Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010438.1 Kokia drynarioides strain JFW-HI SEQ_125328, 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: 56236
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 54 characters in sequence are not A, C, G, or T
Found at i:709 original size:18 final size:17
Alignment explanation
Indices: 686--796 Score: 141
Period size: 17 Copynumber: 6.4 Consensus size: 17
676 TTATAGTATT
686 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
704 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
*
721 TTTAAATTCAAAATAAA
1 TTTAAATTTAAAATAAA
738 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
755 TTTAAATTTTTAAACAAA
1 TTTAAA-TTTAAAATAAA
*
773 TTTAATTTTTAAAATAAA
1 TTTAA-ATTTAAAATAAA
791 TTTAAA
1 TTTAAA
797 GGGAGTTCGG
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
17 43 0.54
18 36 0.46
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:751 original size:7 final size:6
Alignment explanation
Indices: 686--763 Score: 74
Period size: 6 Copynumber: 13.5 Consensus size: 6
676 TTATAGTATT
* * *
686 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTCAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
733 -ATAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
764 TTAAACAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
5 15 0.26
6 40 0.69
7 3 0.05
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:761 original size:23 final size:23
Alignment explanation
Indices: 700--749 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
690 AATTTGAAAA
* *
700 TAAATTTAAACTTAAATTAAATT
1 TAAATTCAAACATAAATTAAATT
723 TAAATTCAAA-ATAAATTTAAATT
1 TAAATTCAAACATAAA-TTAAATT
746 TAAA
1 TAAA
750 ATAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATTCAAACATAAATTAAATT
Found at i:1683 original size:27 final size:25
Alignment explanation
Indices: 1641--1694 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
1631 TGGGTAAATT
* * *
1641 ATTTTTTGACCTTTACAAGTTCAAA
1 ATTTTTTGACCCTTACAAATTAAAA
1666 ATTTTTTGACCCCCTTACAAATTAAAA
1 ATTTTTTGA--CCCTTACAAATTAAAA
1693 AT
1 AT
1695 ACACAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.41
Consensus pattern (25 bp):
ATTTTTTGACCCTTACAAATTAAAA
Found at i:2152 original size:14 final size:14
Alignment explanation
Indices: 2120--2196 Score: 50
Period size: 14 Copynumber: 5.1 Consensus size: 14
2110 ATAATTTTGC
* *
2120 TATTATATTATTAC
1 TATTTTATTATTAT
2134 TATTTTATTATTAT
1 TATTTTATTATTAT
2148 TATTTGGATATTATATAACTCT
1 TATTT---TATTAT-T-A---T
2170 TATTTTATTATTA-
1 TATTTTATTATTAT
2183 -ATTTTATTATTAT
1 TATTTTATTATTAT
2196 T
1 T
2197 TTAGAAATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
12 12 0.24
14 17 0.33
17 7 0.14
18 2 0.04
19 7 0.14
22 6 0.12
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (14 bp):
TATTTTATTATTAT
Found at i:2188 original size:12 final size:11
Alignment explanation
Indices: 2169--2199 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
2159 TATATAACTC
2169 TTATTTTATTA
1 TTATTTTATTA
2180 TTAATTTTATTA
1 TT-ATTTTATTA
2192 TTATTTTA
1 TTATTTTA
2200 GAAATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:2199 original size:11 final size:11
Alignment explanation
Indices: 2120--2199 Score: 54
Period size: 11 Copynumber: 6.9 Consensus size: 11
2110 ATAATTTTGC
*
2120 TATTATATTAT
1 TATTATTTTAT
*
2131 TACTATTTTAT
1 TATTATTTTAT
2142 TATTATTATT-T
1 TATTATT-TTAT
* * *
2153 GGATATTATATAAC
1 ---TATTATTTTAT
*
2167 TCTTATTTTAT
1 TATTATTTTAT
2178 TATTAATTTTAT
1 TATT-ATTTTAT
