Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013142.1 Kokia drynarioides strain JFW-HI SEQ_128161, 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: 71874
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Warning! 122 characters in sequence are not A, C, G, or T
Found at i:2364 original size:21 final size:20
Alignment explanation
Indices: 2318--2367 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2308 TATTAGTTTT
*
2318 TAATTTTTTTTTAAATTATA
1 TAATTTTATTTTAAATTATA
*
2338 TTATTTTATTTTAATATT-TAA
1 TAATTTTATTTTAA-ATTAT-A
2359 TAATTTTAT
1 TAATTTTAT
2368 AAAATTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TAATTTTATTTTAAATTATA
Found at i:9738 original size:6 final size:6
Alignment explanation
Indices: 9727--9763 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
9717 GAGGTAGACT
* *
9727 CTCTCA CTCTCA CGCTCA CTCTCA CGCTCA CTCTCA C
1 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA C
9764 CTACACTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.16, C:0.51, G:0.05, T:0.27
Consensus pattern (6 bp):
CTCTCA
Found at i:9771 original size:12 final size:12
Alignment explanation
Indices: 9729--9763 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
9719 GGTAGACTCT
9729 CTCACTCTCACG
1 CTCACTCTCACG
9741 CTCACTCTCACG
1 CTCACTCTCACG
9753 CTCACTCTCAC
1 CTCACTCTCAC
9764 CTACACTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.51, G:0.06, T:0.26
Consensus pattern (12 bp):
CTCACTCTCACG
Found at i:11522 original size:23 final size:23
Alignment explanation
Indices: 11466--11514 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
11456 GATCTAAAAT
11466 TTTTTATTTTATTACTAATATATA
1 TTTTTATTTTATTAC-AATATATA
11490 TTTTTATTTTATTA-AAT-TATA
1 TTTTTATTTTATTACAATATATA
11511 TTTT
1 TTTT
11515 ATAATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 8 0.32
22 3 0.12
24 14 0.56
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTATTTTATTACAATATATA
Found at i:11525 original size:21 final size:21
Alignment explanation
Indices: 11466--11526 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 21
11456 GATCTAAAAT
*
11466 TTTTTATTTTATTACTAATATATA
1 TTTTTAATTTATTA--AAT-TATA
*
11490 TTTTTATTTTATTAAATTATA
1 TTTTTAATTTATTAAATTATA
11511 TTTTATAATTT-TTAAA
1 TTTT-TAATTTATTAAA
11527 AGGAATCCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
21 13 0.37
22 8 0.23
24 14 0.40
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTAATTTATTAAATTATA
Found at i:13617 original size:4 final size:4
Alignment explanation
Indices: 13596--13634 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
13586 GAGAGAGGCA
* * *
13596 GAGT GTGT GTGT GTGT GAGT GAGT GAGT GAGT GAGT GAG
1 GAGT GAGT GAGT GAGT GAGT GAGT GAGT GAGT GAGT GAG
13635 GGAAATGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.51, T:0.31
Consensus pattern (4 bp):
GAGT
Found at i:17900 original size:13 final size:13
Alignment explanation
Indices: 17884--17908 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17874 TTCTTTTCTT
17884 TTTTTCTCCTTTC
1 TTTTTCTCCTTTC
17897 TTTTTCTCCTTT
1 TTTTTCTCCTTT
17909 TATTTCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTCTCCTTTC
Found at i:18160 original size:20 final size:20
Alignment explanation
Indices: 18135--18196 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
18125 CATATTCCCC
*
18135 TTTTTCTCCACCCTCTGTTT
1 TTTTTCTCCACTCTCTGTTT
*
18155 TTTTTCTCCACTCTCAGTTT
1 TTTTTCTCCACTCTCTGTTT
**
18175 TTCCTCTCCACTCTCTGTTT
1 TTTTTCTCCACTCTCTGTTT
18195 TT
1 TT
18197 CCAATGTCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.06, C:0.34, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTTTCTCCACTCTCTGTTT
Found at i:22827 original size:5 final size:5
Alignment explanation
Indices: 22817--22841 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
22807 GGGTTGATAC
22817 AGAGG AGAGG AGAGG AGAGG AGAGG
