Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011439.1 Kokia drynarioides strain JFW-HI SEQ_126423, 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: 18839
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Found at i:852 original size:23 final size:23
Alignment explanation
Indices: 826--974 Score: 130
Period size: 23 Copynumber: 6.5 Consensus size: 23
816 ACACTAGCGC
826 GCTTACTATTTCGCACTGTGTGT
1 GCTTACTATTTCGCACTGTGTGT
*
849 GCTTACTGTTTCGCACT-TCGTGT
1 GCTTACTATTTCGCACTGT-GTGT
* * *
872 GCTTACTGTTTCGTACTTTGTGT
1 GCTTACTATTTCGCACTGTGTGT
* * *
895 GCCTACTGATTT-GCACTATGTGC
1 GCTTACT-ATTTCGCACTGTGTGT
*
918 GCCTACTGA-TT-GCACTGTGTGT
1 GCTTACT-ATTTCGCACTGTGTGT
940 GCTTACTGGA-TT-GCACTGTGTGT
1 GCTTACT--ATTTCGCACTGTGTGT
*
963 GCTTACTGTTTC
1 GCTTACTATTTC
975 CCCAGCACTT
Statistics
Matches: 109, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
22 20 0.18
23 85 0.78
24 4 0.04
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.42
Consensus pattern (23 bp):
GCTTACTATTTCGCACTGTGTGT
Found at i:894 original size:46 final size:45
Alignment explanation
Indices: 826--974 Score: 167
Period size: 46 Copynumber: 3.3 Consensus size: 45
816 ACACTAGCGC
*
826 GCTTACTATTTCGCACTGTGTGTGCTTACTGTTTCGCACT-TCGTGT
1 GCTTACTGTTTCGCACTGTGTGTGCTTACTGTTT-GCACTAT-GTGT
* * * *
872 GCTTACTGTTTCGTACTTTGTGTGCCTACTGATTTGCACTATGTGC
1 GCTTACTGTTTCGCACTGTGTGTGCTTACTG-TTTGCACTATGTGT
* * * *
918 GCCTACTGATT-GCACTGTGTGTGCTTACTGGATTGCACTGTGTGT
1 GCTTACTGTTTCGCACTGTGTGTGCTTACT-GTTTGCACTATGTGT
963 GCTTACTGTTTC
1 GCTTACTGTTTC
975 CCCAGCACTT
Statistics
Matches: 84, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
45 35 0.42
46 45 0.54
47 4 0.05
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.42
Consensus pattern (45 bp):
GCTTACTGTTTCGCACTGTGTGTGCTTACTGTTTGCACTATGTGT
Found at i:1415 original size:15 final size:15
Alignment explanation
Indices: 1392--1424 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1382 TTGATAAAAT
*
1392 TAAGCAATAAATAAA
1 TAAGAAATAAATAAA
1407 TAAGAAATAAATAAA
1 TAAGAAATAAATAAA
1422 TAA
1 TAA
1425 TTATCTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (15 bp):
TAAGAAATAAATAAA
Found at i:2535 original size:26 final size:27
Alignment explanation
Indices: 2498--2559 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
2488 TCGTTGAAAA
* *
2498 TTAAACATGAGGTAG-TCGCCAGGACG
1 TTAAACACGAGGTAGTTAGCCAGGACG
*
2524 TTAAACACGAGGTAGTTAGCCGGGACG
1 TTAAACACGAGGTAGTTAGCCAGGACG
2551 TTAAACACG
1 TTAAACACG
2560 GGGCAGTCTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 14 0.44
27 18 0.56
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.19
Consensus pattern (27 bp):
TTAAACACGAGGTAGTTAGCCAGGACG
Found at i:4484 original size:6 final size:6
Alignment explanation
Indices: 4475--4509 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
4465 AATTTGTTAA
4475 AAATTT AAA-TT AAATTT AAA-TT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT A
4510 TTTTCGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:4489 original size:11 final size:11
Alignment explanation
Indices: 4475--4507 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
4465 AATTTGTTAA
4475 AAATTTAAATT
1 AAATTTAAATT
4486 AAATTTAAATT
1 AAATTTAAATT
4497 AAATTTAAATT
1 AAATTTAAATT
4508 TATTTTCGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AAATTTAAATT
