Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001053.1 Kokia drynarioides strain JFW-HI SEQ_112297, 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: 11270
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Found at i:5774 original size:503 final size:500
Alignment explanation
Indices: 4167--6886 Score: 2512
Period size: 505 Copynumber: 5.4 Consensus size: 500
4157 ACCAAACCAC
* * * * * * *
4167 AAAACCAAAATAAATTCAAAACAATCTGCAGAAATGGAAACCCAGCAAACCCAAATCAAAAGCAA
1 AAAAACAAAACAAACTCAAAACAATCTGTAAAAATGAAAAACCAGCAAACCCAAATCAAAAGCAA
* * * * * * *
4232 ATCTAAACAGGACAGATTATATCAAGCCATCCAAATTTTTAACATATGTAAAATAATAATAGAAA
66 ATCAAAACAGAACAGATTACAACAAACCATTCAAATTCTTAACATATGTAAAATAATAATAGAAA
* * * *
4297 TATATTATCTAATGATTATAATATGCATTAATTATGAAATGTAGATTTCATACTAATACAAATTT
131 TATATTATATAATGATTATAATATGCATTAATTATGAAATGTGGATTCCGTACTAATACAAATTT
* ** *
4362 AAAATTTAGCATCTAAAATTAATCCTTTAAAATAATAATACTAAGCAAAAATAATAATACATTAA
196 AAAATTTAGCATCCAAAATTAATTATTTAAAATAATAATACTTAGCAAAAATAATAATACATTAA
* * ** * * * * *
4427 TAAAGATAGTTAGATTAAAACTCAAAAATATTGAAAATAAATTAAATATTTTCAAAACTTTGAAA
261 TAAAGACAGTTAAAACAGAACTCGAAAATATTGAAAACAAATTGAATATTTTCAAAAC-TTAAAA
** * * **
4492 TACCTACTCTTTTTTTACTCTGATATCAGATTGTATAAAAAATTATTCAAATTTTTTTTAATAAA
325 TATATACTCTTTCTTGACTCTGATATCAGATTGTATCGAAAATTATT--AA-TTTTTTTAATAAA
* * * * * *
4557 TATGTCGACATCATTTTTTATAGCAATTTAAAAGAGACCATACTCAATCACGCACTCAAAAATTG
387 TATGTCGACATCATTTATTATAACAATTTAAAAGAGACAATACTCAACCACCCACTCAAAAGTTG
* * * * * *
4622 AGTGGATAGAAAA-TCACAAATCAAAACAAACAATAAAAATAGAAAACCA
452 AGTGAATAGAAAACT-ACAAATCAAACCAAACTACAAAAATAAAAAATCA
* * * *
4671 TAAAACTAAAACAAACTCAAAACAATCAGTAGAAATGAAAAATCAGCAAACCCAAATCAAAAGCA
1 AAAAAC-AAAACAAACTCAAAACAATCTGTAAAAATGAAAAACCAGCAAACCCAAATCAAAAGCA
* * * * *
4736 AATCAAAATATAACATATTACAACAAACTATTCAAATTCTTAACATATTTAAAATAATAATAGAA
65 AATCAAAACAGAACAGATTACAACAAACCATTCAAATTCTTAACATATGTAAAATAATAATAG-A
* * ** *
4801 ATATATTATATATATATATATATTATAATATGCATTAATTATGAAATGTGAATTCTATATTAATA
129 A-ATA-TAT-TATATA-AT-GATTATAATATGCATTAATTATGAAATGTGGATTCCGTACTAATA
* * * * * * *
4866 AAAATTTAAAAATTAACATCCAAATTTAATCT-TTTAAAATAACAATAC-TCGAAAATAATAATA
189 CAAATTTAAAATTTAGCATCCAAAATTAAT-TATTTAAAATAATAATACTTAGCAAA-AATAATA
* * * * * *
4929 ATACATTAACAAAGACAGTTAAATCAGAACTTGAAAACATTGAAAACAAATTAAATATTTT-TAA
252 ATACATTAATAAAGACAGTTAAAACAGAACTCGAAAATATTGAAAACAAATTGAATATTTTCAAA
