Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013193.1 Kokia drynarioides strain JFW-HI SEQ_128212, 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: 54078
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1912 original size:2 final size:2
Alignment explanation
Indices: 1905--1930 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1895 AAGCTTTAAC
1905 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
1931 GATAGATAGA
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:3465 original size:37 final size:37
Alignment explanation
Indices: 3415--3488 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
3405 TTTATGAAAA
3415 TTAGTTAAATTACAAACTAATGACAAAATTATATTTT
1 TTAGTTAAATTACAAACTAATGACAAAATTATATTTT
3452 TTAGTTAAATTACAAACTAATGACAAAATTATATTTT
1 TTAGTTAAATTACAAACTAATGACAAAATTATATTTT
3489 AACTTTCACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (37 bp):
TTAGTTAAATTACAAACTAATGACAAAATTATATTTT
Found at i:3593 original size:3 final size:3
Alignment explanation
Indices: 3578--3615 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3568 CTAGAGAGAT
*
3578 ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3616 TGTGAAATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:13313 original size:17 final size:17
Alignment explanation
Indices: 13291--13327 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
13281 TTTAGTCCTT
13291 AAACTCTAATTTCATCA
1 AAACTCTAATTTCATCA
*
13308 AAACTCTAATTTTATCA
1 AAACTCTAATTTCATCA
13325 AAA
1 AAA
13328 ATAATTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (17 bp):
AAACTCTAATTTCATCA
Found at i:13342 original size:14 final size:15
Alignment explanation
Indices: 13314--13342 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13304 ATCAAAACTC
13314 TAATTTTATCAAAAA
1 TAATTTTATCAAAAA
13329 TAATTTTA-CAAAAA
1 TAATTTTATCAAAAA
13343 GATTTTACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATTTTATCAAAAA
Found at i:21601 original size:16 final size:16
Alignment explanation
Indices: 21580--21611 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
21570 TGTTATGACC
21580 TACCTGCAACAACACA
1 TACCTGCAACAACACA
21596 TACCTGCAACAACACA
1 TACCTGCAACAACACA
21612 AGTATGTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.38, G:0.06, T:0.12
Consensus pattern (16 bp):
TACCTGCAACAACACA
Found at i:24230 original size:11 final size:11
Alignment explanation
Indices: 24214--24238 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24204 TTCCAAACCA
24214 TTTCTTTTTCT
1 TTTCTTTTTCT
24225 TTTCTTTTTCT
1 TTTCTTTTTCT
24236 TTT
1 TTT
24239 TCTCGTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:28528 original size:26 final size:25
Alignment explanation
Indices: 28497--28553 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
28487 TTAACTCATT
28497 ACGAGCACAAACAACATTTAACCCAC
1 ACGAGC-CAAACAACATTTAACCCAC
** *
28523 ACGAG-CTGACAACATTTAGCCCAC
1 ACGAGCCAAACAACATTTAACCCAC
28547 ACGAGCC
1 ACGAGCC
28554 CATAATGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 21 0.78
25 1 0.04
26 5 0.19
ACGTcount: A:0.39, C:0.35, G:0.14, T:0.12
Consensus pattern (25 bp):
ACGAGCCAAACAACATTTAACCCAC
Found at i:28536 original size:24 final size:24
Alignment explanation
Indices: 28507--28552 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
28497 ACGAGCACAA
28507 ACAACATTTAACCCACACGAGCTG
1 ACAACATTTAACCCACACGAGCTG
*
28531 ACAACATTTAGCCCACACGAGC
1 ACAACATTTAACCCACACGAGC
28553 CCATAATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.35, G:0.13, T:0.15
Consensus pattern (24 bp):
ACAACATTTAACCCACACGAGCTG
Found at i:28574 original size:24 final size:24
Alignment explanation
Indices: 28547--28721 Score: 188
Period size: 24 Copynumber: 7.3 Consensus size: 24
28537 TTTAGCCCAC
* *
28547 ACGAGCCCATAATGATTAGCTCTT
1 ACGAGCCCAAAATGGTTAGCTCTT
* *
28571 ACGAGCCTAAAATGGTTAACTCTT
1 ACGAGCCCAAAATGGTTAGCTCTT
*
28595 ACGAGCCCAAAATGATTAGCTCTT
1 ACGAGCCCAAAATGGTTAGCTCTT
*
28619 ACGATCCCAAAATGGTTAGCTCTT
1 ACGAGCCCAAAATGGTTAGCTCTT
** * *
28643 ACGAGCTTAGAATGGTTTGCTCTT
1 ACGAGCCCAAAATGGTTAGCTCTT
* * ** *
28667 ACGAGCCGATAATAATTAGCTTTT
1 ACGAGCCCAAAATGGTTAGCTCTT
* * *
