Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002675.1 Kokia drynarioides strain JFW-HI SEQ_114931, 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: 77787
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:8752 original size:29 final size:30
Alignment explanation
Indices: 8712--8772 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
8702 TTATAATAGT
* *
8712 AAAATTATATTTTATC-TCTCAAAATTATA
1 AAAATTATATTTAATCTTCTAAAAATTATA
*
8741 AAAATT-TGATTTAATCTTTTAAAAATTATA
1 AAAATTAT-ATTTAATCTTCTAAAAATTATA
8771 AA
1 AA
8773 TATAAAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.04
29 13 0.48
30 13 0.48
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.44
Consensus pattern (30 bp):
AAAATTATATTTAATCTTCTAAAAATTATA
Found at i:10734 original size:19 final size:20
Alignment explanation
Indices: 10710--10753 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
10700 TTTCTTTATG
10710 TTTTTT-TATAATTTT-AAT
1 TTTTTTATATAATTTTGAAT
*
10728 ATTTTTTATATTATTTTGAAT
1 -TTTTTTATATAATTTTGAAT
10749 TTTTT
1 TTTTT
10754 AATTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 13 0.59
21 3 0.14
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTTATATAATTTTGAAT
Found at i:10754 original size:19 final size:20
Alignment explanation
Indices: 10710--10754 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
10700 TTTCTTTATG
10710 TTTTTT-TATAATTTTAATA
1 TTTTTTATATAATTTTAATA
* *
10729 TTTTTTATATTATTTTGA-A
1 TTTTTTATATAATTTTAATA
10748 TTTTTTA
1 TTTTTTA
10755 ATTTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTTATATAATTTTAATA
Found at i:11788 original size:16 final size:15
Alignment explanation
Indices: 11769--11822 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
11759 GTGAAAAAAA
11769 AAAAATTTGAAAGATG
1 AAAAA-TTGAAAGATG
11785 AAAAATTGAAAGGATAG
1 AAAAATTGAAA-GAT-G
*
11802 AAAAATAGAAAGATG
1 AAAAATTGAAAGATG
*
11817 GAAAAT
1 AAAAAT
11823 ATAATTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 12 0.35
16 11 0.32
17 11 0.32
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.19
Consensus pattern (15 bp):
AAAAATTGAAAGATG
Found at i:12888 original size:20 final size:20
Alignment explanation
Indices: 12863--12904 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
12853 ATTGGACTTA
12863 TAGACGACATAATAGTCCCT
1 TAGACGACATAATAGTCCCT
12883 TAGACGACATAATAGTCCCT
1 TAGACGACATAATAGTCCCT
12903 TA
1 TA
12905 TTATTTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (20 bp):
TAGACGACATAATAGTCCCT
Found at i:14008 original size:90 final size:91
Alignment explanation
Indices: 13832--14014 Score: 253
Period size: 90 Copynumber: 2.0 Consensus size: 91
13822 AACAAATTAA
* * *
13832 ACCCAAACCTAATTTTTTTAAAAATAAATAAAGAAAAAGCAATAGAAAAATTAAAAAAAAACAAC
1 ACCCAAACCCAATTTTTTAAAAAATAAATAAAGAAAAAGCAAGAGAAAAA-TAAAAAAAAAC-AC
* *
13897 AAAAGGCGGTAAACCATAGGAGAGTTAT
64 AAAAGACGGTAAAACATAGGAGAGTTAT
* * *
13925 ACCCAAACCCAATTTTTTAAAAAAGTAAATAAAGACAAGGCAAGGGAAAAA-AAAAAAAAAC-CA
1 ACCCAAACCCAATTTTTTAAAAAA-TAAATAAAGAAAAAGCAAGAGAAAAATAAAAAAAAACACA
13988 AAAGACGGTAAAACATAGGAGAGTTAT
65 AAAGACGGTAAAACATAGGAGAGTTAT
14015 TTTCGCTCGC
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
90 27 0.33
92 10 0.12
93 22 0.27
94 22 0.27
ACGTcount: A:0.57, C:0.13, G:0.14, T:0.17
Consensus pattern (91 bp):
ACCCAAACCCAATTTTTTAAAAAATAAATAAAGAAAAAGCAAGAGAAAAATAAAAAAAAACACAA
AAGACGGTAAAACATAGGAGAGTTAT
Found at i:22358 original size:22 final size:22
Alignment explanation
Indices: 22311--22364 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
22301 TTTTATATTT
* **
22311 TTTTGATTTGTTTATCATAATT
