Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013993.1 Kokia drynarioides strain JFW-HI SEQ_129024, 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: 24492
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:578 original size:30 final size:29
Alignment explanation
Indices: 527--803 Score: 245
Period size: 30 Copynumber: 9.3 Consensus size: 29
517 AAAAATTTCG
*
527 TTTTAACCCTCGAACTTCCAAAAATCCCAT
1 TTTTTACCCT-GAACTTCCAAAAATCCCAT
*
557 TTTTTACACCTGAAGTTCCAAAAATCCCAT
1 TTTTTAC-CCTGAACTTCCAAAAATCCCAT
* *
587 TTTTTACACCTGAAGTTCCAAAAATCCCAC
1 TTTTTAC-CCTGAACTTCCAAAAATCCCAT
* ** *
617 TTTTGACCCCAAAACTTCCAAAAATTCCAT
1 TTTTTA-CCCTGAACTTCCAAAAATCCCAT
* *
647 TTTTTACCCCCGAACATCCAAAAATCCCAT
1 TTTTTA-CCCTGAACTTCCAAAAATCCCAT
* ** * *
677 TTTTGACCTCAAAACTTCCAAAAATTCTA-
1 TTTTTACC-CTGAACTTCCAAAAATCCCAT
706 TTTTTACCCTCGAACTTCCAAAAATCCCAT
1 TTTTTACCCT-GAACTTCCAAAAATCCCAT
* * **
736 TATTGA-CCTCGAAACTTCCAAAAATTTCA-
1 TTTTTACCCT-G-AACTTCCAAAAATCCCAT
* *
765 TTTTTACCCTTAAACTTCCAAAAATACCAT
1 TTTTTACCC-TGAACTTCCAAAAATCCCAT
*
795 TTTTAACCC
1 TTTTTACCC
804 CAAAATTTCC
Statistics
Matches: 203, Mismatches: 35, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
28 1 0.00
29 48 0.24
30 149 0.73
31 5 0.02
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (29 bp):
TTTTTACCCTGAACTTCCAAAAATCCCAT
Found at i:609 original size:60 final size:58
Alignment explanation
Indices: 527--814 Score: 310
Period size: 60 Copynumber: 4.8 Consensus size: 58
517 AAAAATTTCG
* * ** * *
527 TTTTAACCCTCGAACTTCCAAAAATCCCATTTTTTACACCTGAAGTTCCAAAAATCCCAT
1 TTTTTACCCT-GAACTTCCAAAAATCCCATTTTTGAC-CCAAAACTTCCAAAAATTCCAT
* *
587 TTTTTACACCTGAAGTTCCAAAAATCCCACTTTTGACCCCAAAACTTCCAAAAATTCCAT
1 TTTTTAC-CCTGAACTTCCAAAAATCCCATTTTTGA-CCCAAAACTTCCAAAAATTCCAT
* * *
647 TTTTTACCCCCGAACATCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTCTA-
1 TTTTTA-CCCTGAACTTCCAAAAATCCCATTTTTGACC-CAAAACTTCCAAAAATTCCAT
* * *
706 TTTTTACCCTCGAACTTCCAAAAATCCCATTATTGACCTCGAAACTTCCAAAAATTTCA-
1 TTTTTACCCT-GAACTTCCAAAAATCCCATTTTTGACC-CAAAACTTCCAAAAATTCCAT
* * * *
765 TTTTTACCCTTAAACTTCCAAAAATACCATTTTTAACCCCAAAATTTCCA
1 TTTTTACCC-TGAACTTCCAAAAATCCCATTTTTGA-CCCAAAACTTCCA
815 TTTTCACCCT
Statistics
Matches: 196, Mismatches: 25, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
58 3 0.02
59 90 0.46
60 98 0.50
61 5 0.03
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.32
Consensus pattern (58 bp):
TTTTTACCCTGAACTTCCAAAAATCCCATTTTTGACCCAAAACTTCCAAAAATTCCAT
Found at i:742 original size:59 final size:60
Alignment explanation
Indices: 527--814 Score: 348
Period size: 59 Copynumber: 4.8 Consensus size: 60
517 AAAAATTTCG
* * * ** * *
527 TTTTAACCCTCGAACTTCCAAAAATCCCATTTTTTACACCTGAAGTTCCAAAAATCCCAT
1 TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCAT
* *
587 TTTTTACACCT-GAAGTTCCAAAAATCCCACTTTTGACCCCAAAACTTCCAAAAATTCCAT
1 TTTTTAC-CCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCAT
* * * *
647 TTTTTACCCCCGAACATCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTCTA-
1 TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCAT
* * * *
706 TTTTTACCCTCGAACTTCCAAAAATCCCATTATTGACCTCGAAACTTCCAAAAATTTCA-
1 TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCAT
** * * *
765 TTTTTACCCTTAAACTTCCAAAAATACCATTTTTAACCCCAAAATTTCCA
1 TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCA
815 TTTTCACCCT
Statistics
Matches: 197, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
59 97 0.49
60 97 0.49
61 3 0.02
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.32
Consensus pattern (60 bp):
TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCAT
Found at i:22560 original size:201 final size:201
Alignment explanation
Indices: 21923--23084 Score: 1720
Period size: 201 Copynumber: 5.8 Consensus size: 201
21913 GCGATTACCC
* * * * *
21923 ACAAACGATGCGGTCATCTTCCTGATGAGATGCTAAGAAGAAGACCAAGTCAAATTCACGATGTG
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGATGTG
* * *
21988 AACAAATCTTCGAACCCAAGCTTCCTGATGAGACACTAAGAAACAGGTCGAAGAAATAAAAGGTT
