Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008499.1 Kokia drynarioides strain JFW-HI SEQ_123174, 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: 23338
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:10334 original size:27 final size:25
Alignment explanation
Indices: 10295--10361 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 25
10285 CCATTAATTA
10295 TAAATAAATTTATATTATAATTATTT
1 TAAATAAATTTATATTATAA-TATTT
* *
10321 TAAATAATTATTATATTTTAATATTT
1 TAAATAAAT-TTATATTATAATATTT
10347 ATGCAAATAAATTTA
1 -T--AAATAAATTTA
10362 GAAATATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 13 0.38
27 11 0.32
28 3 0.09
29 7 0.21
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (25 bp):
TAAATAAATTTATATTATAATATTT
Found at i:11356 original size:6 final size:6
Alignment explanation
Indices: 11345--11370 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11335 AACCTTCTCG
11345 AGATAC AGATAC AGATAC AGATAC AG
1 AGATAC AGATAC AGATAC AGATAC AG
11371 GACCAGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.15
Consensus pattern (6 bp):
AGATAC
Found at i:15058 original size:13 final size:13
Alignment explanation
Indices: 15040--15102 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
15030 AGCTTTTCAA
15040 TTTCAAAAGTACT
1 TTTCAAAAGTACT
15053 TTTCAAAA-TAACT
1 TTTCAAAAGT-ACT
* * *
15066 CTTCCAAAGCACT
1 TTTCAAAAGTACT
*
15079 TTTTAAAAGTACT
1 TTTCAAAAGTACT
*
15092 TCTCAAAAGTA
1 TTTCAAAAGTA
15103 ATGATAAACT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
12 1 0.03
13 38 0.97
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (13 bp):
TTTCAAAAGTACT
Found at i:16633 original size:15 final size:15
Alignment explanation
Indices: 16613--16642 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16603 CATTTAACCG
16613 AATTAACCAAATTAA
1 AATTAACCAAATTAA
*
16628 AATTAACCGAATTAA
1 AATTAACCAAATTAA
16643 CTAAAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (15 bp):
AATTAACCAAATTAA
Found at i:16633 original size:24 final size:25
Alignment explanation
Indices: 16606--16652 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
16596 TAATATTCAT
*
16606 TTAACCGAATTAAC-CAAATTAAAA
1 TTAACCGAATTAACTAAAATTAAAA
16630 TTAACCGAATTAACTAAAATTAA
1 TTAACCGAATTAACTAAAATTAA
16653 CCAAATTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.53, C:0.15, G:0.04, T:0.28
Consensus pattern (25 bp):
TTAACCGAATTAACTAAAATTAAAA
Found at i:16658 original size:9 final size:9
Alignment explanation
Indices: 16606--16659 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
16596 TAATATTCAT
*
16606 TTAACCGAA
1 TTAACCAAA
16615 TTAACCAAA
1 TTAACCAAA
16624 TT-A--AAA
1 TTAACCAAA
*
16630 TTAACCGAA
1 TTAACCAAA
*
16639 TTAACTAAAA
1 TTAAC-CAAA
16649 TTAACCAAA
1 TTAACCAAA
16658 TT
1 TT
16660 GGTAATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
6 5 0.14
7 1 0.03
8 1 0.03
9 22 0.61
10 7 0.19
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.28
Consensus pattern (9 bp):
TTAACCAAA
Found at i:17632 original size:34 final size:34
Alignment explanation
Indices: 17547--17632 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 34
17537 ACACGGTTAA
* * *
17547 CCATCAAGCACACTAGATGCTTCTATGAGCTAAT
1 CCATCCAGCACACCAAATGCTTCTATGAGCTAAT
* * *
17581 CCATCCAGTAGATCAAATGC-TCGTATGAGCTAAT
1 CCATCCAGCACACCAAATGCTTC-TATGAGCTAAT
17615 CCATCCAGCACACCAAAT
1 CCATCCAGCACACCAAAT
17633 AACACTGTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
33 2 0.05
34 40 0.95
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (34 bp):