1 TTTTGATTTTTTTATCATAAAA
22333 TTTTGATTTTTTTAT-ATTAAAA
1 TTTTGATTTTTTTATCA-TAAAA
22355 TTTTG-TTTTT
1 TTTTGATTTTT
22365 ATTTTTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (22 bp):
TTTTGATTTTTTTATCATAAAA
Found at i:24278 original size:21 final size:19
Alignment explanation
Indices: 24256--24308 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
24246 TTAAAAGATA
24256 TATTAATTAATAATAATAT
1 TATTAATTAATAATAATAT
*
24275 TA-TAATAAATAATAATATTT
1 TATTAATTAATAATAATA--T
24295 TATTAATTTAATAA
1 TATTAA-TTAATAA
24309 ATAAAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 14 0.50
19 2 0.07
20 3 0.11
21 3 0.11
22 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTAATTAATAATAATAT
Found at i:25729 original size:4 final size:4
Alignment explanation
Indices: 25720--25754 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
25710 TTAAAAAGAT
*
25720 TTTA TTTA TTTA TTTA TTTA GTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
25755 TTATCAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:30223 original size:16 final size:15
Alignment explanation
Indices: 30199--30232 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
30189 CTTCTATTAT
*
30199 TTTTCTTTTTTCTCC
1 TTTTCTTTTTTATCC
30214 TTTTCATTTTTTATCC
1 TTTTC-TTTTTTATCC
30230 TTT
1 TTT
30233 ATGTACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTCTTTTTTATCC
Found at i:31328 original size:6 final size:6
Alignment explanation
Indices: 31290--31324 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
31280 AGGAATGGGG
*
31290 AAGGAA AAGGAA AAGGAA AAGGAA AAGGAG AAGGA
1 AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGA
31325 GAAGAAGCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (6 bp):
AAGGAA
Found at i:39162 original size:2 final size:2
Alignment explanation
Indices: 39155--39180 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39145 TCTATCTGTC
39155 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
39181 AATTTCCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42377 original size:11 final size:10
Alignment explanation
Indices: 42352--42376 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42342 TGAGGTCCTA
42352 TTTTTATTTT
1 TTTTTATTTT
42362 TTTTTATTTT
1 TTTTTATTTT
42372 TTTTT
1 TTTTT
42377 TCAATTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:50637 original size:15 final size:13
Alignment explanation
Indices: 50587--50639 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
50577 AATTTAAAAA
*
50587 ATAAATTTTTAAT
1 ATAAATTTTTATT
* *
50600 ATTAA-TTTCATT
1 ATAAATTTTTATT
50612 ATAAATTTTTATT
1 ATAAATTTTTATT
50625 ATAAATTTTT-TT
1 ATAAATTTTTATT
50637 ATA
1 ATA
50640 TGATGTCTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
12 14 0.41
13 20 0.59
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (13 bp):
ATAAATTTTTATT
Found at i:50731 original size:13 final size:13
Alignment explanation
Indices: 50706--50742 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
50696 TGAAATATTT
50706 AAAAA-AAAA-AA
1 AAAAACAAAACAA
50717 AAAAACAAAACAA
1 AAAAACAAAACAA
50730 AAAAACAAAACAA
1 AAAAACAAAACAA
50743 CCTTAGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 5 0.21
12 4 0.17
13 15 0.62
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAACAA
Found at i:50733 original size:18 final size:17
Alignment explanation
Indices: 50706--50742 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
50696 TGAAATATTT
50706 AAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAC
*
50723 AAAACAAAAAAACAAAAC
1 AAAA-AAAAAAAAAAAAC
50741 AA
1 AA
