Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005422.1 Kokia drynarioides strain JFW-HI SEQ_119444, 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: 56756
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 47 characters in sequence are not A, C, G, or T
Found at i:14556 original size:2 final size:2
Alignment explanation
Indices: 14543--14576 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
14533 TCATATGGAG
* *
14543 AT AT AG AT AT AT AT AT AT AC 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
14577 TCATGTCTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:22726 original size:16 final size:16
Alignment explanation
Indices: 22673--22727 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
22663 TTTATCTATT
*
22673 TTTAAATTTAAATTTGC
1 TTTAAATTTAAA-TTGA
22690 TTTAAATTTAAATTGA
1 TTTAAATTTAAATTGA
*
22706 ATTAAATTTGAAA-TGA
1 TTTAAATTT-AAATTGA
22722 TTTAAA
1 TTTAAA
22728 ACTTAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 19 0.56
17 15 0.44
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (16 bp):
TTTAAATTTAAATTGA
Found at i:24675 original size:59 final size:59
Alignment explanation
Indices: 24608--24805 Score: 158
Period size: 59 Copynumber: 3.4 Consensus size: 59
24598 CCCTAACATA
* * * *
24608 TCCAAAAATTACATTTTGACCACCAATCTTTTTAAAAATTAAAATTTT-ACCCTT-GAACT
1 TCCAAAAATTACATTTTAACC-CCAAACTTTCTAAAAATT-AAATTTTCACCCTTAAAACT
* * * * *
24667 TCCTAAAATTCCATTTTTAACCCTAAACTTTCTAAAAATTACATTTTCACCCTTAAAATT
1 TCCAAAAATTACA-TTTTAACCCCAAACTTTCTAAAAATTAAATTTTCACCCTTAAAACT
* * * *
24727 TCCAAAAATTACA-TTT-ACCCCTAAATTTTCT-AAAATTCCATTTTTAACCC-T-AAACTT
1 TCCAAAAATTACATTTTAACCCC-AAACTTTCTAAAAATT-AAATTTTCACCCTTAAAAC-T
* *
24784 TCTAAAAATTACATTTTCACCC
1 TCCAAAAATTACATTTTAACCC
24806 TAAAATTTTC
Statistics
Matches: 112, Mismatches: 19, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
56 3 0.03
57 24 0.21
58 28 0.25
59 36 0.32
60 21 0.19
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.38
Consensus pattern (59 bp):
TCCAAAAATTACATTTTAACCCCAAACTTTCTAAAAATTAAATTTTCACCCTTAAAACT
Found at i:24684 original size:29 final size:28
Alignment explanation
Indices: 24642--24973 Score: 185
Period size: 29 Copynumber: 11.5 Consensus size: 28
24632 AATCTTTTTA
* * *
24642 AAAATTAAAATTTTACCCTTGAACTTCCT
1 AAAATTACATTTTTACCC-TAAACTTCCT
* *
24671 AAAATTCCATTTTTAACCCTAAACTTTCT
1 AAAATTACATTTTT-ACCCTAAACTTCCT
* * *
24700 AAAAATTACATTTTCACCCTTAAAATTTCCA
1 -AAAATTACATTTTTACCC-T-AAACTTCCT
* *
24731 AAAATTACA--TTTACCCCTAAATTTTCT
1 AAAATTACATTTTTA-CCCTAAACTTCCT
* *
24758 AAAATTCCATTTTTAACCCTAAACTTTCT
1 AAAATTACATTTTT-ACCCTAAACTTCCT
* *
24787 AAAAATTACATTTTCACCCTAAAATTTTCC-
1 -AAAATTACATTTTTACCCT-AAA-CTTCCT
* * **
24817 AAAATTCCATTTTAACCC-AAACTTTTT
1 AAAATTACATTTTTACCCTAAACTTCCT
* * *
24844 AAAAATTACATTTTTGGCCCTCGAGCTTTCC-
1 -AAAATTACATTTTT-ACCCT-AAAC-TTCCT
* * * *
24875 AAAATTCCATTTTTGACACTAAATTTTCCA
1 AAAATTACATTTTT-ACCCTAAA-CTTCCT
*
24905 AAAATTACA-TTTTACCCCTAAACTTTCT
1 AAAATTACATTTTTA-CCCTAAACTTCCT
* *
24933 AAAATTCCATTTTGA-CCTAAACTTTCC-
1 AAAATTACATTTTTACCCTAAAC-TTCCT
24960 AAAATTACCATTTT
1 AAAATTA-CATTTT
24974 GCCCCCTCGA
Statistics
Matches: 234, Mismatches: 46, Indels: 47
0.72 0.14 0.14
Matches are distributed among these distances:
26 2 0.01
27 31 0.13
28 37 0.16
29 84 0.36
30 67 0.29
31 11 0.05
32 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (28 bp):
AAAATTACATTTTTACCCTAAACTTCCT
Found at i:24757 original size:58 final size:57
Alignment explanation
Indices: 24608--24978 Score: 308
Period size: 58 Copynumber: 6.4 Consensus size: 57
24598 CCCTAACATA
* * ** *
24608 TCCAAAAATTACATTTTGACCACC-AATCTTTTTAAAAATTAAAATTTT-ACCCTTGAAC-T
