Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014747.1 Kokia drynarioides strain JFW-HI SEQ_129786, 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: 69574
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 78 characters in sequence are not A, C, G, or T
Found at i:9893 original size:23 final size:25
Alignment explanation
Indices: 9853--9899 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
9843 TTTAAATTAA
* *
9853 TAAAAATAAATTATATTTT-ATTTT
1 TAAAAATAAATAAAATTTTGATTTT
9877 TAAAAAT-AATAAAATTTTGATTT
1 TAAAAATAAATAAAATTTTGATTT
9900 AATTCTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TAAAAATAAATAAAATTTTGATTTT
Found at i:10051 original size:24 final size:24
Alignment explanation
Indices: 10024--10069 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
10014 TAAAATCAAT
10024 CTATTTCTTTAAATAACTCAAAAC
1 CTATTTCTTTAAATAACTCAAAAC
10048 CTATTTCTTTAAATAACTCAAA
1 CTATTTCTTTAAATAACTCAAA
10070 CCCCAACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (24 bp):
CTATTTCTTTAAATAACTCAAAAC
Found at i:16487 original size:29 final size:29
Alignment explanation
Indices: 16425--16505 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
16415 ATAAATCTCA
* *
16425 AATTTATATATGAATTTTAATTTAATGTGT
1 AATTTATATATGAATTTTAATTT-ACGTAT
*
16455 AATTTGATATATGAATTTTGATTT-CGTAT
1 AATTT-ATATATGAATTTTAATTTACGTAT
* * *
16484 AATTATACACATGAACTTTAAT
1 AATT-TATATATGAATTTTAAT
16506 GGTTGTCCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
29 19 0.45
30 6 0.14
31 17 0.40
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (29 bp):
AATTTATATATGAATTTTAATTTACGTAT
Found at i:16717 original size:30 final size:30
Alignment explanation
Indices: 16680--16760 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
16670 AAATTCGGTC
16680 AAATCAAAATTTCATGTATAAATTTACATA
1 AAATCAAAATTTCATGTATAAATTTACATA
* * *
16710 AACTCAAAATTTTATGTATAAATTTATATA
1 AAATCAAAATTTCATGTATAAATTTACATA
*
16740 AAATCAAAA-TTCATATATAAA
1 AAATCAAAATTTCATGTATAAA
16761 ATTGGATATT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
29 10 0.22
30 35 0.78
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAATTTACATA
Found at i:17076 original size:13 final size:13
Alignment explanation
Indices: 17045--17087 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
17035 ATATTTGGGT
17045 TAATATTAA-AAA
1 TAATATTAATAAA
17057 T-AT-TTAATAAA
1 TAATATTAATAAA
17068 TAATATTAATAAA
1 TAATATTAATAAA
*
17081 TCATATT
1 TAATATT
17088 TCATTTTGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.15
11 6 0.22
12 3 0.11
13 14 0.52
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (13 bp):
TAATATTAATAAA
Found at i:19552 original size:84 final size:83
Alignment explanation
Indices: 19418--19600 Score: 239
Period size: 84 Copynumber: 2.2 Consensus size: 83
19408 TTGACGCCCA
* * *
19418 AAAAATG-AAAAAAAA-TTCAATTCAATCCTCTTATAAATAGAGAAACTATAAATTAATATAGTA
1 AAAAATGAAAAAAAAATTTCAATTCAATCCTCTTATAAATAAAGAAACTATAAACTAATATAGAA
* *
19481 AAATTATACTTTGATCA-TT
66 AAATT-CACTTT-AACACTT
* *
19500 CAAAATGAAAAAAAAATTTCAATTCAATCCGT-TTATAAATAAAGAAATTATAAACTAATATAGA
1 AAAAATGAAAAAAAAATTTCAATTCAATCC-TCTTATAAATAAAGAAACTATAAACTAATATAGA
19564 AAAATTCACTTTAACACCTT
65 AAAATTCACTTTAACA-CTT
19584 AAAAATGAAAAAAAAAT
1 AAAAATGAAAAAAAAAT
19601 AATCCCTTAA
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
82 9 0.10
83 13 0.15
84 65 0.74
85 1 0.01
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (83 bp):
AAAAATGAAAAAAAAATTTCAATTCAATCCTCTTATAAATAAAGAAACTATAAACTAATATAGAA
AAATTCACTTTAACACTT
Found at i:20686 original size:3 final size:3
Alignment explanation
Indices: 20671--20701 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
20661 CCACCCCAAA
*