* * * * * * * * * * **
4993 ATTTAGAAATATTTGCTCCTCCTTGACTTTAATATTAAATTGT-CCTG-AAATT-TTTTTTTTTT
317 ACTTA-AAATATATACTCTTTCTTGACTCTGATATCAGATTGTATC-GAAAATTATTAATTTTTT
* * * * *
5055 TAAATAAATATGTCGGCATCATTTATTATAACAATTTAAAAGAGACAGTATTTAACTACCCACT-
380 T-AATAAATATGTCGACATCATTTATTATAACAATTTAAAAGAGACAATACTCAACCACCCACTC
* * * * * *
5119 AAGAAGTTAAGTGAACAAAAAACCACAAATAAAACCAAA-TCACAAAAATCAAAAATCA
444 AA-AAGTTGAGTGAATAGAAAACTACAAATCAAACCAAACT-ACAAAAATAAAAAATCA
* * * * *
5177 AAAAACCAAAACAAATTCAAAACAATCTATAAAAATGGAAAACAAGCAAACCCAAATTAAAAGCA
1 AAAAA-CAAAACAAACTCAAAACAATCTGTAAAAATGAAAAACCAGCAAACCCAAATCAAAAGCA
* * * *
5242 AATCAAAACAGAATAAATTACAGCAAACCATTCAAATTCTTAACATATGTAAAATAACAATAGAA
65 AATCAAAACAGAACAGATTACAACAAACCATTCAAATTCTTAACATATGTAAAATAATAATAGAA
* *
5307 ATATATTATATAATGATTATAATATGCATTAATTATAAAATATGGATTCCGTACTAATACAAATT
130 ATATATTATATAATGATTATAATATGCATTAATTATGAAATGTGGATTCCGTACTAATACAAATT
*
5372 TAAAATTTAGCATCCAAAATTAATTATTTAAAATAATAATACTTAGCAAAAATAATAACACATTA
195 TAAAATTTAGCATCCAAAATTAATTATTTAAAATAATAATACTTAGCAAAAATAATAATACATTA
* * * * * *
5437 ATAAAAACAGTTAAAACAGATCTCGAAAATATTTAAAATATATTGAATATTTTTAAAACTTAAAA
260 ATAAAGACAGTTAAAACAGAACTCGAAAATATTGAAAACAAATTGAATATTTTCAAAACTTAAAA
* * * *
5502 GTATATGCTCTTTCTTGACTCTGATACCAGATTATCTCGAAAATTATATAATTTTTTTAATAAAT
325 -TATATACTCTTTCTTGACTCTGATATCAGATTGTATCGAAAATTAT-TAATTTTTTTAATAAAT
* * * * * * *
5567 ATATCGACATCATTTATTATATCAATTTAAATGAGACAATATTCAACCACCAACTTAGAAGTTGA
388 ATGTCGACATCATTTATTATAACAATTTAAAAGAGACAATACTCAACCACCCACTCAAAAGTTGA
*
5632 GTGAATAGAAAACTACATATCAAACCAAACTACAAAAATAAAAAATCA
453 GTGAATAGAAAACTACAAATCAAACCAAACTACAAAAATAAAAAATCA
* * * * * *
5680 CAAATCAAAATAAACTCAAAATAATATGTAAAAATGAAAAACCAGCAAACCCAAATAAAAAAGCA
1 AAAAACAAAACAAACTCAAAACAATCTGTAAAAATGAAAAACCAGCAAACCCAAAT-CAAAAGCA
* * *
5745 AA-CGTAAACATAACAGATTACAACAAACCATTCAAATTCTTAACATATATAAAATAATAATACG
65 AATC-AAAACAGAACAGATTACAACAAACCATTCAAATTCTTAACATATGTAAAATAATAATA-G
* * * * * *
5809 -AATATATTATATAATGATTATAATATGCATTAATAATGGAATGTGGGTTCTGTCCCAATACAAA
128 AAATATATTATATAATGATTATAATATGCATTAATTATGAAATGTGGATTCCGTACTAATACAAA
* * * * * * *
5873 TTTAAAATTTAGCAT-AAAATATTAAATATTTATAATAATAATAATT-GAAAAAAATAAAAATAT
193 TTTAAAATTTAGCATCCAAA-ATTAATTATTTAAAATAATAATACTTAG-CAAAAATAATAATAC
* * * *
5936 ATTAATAAATACACTT-AAACTAGAACTCGAAAATATTGAAAACAAATAGAGTA-TTTCAAATA-
256 ATTAATAAAGACAGTTAAAAC-AGAACTCGAAAATATTGAAAACAAATTGAATATTTTCAAA-AC