50743 CCTTAGAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAAC
Found at i:50910 original size:20 final size:20
Alignment explanation
Indices: 50882--50923 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
50872 CAATTATAAT
*
50882 ATAAAAAAAGAA-CATAAAAA
1 ATAAAAAAA-AATAATAAAAA
*
50902 ATAATAAAAAATAATAAAAA
1 ATAAAAAAAAATAATAAAAA
50922 AT
1 AT
50924 TGTAAAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (20 bp):
ATAAAAAAAAATAATAAAAA
Found at i:50930 original size:10 final size:10
Alignment explanation
Indices: 50895--50923 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
50885 AAAAAAGAAC
50895 ATAAAAAATA
1 ATAAAAAATA
50905 ATAAAAAATA
1 ATAAAAAATA
50915 ATAAAAAAT
1 ATAAAAAAT
50924 TGTAAAAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:54751 original size:14 final size:14
Alignment explanation
Indices: 54688--54752 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
54678 TCGGCAATAT
*
54688 ATAAATAACTTATA
1 ATAAATAATTTATA
54702 ATAAAT-ATTATATA
1 ATAAATAATT-TATA
* * *
54716 ATTTAATTAAAATTAAA
1 A--TAAAT-AATTTATA
54733 ATAAATAATTTATA
1 ATAAATAATTTATA
54747 ATAAAT
1 ATAAAT
54753 TGGTAGGTCA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
13 2 0.05
14 23 0.59
15 4 0.10
16 4 0.10
17 4 0.10
18 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAAATAATTTATA
Found at i:54854 original size:8 final size:8
Alignment explanation
Indices: 54841--54866 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
54831 GTGGAAGTAT
54841 ATTTTAAA
1 ATTTTAAA
54849 ATTTTAAA
1 ATTTTAAA
54857 ATTTTAAA
1 ATTTTAAA
54865 AT
1 AT
54867 ATTATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTTTAAA
Found at i:55808 original size:18 final size:18
Alignment explanation
Indices: 55771--55814 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
55761 TATAAAATTT
*
55771 AAATTTATAAATTTATAA
1 AAATTTATAAATTCATAA
55789 AAATATTATAAATTCA-AA
1 AAAT-TTATAAATTCATAA
*
55807 AATTTTAT
1 AAATTTAT
55815 TTTTTATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 9 0.39
19 10 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTATAAATTCATAA
Found at i:57948 original size:5 final size:5
Alignment explanation
Indices: 57931--57963 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
57921 AGGTGAGTAT
*
57931 TCGA- TCGAG TCGAA TCGAG TCGAG TCGAG TCGA
1 TCGAG TCGAG TCGAG TCGAG TCGAG TCGAG TCGA
57964 ATCAAGTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.21
Consensus pattern (5 bp):
TCGAG
Found at i:57949 original size:10 final size:10
Alignment explanation
Indices: 57934--57980 Score: 67
Period size: 10 Copynumber: 4.7 Consensus size: 10
57924 TGAGTATTCG
57934 ATCGAGTCGA
1 ATCGAGTCGA
57944 ATCGAGTCGA
1 ATCGAGTCGA
*
57954 GTCGAGTCGA
1 ATCGAGTCGA
* *
57964 ATCAAGTTGA
1 ATCGAGTCGA
57974 ATCGAGT
1 ATCGAGT
57981 AAAAAAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (10 bp):
ATCGAGTCGA
Found at i:61068 original size:13 final size:13
Alignment explanation
Indices: 61050--61074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61040 AATGAGTCAA
61050 ATCTCAATATATC
1 ATCTCAATATATC
61063 ATCTCAATATAT
1 ATCTCAATATAT
61075 AAAAGAGTGC
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:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
ATCTCAATATATC
Found at i:64829 original size:7 final size:7
Alignment explanation
Indices: 64817--64842 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
64807 TATTTATTAA
64817 TTTAAAT
1 TTTAAAT
64824 TTTAAAT
1 TTTAAAT
64831 TTTAAAT
1 TTTAAAT
64838 TTTAA
1 TTTAA
64843 TTATTACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTAAAT
Done.