Found at i:5181 original size:24 final size:24
Alignment explanation
Indices: 5148--5198 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5138 TAACTCTTAA
* * *
5148 TAATATTAATAACTGTTTTAATAT
1 TAATACTAATAACTCTATTAATAT
*
5172 TAATACTAATGACTCTATTAATAT
1 TAATACTAATAACTCTATTAATAT
5196 TAA
1 TAA
5199 ATAAGTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (24 bp):
TAATACTAATAACTCTATTAATAT
Found at i:5259 original size:12 final size:13
Alignment explanation
Indices: 5244--5281 Score: 60
Period size: 12 Copynumber: 2.9 Consensus size: 13
5234 TGTTTTGATA
5244 ATTATTAATAAT-
1 ATTATTAATAATG
5256 ATTATTAATAATG
1 ATTATTAATAATG
5269 ATTAATTAATAAT
1 ATT-ATTAATAAT
5282 TAATAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 3 0.12
14 9 0.38
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
ATTATTAATAATG
Found at i:6460 original size:29 final size:29
Alignment explanation
Indices: 6413--6705 Score: 275
Period size: 29 Copynumber: 10.0 Consensus size: 29
6403 GAAATCCTAT
* *
6413 TTTTGACCTCGAACCTTCCAAAAATTATCA
1 TTTTGACCCCGAA-CTTCCAAAAATTACCA
*
6443 TTTT-ACCCCTGAACTTCCAAAAATCA-CA
1 TTTTGACCCC-GAACTTCCAAAAATTACCA
*
6471 TTTTTAACCCCGAACCTTCCAAAAATTACCA
1 -TTTTGACCCCGAA-CTTCCAAAAATTACCA
* *
6502 TTTT-ACCCCCAAACTTTCAAAAA-TACCA
1 TTTTGA-CCCCGAACTTCCAAAAATTACCA
* *
6530 GTTTTGACCCCAAACTTCCAAAAA-TGCCA
1 -TTTTGACCCCGAACTTCCAAAAATTACCA
6559 TTTTTGACCCCGAACCTTCCAAAAATTACCA
1 -TTTTGACCCCGAA-CTTCCAAAAATTACCA
* *
6590 -TTTCACCCCCGAACTTCCAAAAA-TCCCA
1 TTTTGA-CCCCGAACTTCCAAAAATTACCA
6618 TTTTGACCCCGAACCTTCCAAAAATTACCA
1 TTTTGACCCCGAA-CTTCCAAAAATTACCA
*
6648 -TTTCATCCCCGAACTTCCAAAAA-T-CTCA
1 TTTTGA-CCCCGAACTTCCAAAAATTAC-CA
*
6676 TTTTTGACCCCGAACCTTTC-AAAATTACCA
1 -TTTTGACCCCGAA-CTTCCAAAAATTACCA
6706 AACCTTCCAA
Statistics
Matches: 225, Mismatches: 17, Indels: 42
0.79 0.06 0.15
Matches are distributed among these distances:
27 1 0.00
28 21 0.09
29 122 0.54
30 74 0.33
31 7 0.03
ACGTcount: A:0.34, C:0.33, G:0.05, T:0.28
Consensus pattern (29 bp):
TTTTGACCCCGAACTTCCAAAAATTACCA
Found at i:6580 original size:88 final size:87
Alignment explanation
Indices: 6431--6705 Score: 303
Period size: 88 Copynumber: 3.1 Consensus size: 87
6421 TCGAACCTTC
*
6431 CAAAAATTATCATTTT-ACCCCTG-AACTTCCAAAAATCACATTTTTAACCCCGAACCTTCCAAA
1 CAAAAA-TACCATTTTGACCCC-GAAACTTCCAAAAATC-CATTTTTAACCCCGAACCTTCCAAA
6494 AATTACCATTTTACCCCCAAACTTT
63 AATTACCATTTTACCCCCAAACTTT
*
6519 CAAAAATACCAGTTTTGACCCC-AAACTTCCAAAAATGCCATTTTTGACCCCGAACCTTCCAAAA
1 CAAAAATACCA-TTTTGACCCCGAAACTTCCAAAAAT-CCATTTTTAACCCCGAACCTTCCAAAA
* * *
6583 ATTACCATTTCACCCCCGAACTTC
64 ATTACCATTTTACCCCCAAACTTT
* * * *
6607 CAAAAATCCCATTTTGACCCCGAACCTTCCAAAAATTACCA-TTTCATCCCCGAA-CTTCCAAAA
1 CAAAAATACCATTTTGACCCCGAAACTTCCAAAAA-T-CCATTTTTAACCCCGAACCTTCCAAAA
* *
6670 A-T-CTCATTTTTGACCCCGAACCTTT
64 ATTAC-CA-TTTT-ACCCCCAAACTTT
*
6695 CAAAATTACCA
1 CAAAAATACCA
6706 AACCTTCCAA
Statistics
Matches: 160, Mismatches: 18, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
85 1 0.01
86 3 0.02
87 27 0.17
88 119 0.74
89 10 0.06
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.28
Consensus pattern (87 bp):
CAAAAATACCATTTTGACCCCGAAACTTCCAAAAATCCATTTTTAACCCCGAACCTTCCAAAAAT
TACCATTTTACCCCCAAACTTT
Found at i:6711 original size:18 final size:18
Alignment explanation
