Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011928.1 Kokia drynarioides strain JFW-HI SEQ_126926, 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: 20037
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--36 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37 TATTTAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92 original size:20 final size:21
Alignment explanation
Indices: 64--107 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
54 TTAATTTTTG
64 TATTATATTTTGGTGTA-TATT
1 TATTATATTTT-GTGTATTATT
*
85 TATT-TATTTTTTGTATTATT
1 TATTATATTTTGTGTATTATT
105 TAT
1 TAT
108 GTAAAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (21 bp):
TATTATATTTTGTGTATTATT
Found at i:199 original size:27 final size:27
Alignment explanation
Indices: 154--257 Score: 102
Period size: 27 Copynumber: 3.9 Consensus size: 27
144 TGTGGGGTTG
* * *
154 GTGCAGCCTGCCAGGTAGGCACCTTT-
1 GTGCCGCCTGTCAGATAGGCACCTTTA
*
180 GATGCCGCCTGTCAGATAGGCACCTCTA
1 G-TGCCGCCTGTCAGATAGGCACCTTTA
* * * *
208 GTGCCGCTTATGAGGTAGGCACCTTTA
1 GTGCCGCCTGTCAGATAGGCACCTTTA
* *
235 GTGTCGCCTGTCAAATAGGCACC
1 GTGCCGCCTGTCAGATAGGCACC
258 ACCCCACTGT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
26 1 0.02
27 59 0.97
28 1 0.02
ACGTcount: A:0.19, C:0.29, G:0.28, T:0.24
Consensus pattern (27 bp):
GTGCCGCCTGTCAGATAGGCACCTTTA
Found at i:5149 original size:36 final size:36
Alignment explanation
Indices: 5108--5294 Score: 257
Period size: 36 Copynumber: 5.1 Consensus size: 36
5098 CATGAACATT
5108 ACATATTTTCTGTCAAATGCCCTGAAGAACATACCC
1 ACATATTTTCTGTCAAATGCCCTGAAGAACATACCC
5144 ACATATTTTCTGTCAAATGCCCTGAAGAACATACCC
1 ACATATTTTCTGTCAAATGCCCTGAAGAACATACCC
* * ***
5180 ACATATTTTTCTATCACATGGAATGAAGAACATACCC
1 ACATA-TTTTCTGTCAAATGCCCTGAAGAACATACCC
*
5217 ACATATTTTCTGTCAAATGCCCTAAAGAACATACCC
1 ACATATTTTCTGTCAAATGCCCTGAAGAACATACCC
* * ***
5253 ACATATTTTTCTATCACATGGAATGAAGAACATACCC
1 ACATA-TTTTCTGTCAAATGCCCTGAAGAACATACCC
5290 ACATA
1 ACATA
5295 ATAGTCATCA
Statistics
Matches: 132, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
36 71 0.54
37 61 0.46
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.28
Consensus pattern (36 bp):
ACATATTTTCTGTCAAATGCCCTGAAGAACATACCC
Found at i:5306 original size:73 final size:73
Alignment explanation
Indices: 5130--5294 Score: 321
Period size: 73 Copynumber: 2.3 Consensus size: 73
5120 TCAAATGCCC
*
5130 TGAAGAACATACCCACATATTTTCTGTCAAATGCCCTGAAGAACATACCCACATATTTTTCTATC
1 TGAAGAACATACCCACATATTTTCTGTCAAATGCCCTAAAGAACATACCCACATATTTTTCTATC
5195 ACATGGAA
66 ACATGGAA
5203 TGAAGAACATACCCACATATTTTCTGTCAAATGCCCTAAAGAACATACCCACATATTTTTCTATC
1 TGAAGAACATACCCACATATTTTCTGTCAAATGCCCTAAAGAACATACCCACATATTTTTCTATC
5268 ACATGGAA
66 ACATGGAA
5276 TGAAGAACATACCCACATA
1 TGAAGAACATACCCACATA
5295 ATAGTCATCA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 91 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.27
Consensus pattern (73 bp):
TGAAGAACATACCCACATATTTTCTGTCAAATGCCCTAAAGAACATACCCACATATTTTTCTATC
ACATGGAA
Found at i:5395 original size:23 final size:23
Alignment explanation
Indices: 5366--6236 Score: 1062
Period size: 23 Copynumber: 37.6 Consensus size: 23
5356 TTAATTCTTT
* *
5366 ACATTAATATTTAATCATAAATC
1 ACATTAATATTTAAGCACAAATC
*
5389 ATATTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
5412 ACATTGATATTTAATCATAAATCATAAATC
1 ACATTAATATTTAAGC----A-C--AAATC
*
5442 ATATTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* * *
5465 ACATTGATATTTAATCATAAATC
1 ACATTAATATTTAAGCACAAATC
*
5488 ATATTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
*
5511 ACATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
*
5534 ACATTAATATTTTAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
*
5557 ACGTTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
5580 ATATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
* *
5603 ACAGTAATATTTAAGTACAAATC
1 ACATTAATATTTAAGCACAAATC
5626 ACATTAATATTTAAGCATC-AATC
1 ACATTAATATTTAAGCA-CAAATC
5649 ACATTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
*
5672 ACATCAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
*
5695 ACATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
* *
5718 ACATTAATATTTGAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
** *
5741 ACATCCATATTTGAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* * *
5764 ATATTAATATTTAAGTACAAATT
1 ACATTAATATTTAAGCACAAATC
*
5787 AAATTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
5810 ACATCAATATTTGAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
5833 ATATTAATATTTGAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
*
5856 ACATTAATATTTAAGCACAAAAC
1 ACATTAATATTTAAGCACAAATC
5879 ACATTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
