Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013249.1 Kokia drynarioides strain JFW-HI SEQ_128269, 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: 17891
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1031 original size:24 final size:26
Alignment explanation
Indices: 1004--1051 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
994 AAGAGAATGT
1004 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
1028 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
1052 CTCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:3216 original size:24 final size:26
Alignment explanation
Indices: 3189--3236 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
3179 AAGAGAATGT
3189 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
3213 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
3237 CTCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:5225 original size:20 final size:20
Alignment explanation
Indices: 5202--5247 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
5192 TCATTTTTCA
* *
5202 ATAAAAATACATA-AAATTTT
1 ATAAAAACACATACAAA-ATT
5222 ATAAAAACACATACAAAATT
1 ATAAAAACACATACAAAATT
5242 ATAAAA
1 ATAAAA
5248 TATTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (20 bp):
ATAAAAACACATACAAAATT
Found at i:6772 original size:13 final size:13
Alignment explanation
Indices: 6754--6794 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
6744 ATTTTTCATA
6754 TTTTTATATAATT
1 TTTTTATATAATT
*
6767 TTTTTATCA-AATA
1 TTTTTAT-ATAATT
6780 TTTTT-TATAATT
1 TTTTTATATAATT
6792 TTT
1 TTT
6795 AAATAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 1 0.04
12 7 0.29
13 15 0.62
14 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTATATAATT
Found at i:7008 original size:14 final size:14
Alignment explanation
Indices: 6989--7015 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6979 TTTTTAAAGA
6989 AAAACATTTTACAT
1 AAAACATTTTACAT
7003 AAAACATTTTACA
1 AAAACATTTTACA
7016 ATTTTAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAT
Found at i:7804 original size:21 final size:21
Alignment explanation
Indices: 7778--7821 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
7768 AATTTTCATT
7778 TCACAAAGTTTAACAATAGTA
1 TCACAAAGTTTAACAATAGTA
7799 TCACAAAGTTTAACAATAGTA
1 TCACAAAGTTTAACAATAGTA
7820 TC
1 TC
7822 GTAGGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (21 bp):
TCACAAAGTTTAACAATAGTA
Found at i:11278 original size:7 final size:7
Alignment explanation
Indices: 11266--11314 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 7
11256 GGTTTCACCC
11266 AAAAAAG
1 AAAAAAG
11273 AAAAAAAGG
1 -AAAAAA-G
11282 AAAAAA-
1 AAAAAAG
11288 AAAAAAG
1 AAAAAAG
11295 -AAAAAG
1 AAAAAAG
*
11301 GAAAAAG
1 AAAAAAG
11308 AAAAAAG
1 AAAAAAG
11315 GAGAGGTCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
6 12 0.32
7 12 0.32
8 12 0.32
9 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:11291 original size:20 final size:20
Alignment explanation
Indices: 11266--11314 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
11256 GGTTTCACCC
*
11266 AAAAAAGAA-AAAAAGGAAA
1 AAAAAAAAAGAAAAAGGAAA
11285 AAAAAAAAAGAAAAAGGAAA
1 AAAAAAAAAGAAAAAGGAAA
*
11305 AAGAAAAAAG
1 AAAAAAAAAG
11315 GAGAGGTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAAAAAGGAAA
Found at i:13505 original size:3 final size:3
Alignment explanation
Indices: 13497--13523 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
13487 TGTTAGCTAC
13497 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
13524 TTACAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:13606 original size:17 final size:18
Alignment explanation
Indices: 13572--13607 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13562 TGAATTTCTA