1 AGAGG AGAGG AGAGG AGAGG AGAGG
22842 CTTACAGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
AGAGG
Found at i:35475 original size:15 final size:16
Alignment explanation
Indices: 35448--35479 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
35438 AGGAACAATT
35448 TTGTTACCAAAAAAAA
1 TTGTTACCAAAAAAAA
35464 TTGTTA-CAAAAAAAA
1 TTGTTACCAAAAAAAA
35479 T
1 T
35480 GAACAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.28
Consensus pattern (16 bp):
TTGTTACCAAAAAAAA
Found at i:36571 original size:21 final size:20
Alignment explanation
Indices: 36536--36602 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
36526 ATACCATTAC
* *
36536 AAAAATGTAAAAAAAATTGT
1 AAAAATTTAACAAAAATTGT
*
36556 AAAAATTATAAC-AAAATTGC
1 AAAAATT-TAACAAAAATTGT
*
36576 AAAACTATTTAACAAAAGTT-T
1 AAAA--ATTTAACAAAAATTGT
36597 AAAAAT
1 AAAAAT
36603 CAAATTTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
19 2 0.05
20 17 0.45
21 11 0.29
22 8 0.21
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAAATTTAACAAAAATTGT
Found at i:43607 original size:6 final size:6
Alignment explanation
Indices: 43598--43658 Score: 67
Period size: 6 Copynumber: 10.7 Consensus size: 6
43588 AAATAGTGCG
* *
43598 AGTGAC AGTGGC AGTGAT AGTGAC AGTGAC AGTGAC A--G-C AGTGAC
1 AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC
43643 AGTGGA- AGTGAC AGTG
1 AGT-GAC AGTGAC AGTG
43659 GAAGCCACAG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 3 0.07
6 38 0.83
7 2 0.04
ACGTcount: A:0.31, C:0.13, G:0.38, T:0.18
Consensus pattern (6 bp):
AGTGAC
Found at i:43642 original size:21 final size:21
Alignment explanation
Indices: 43616--43656 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
43606 TGGCAGTGAT
43616 AGTGACAGT-GACAGTGACAGC
1 AGTGACAGTGGA-AGTGACAGC
43637 AGTGACAGTGGAAGTGACAG
1 AGTGACAGTGGAAGTGACAG
43657 TGGAAGCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.34, C:0.15, G:0.37, T:0.15
Consensus pattern (21 bp):
AGTGACAGTGGAAGTGACAGC
Found at i:48536 original size:14 final size:14
Alignment explanation
Indices: 48517--48547 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
48507 TAGGTTTTAA
48517 AAATTTAATTAATT
1 AAATTTAATTAATT
*
48531 AAATTTATTTAATT
1 AAATTTAATTAATT
48545 AAA
1 AAA
48548 AATCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:56379 original size:8 final size:8
Alignment explanation
Indices: 56366--56397 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
56356 TTGATTGGCA
56366 ACAGAATT
1 ACAGAATT
56374 ACAGAATT
1 ACAGAATT
56382 ACAGAATT
1 ACAGAATT
*
56390 GCAGAATT
1 ACAGAATT
56398 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (8 bp):
ACAGAATT
Found at i:57680 original size:16 final size:16
Alignment explanation
Indices: 57645--57677 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57635 ATGAAACTTT
*
57645 AATTACATATATATTA
1 AATTAAATATATATTA
57661 AATTAAATATAT-TTA
1 AATTAAATATATATTA
57676 AA
1 AA
57678 ATTTTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTAAATATATATTA
Found at i:71763 original size:23 final size:22
Alignment explanation
Indices: 71706--71854 Score: 79
Period size: 23 Copynumber: 6.4 Consensus size: 22
71696 CGGAAGCGCT
*
71706 CTTACTGTTTCGCACTTTGTGTG
1 CTTACTGTTT-GCACCTTGTGTG
*
71729 TTTACTGTTTTGCACCTTGTGTG
1 CTTACTG-TTTGCACCTTGTGTG
* * *
71752 CTTACTGATTTGC-GCTATATGCG
1 CTTACTG-TTTGCACCT-TGTGTG
* * *
71775 CCTACTGATTGCA-GTATGTGTG
1 CTTACTGTTTGCACCT-TGTGTG
* *
71797 CCTACTGGATTGCA-CTGTGTGTG
1 CTTACT-GTTTGCACCT-TGTGTG
*
71820 CTTACTGTTTCCCCAGCACTTGTGTG
1 CTTACTGTTT--GCA-C-CTTGTGTG
71846 CTTACTGTT
1 CTTACTGTT
71855 AAGTACTTCG
Statistics
Matches: 100, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
22 21 0.21
23 57 0.57
24 5 0.05
26 15 0.15
27 2 0.02
ACGTcount: A:0.13, C:0.22, G:0.23, T:0.42
Consensus pattern (22 bp):
CTTACTGTTTGCACCTTGTGTG
Done.