5902 ACAGTAATATTTATGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
5925 ACATTAA-ATTTGAGCACAAATA
1 ACATTAATATTTAAGCACAAATC
* * * *
5947 ATATTAATATTTGAGTATAAATC
1 ACATTAATATTTAAGCACAAATC
* *
5970 ACATTAAAATTTGAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
5993 ACATTAATATTTATGCATAAATC
1 ACATTAATATTTAAGCACAAATC
* * * *
6016 ACATTGATATTTATGAATAAATC
1 ACATTAATATTTAAGCACAAATC
* *
6039 TCATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
*
6062 ACATTAATATTTTAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
6085 ATATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
* *
6108 ATATTAATATTTGAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* * *
6131 ATATTAATATTTAAACATAAATC
1 ACATTAATATTTAAGCACAAATC
* * *
6154 ATAGTAATACTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
6177 ACATTAATATTTAATCATAAATC
1 ACATTAATATTTAAGCACAAATC
*
6200 ATATTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
*
6223 ATATTAATATTTAA
1 ACATTAATATTTAA
6237 ACATAGATAT
Statistics
Matches: 734, Mismatches: 104, Indels: 20
0.86 0.12 0.02
Matches are distributed among these distances:
22 19 0.03
23 692 0.94
24 1 0.00
25 1 0.00
26 1 0.00
27 1 0.00
28 1 0.00
30 18 0.02
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.34
Consensus pattern (23 bp):
ACATTAATATTTAAGCACAAATC
Found at i:5426 original size:30 final size:30
Alignment explanation
Indices: 5392--5479 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 30
5382 ATAAATCATA
5392 TTAATATTTAAGCACAAATCACATTGATAT
1 TTAATATTTAAGCACAAATCACATTGATAT
* * *
5422 TTAATCA-TAAATCATAAAT--C----ATA-
1 TTAAT-ATTTAAGCACAAATCACATTGATAT
5445 TTAATATTTAAGCACAAATCACATTGATAT
1 TTAATATTTAAGCACAAATCACATTGATAT
5475 TTAAT
1 TTAAT
5480 CATAAATCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 18
0.64 0.09 0.27
Matches are distributed among these distances:
22 1 0.02
23 14 0.33
24 3 0.07
25 1 0.02
28 1 0.02
29 3 0.07
30 19 0.44
31 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (30 bp):
TTAATATTTAAGCACAAATCACATTGATAT
Found at i:7621 original size:15 final size:15
Alignment explanation
Indices: 7579--7626 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
7569 TAATTATAAT
*
7579 TTATTAAATAAAAT-
1 TTATTTAATAAAATA
*
7593 TTATCTTAATTAAATTA
1 TTAT-TTAA-TAAAATA
7610 TTATTTAATAAAATA
1 TTATTTAATAAAATA
7625 TT
1 TT
7627 TAAATTCCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 4 0.14
15 11 0.39
16 9 0.32
17 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATTTAATAAAATA
Found at i:9878 original size:5 final size:6
Alignment explanation
Indices: 9852--9876 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9842 CACTTTTGTC
9852 TTCTTT TTCTTT TTCTTT TTCTTT T
1 TTCTTT TTCTTT TTCTTT TTCTTT T
9877 CTCAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:9901 original size:16 final size:16
Alignment explanation
Indices: 9882--9931 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
9872 CTTTTCTCAA
9882 TTTTTTTTCAATTCTT
1 TTTTTTTTCAATTCTT
9898 TTTTTTTTC-ATT-TT
1 TTTTTTTTCAATTCTT
* *
9912 TTTGTTTTTGACTTCTT
1 TTT-TTTTTCAATTCTT
9929 TTT
1 TTT
9932 CTAAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 5 0.17
15 8 0.28
16 11 0.38
17 5 0.17
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.78
Consensus pattern (16 bp):
TTTTTTTTCAATTCTT
Found at i:10877 original size:11 final size:11
Alignment explanation
Indices: 10872--10920 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
10862 TTTTTTTGAA
*
10872 TTTTTTGAATT
1 TTTTTTCAATT
* *
10883 GTTTTTCAAAT
1 TTTTTTCAATT
10894 TTTTTT-AATT
1 TTTTTTCAATT
10904 TTTTTTCAATT
1 TTTTTTCAATT
10915 TTTTTT
1 TTTTTT
10921 AAAAAAAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (11 bp):
TTTTTTCAATT
Found at i:10908 original size:9 final size:10
Alignment explanation
Indices: 10862--10919 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
10852 AATATACTTT
*
10862 TTTTTTTGAA
1 TTTTTTTCAA
*
10872 -TTTTTTGAA
1 TTTTTTTCAA
10881 TTGTTTTTCAAA
1 TT-TTTTTC-AA
10893 TTTTTTT-AA
1 TTTTTTTCAA
10902 TTTTTTTTCAA
1 -TTTTTTTCAA
10913 TTTTTTT
1 TTTTTTT
10920 TAAAAAAAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
9 11 0.26
10 15 0.36
11 12 0.29
12 4 0.10
ACGTcount: A:0.19, C:0.03, G:0.05, T:0.72
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:10922 original size:21 final size:20
Alignment explanation
Indices: 10861--10919 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 20
10851 AAATATACTT
* *
10861 TTTTTTTTGAATTTTTTGAA
1 TTTTTTTTCAATTTTTTTAA
*
10881 TTGTTTTTCAAATTTTTTTAA
1 TTTTTTTTC-AATTTTTTTAA
10902 TTTTTTTTCAATTTTTTT
1 TTTTTTTTCAATTTTTTT
10920 TAAAAAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.19, C:0.03, G:0.05, T:0.73
Consensus pattern (20 bp):
TTTTTTTTCAATTTTTTTAA
Done.