Indices: 6688--6723 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6678 TTTGACCCCG
*
6688 AACCTTTCAAAATTACCA
1 AACCTTCCAAAATTACCA
6706 AACCTTCCAAAATTACCA
1 AACCTTCCAAAATTACCA
6724 TTTTACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (18 bp):
AACCTTCCAAAATTACCA
Found at i:6756 original size:29 final size:29
Alignment explanation
Indices: 6706--6785 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 29
6696 AAAATTACCA
*
6706 AACCTTCCAAAATTACCATTTT-ACCCTCG
1 AACCTTCCAAAAATACCATTTTGACCCT-G
*
6735 AA-CTTCCAAAAATCCCATTTTTGACCCTG
1 AACCTTCCAAAAATACCA-TTTTGACCCTG
6764 AACCTTCCAAAAATTACCATTT
1 AACCTTCCAAAAA-TACCATTT
6786 ACCCCCGAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 13 0.30
29 9 0.20
30 18 0.41
31 4 0.09
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (29 bp):
AACCTTCCAAAAATACCATTTTGACCCTG
Found at i:6756 original size:76 final size:78
Alignment explanation
Indices: 6629--6782 Score: 242
Period size: 76 Copynumber: 2.0 Consensus size: 78
6619 TTTGACCCCG
*
6629 AACCTTCCAAAAATTACCATTTCATCCCCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTT
1 AACCTTCCAAAAATTACCATTTCATCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
*
6694 TC-AAAATTACCA
66 CCAAAAATTACCA
* *
6706 AACCTTCC-AAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGACCCTGAACCT
1 AACCTTCCAAAAATTACCATTTCATCCC-CGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
6769 TCCAAAAATTACCA
65 TCCAAAAATTACCA
6783 TTTACCCCCG
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
75 3 0.04
76 50 0.70
77 18 0.25
ACGTcount: A:0.35, C:0.32, G:0.04, T:0.29
Consensus pattern (78 bp):
AACCTTCCAAAAATTACCATTTCATCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
CCAAAAATTACCA
Found at i:6771 original size:30 final size:29
Alignment explanation
Indices: 6706--6794 Score: 103
Period size: 28 Copynumber: 3.1 Consensus size: 29
6696 AAAATTACCA
*
6706 AACCTTCCAAAATTACCATTTTACCCTCG
1 AACCTTCCAAAAATACCATTTTACCCTCG
*
6735 AA-CTTCCAAAAATCCCATTTTTGACCCT-G
1 AACCTTCCAAAAATACCA-TTTT-ACCCTCG
*
6764 AACCTTCCAAAAATTACCA-TTTACCCCCG
1 AACCTTCCAAAAA-TACCATTTTACCCTCG
6793 AA
1 AA
6795 TGTTTGAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
28 17 0.33
29 15 0.29
30 15 0.29
31 4 0.08
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.28
Consensus pattern (29 bp):
AACCTTCCAAAAATACCATTTTACCCTCG
Found at i:9840 original size:21 final size:21
Alignment explanation
Indices: 9802--9841 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9792 CTGGAAAGCC
* *
9802 AAGCTGAAGTAGCTGAATTAA
1 AAGCTCAAGTAGCAGAATTAA
*
9823 AAGCTCAAGTAGGAGAATT
1 AAGCTCAAGTAGCAGAATT
9842 GGAGGAATCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (21 bp):
AAGCTCAAGTAGCAGAATTAA
Found at i:18745 original size:42 final size:41
Alignment explanation
Indices: 18667--18748 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 41
18657 AAAACTCCCC
* *
18667 TTTAAATTTATTTTAAGATTAAATTTGTTAAAAATTTAAAT
1 TTTAAATTTATTTTAAGATTAAAATTATTAAAAATTTAAAT
* *
18708 TTTAAATTTATTTTCGAA-TTTAAAATTATTATAAATTTAAA
1 TTTAAATTTATTTT--AAGATTAAAATTATTAAAAATTTAAA
18749 ATAAGTGTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 14 0.40
42 19 0.54
43 2 0.06
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (41 bp):
TTTAAATTTATTTTAAGATTAAAATTATTAAAAATTTAAAT
Done.