1 TCCAAAAATTACATTTT-ACC-CCTAAACTTTCT-AAAATT-CCATTTTAACCC-TAAACTT
* * * * * *
24667 TCCTAAAATTCCATTTTTAACCCTAAACTTTCTAAAAATTACATTTTCACCCTTAAAATT
1 TCCAAAAATTACA-TTTTACCCCTAAACTTTCT-AAAATTCCATTTTAACCC-TAAACTT
*
24727 TCCAAAAATTACA-TTTACCCCTAAATTTTCTAAAATTCCATTTTTAACCCTAAACTT
1 TCCAAAAATTACATTTTACCCCTAAACTTTCTAAAATTCCA-TTTTAACCCTAAACTT
* * *
24784 TCTAAAAATTACATTTT-CACCCTAAAATTTTCCAAAATTCCATTTTAACCC-AAACTT
1 TCCAAAAATTACATTTTAC-CCCT-AAACTTTCTAAAATTCCATTTTAACCCTAAACTT
** ** * * * * * *
24841 TTTAAAAATTACATTTTTGGCCCTCGAGCTTTCCAAAATTCCATTTTTGACACTAAATTT
1 TCCAAAAATTACA-TTTTACCCCT-AAACTTTCTAAAATTCCA-TTTTAACCCTAAACTT
*
24901 TCCAAAAATTACATTTTACCCCTAAACTTTCTAAAATTCCATTTTGA-CCTAAACTT
1 TCCAAAAATTACATTTTACCCCTAAACTTTCTAAAATTCCATTTTAACCCTAAACTT
*
24957 TCC-AAAATTACCATTTTGCCCC
1 TCCAAAAATTA-CATTTTACCCC
24979 CTCGAGTGTC
Statistics
Matches: 263, Mismatches: 36, Indels: 29
0.80 0.11 0.09
Matches are distributed among these distances:
55 7 0.03
56 20 0.08
57 51 0.19
58 86 0.33
59 67 0.25
60 32 0.12
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (57 bp):
TCCAAAAATTACATTTTACCCCTAAACTTTCTAAAATTCCATTTTAACCCTAAACTT
Found at i:24776 original size:87 final size:86
Alignment explanation
Indices: 24641--24973 Score: 354
Period size: 87 Copynumber: 3.8 Consensus size: 86
24631 CAATCTTTTT
* * * * *
24641 AAAAATTAAAATTTTACCCTTGAACTTCCTAAAATTCCATTTTTAACCCTAAACTTTCTAAAAAT
1 AAAAATT-ACATTTTACCCCTAAATTTTCTAAAATTCCATTTTTAACCCTAAACTTTC-AAAAAT
24706 TACATTTTCACCCTTAAAATTTCC
64 TACATTTTCACCC-TAAAATTTCC
24730 AAAAATTACA-TTTACCCCTAAATTTTCTAAAATTCCATTTTTAACCCTAAACTTTCTAAAAATT
1 AAAAATTACATTTTACCCCTAAATTTTCTAAAATTCCATTTTTAACCCTAAACTTTC-AAAAATT
24794 ACATTTTCACCCTAAAATTTTCC
65 ACATTTTCACCCTAAAA-TTTCC
* * * ** * * *
24817 -AAAATTCCATTTTAACCC-AAACTTTT-TAAAAATTACATTTTTGGCCCTCGAGCTTTCCAAAA
1 AAAAATTACATTTTACCCCTAAA-TTTTCT-AAAATTCCATTTTTAACCCT-AAACTTTCAAAAA
* * * *
24879 TTCCATTTTTGACACTAAATTTTCC
63 TTACA-TTTTCACCCTAAAATTTCC
* * *
24904 AAAAATTACATTTTACCCCTAAACTTTCTAAAATTCCA-TTTTGA-CCTAAACTTTCCAAAATTA
1 AAAAATTACATTTTACCCCTAAATTTTCTAAAATTCCATTTTTAACCCTAAACTTTCAAAAATTA
24967 CCATTTT
66 -CATTTT
24974 GCCCCCTCGA
Statistics
Matches: 209, Mismatches: 25, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
85 17 0.08
86 22 0.11
87 113 0.54
88 46 0.22
89 11 0.05
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (86 bp):
AAAAATTACATTTTACCCCTAAATTTTCTAAAATTCCATTTTTAACCCTAAACTTTCAAAAATTA
CATTTTCACCCTAAAATTTCC
Found at i:32326 original size:7 final size:7
Alignment explanation
Indices: 32314--32341 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
32304 GTGATGCAAC
32314 GAATCTT
1 GAATCTT
32321 GAATCTT
1 GAATCTT
32328 GAATCTT
1 GAATCTT
32335 GAATCTT
1 GAATCTT
32342 TGAGCTTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (7 bp):
GAATCTT
Found at i:33376 original size:2 final size:2
Alignment explanation
Indices: 33369--33403 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
33359 CTGTAATTCA
33369 AT AT AT AT AT AT AT AT AT AT A- AT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
33404 CATACTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:33408 original size:11 final size:11
Alignment explanation
Indices: 33369--33412 Score: 58
Period size: 10 Copynumber: 4.3 Consensus size: 11
33359 CTGTAATTCA
33369 ATATATATA-T
1 ATATATATACT
33379 ATATATATA-T
1 ATATATATACT
33389 A-ATATATACT
1 ATATATATACT
*
33399 ATATACATACT
1 ATATATATACT
33410 ATA
1 ATA
33413 ACAGGACCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
9 7 0.23
10 13 0.42
11 11 0.35
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (11 bp):
ATATATATACT
Found at i:39284 original size:2 final size:2
