Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015762.1 Corchorus capsularis cultivar CVL-1 contig15783, 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: 55885
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:80 original size:2 final size:2
Alignment explanation
Indices: 73--159 Score: 71
Period size: 2 Copynumber: 46.5 Consensus size: 2
63 CTCGTACTTT
*
73 TA TA TA TA GTA TA GA T- TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
114 TA TA -A TA TA -A TA TA T- TA T- TA TC TA T- TA TA TC TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
151 TA TA CA TA T
1 TA TA TA TA T
160 CTATCTATCT
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
1 7 0.10
2 58 0.87
3 2 0.03
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:115 original size:7 final size:7
Alignment explanation
Indices: 75--143 Score: 68
Period size: 7 Copynumber: 9.7 Consensus size: 7
65 CGTACTTTTA
*
75 TATATAG
1 TATATAT
*
82 TATAGAT
1 TATATAT
89 TATATA-
1 TATATAT
95 TATATAT
1 TATATAT
102 ATATATAT
1 -TATATAT
110 TATATAT
1 TATATAT
* *
117 AATATAA
1 TATATAT
124 TATATTAT
1 TATA-TAT
*
132 TATCTAT
1 TATATAT
139 TATAT
1 TATAT
144 CTATATCTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
6 6 0.12
7 32 0.64
8 12 0.24
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (7 bp):
TATATAT
Found at i:128 original size:35 final size:36
Alignment explanation
Indices: 72--149 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 36
62 ACTCGTACTT
*
72 TTATATATAGTATAGATTATA-TATATATATATATATA
1 TTATATATAATATAGATTATATTAT-TATATAT-TATA
*
109 TTATATATAATATA-A-TATATTATTATCTATTATA
1 TTATATATAATATAGATTATATTATTATATATTATA
143 TCTATAT
1 T-TATAT
150 CTATACATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
34 5 0.14
35 15 0.41
36 4 0.11
37 13 0.35
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (36 bp):
TTATATATAATATAGATTATATTATTATATATTATA
Found at i:166 original size:4 final size:4
Alignment explanation
Indices: 147--215 Score: 102
Period size: 4 Copynumber: 16.8 Consensus size: 4
137 ATTATATCTA
* *
147 TATC TATAC ATATC TATC TATC TATC TATC TATC TATG TATC TATC TATT
1 TATC TAT-C -TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
197 TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TAT
216 TTATACCTCT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
4 54 0.92
5 2 0.03
6 3 0.05
ACGTcount: A:0.28, C:0.20, G:0.01, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:6742 original size:23 final size:23
Alignment explanation
Indices: 6716--6786 Score: 58
Period size: 23 Copynumber: 3.1 Consensus size: 23
6706 TCAGCAAAAA
6716 CAAAACACCATGAATAAGAAACT
1 CAAAACACCATGAATAAGAAACT
** * *
6739 C-AAAGGCC-T-AATATCACAAAAT
1 CAAAACACCATGAATA--AGAAACT
*
6761 CAGAACACCATGAATAAGAAACT
1 CAAAACACCATGAATAAGAAACT
6784 CAA
1 CAA
6787 TGGCCTATTA
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
20 4 0.12
21 1 0.03
22 11 0.33
23 12 0.36
24 1 0.03
25 4 0.12
ACGTcount: A:0.54, C:0.23, G:0.10, T:0.14
Consensus pattern (23 bp):
CAAAACACCATGAATAAGAAACT
Found at i:13782 original size:32 final size:32
Alignment explanation
Indices: 13695--13795 Score: 103
Period size: 32 Copynumber: 3.1 Consensus size: 32
13685 TTAAGTAAGG
* * * **
13695 TCGGGTTAAATATGGGGTCAGGTTGATTCAAGT
1 TCGGGTCAAAT-TTGGGTAAGGTTGATTCGGGT
*
13728 TCGGGTTAAATTTGGGTAAGGTTGATTCGGGT
1 TCGGGTCAAATTTGGGTAAGGTTGATTCGGGT
* * * *
13760 TCGGGTCAATTTTGTGTTAGGTTAATTCGGGT
1 TCGGGTCAAATTTGGGTAAGGTTGATTCGGGT
13792 TCGG
1 TCGG
13796 ATTCGGGCTG
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
32 48 0.81
33 11 0.19
ACGTcount: A:0.19, C:0.09, G:0.35, T:0.38
Consensus pattern (32 bp):
TCGGGTCAAATTTGGGTAAGGTTGATTCGGGT
Found at i:13972 original size:20 final size:20
Alignment explanation
Indices: 13939--13977 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13929 CATAAATGAA
*
13939 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
13959 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
