Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010268.1 Kokia drynarioides strain JFW-HI SEQ_125107, 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: 48136
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:2438 original size:96 final size:96
Alignment explanation
Indices: 2264--2445 Score: 226
Period size: 96 Copynumber: 1.9 Consensus size: 96
2254 AAGGATATTT
** * *
2264 GATTATCTCGATTCGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAATATTTCAGAATTGAAGA
1 GATTATCTCGATTCGAAGAAAGAATGCACCTAATAAGTTAAGGCACAATATTTCAGAATCGAAGA
2329 TAAGGAAACATTGCCTCGATTAAGGGTGTTC
66 TAAGGAAACATTGCCTCGATTAAGGGTGTTC
* * * **
2360 GATTATTTCGATTTGAAGAAAGAATGCACCTAATGAGTTAAGGCACAA-ATTTTTGAAACTCGAA
1 GATTATCTCGATTCGAAGAAAGAATGCACCTAATAAGTTAAGGCACAATATTTCAG-AA-TCGAA
*
2424 -ATAAAGG-AATATTGCCTCGATT
64 GAT-AAGGAAACATTGCCTCGATT
2446 TTTTTAAATA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
95 5 0.07
96 60 0.82
97 8 0.11
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (96 bp):
GATTATCTCGATTCGAAGAAAGAATGCACCTAATAAGTTAAGGCACAATATTTCAGAATCGAAGA
TAAGGAAACATTGCCTCGATTAAGGGTGTTC
Found at i:2467 original size:11 final size:11
Alignment explanation
Indices: 2451--2475 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2441 CGATTTTTTT
2451 AAATAAAATAA
1 AAATAAAATAA
2462 AAATAAAATAA
1 AAATAAAATAA
2473 AAA
1 AAA
2476 ATATTTCGAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:2862 original size:59 final size:59
Alignment explanation
Indices: 2668--2861 Score: 336
Period size: 59 Copynumber: 3.3 Consensus size: 59
2658 GATGCACGGT
* * *
2668 GGTAAAATGGTAATTTTTAGAAGGTTTGGGGTCAAAAATAGGATTTGTGGAAGTTCGGG
1 GGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGG
2727 GGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGG
1 GGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGG
* *
2786 GGTAAAATGGTAATTTTTAGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGGG
1 GGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGG
2845 GGT-AAATGGTAATTTTT
1 GGTAAAATGGTAATTTTT
2862 TGAAAAGTTT
Statistics
Matches: 130, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
58 14 0.11
59 116 0.89
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (59 bp):
GGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGG
Found at i:2863 original size:29 final size:29
Alignment explanation
Indices: 2668--2861 Score: 177
Period size: 30 Copynumber: 6.6 Consensus size: 29
2658 GATGCACGGT
* *
2668 GGTAAAATGGTAATTTTTAGAAGGTT-TGG
1 GGTAAAATGGTAATTTTTGGAA-GTTCGGG
*
2697 GGTCAAAAATAGG--ATTTGTGGAAGTTCGGG
1 GGT--AAAAT-GGTAATTTTTGGAAGTTCGGG
*
2727 GGTAAAATGGTAATTTTTAGAAGGTTC-GG
1 GGTAAAATGGTAATTTTTGGAA-GTTCGGG
*
2756 GGTCAAAAATGG-GATTTTTGGAAGTTCGGG
1 GGT--AAAATGGTAATTTTTGGAAGTTCGGG
* *
2786 GGTAAAATGGTAATTTTTAGAAGGTTCGAG
1 GGTAAAATGGTAATTTTTGGAA-GTTCGGG
* *
2816 GTTAAAAATGG-GATTTTTGGAAGTTCGGG
1 GGT-AAAATGGTAATTTTTGGAAGTTCGGG
2845 GGT-AAATGGTAATTTTT
1 GGTAAAATGGTAATTTTT
2862 TGAAAAGTTT
Statistics
Matches: 135, Mismatches: 16, Indels: 29
0.75 0.09 0.16
Matches are distributed among these distances:
27 8 0.06
28 18 0.13
29 40 0.30
30 48 0.36
31 19 0.14
32 2 0.01
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (29 bp):
GGTAAAATGGTAATTTTTGGAAGTTCGGG
Found at i:4685 original size:17 final size:17
Alignment explanation
Indices: 4658--4740 Score: 103
Period size: 17 Copynumber: 4.8 Consensus size: 17
4648 TTGGACATTT
*
4658 TAAATTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
* *
4676 TAAATTTAAATTTCAGA
1 TAAATTTAAATTTAAAA
4693 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
4710 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
4727 TAAATTTAAGTTTA
1 TAAATTTAAATTTA
4741 TTGGACCCAG
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
17 52 0.93
18 4 0.07