Alignment explanation
Indices: 39277--39309 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39267 AAATTAATAG
39277 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
39310 TATAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:41297 original size:15 final size:15
Alignment explanation
Indices: 41274--41303 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41264 TAACAATATA
*
41274 TATATAAATAGCAAT
1 TATAAAAATAGCAAT
41289 TATAAAAATAGCAAT
1 TATAAAAATAGCAAT
41304 AGCATTATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (15 bp):
TATAAAAATAGCAAT
Found at i:44942 original size:20 final size:20
Alignment explanation
Indices: 44909--44949 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
44899 ATATAAATAA
*
44909 TAAAATTCAATAATTCAATT
1 TAAAATTCAATAATTAAATT
**
44929 TAAAATTCTTTAATTAAATT
1 TAAAATTCAATAATTAAATT
44949 T
1 T
44950 GATTTAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAAATTCAATAATTAAATT
Found at i:44988 original size:28 final size:27
Alignment explanation
Indices: 44927--44990 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
44917 AATAATTCAA
*
44927 TTTAAAAT-TCTTTAATTAAATTTGAT
1 TTTAAAATATCTTTAATTAAATTTAAT
*
44953 TTAAAAAATAT-TTTAATATAAATTTAAT
1 TT-TAAAATATCTTTAAT-TAAATTTAAT
44981 TATTAAAATA
1 T-TTAAAATA
44991 AAATTTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 2 0.06
27 11 0.35
28 17 0.55
29 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
TTTAAAATATCTTTAATTAAATTTAAT
Found at i:45133 original size:5 final size:5
Alignment explanation
Indices: 45123--45147 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
45113 TTCCAATGTA
45123 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
45148 CTCCTTCGTC
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:53199 original size:42 final size:42
Alignment explanation
Indices: 53140--53220 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
53130 GTTGTCAAAT
53140 GGTTAAGAAAATATGAACAGATATTACTATGTAATCACACCC
1 GGTTAAGAAAATATGAACAGATATTACTATGTAATCACACCC
53182 GGTTAAGAAAATATGAACAGATATTACTATGTAATCACA
1 GGTTAAGAAAATATGAACAGATATTACTATGTAATCACA
53221 TCAGTATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (42 bp):
GGTTAAGAAAATATGAACAGATATTACTATGTAATCACACCC
Found at i:53691 original size:28 final size:30
Alignment explanation
Indices: 53660--53718 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 30
53650 TTCTAAATTT
53660 TTATATTATT-TAAAAAATAAA-AAAAAAA
1 TTATATTATTATAAAAAATAAATAAAAAAA
* *
53688 -T-TATTATTATCAATAATAAATAAAAAAA
1 TTATATTATTATAAAAAATAAATAAAAAAA
53716 TTA
1 TTA
53719 AAAATACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
26 7 0.28
27 10 0.40
28 7 0.28
29 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (30 bp):
TTATATTATTATAAAAAATAAATAAAAAAA
Found at i:53694 original size:26 final size:28
Alignment explanation
Indices: 53663--53718 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
53653 TAAATTTTTA
53663 TATTATT-TAAAAAATAAA-AAAAAAAT
1 TATTATTATAAAAAATAAATAAAAAAAT
* *
53689 TATTATTATCAATAATAAATAAAAAAAT
1 TATTATTATAAAAAATAAATAAAAAAAT
53717 TA
1 TA
53719 AAAATACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 7 0.27
27 9 0.35
28 10 0.38
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (28 bp):
TATTATTATAAAAAATAAATAAAAAAAT
Found at i:54549 original size:6 final size:6
Alignment explanation
Indices: 54538--54568 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
54528 CAAACCTTAT
54538 CCTAGA CCTAGA CCTAGA CCTAGA CCTAGA C
1 CCTAGA CCTAGA CCTAGA CCTAGA CCTAGA C
54569 TTAAGTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.35, G:0.16, T:0.16
Consensus pattern (6 bp):
CCTAGA
Done.