* * * * * * * *
5998 ATAGAAATACT-TACTCCTCCCTGACACTGATACCAAATTGTATCAAAAATTATTCATATATTTT
319 TTA-AAATA-TATACTCTTTCTTGACTCTGATATCAGATTGTATCGAAAATTA-T--TA-ATTTT
* * * * *
6062 TTTAATAAATATGTCGATATAATTTATTATAACAATTTAAAGGAGACAATGCTCAACTACCCACT
378 TTTAATAAATATGTCGACATCATTTATTATAACAATTTAAAAGAGACAATACTCAACCACCCACT
* * * * * * * * *
6127 CAAAAGTTGAGTGGATAGAAAACAACAAATCAAACTAACCCATAGATATGAAAAATCA
443 CAAAAGTTGAGTGAATAGAAAACTACAAATCAAACCAAACTACAAAAATAAAAAATCA
* * * *
6185 AAAAACTTAAACAAACTCAAAATAATCTG-AAGAAATGAAAAACCAACAAATCCAAATCAAAAGC
1 AAAAAC-AAAACAAACTCAAAACAATCTGTAA-AAATGAAAAACCAGCAAACCCAAATCAAAAGC
* * * *
6249 AAATCAAAACAAAACA-ATTTACAACAAACCATTCGAATTCTTAACGTATGTAAAATAATAATAT
64 AAATCAAAACAGAACAGA-TTACAACAAACCATTCAAATTCTTAACATATGTAAAATAATAATAG
* * * * * * *
6313 AAATATATTATATAATAATTATAATATACATTATTTATGAAATATGGATTTCGTATTAATAAAAA
128 AAATATATTATATAATGATTATAATATGCATTAATTATGAAATGTGGATTCCGTACTAATACAAA
* * * *
6378 TTTAAATTTTAGCATCCAAAATTAATCATTTAAAATAATAATACTCAGCAAAAATGATAATACAT
193 TTTAAAATTTAGCATCCAAAATTAATTATTTAAAATAATAATACTTAGCAAAAATAATAATACAT
* * * * ** *
6443 TAATAAAGATAATT-AGACTAGAATTTAAAAATATTAAAAACAAATTGAATATTTTCAAAACTTA
258 TAATAAAGACAGTTAAAAC-AGAACTCGAAAATATTGAAAACAAATTGAATATTTTCAAAACTTA
*
6507 AAA-ATAT-CTACTTCTCTTTGACTCTGATATCAGATTATATCGAAAATTATTCAAATTCTTTTT
322 AAATATATACT-CTT-TC-TTGACTCTGATATCAGATTGTATCGAAAATTATT--AA------TT
* * * * * * *
6570 TTTTTAAATAAATATG-CTGGCATAATTCATTATAACAATTTAAAAAAAAATAATACTCAACCAT
376 TTTTT-AATAAATATGTC-GACATCATTTATTATAACAATTT-AAAAGAGACAATACTCAACCAC
** * * * * * ** * * * **
6634 CTTCCCAGAAGTTGAGT-AGATAAAAAACCATAAATCAAATTAACCCACATAAATGGAAAATCA
438 CCACTCAAAAGTTGAGTGA-ATAGAAAACTACAAATCAAACCAAACTACAAAAATAAAAAATCA
* * * * * * * ** *
6697 CAAAACTAAAACAAATTCAAAATAATCTATAAAAATAAAAAATCA-AAAAAACAAAACAAAAGCA
1 AAAAAC-AAAACAAACTCAAAACAATCTGTAAAAATGAAAAACCAGCAAACCCAAATCAAAAGCA
* * ** * * *
6761 AATCAAAACAAAACAAATTACCCCAAACCATTCAAATTCTTAATATATATAAAATAAAAATAGAA
65 AATCAAAACAGAACAGATTACAACAAACCATTCAAATTCTTAACATATGTAAAATAATAATAGAA
* * * *
6826 ATA-A--A-CTAATGATTATAATGTGCATTAATTATGAAATGTGGA-TCGTGTACTAATAAAAAT
130 ATATATTATATAATGATTATAATATGCATTAATTATGAAATGTGGATTC-CGTACTAATACAAAT
6886 T
194 T
6887 ATGAAATGTG
Statistics
Matches: 1809, Mismatches: 341, Indels: 129
0.79 0.15 0.06
Matches are distributed among these distances:
499 1 0.00
500 139 0.08
501 39 0.02
502 107 0.06
503 322 0.18
504 27 0.01