13572 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
13590 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
13607 T
1 T
13608 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:16671 original size:29 final size:28
Alignment explanation
Indices: 16639--16702 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
16629 AAAATAAGAC
**
16639 TTTTCGGATACCCGGGGGTAAAATGGTAA
1 TTTT-GGATACCCGGGGCAAAAATGGTAA
* *
16668 TTTTGGATTCTCGGGGCAAAAATGGTAA
1 TTTTGGATACCCGGGGCAAAAATGGTAA
16696 TTTTGGA
1 TTTTGGA
16703 AATTTTAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.27, C:0.11, G:0.30, T:0.33
Consensus pattern (28 bp):
TTTTGGATACCCGGGGCAAAAATGGTAA
Found at i:16758 original size:30 final size:29
Alignment explanation
Indices: 16685--16943 Score: 170
Period size: 30 Copynumber: 8.7 Consensus size: 29
16675 TTCTCGGGGC
* *
16685 AAAAATGGTAATTTTGGAAATTTTAGAGTTT
1 AAAAATGG-AATTTTGGAAGTTTT-GAGGTT
16716 AAAAGA-GTG-ATTTTGAGAA-TTTTGAGGTT
1 AAAA-ATG-GAATTTTG-GAAGTTTTGAGGTT
* * **
16745 AAAAATGGAGATTTTAGAGGTTTAAAGG-T
1 AAAAATGGA-ATTTTGGAAGTTTTGAGGTT
* * *
16774 AAAAATGGAATTTTTGGAAGTTTCGAGATA
1 AAAAATGGAA-TTTTGGAAGTTTTGAGGTT
* * *
16804 AAAAATGGCATTTTTGGAAG-TTTGGGGGT
1 AAAAATGG-AATTTTGGAAGTTTTGAGGTT
* *
16833 AAAAATGGAATTTTTGGAAGTTTCGGGGTT
1 AAAAATGGAA-TTTTGGAAGTTTTGAGGTT
* * *
16863 AAAAATAGGATTTTTGGAAGTTCT-AGGGT
1 AAAAAT-GGAATTTTGGAAGTTTTGAGGTT
* * * *
16892 AAAAATGAAATTTTTAGAAGTTTTGGGGTC
1 AAAAATGGAA-TTTTGGAAGTTTTGAGGTT
*
16922 AAAAATAGGATTTTTGGAAGTT
1 AAAAAT-GGAATTTTGGAAGTT
16944 CAGGGGTAAA
Statistics
Matches: 177, Mismatches: 35, Indels: 33
0.72 0.14 0.13
Matches are distributed among these distances:
28 6 0.03
29 75 0.42
30 80 0.45
31 14 0.08
32 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (29 bp):
AAAAATGGAATTTTGGAAGTTTTGAGGTT
Found at i:16788 original size:29 final size:29
Alignment explanation
Indices: 16771--16974 Score: 218
Period size: 30 Copynumber: 6.9 Consensus size: 29
16761 GAGGTTTAAA
*
16771 GGTAAAAATGGAATTTTTGGAAGTTTCGA
1 GGTAAAAATGGAATTTTTGGAAGTTTCGG
* * *
16800 GATAAAAAATGGCATTTTTGGAAGTTTGGG
1 GGT-AAAAATGGAATTTTTGGAAGTTTCGG
16830 GGTAAAAATGGAATTTTTGGAAGTTTCGG
1 GGTAAAAATGGAATTTTTGGAAGTTTCGG
*
16859 GGTTAAAAATAGG-ATTTTTGGAAG-TTCTAG
1 GG-TAAAAAT-GGAATTTTTGGAAGTTTC-GG
* * *
16889 GGTAAAAATGAAATTTTTAGAAGTTTTGG
1 GGTAAAAATGGAATTTTTGGAAGTTTCGG
16918 GGTCAAAAATAGG-ATTTTTGGAAG-TTCAGG
1 GGT-AAAAAT-GGAATTTTTGGAAGTTTC-GG
**
16948 GGTAAAAATAAAATTTTTGGATAGTTT
1 GGTAAAAATGGAATTTTTGGA-AGTTT
16975 AGGGACCTCT
Statistics
Matches: 146, Mismatches: 17, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
28 1 0.01
29 69 0.47
30 71 0.49
31 5 0.03
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
GGTAAAAATGGAATTTTTGGAAGTTTCGG
Found at i:16835 original size:59 final size:58
Alignment explanation
Indices: 16771--16974 Score: 257
Period size: 59 Copynumber: 3.4 Consensus size: 58
16761 GAGGTTTAAA
* * *
16771 GGTAAAAATGGAATTTTTGGAAGTTTCGAGATAAAAAAT-GGCATTTTTGGAAGTTTGGG
1 GGTAAAAATGAAATTTTTGGAAGTTTCGGGGTAAAAAATAGG-ATTTTTGGAAGTTT-GG
* * *
16830 GGTAAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATAGGATTTTTGGAAGTTCTAG
1 GGTAAAAATGAAATTTTTGGAAGTTTCGGGGTAAAAAATAGGATTTTTGGAAGTT-TGG
* * * *
16889 GGTAAAAATGAAATTTTTAGAAGTTTTGGGGTCAAAAATAGGATTTTTGGAAGTTCAGG
1 GGTAAAAATGAAATTTTTGGAAGTTTCGGGGTAAAAAATAGGATTTTTGGAAGTT-TGG
*
16948 GGTAAAAATAAAATTTTTGGATAGTTT
1 GGTAAAAATGAAATTTTTGGA-AGTTT
16975 AGGGACCTCT
Statistics
Matches: 130, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
59 122 0.94
60 8 0.06
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (58 bp):
GGTAAAAATGAAATTTTTGGAAGTTTCGGGGTAAAAAATAGGATTTTTGGAAGTTTGG
Done.