28691 ATGAGCCGAGAATGGTTAGCTCTT
1 ACGAGCCCAAAATGGTTAGCTCTT
28715 ACGAGCC
1 ACGAGCC
28722 TAGACAGAGT
Statistics
Matches: 124, Mismatches: 27, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 124 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (24 bp):
ACGAGCCCAAAATGGTTAGCTCTT
Found at i:28638 original size:72 final size:72
Alignment explanation
Indices: 28547--28723 Score: 228
Period size: 72 Copynumber: 2.5 Consensus size: 72
28537 TTTAGCCCAC
* * *
28547 ACGAGCCCATAATGATTAGCTCTTACGAGCCTAAAATGGTTAACTCTTACGAGCCCAAAATGATT
1 ACGAGCCCAAAATGGTTAGCTCTTACGAGCCTAAAATGGTTAACTCTTACGAGCCCAAAATAATT
28612 AGCTCTT
66 AGCTCTT
* * * ** * *
28619 ACGATCCCAAAATGGTTAGCTCTTACGAGCTTAGAATGGTTTGCTCTTACGAGCCGATAATAATT
1 ACGAGCCCAAAATGGTTAGCTCTTACGAGCCTAAAATGGTTAACTCTTACGAGCCCAAAATAATT
*
28684 AGCTTTT
66 AGCTCTT
* * *
28691 ATGAGCCGAGAATGGTTAGCTCTTACGAGCCTA
1 ACGAGCCCAAAATGGTTAGCTCTTACGAGCCTA
28724 GACAGAGTTT
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 89 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (72 bp):
ACGAGCCCAAAATGGTTAGCTCTTACGAGCCTAAAATGGTTAACTCTTACGAGCCCAAAATAATT
AGCTCTT
Found at i:31946 original size:22 final size:22
Alignment explanation
Indices: 31921--31963 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
31911 AAAATTATTT
*
31921 AATAATTTTATTATTTCAAAAA
1 AATAATTTTAATATTTCAAAAA
*
31943 AATAATTTTAATATTTTAAAA
1 AATAATTTTAATATTTCAAAA
31964 TCATTTGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AATAATTTTAATATTTCAAAAA
Found at i:36668 original size:11 final size:12
Alignment explanation
Indices: 36643--36674 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
36633 TTAAATTTAC
36643 TTTAAATTCATT
1 TTTAAATTCATT
36655 TTTAAATTCATT
1 TTTAAATTCATT
36667 TTTAAATT
1 TTTAAATT
36675 TAAAATCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTAAATTCATT
Found at i:37472 original size:3 final size:3
Alignment explanation
Indices: 37464--37599 Score: 85
Period size: 3 Copynumber: 43.0 Consensus size: 3
37454 ATAACCGTTT
* ** * *
37464 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTC TAA TAA CAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
37512 TAA TAA TAA -ACA GTAA TAA TAAA TGA CAA TTAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TA-A -TAA TAA T-AA TAA TAA -TAA TAA TAA TAA TAA TAA
** * *
37560 CTGTT TCAA TAA TAA TAA TAA TTAA TAT TAA TAT TAA TAA
1 -T-AA T-AA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
37600 ATTTTAATAA
Statistics
Matches: 101, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
2 1 0.01
3 87 0.86
4 12 0.12
5 1 0.01
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:37591 original size:16 final size:16
Alignment explanation
Indices: 37567--37609 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
37557 TAACTGTTTC
* *
37567 AATAATAATAATAATT
1 AATATTAATAATAATA
*
37583 AATATTAATATTAATA
1 AATATTAATAATAATA
*
37599 AATTTTAATAA
1 AATATTAATAA
37610 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATTAATAATAATA
Found at i:37617 original size:40 final size:40
Alignment explanation
Indices: 37525--37617 Score: 100
Period size: 40 Copynumber: 2.3 Consensus size: 40
37515 TAATAAACAG
* * *
37525 TAATAATAAATGACAATTAATAATATTAATAATAACTGTT
1 TAATAATAAATAACAATTAATAATAATAATAATAAATGTT
* * *
37565 TCAATAAT-AATAATAATTAATATTAATATTAATAAAT-TT
1 T-AATAATAAATAACAATTAATAATAATAATAATAAATGTT
37604 TAATAAATAAATAA
1 TAAT-AATAAATAA
37618 AAAAGGAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
38 3 0.07
39 6 0.14
40 29 0.66
41 6 0.14
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (40 bp):
TAATAATAAATAACAATTAATAATAATAATAATAAATGTT
Found at i:38770 original size:29 final size:30
Alignment explanation
Indices: 38713--38850 Score: 120
Period size: 29 Copynumber: 4.5 Consensus size: 30
38703 CCTAAACTGT
*
38713 CAAAAATTCCATTTTTTTACCTCGAAACTTC
1 CAAAAATTCCA-TTTTTCACCTCGAAACTTC
* *
38744 CAAAAATTACATTTTTCCCCTCG-AACTTC
1 CAAAAATTCCATTTTTCACCTCGAAACTTC
* *
38773 CAAAAATTCCATTTTTTTTTACCTCGAAACTTT
1 CAAAAATTCCA---TTTTTCACCTCGAAACTTC
** * * *
38806 TGAAAATTTCA-TTTT-ACCCCTAAACTTC
1 CAAAAATTCCATTTTTCACCTCGAAACTTC
38834 CAAAAAATTCCATTTTT
1 C-AAAAATTCCATTTTT