20671 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20702 CTGCCTACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:30102 original size:7 final size:7
Alignment explanation
Indices: 30090--30125 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
30080 CAGCAGTGTG
30090 GTTGGGA
1 GTTGGGA
30097 GTTGGGA
1 GTTGGGA
*
30104 GCTGGGA
1 GTTGGGA
30111 GTTGGGA
1 GTTGGGA
*
30118 CTTGGGA
1 GTTGGGA
30125 G
1 G
30126 GGGAGGTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.14, C:0.06, G:0.56, T:0.25
Consensus pattern (7 bp):
GTTGGGA
Found at i:35675 original size:41 final size:38
Alignment explanation
Indices: 35575--35678 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
35565 TTCGAAGCAA
* *
35575 TAAAGTGACACCCAGTGTCTCATCG-ACCTAGCTGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
35612 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
35650 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
35679 GTCGAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:40035 original size:24 final size:24
Alignment explanation
Indices: 39989--40035 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
39979 CTAATAGATG
* *
39989 CATAAAACGCATCGTATAGCTAAA
1 CATAAAACGCAACGTATAACTAAA
*
40013 CATAAAACGCAACGTTTAACTAA
1 CATAAAACGCAACGTATAACTAA
40036 TAGTACTCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (24 bp):
CATAAAACGCAACGTATAACTAAA
Found at i:45661 original size:30 final size:30
Alignment explanation
Indices: 45625--45688 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
45615 CACTCTAAAT
*
45625 AAAAAAATTTAAATGACAAGTATGTTTATA
1 AAAAAAATTTAAATGACAAATATGTTTATA
*
45655 AAAAAAATTTATATGACAAATATGTTTATA
1 AAAAAAATTTAAATGACAAATATGTTTATA
45685 AAAA
1 AAAA
45689 GCTCATAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (30 bp):
AAAAAAATTTAAATGACAAATATGTTTATA
Found at i:53048 original size:29 final size:30
Alignment explanation
Indices: 53015--53084 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
53005 ATCATTCAAT
*
53015 TTCAAAAGTTACAAAT-GGTCATTGAACTA
1 TTCAAAAGTTACAAATAAGTCATTGAACTA
* * *
53044 TTCAAAAGTTTTCATATAAGTCATTGAATTA
1 TTCAAAAG-TTACAAATAAGTCATTGAACTA
53075 TTCAAAAGTT
1 TTCAAAAGTT
53085 TTTATTCAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.23
30 8 0.23
31 19 0.54
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (30 bp):
TTCAAAAGTTACAAATAAGTCATTGAACTA
Found at i:57430 original size:22 final size:22
Alignment explanation
Indices: 57398--57514 Score: 144
Period size: 22 Copynumber: 5.2 Consensus size: 22
57388 ACGCTAGCAC
*
57398 GCTTATGTTCAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
*
57420 GCTTCTATTCAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* * *
57442 GCTTCTGTTTAGCATTATGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* *
57464 GCTTCTGTTTAGCACTATGTGT
1 GCTTCTGTTCAGCACTGTGTGT
57486 GCTTCTGTTACCCAGCACTGTGTGT
1 GCTTCTGTT---CAGCACTGTGTGT
57511 GCTT
1 GCTT
57515 TTATTTCCTC
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
22 68 0.82
25 15 0.18
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.43
Consensus pattern (22 bp):
GCTTCTGTTCAGCACTGTGTGT
Found at i:62896 original size:19 final size:19
Alignment explanation
Indices: 62872--62914 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
62862 AAACATAAAT
62872 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
62891 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
62910 TAAAT
1 TAAAT
62915 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:63574 original size:30 final size:30
Alignment explanation
Indices: 63498--63576 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 30
63488 TTTTTTAAAA
*
63498 TTTTGAAAATTCAAAAGAT-ATATAAAAGTTAT
1 TTTTAAAAATT-AAAA-ATCAT-TAAAAGTTAT
63530 TTTTAAAAATTAAAAATCATTAAAA-TTA-