66 AACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATAAAAGGTT
* *
22053 AGCTTCCTGATGAGATACTGCGAAG-CAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
131 AGCTTCCTGATGAGATACTGAGAAGTGA-ACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
22117 AATTGAA
195 AATTGAA
*
22124 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAATCCACGATGTG
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGATGTG
* * * *
22189 AACAAATCTTCGAACCTCAGCTTCCTGACGAGAAACTGAAAAACAGGT-GAAGCAATAAAAGGTT
66 AACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATAAAAGGTT
* * ** *
22253 AGCTTCCTGGTGAGATACAGAGAAGTGAACCAAATTTATCTTCCTGATGATATACAGAGAAGCGA
131 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA
22318 ATTGAA
196 ATTGAA
* * *
22324 ACAAACGACGTGGTCATCTTCCTGATGAGATACTGAGTAGAAGACCAAATCAAATCCACGGTGTG
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGATGTG
* * *
22389 AACAAATCTTCGAACCCCAGTTTCCTGATGAGACACTGAGAAACAGGTCAAAGCAATAAAAGTTT
66 AACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATAAAAGGTT
* *
22454 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTT-CTAGATGAGATACAAAGAAGCA
131 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCT-GATGAGATACAGAGAAGCG
22518 AATTGAA
195 AATTGAA
* * * *
22525 ACAAACGACGCGATCATCTTCCTGATGAAATACTGAGAAGAAGACCAAATCAAATTCACGATGTC
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGATGTG
* *
22590 AATAAATCTTCGAACCCCAGCTTCCTGGTGAGACACTGAGAAACAGGTCGAAGCAATAAAAGGTT
66 AACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATAAAAGGTT
* *
22655 AGCTTCCTGGTGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA
131 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA
22720 ATTGAA
196 ATTGAA
* * * **
22726 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAATACCAAACCAAATCCACGGCGTG
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGATGTG
* *
22791 AACAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAAAAACAGGTCGAAGCAATAAAAGGTT
66 AACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATAAAAGGTT
* * * * *
22855 AGCTTCCTGGTGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGATGATATACAGAGAAGCGA
131 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA
22920 ATTGAA
196 ATTGAA
* * *
22926 ACAAACGACGTGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCA----CGA
* * * * * *
22991 CGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAC
62 TGTGAACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATAAAA
*
23056 GGTTAGCTTCCTAATGAGATACTGAGAAG
127 GGTTAGCTTCCTGATGAGATACTGAGAAG
23085 AAGGCTATGT
Statistics
Matches: 866, Mismatches: 86, Indels: 14
0.90 0.09 0.01
Matches are distributed among these distances:
200 350 0.40
201 428 0.49
202 2 0.00
204 19 0.02
205 67 0.08
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (201 bp):
ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGATGTG
AACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATAAAAGGTT
AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA
ATTGAA
Found at i:22817 original size:401 final size:401
Alignment explanation
Indices: 21923--23084 Score: 1736
Period size: 401 Copynumber: 2.9 Consensus size: 401
21913 GCGATTACCC
* * * * * *
21923 ACAAACGATGCGGTCATCTTCCTGATGAGATGCTAAGAAGAAGACCAAGTCAAATTCACGATGTG
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGGTGTG
* *
21988 AACAAATCTTCGAACCCAAGCTTCCTGATGAGACACTAAGAAACAGGTCGAAGAAATAAAAGGTT
66 AACAAATCTTCGAACCC-AGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATAAAAGGTT
* *
22053 AGCTTCCTGATGAGATACTGCGAAG-CAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
130 AGCTTCCTGATGAGATACTGAGAAGTGA-ACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
*
22117 AATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAATCCA
194 AATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCA
* * * *
22182 CGATGTGAACAAATCTTCGAACCTCAGCTTCCTGACGAGAAACTGAAAAACAGGT-GAAGCAATA
259 CGATGTGAACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATA
* * *
22246 AAAGGTTAGCTTCCTGGTGAGATACAGAGAAGTGAACCAAATTTATCTTCCTGATGATATACAGA
324 AAAGGTTAGCTTCCTGGTGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGA
22311 GAAGCGAATTGAA
389 GAAGCGAATTGAA
* *
22324 ACAAACGACGTGGTCATCTTCCTGATGAGATACTGAGTAGAAGACCAAATCAAATCCACGGTGTG
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGGTGTG
* * *
22389 AACAAATCTTCGAACCCCAGTTTCCTGATGAGACACTGAGAAACAGGTCAAAGCAATAAAAGTTT
66 AACAAATCTTCGAA-CCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATAAAAGGTT
* *
22454 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTT-CTAGATGAGATACAAAGAAGCA
130 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCT-GATGAGATACAGAGAAGCG
* * *
22518 AATTGAAACAAACGACGCGATCATCTTCCTGATGAAATACTGAGAAGAAGACCAAATCAAATTCA
194 AATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCA
* * *
22583 CGATGTCAATAAATCTTCGAACCCCAGCTTCCTGGTGAGACACTGAGAAACAGGTCGAAGCAATA
259 CGATGTGAACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATA
* *
22648 AAAGGTTAGCTTCCTGGTGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGA
324 AAAGGTTAGCTTCCTGGTGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGA
22713 GAAGCGAATTGAA
389 GAAGCGAATTGAA
* * * *
22726 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAATACCAAACCAAATCCACGGCGTG
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGGTGTG
* *
22791 AACAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAAAAACAGGTCGAAGCAATAAAAGGTTA
66 AACAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATAAAAGGTTA
* * * * *
22856 GCTTCCTGGTGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGATGATATACAGAGAAGCGAA
131 GCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
* * *
22921 TTGAAACAAACGACGTGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
196 TTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCA--
* * * * *
22986 CTCGACGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAA
259 --CGATGTGAACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAA
* **
23051 TAAACGGTTAGCTTCCTAATGAGATACTGAGAAG
322 TAAAAGGTTAGCTTCCTGGTGAGATACTGAGAAG
23085 AAGGCTATGT
Statistics
Matches: 684, Mismatches: 68, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
400 2 0.00
401 435 0.64
402 161 0.24
405 86 0.13
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (401 bp):
ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGGTGTG
AACAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATAAAAGGTTA
GCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
TTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACG
ATGTGAACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATAAA
AGGTTAGCTTCCTGGTGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGA
AGCGAATTGAA
Found at i:23441 original size:11 final size:10
Alignment explanation
Indices: 23412--23463 Score: 59
Period size: 10 Copynumber: 4.8 Consensus size: 10
23402 GGCCCAACAA
23412 ATTTAAATTT
1 ATTTAAATTT
23422 ATTTAAATTT
1 ATTTAAATTT
23432 ATTATAAATTT
1 ATT-TAAATTT
*
23443 AAATTTAAAATTC
1 --ATTT-AAATTT
23456 ATTTAAAT
1 ATTTAAAT
23464 AATGTCCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 17 0.46
11 11 0.30
12 1 0.03
13 8 0.22
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:23459 original size:17 final size:17
Alignment explanation
Indices: 23410--23463 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
23400 TGGGCCCAAC
*
23410 AAATTT-AAATTTATTT
1 AAATTTAAAATTAATTT
** *
23426 AAATTTATTATAAATTT
1 AAATTTAAAATTAATTT
*
23443 AAATTTAAAATTCATTT
1 AAATTTAAAATTAATTT
23460 AAAT
1 AAAT
23464 AATGTCCAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 6 0.21
17 23 0.79
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTTAAAATTAATTT
Found at i:24206 original size:9 final size:9
Alignment explanation
Indices: 24194--24235 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
24184 TTCAATAATA
24194 ATAATAAAT
1 ATAATAAAT
24203 ATAATAAAT
1 ATAATAAAT
*
24212 AT-ATTAAT
1 ATAATAAAT
24220 ATTAATAAA-
1 A-TAATAAAT
24229 ATAATAA
1 ATAATAA
24236 TAAAATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 12 0.41
9 13 0.45
10 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATAATAAAT
Done.