13978 GGATTCGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:14349 original size:15 final size:14
Alignment explanation
Indices: 14324--14387 Score: 65
Period size: 15 Copynumber: 4.4 Consensus size: 14
14314 GAAATTAAAA
14324 AATTTGAAATTCTT
1 AATTTGAAATTCTT
* **
14338 TATTTGAGAATTAGT
1 AATTTGA-AATTCTT
14353 AATTTGAAATTCTGT
1 AATTTGAAATTCT-T
*
14368 AATTTCAAATTCTT
1 AATTTGAAATTCTT
*
14382 TATTTG
1 AATTTG
14388 GATAACTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
14 15 0.38
15 24 0.62
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (14 bp):
AATTTGAAATTCTT
Found at i:19880 original size:200 final size:197
Alignment explanation
Indices: 19538--19931 Score: 698
Period size: 200 Copynumber: 2.0 Consensus size: 197
19528 TTGGGTGATG
*
19538 CGCGCGCGGCATGGCCCCCGACTCCCCTTGGGCGCCCATGTCGCAGGCTTGAGCCAGGGCGTTGG
1 CGCGCGCGGCATGGCCCCCGACTCCCCCTGGGCGCCCATGTCGCAGGCTTGAGCCAGGGCGTTGG
*
19603 TCTCAGGCCCCAGGTCTCCTGCGCCCATGTTGGTGCTGGTGGCATGTCTCGACTAGCGCTGGGCG
66 TCTCAGGCCCAAGGTCTCCTGCGCCCATGTTGGTGCTGGTGGCATGTCTCGACTAGCGCTGGGCG
* *
19668 CCCATGTGGTATGCTTGGCACCCTATATGGTTTGCCTCGCGACCCATGTACTCCAGTGCTACGAC
131 CCCATATGGTATGCTTGGCACCCCATATGGTTTGCCTCGCGACCCATGTACTCCAGTGCTACGAC
19733 GC
196 GC
*
19735 CGCGCGCGGCATGGCCCCCGACTCCCCCTGGGCGCCCATGTCGCAGGTTTGAGCGCCCAGGGCGT
1 CGCGCGCGGCATGGCCCCCGACTCCCCCTGGGCGCCCATGTCGCAGGCTTGA--G-CCAGGGCGT
19800 TGGTCTCAGGCCCAAGGTCTCCTGCGCCCATGTTGGTGCTGGTGGCATGTCTCGACTAGCGCTGG
63 TGGTCTCAGGCCCAAGGTCTCCTGCGCCCATGTTGGTGCTGGTGGCATGTCTCGACTAGCGCTGG
* *
19865 GCGCCCATATGGTATGCTTGGTACCCCATGTGGTTTGCCTCGCGACCCATGTACTCCAGTGCTAC
128 GCGCCCATATGGTATGCTTGGCACCCCATATGGTTTGCCTCGCGACCCATGTACTCCAGTGCTAC
19930 GA
193 GA
19932 AACCTCTTGA
Statistics
Matches: 187, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
197 50 0.27
199 1 0.01
200 136 0.73
ACGTcount: A:0.12, C:0.34, G:0.31, T:0.22
Consensus pattern (197 bp):
CGCGCGCGGCATGGCCCCCGACTCCCCCTGGGCGCCCATGTCGCAGGCTTGAGCCAGGGCGTTGG
TCTCAGGCCCAAGGTCTCCTGCGCCCATGTTGGTGCTGGTGGCATGTCTCGACTAGCGCTGGGCG
CCCATATGGTATGCTTGGCACCCCATATGGTTTGCCTCGCGACCCATGTACTCCAGTGCTACGAC
GC
Found at i:28542 original size:13 final size:13
Alignment explanation
Indices: 28521--28550 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28511 GATCAAGTGT
*
28521 AAAAGTAAAAAGG
1 AAAAATAAAAAGG
28534 AAAAATAAAAAGG
1 AAAAATAAAAAGG
28547 AAAA
1 AAAA
28551 CAAATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (13 bp):
AAAAATAAAAAGG
Found at i:48661 original size:95 final size:95
Alignment explanation
Indices: 48498--48689 Score: 384
Period size: 95 Copynumber: 2.0 Consensus size: 95
48488 CTCTTAAGAA
48498 GACCGCTTTTGATCGCAGCAAGTATGAAGTTTGACGCACAAGACGGAACGAAGCCAATTGTTTTC
1 GACCGCTTTTGATCGCAGCAAGTATGAAGTTTGACGCACAAGACGGAACGAAGCCAATTGTTTTC
48563 AACATAAATGAAGCCATGAAAGCTCCTGCC
66 AACATAAATGAAGCCATGAAAGCTCCTGCC
48593 GACCGCTTTTGATCGCAGCAAGTATGAAGTTTGACGCACAAGACGGAACGAAGCCAATTGTTTTC
1 GACCGCTTTTGATCGCAGCAAGTATGAAGTTTGACGCACAAGACGGAACGAAGCCAATTGTTTTC
48658 AACATAAATGAAGCCATGAAAGCTCCTGCC
66 AACATAAATGAAGCCATGAAAGCTCCTGCC
48688 GA
1 GA
48690 AATCCATTTT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 97 1.00
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (95 bp):
GACCGCTTTTGATCGCAGCAAGTATGAAGTTTGACGCACAAGACGGAACGAAGCCAATTGTTTTC
AACATAAATGAAGCCATGAAAGCTCCTGCC
Found at i:52669 original size:13 final size:13
Alignment explanation
Indices: 52651--52680 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
52641 ATTTTTGAGA
52651 AGAGAAGTCGACT
1 AGAGAAGTCGACT
*
52664 AGAGAAGTCGATT
1 AGAGAAGTCGACT
52677 AGAG
1 AGAG
52681 GAAGCAAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.33, T:0.17
Consensus pattern (13 bp):
AGAGAAGTCGACT
Found at i:55304 original size:19 final size:18
Alignment explanation
Indices: 55280--55316 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
55270 TTGAAGATTT
55280 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
55299 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
55317 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Done.