1 TTTTAAAAATTAAAAATCATTAAAAGTTAT
63558 TTTTAAAAAGTATAAAAAT
1 TTTTAAAAA-T-TAAAAAT
63577 TACAAAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
28 9 0.21
29 4 0.09
30 14 0.33
31 6 0.14
32 10 0.23
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (30 bp):
TTTTAAAAATTAAAAATCATTAAAAGTTAT
Found at i:65639 original size:29 final size:28
Alignment explanation
Indices: 65608--65979 Score: 386
Period size: 29 Copynumber: 12.8 Consensus size: 28
65598 TTCGGAGTCA
65608 AAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
65636 AAAATGGTAATTTTGGAAGGTTC-GGGAT
1 AAAATGGGATTTTTGGAA-GTTCGGGGGT
65664 AAAAAATGGGACTTTTTGGAAGTTCGGGGGT
1 --AAAATGGGA-TTTTTGGAAGTTCGGGGGT
* ** *
65695 AAAATGGTAATTTTTGGAAGGTTTAGGGTT
1 AAAATGG-GATTTTTGGAA-GTTCGGGGGT
*
65725 AAAAATGGGATTTTTGGAAGTTTGGGGGT
1 -AAAATGGGATTTTTGGAAGTTCGGGGGT
* * * *
65754 AAAATGGTAATTTTGGAATGTTCGAGGTT
1 AAAATGGGATTTTTGGAA-GTTCGGGGGT
65783 AAAAATGGGATTTTTGGAAGTTCGGGGGT
1 -AAAATGGGATTTTTGGAAGTTCGGGGGT
* *
65812 AAAATGGCATTTTTGGAAGGTTCGGGGTT
1 AAAATGGGATTTTTGGAA-GTTCGGGGGT
* *
65841 AAAAACGGGATTTTTGGAAGTTCAGGGGT
1 -AAAATGGGATTTTTGGAAGTTCGGGGGT
* *
65870 AAAATGGTAATTTTTGGAAGGTTCGGGGTT
1 AAAATGG-GATTTTTGGAA-GTTCGGGGGT
*
65900 AAAAATGGGATTTTTGGAAGTTTGGGGGT
1 -AAAATGGGATTTTTGGAAGTTCGGGGGT
* ** *
65929 AAAATGGTAATTTTTGGAAGGTTCTAGGTT
1 AAAATGG-GATTTTTGGAA-GTTCGGGGGT
65959 AAAATGGGATTTTTGGAAGTT
1 AAAATGGGATTTTTGGAAGTT
65980 TAGAGACCTC
Statistics
Matches: 286, Mismatches: 41, Indels: 34
0.79 0.11 0.09
Matches are distributed among these distances:
28 69 0.24
29 98 0.34
30 93 0.33
31 26 0.09
ACGTcount: A:0.29, C:0.03, G:0.34, T:0.34
Consensus pattern (28 bp):
AAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:65696 original size:59 final size:57
Alignment explanation
Indices: 65569--65979 Score: 581
Period size: 58 Copynumber: 7.0 Consensus size: 57
65559 TCCAGATGCA
* * *
65569 CGGGGGCAAAATGGTAGTTTTGGGGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTT--GGAAGGTTCGG-GTTAAAAATGGGATTTTTGGAAGTT
*
65629 CGGGGGTAAAATGGTAATTTTGGAAGGTTCGGGATAAAAAATGGGACTTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTGGAAGGTTCGGG-TTAAAAATGGGA-TTTTTGGAAGTT
*
65688 CGGGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGTTAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAA-TTTTGGAAGG-TTCGGGTTAAAAATGGGATTTTTGGAAGTT
* *
65747 TGGGGGTAAAATGGTAATTTTGGAATGTTCGAGGTTAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTGGAAGGTTCG-GGTTAAAAATGGGATTTTTGGAAGTT
* * *
65805 CGGGGGTAAAATGGCATTTTTGGAAGGTTCGGGGTTAAAAACGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTGGAAGGTTC-GGGTTAAAAATGGGATTTTTGGAAGTT
*
65863 CAGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAA-TTTTGGAAGGTTC-GGGTTAAAAATGGGATTTTTGGAAGTT
* *
65922 TGGGGGTAAAATGGTAATTTTTGGAAGGTTCTAGGTT-AAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAA-TTTTGGAAGGTTC-GGGTTAAAAATGGGATTTTTGGAAGTT
65980 TAGAGACCTC
Statistics
Matches: 323, Mismatches: 21, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
57 4 0.01
58 143 0.44
59 131 0.41
60 40 0.12
61 5 0.02
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (57 bp):
CGGGGGTAAAATGGTAATTTTGGAAGGTTCGGGTTAAAAATGGGATTTTTGGAAGTT
Found at i:67799 original size:17 final size:16
Alignment explanation
Indices: 67777--67839 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
67767 TTGACTTTTC
67777 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
*
67794 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTTAAA
* *
67811 TAAACTTAAATTTAAAA
1 TAAA-TTTAATTTTAAA
*
67828 TAAATTGAATTT
1 TAAATTTAATTT
67840 CCAACGGGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 7 0.17
17 25 0.62
18 8 0.20
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Done.