9618 AGGTTCATGATTTCTATGGAAT-ACTCACCATATCAATTTCCGAATGATCGCAAAAAACCTTAAC
1 AGGTTCATGATTTCTATGGAATAAC-CACCATATCAATTTCCGAATGATCGCAAAAAAACTTAAC
9682 ATGATAGCTTTCAAAGTCTCCTTCAAACCCTAAGAAATGCACAAAAAGC
65 ATGATAGCTTTCAAAGTCTCCTTCAAACCCTAAGAAATGCACAAAAAGC
9731 CTCATCAATG
Statistics
Matches: 110, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
112 2 0.02
113 108 0.98
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (113 bp):
AGGTTCATGATTTCTATGGAATAACCACCATATCAATTTCCGAATGATCGCAAAAAAACTTAACA
TGATAGCTTTCAAAGTCTCCTTCAAACCCTAAGAAATGCACAAAAAGC
Found at i:11048 original size:12 final size:12
Alignment explanation
Indices: 11031--11055 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11021 GGTATTTACA
11031 TTCTTTTTTTTT
1 TTCTTTTTTTTT
11043 TTCTTTTTTTTT
1 TTCTTTTTTTTT
11055 T
1 T
11056 CCAATTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTCTTTTTTTTT
Done.