CCATCCAGCACACCAAATGCTTCTATGAGCTAAT
Found at i:22440 original size:22 final size:22
Alignment explanation
Indices: 22373--22441 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 22
22363 TAGAAAAATA
*
22373 ATATTTTAAAATTATAAT--CT
1 ATATTTTAAATTTATAATAACT
* *
22393 AT-TTTTAAATTAATAGTAGA-T
1 ATATTTTAAATTTATAATA-ACT
22414 A-ATTTTAAATTTATAATAACT
1 ATATTTTAAATTTATAATAACT
22435 ATATTTT
1 ATATTTT
22442 CCCGTTTTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 12 0.32
20 3 0.08
21 18 0.47
22 5 0.13
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (22 bp):
ATATTTTAAATTTATAATAACT
Found at i:22997 original size:25 final size:26
Alignment explanation
Indices: 22943--22997 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
22933 CCATTAATTA
* * *
22943 TAAATAAATTTGTCTTATAATTTTTT
1 TAAATAAATTTATCTTATAATTATTG
22969 TAAATAAATTTAT-TTAT-ATATATTG
1 TAAATAAATTTATCTTATAAT-TATTG
22994 TAAA
1 TAAA
22998 AACAAGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 2 0.08
25 11 0.44
26 12 0.48
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (26 bp):
TAAATAAATTTATCTTATAATTATTG
Found at i:23301 original size:364 final size:364
Alignment explanation
Indices: 22619--23338 Score: 1199
Period size: 364 Copynumber: 2.0 Consensus size: 364
22609 AATTTATAAA
*
22619 TATATATATTGTAAAAACAAGTATAAAACATGTCAAAATAAATAAATTGATAATGTTCATTTGAG
1 TATATATATTGTAAAAACAAGTATAAAACATGTCAAAATAAATAAATTGATAATGTTCATTTGAC
*
22684 CAAATTATCCAAATTAACCGAATTAGTAATAGCCTAATACATATAATATATAATATTATTTATTA
66 CAAATTATCCAAATTAACCGAATTAGTAATAGCCTAATACAAATAATATATAATATTATTTATTA
** *
22749 AATTCGGTTAATTCGGTTAATAACCCGATTTCGAATTGAATTAATCGTTAACTAAAATTCCAAAA
131 AATTCGGTTAATTCGGTTAATAACCCGATTTCGAACCGAATTAACCGTTAACTAAAATTCCAAAA
* * *
22814 AAACATTTAACCGACTTTCGATTGAACTAGATCAGTTAATCAACCGATTAATCGAATTAGACCAA
196 AAACATTTAACCGACTTCCGATCGAACTAGATCAGTTAATCAACCAATTAATCGAATTAGACCAA
* **
22879 TTCGACCGGTTAATTCGATTTTAACCGAAATTTGAACACCCTTAAGAATGTTAACCATTAATTAT
261 TTCGACCGGTTAATTCGATTTTAACCGAAATTTGAACACCCCTAAGAATGCCAACCATTAATTAT
* *
22944 AAATAAATTTGTCTTATAATTTTTTTAAATAAATTTATT
326 AAATAAATTTATCTTATAATTATTTTAAATAAATTTATT
*
22983 TATATATATTGTAAAAACAAGTATAAAACGTGTCAAAATAAATAAATTGATAATGTTCATTTGAC
1 TATATATATTGTAAAAACAAGTATAAAACATGTCAAAATAAATAAATTGATAATGTTCATTTGAC
*
23048 CGAATTATCCAAATTAACCGAATTAGTAATAGCCTAATACAAATAATATATAATATTATTTATTA
66 CAAATTATCCAAATTAACCGAATTAGTAATAGCCTAATACAAATAATATATAATATTATTTATTA
* *
23113 AGTTCGGTTAATTCGGTTAATAACCCGATTTCGAACCGAATTAACCGTTAACTGAAATTCCAAAA
131 AATTCGGTTAATTCGGTTAATAACCCGATTTCGAACCGAATTAACCGTTAACTAAAATTCCAAAA
* ** **
23178 AAACTTTTAACCGAGC-TCCGATCGAACTAGATCAGTTAATTGACCAATTAATCGAATTAGATTA
196 AAACATTTAACCGA-CTTCCGATCGAACTAGATCAGTTAATCAACCAATTAATCGAATTAGACCA
* * *
23242 ATTCGATCTGTTAATTCGATTTTAACCGAAATTTGAACACCCCTAATAATGCCAACCATTAATTA
260 ATTCGACCGGTTAATTCGATTTTAACCGAAATTTGAACACCCCTAAGAATGCCAACCATTAATTA
23307 TAAATAAATTTATCTTATAATTATTTTAAATA
325 TAAATAAATTTATCTTATAATTATTTTAAATA
Statistics
Matches: 330, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
364 329 1.00
365 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (364 bp):
TATATATATTGTAAAAACAAGTATAAAACATGTCAAAATAAATAAATTGATAATGTTCATTTGAC
CAAATTATCCAAATTAACCGAATTAGTAATAGCCTAATACAAATAATATATAATATTATTTATTA
AATTCGGTTAATTCGGTTAATAACCCGATTTCGAACCGAATTAACCGTTAACTAAAATTCCAAAA
AAACATTTAACCGACTTCCGATCGAACTAGATCAGTTAATCAACCAATTAATCGAATTAGACCAA
TTCGACCGGTTAATTCGATTTTAACCGAAATTTGAACACCCCTAAGAATGCCAACCATTAATTAT
AAATAAATTTATCTTATAATTATTTTAAATAAATTTATT
Done.