2190 TATTATTTTA
1 TATTATTTTA
2200 GAAATATTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
11 32 0.62
12 13 0.25
13 1 0.02
14 6 0.12
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:5296 original size:22 final size:22
Alignment explanation
Indices: 5246--5296 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
5236 TACTCACCTT
*
5246 ATAATTTTTTTTAATTATTCTC
1 ATAATTTTTTTTAATTATCCTC
*
5268 TTAAATTTTTTTTATATT-TCCTC
1 AT-AATTTTTTTTA-ATTATCCTC
5291 ATAATT
1 ATAATT
5297 AAAATAAGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 5 0.21
23 16 0.67
24 3 0.12
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (22 bp):
ATAATTTTTTTTAATTATCCTC
Found at i:6345 original size:51 final size:51
Alignment explanation
Indices: 6269--6371 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
6259 TGTTAAAGAG
*
6269 GATCAAGAGGAGAGGTTGGAACTGAGAGTGGATATTGGAATTGGGGATAAT
1 GATCAAGAGGAGAGGTTGGAACTGAGAGTGGATACTGGAATTGGGGATAAT
6320 GATCAAGAGGAGAGGTTGGAACTGAGAGTGGATACTGGAATTGGGGATAAT
1 GATCAAGAGGAGAGGTTGGAACTGAGAGTGGATACTGGAATTGGGGATAAT
6371 G
1 G
6372 CAGTTGTAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.05, G:0.40, T:0.22
Consensus pattern (51 bp):
GATCAAGAGGAGAGGTTGGAACTGAGAGTGGATACTGGAATTGGGGATAAT
Found at i:15909 original size:18 final size:17
Alignment explanation
Indices: 15865--15909 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
15855 CGTTTTTAAG
*
15865 TATATAATATTTTATAT
1 TATATAATTTTTTATAT
* *
15882 TATGTTATTTTTATATAT
1 TATATAATTTTT-TATAT
15900 TATATAATTT
1 TATATAATTT
15910 GTAACAAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TATATAATTTTTTATAT
Found at i:17661 original size:24 final size:24
Alignment explanation
Indices: 17632--17706 Score: 116
Period size: 24 Copynumber: 3.1 Consensus size: 24
17622 AAAAATAATC
17632 TTTCAATTAAACTCTTTTTATTTG
1 TTTCAATTAAACTCTTTTTATTTG
*
17656 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTTTTTATTTG
*
17680 TTTCAATTAAACT-TTGTTTAGTTG
1 TTTCAATTAAACTCTT-TTTATTTG
17704 TTT
1 TTT
17707 GAGTCAAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.24, C:0.11, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTTTTTATTTG
Found at i:19646 original size:24 final size:24
Alignment explanation
Indices: 19617--19667 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
19607 AGAAATAATC
*
19617 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
19641 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
19665 TTT
1 TTT
19668 GAGTCAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:21626 original size:36 final size:36
Alignment explanation
Indices: 21574--21694 Score: 106
Period size: 36 Copynumber: 3.5 Consensus size: 36
21564 TTGAATACAT
* *
21574 ATGAGTTTAATTGAGCTTGAGTACAAAAATTGATAA
1 ATGAGCTTAATCGAGCTTGAGTACAAAAATTGATAA
** ** * *
21610 ATGAGCTTAATCGAGCTCAAG--CTTAAA-T-ACAT
1 ATGAGCTTAATCGAGCTTGAGTACAAAAATTGATAA
* *
21642 ATGAGCTTAGTTGAGCTTGAGTACAAAAATTGATAA
1 ATGAGCTTAATCGAGCTTGAGTACAAAAATTGATAA
* *
21678 ATAAACTTAATCGAGCT
1 ATGAGCTTAATCGAGCT
21695 CAAACTTGAA
Statistics
Matches: 61, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
32 19 0.31
33 1 0.02
34 8 0.13
35 1 0.02
36 32 0.52
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.31
Consensus pattern (36 bp):
ATGAGCTTAATCGAGCTTGAGTACAAAAATTGATAA
Found at i:21633 original size:68 final size:68
Alignment explanation
Indices: 21555--21706 Score: 250
Period size: 68 Copynumber: 2.2 Consensus size: 68
21545 AATCGAGTTA
* * *