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:8471 original size:20 final size:20
Alignment explanation
Indices: 8432--8473 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
8422 TCACTGGTAG
* *
8432 AACTTCACTTCTATCGATAC
1 AACTTCACTTCTACCAATAC
*
8452 AACTTCAGTTCTACCAATAC
1 AACTTCACTTCTACCAATAC
8472 AA
1 AA
8474 GTATTCTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.29, G:0.05, T:0.31
Consensus pattern (20 bp):
AACTTCACTTCTACCAATAC
Found at i:11572 original size:20 final size:20
Alignment explanation
Indices: 11535--11590 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
11525 CTACCCTGGG
* *
11535 ACTTCTATCGGTAGAACTTC
1 ACTTCTATCGATACAACTTC
*
11555 ACTTCTATCGATACAACTTT
1 ACTTCTATCGATACAACTTC
* *
11575 AGTTCTACCGATACAA
1 ACTTCTATCGATACAA
11591 GTATGCTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (20 bp):
ACTTCTATCGATACAACTTC
Found at i:24588 original size:21 final size:22
Alignment explanation
Indices: 24552--24602 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
24542 TTTTTAAAAA
24552 ATATTTATATAATTTTATTTTT
1 ATATTTATATAATTTTATTTTT
*
24574 ATATTTA-ATAGTTTTATTTTT
1 ATATTTATATAATTTTATTTTT
*
24595 TTATTTAT
1 ATATTTAT
24603 TGAAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
ATATTTATATAATTTTATTTTT
Found at i:39128 original size:12 final size:12
Alignment explanation
Indices: 39089--39134 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
39079 AAGAGGCACC
39089 AAAGAAGAAGGA
1 AAAGAAGAAGGA
39101 CAAA-AAGAAAGG-
1 -AAAGAAG-AAGGA
39113 AAAGAAGAAGGA
1 AAAGAAGAAGGA
39125 AAAGCAAGAA
1 AAAG-AAGAA
39135 AATGCGCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 7 0.24
12 10 0.34
13 12 0.41
ACGTcount: A:0.67, C:0.04, G:0.28, T:0.00
Consensus pattern (12 bp):
AAAGAAGAAGGA
Found at i:40822 original size:17 final size:16
Alignment explanation
Indices: 40788--40840 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
40778 AGTCTCTTAT
*
40788 AAAAAAATAACAAAAAG
1 AAAAAAA-AAGAAAAAG
40805 AAAAAAAAAGAAAGAAG
1 AAAAAAAAAGAAA-AAG
* *
40822 AAGAAAAGAG-AAAAG
1 AAAAAAAAAGAAAAAG
40837 AAAA
1 AAAA
40841 TAGATATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 6 0.19
16 7 0.23
17 18 0.58
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:45480 original size:21 final size:21
Alignment explanation
Indices: 45454--45512 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
45444 TCAGCACACT
*
45454 CAGATGCATCCACAACAAAGC
1 CAGATGCATCCACAACAAAAC
* *
45475 CAGATGCATCCACACCAAAAT
1 CAGATGCATCCACAACAAAAC
*
45496 CAGATGCAGCCACAACA
1 CAGATGCATCCACAACA
45513 CTCTTCAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.42, C:0.34, G:0.14, T:0.10
Consensus pattern (21 bp):
CAGATGCATCCACAACAAAAC
Found at i:47244 original size:46 final size:46
Alignment explanation
Indices: 47191--47288 Score: 133
Period size: 46 Copynumber: 2.1 Consensus size: 46
47181 CTGGGGAAAT
* *
47191 AGTAAGCACACACAGTGCAAATCAGTAGGCACACACGGTGCAAAAC
1 AGTAAGCACACACAGTGCAAATCAGTAAGCACACACAGTGCAAAAC
* * * **
47237 AGTAAGCACATATAGTGCGAATCAGTAAGCACACACAGTGCTGAAC
1 AGTAAGCACACACAGTGCAAATCAGTAAGCACACACAGTGCAAAAC
47283 AGTAAG
1 AGTAAG
47289 TACGCTAATG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (46 bp):
AGTAAGCACACACAGTGCAAATCAGTAAGCACACACAGTGCAAAAC
Found at i:47288 original size:23 final size:23
Alignment explanation
Indices: 47187--47277 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
47177 AGTGCTGGGG
47187 AAAT-AGTAAGCACACACAGTGC
1 AAATCAGTAAGCACACACAGTGC
* *
47209 AAATCAGTAGGCACACACGGTGC
1 AAATCAGTAAGCACACACAGTGC
* * *
47232 AAAACAGTAAGCACATATAGTGC
1 AAATCAGTAAGCACACACAGTGC
*
47255 GAATCAGTAAGCACACACAGTGC
1 AAATCAGTAAGCACACACAGTGC
47278 TGAACAGTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
22 4 0.07
23 53 0.93
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (23 bp):
AAATCAGTAAGCACACACAGTGC
Done.