38851 GACCCCAAAA
Statistics
Matches: 85, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
28 10 0.12
29 28 0.33
30 14 0.16
31 10 0.12
32 10 0.12
33 13 0.15
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.40
Consensus pattern (30 bp):
CAAAAATTCCATTTTTCACCTCGAAACTTC
Found at i:38812 original size:62 final size:59
Alignment explanation
Indices: 38713--38900 Score: 213
Period size: 62 Copynumber: 3.1 Consensus size: 59
38703 CCTAAACTGT
** *
38713 CAAAAATTCCATTTTTTTACCTCGAAACTTCCAAAAATTACATTTTTCCCCTCGAACTTC
1 CAAAAATTCCATTTTTTTACCTCGAAACTT-TTAAAATTACATTTTACCCCTCGAACTTC
* *
38773 CAAAAATTCCATTTTTTTTTACCTCGAAACTTTTGAAAATTTCATTTTACCCCT-AAACTTC
1 CAAAAATTCCA--TTTTTTTACCTCGAAACTTTT-AAAATTACATTTTACCCCTCGAACTTC
* * *
38834 CAAAAAATTCCA-TTTTTGACCCCAAAACTTTTAAAATTACCATTTTACCCC-CGAA-TGTC
1 C-AAAAATTCCATTTTTTTACCTCGAAACTTTTAAAATTA-CATTTTACCCCTCGAACT-TC
38893 CAAAAATT
1 CAAAAATT
38901 TCGTTTTTGA
Statistics
Matches: 111, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
58 14 0.13
59 33 0.30
60 11 0.10
61 7 0.06
62 46 0.41
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.37
Consensus pattern (59 bp):
CAAAAATTCCATTTTTTTACCTCGAAACTTTTAAAATTACATTTTACCCCTCGAACTTC
Found at i:40162 original size:3 final size:3
Alignment explanation
Indices: 40154--40229 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
40144 AATTTTTTGT
40154 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40202 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
40230 ATGAAATTAG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42994 original size:28 final size:22
Alignment explanation
Indices: 42939--42982 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
42929 AAAGAAAGAT
42939 TAATAATTTAAATTTAGATGAA
1 TAATAATTTAAATTTAGATGAA
42961 TAATAATTTAAATTTAGATGAA
1 TAATAATTTAAATTTAGATGAA
42983 GAAATAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (22 bp):
TAATAATTTAAATTTAGATGAA
Found at i:46924 original size:22 final size:23
Alignment explanation
Indices: 46899--46959 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
46889 AAAAACAAAA
*
46899 ATGAATAGTGAAATTCTCTTA-C
1 ATGAATAGTGAAATTCTCCTATC
*
46921 ATGAATAGTGATATT-TCCTATC
1 ATGAATAGTGAAATTCTCCTATC
* *
46943 ATGAATATTGAGATTCT
1 ATGAATAGTGAAATTCT
46960 TTGACAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 4 0.12
22 28 0.85
23 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (23 bp):
ATGAATAGTGAAATTCTCCTATC
Found at i:47024 original size:18 final size:19
Alignment explanation
Indices: 47001--47041 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
46991 AATCAAAGAA
47001 TATATTCT-CTGAAAAAGT
1 TATATTCTACTGAAAAAGT
*
47019 TATATTCTGATTGAAAAAGT
1 TATATTCT-ACTGAAAAAGT
47039 TAT
1 TAT
47042 GTAATGTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (19 bp):
TATATTCTACTGAAAAAGT
Found at i:47251 original size:14 final size:14
Alignment explanation
Indices: 47211--47251 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
47201 TTTCAAAATT
47211 AAATTTAAGTTTTA
1 AAATTTAAGTTTTA
* *
47225 AAATTCAAATTTTA
1 AAATTTAAGTTTTA
*
47239 TAATTTAAGTTTT
1 AAATTTAAGTTTT
47252 CAAGTTTTAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (14 bp):
AAATTTAAGTTTTA
Found at i:48399 original size:43 final size:43
Alignment explanation
Indices: 48343--48435 Score: 168
Period size: 43 Copynumber: 2.2 Consensus size: 43
48333 GCAATGATAT
*
48343 ATATATCCAAAACCATCCAGACCTAAACAACATAGCAATTAAC
1 ATATATCCAAAACCATCCAAACCTAAACAACATAGCAATTAAC
*
48386 ATATATCCGAAACCATCCAAACCTAAACAACATAGCAATTAAC
1 ATATATCCAAAACCATCCAAACCTAAACAACATAGCAATTAAC
48429 ATATATC
1 ATATATC
48436 GATCATCCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.48, C:0.27, G:0.04, T:0.20
Consensus pattern (43 bp):
ATATATCCAAAACCATCCAAACCTAAACAACATAGCAATTAAC
Found at i:52563 original size:18 final size:18
Alignment explanation
Indices: 52540--52574 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52530 AATATGGAAA
*
52540 GTAATCTTAGAAGATTTT
1 GTAATCTAAGAAGATTTT
*
52558 GTAATCTAATAAGATTT
1 GTAATCTAAGAAGATTT
52575 GATTTTCTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (18 bp):
GTAATCTAAGAAGATTTT
Done.