21555 AGCTCAAGCTTGAATACATATGAGTTTAATTGAGCTTGAGTACAAAAATTGATAAATGAGCTTAA
1 AGCTCAAGCTTGAATACATATGAGCTTAATTGAGCTTGAGTACAAAAATTGATAAATAAACTTAA
21620 TCG
66 TCG
* *
21623 AGCTCAAGCTTAAATACATATGAGCTTAGTTGAGCTTGAGTACAAAAATTGATAAATAAACTTAA
1 AGCTCAAGCTTGAATACATATGAGCTTAATTGAGCTTGAGTACAAAAATTGATAAATAAACTTAA
21688 TCG
66 TCG
*
21691 AGCTCAAACTTGAATA
1 AGCTCAAGCTTGAATA
21707 ACTCAATTAT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 77 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (68 bp):
AGCTCAAGCTTGAATACATATGAGCTTAATTGAGCTTGAGTACAAAAATTGATAAATAAACTTAA
TCG
Found at i:25838 original size:25 final size:26
Alignment explanation
Indices: 25797--25845 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
25787 ATAGTAATTC
25797 TTTTACAAATATATAATTTATTATTA
1 TTTTACAAATATATAATTTATTATTA
* *
25823 TTTTATAAA-ATATAATTTTTTAT
1 TTTTACAAATATATAATTTATTAT
25846 GTTAAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTTACAAATATATAATTTATTATTA
Found at i:37001 original size:117 final size:117
Alignment explanation
Indices: 36781--37009 Score: 424
Period size: 117 Copynumber: 2.0 Consensus size: 117
36771 CCCATAGATC
* *
36781 TATCCTGTTATTTTAACAGTTTAATTAATAATTTCAATAATATAAAGGATATAACCCCAACATCT
1 TATCCTGTTATTTTAACAGTTCAATTAATAATTTCAATAAAATAAAGGATATAACCCCAACATCT
36846 TTTAAATGACAAACGTTTTAAACAATTTCAATGATGTAAAGACTGTAAAGACG
66 TTTAAATGACAAACGTTTTAAACAATTTCAATGATGTAAAGAC-GTAAAGACG
36899 TATCCTGTTATTTTAACAGTTCAATTAATAATTTCAATAAAATAAAGGATAT-ACCCCAACATCT
1 TATCCTGTTATTTTAACAGTTCAATTAATAATTTCAATAAAATAAAGGATATAACCCCAACATCT
36963 TTTAAATGACAAACGTTTTAAACAATTTCAATGATGTAAAGACGTAA
66 TTTAAATGACAAACGTTTTAAACAATTTCAATGATGTAAAGACGTAA
37010 TTAATATATC
Statistics
Matches: 109, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
116 4 0.04
117 55 0.50
118 50 0.46
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (117 bp):
TATCCTGTTATTTTAACAGTTCAATTAATAATTTCAATAAAATAAAGGATATAACCCCAACATCT
TTTAAATGACAAACGTTTTAAACAATTTCAATGATGTAAAGACGTAAAGACG
Found at i:54812 original size:22 final size:21
Alignment explanation
Indices: 54774--54815 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
54764 TAAAGTATGT
*
54774 AAAAATAGAAATAAATATATA
1 AAAAATACAAATAAATATATA
*
54795 AAAAATACAGAATGAATATAT
1 AAAAATACA-AATAAATATAT
54816 TATAATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (21 bp):
AAAAATACAAATAAATATATA
Found at i:54815 original size:2 final size:2
Alignment explanation
Indices: 54810--54847 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
54800 TACAGAATGA
54810 AT AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54848 GTATGTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54966 original size:24 final size:25
Alignment explanation
Indices: 54908--54971 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
54898 AAAAATGAAA
* *
54908 AAAAATTAAAAATATAAAAATTTGT
1 AAAAATTATATATATAAAAATTTGT
* * *
54933 AAAAA-AATATATTTAAAACTTT-T
1 AAAAATTATATATATAAAAATTTGT
54956 AAAAATTATATATATA
1 AAAAATTATATATATA
54972 TAAGTATTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 6 0.19
24 20 0.65
25 5 0.16
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (25 bp):
AAAAATTATATATATAAAAATTTGT
Found at i:55622 original size:13 final size:13
Alignment explanation
Indices: 55601--55635 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
55591 TTAGCATTGC
*
55601 TTTTAAAAAGTAA
1 TTTTGAAAAGTAA
*
55614 TTTTGAAAAGTAC
1 TTTTGAAAAGTAA
55627 TTTTGAAAA
1 TTTTGAAAA
55636 ACTTAGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (13 bp):
TTTTGAAAAGTAA
Done.