505 433 0.24
506 286 0.16
507 49 0.03
508 6 0.00
509 12 0.01
510 44 0.02
511 241 0.13
512 101 0.06
513 2 0.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (500 bp):
AAAAACAAAACAAACTCAAAACAATCTGTAAAAATGAAAAACCAGCAAACCCAAATCAAAAGCAA
ATCAAAACAGAACAGATTACAACAAACCATTCAAATTCTTAACATATGTAAAATAATAATAGAAA
TATATTATATAATGATTATAATATGCATTAATTATGAAATGTGGATTCCGTACTAATACAAATTT
AAAATTTAGCATCCAAAATTAATTATTTAAAATAATAATACTTAGCAAAAATAATAATACATTAA
TAAAGACAGTTAAAACAGAACTCGAAAATATTGAAAACAAATTGAATATTTTCAAAACTTAAAAT
ATATACTCTTTCTTGACTCTGATATCAGATTGTATCGAAAATTATTAATTTTTTTAATAAATATG
TCGACATCATTTATTATAACAATTTAAAAGAGACAATACTCAACCACCCACTCAAAAGTTGAGTG
AATAGAAAACTACAAATCAAACCAAACTACAAAAATAAAAAATCA
Found at i:5910 original size:21 final size:20
Alignment explanation
Indices: 5865--5915 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
5855 GTTCTGTCCC
5865 AATACAAAT-TTAAAATTTAG
1 AATA-AAATATTAAAATTTAG
* *
5885 CATAAAATATTAAATATTTAT
1 AATAAAATATTAAA-ATTTAG
5906 AATAATAATA
1 AATAA-AATA
5916 ATTGAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 4 0.16
20 8 0.32
21 9 0.36
22 4 0.16
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
AATAAAATATTAAAATTTAG
Found at i:6329 original size:21 final size:23
Alignment explanation
Indices: 6303--6346 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6293 CGTATGTAAA
*
6303 ATAATAA-TATAA-ATATATTAT
1 ATAATAATTATAATATACATTAT
6324 ATAATAATTATAATATACATTAT
1 ATAATAATTATAATATACATTAT
6347 TTATGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAATAATTATAATATACATTAT
Found at i:6752 original size:5 final size:5
Alignment explanation
Indices: 6744--6777 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
6734 AAAAATCAAA
*
6744 AAAAC AAAAC AAAAGC AAATC AAAAC AAAAC AAA
1 AAAAC AAAAC AAAA-C AAAAC AAAAC AAAAC AAA
6778 TTACCCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.76, C:0.18, G:0.03, T:0.03
Consensus pattern (5 bp):
AAAAC
Found at i:6767 original size:16 final size:15
Alignment explanation
Indices: 6735--6778 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
6725 ATAAAAATAA
6735 AAAATCAAAA-AAA-C
1 AAAA-CAAAACAAATC
6749 AAAACAAAAGCAAATC
1 AAAACAAAA-CAAATC
6765 AAAACAAAACAAAT
1 AAAACAAAACAAAT
6779 TACCCCAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.19
14 4 0.15
15 8 0.30
16 10 0.37
ACGTcount: A:0.75, C:0.16, G:0.02, T:0.07
Consensus pattern (15 bp):
AAAACAAAACAAATC
Done.