Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010743.1 Kokia drynarioides strain JFW-HI SEQ_125698, 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: 3397
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:218 original size:29 final size:28
Alignment explanation
Indices: 167--659 Score: 231
Period size: 29 Copynumber: 17.1 Consensus size: 28
157 AAGGTCCCTA
167 AACTATCCAAAAATTACCATTTTACCCCCG
1 AACT-TCCAAAAA-TACCATTTTACCCCCG
* *
197 AACTTCCAAAAATCCCATTTTTGA-CCCCT
1 AACTTCCAAAAATACCA-TTTT-ACCCCCG
**
226 AACTTCCAAAAATTACCATTTTACCCCTA
1 AACTTCCAAAAA-TACCATTTTACCCCCG
* *
255 AACTTCCAAAAATCCCATTTTTAACCCCG
1 AACTTCCAAAAATACCA-TTTTACCCCCG
*
284 AACCTTCCAAAAAATACCATTTTACCCTCG
1 AA-CTTCC-AAAAATACCATTTTACCCCCG
* *** ** ** ** *
314 AAC--NC-ATTTTACCCCTAAACTTCCA
1 AACTTCCAAAAATACCATTTTACCCCCG
** * * * **
339 AAAATCC---CAT---TTTTAACCCCGA
1 AACTTCCAAAAATACCATTTTACCCCCG
*
361 ACCTTCCAAAAAATACCATTTTACCCCCG
1 AACTTCC-AAAAATACCATTTTACCCCCG
* * **
390 AACTTCCAAAAGTCCCATTTTTTTA-CCCTA
1 AACTTCCAAAAATACCA---TTTTACCCCCG
*
420 AACCTTCCAAAAATTACCATTTTACCCCCA
1 AA-CTTCCAAAAA-TACCATTTTACCCCCG
* * *
450 AACTTCCAAAAGTCCCATTTTTTTTA-CCCCA
1 AACTTCCAAAAATACCA----TTTTACCCCCG
*
481 AACCTTCCAAAAATTACCATTTTACCCCCA
1 AA-CTTCCAAAAA-TACCATTTTACCCCCG
* * *
511 AACTTCCAAAAGTCCCATTTTTGA-CCTCG
1 AACTTCCAAAAATACCA-TTTT-ACCCCCG
*
540 AACCTTCCAAAAATTACCATTTTACCCTCG
1 AA-CTTCCAAAAA-TACCATTTTACCCCCG
* *
570 ACCTTCCAAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAA-TACCATTTTACCCCCG
* *
599 AACTTCCAAAGAT-CCTATTTTTAACCCCG
1 AACTTCCAAAAATACC-A-TTTTACCCCCG
*
628 AACCTTCCAAAAATTACCCTTTTACCCCCG
1 AA-CTTCCAAAAA-TACCATTTTACCCCCG
658 AA
1 AA
660 TGTTTGAAAT
Statistics
Matches: 356, Mismatches: 68, Indels: 78
0.71 0.14 0.16
Matches are distributed among these distances:
22 10 0.03
25 12 0.03
26 2 0.01
27 4 0.01
28 27 0.08
29 158 0.44
30 84 0.24
31 35 0.10
32 20 0.06
33 4 0.01
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.29
Consensus pattern (28 bp):
AACTTCCAAAAATACCATTTTACCCCCG
Found at i:240 original size:58 final size:58
Alignment explanation
Indices: 162--659 Score: 261
Period size: 59 Copynumber: 8.6 Consensus size: 58
152 TCCCGAAGGT
*
162 CCCTAAACTATCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGAC
1 CCCT-AACT-TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAAC
**
222 CCCTAACTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAAC
1 CCCTAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAAC
* * * * *
280 CCCGAACCTTCCAAAAAATACCATTTTA---CC---C-T-C--GAA-CNCA-TTTTACC
1 CCCTAA-CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAAC
** ** * * *
327 CCTAAACTTCCAAAAATCC-CATTTTTAACCCCGAACCTTCCAAAAAATACCA-TTTTACC
1 CCCTAACTTCCAAAAATTACCA-TTTTACCCCCGAA-CTTCC-AAAAATCCCATTTTTAAC
* * * ** * *
386 CCCGAACTTCC-AAAAGTCCCATTTTTTTA-CCCTAAACCTTCCAAAAATTACCA-TTTTACC
1 CCCTAACTTCCAAAAATTACCA---TTTTACCCCCGAA-CTTCCAAAAA-TCCCATTTTTAAC
* * * * * *
446 CCCAAACTTCC-AAAAGTCCCATTTTTTTTA-CCCCAAACCTTCCAAAAATTACCA-TTTTACC
1 CCCTAACTTCCAAAAATTACCA----TTTTACCCCCGAA-CTTCCAAAAA-TCCCATTTTTAAC
* * * * *
507 CCCAAACTTCC-AAAAGTCCCATTTTTGA-CCTCGAACCTTCCAAAAATTACCA-TTTT-AC
1 CCCTAACTTCCAAAAATTACCA-TTTT-ACCCCCGAA-CTTCCAAAAA-TCCCATTTTTAAC
* * * * *
565 CCTCGACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAGATCCTATTTTTAAC
1 CC-CTAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAAC
* *
624 CCCGAACCTTCCAAAAATTACCCTTTTACCCCCGAA
1 CCCTAA-CTTCCAAAAATTACCATTTTACCCCCGAA
660 TGTTTGAAAT
Statistics
Matches: 373, Mismatches: 38, Indels: 55
0.80 0.08 0.12
Matches are distributed among these distances:
45 2 0.01
46 15 0.04
47 10 0.03
48 3 0.01
49 4 0.01
51 1 0.00
52 1 0.00
53 2 0.01
54 1 0.00
55 1 0.00
56 1 0.00
57 3 0.01
58 84 0.23
59 125 0.34
60 55 0.15
61 65 0.17
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.29
Consensus pattern (58 bp):
CCCTAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAAC
Found at i:353 original size:46 final size:46
Alignment explanation
Indices: 273--363 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 46
263 AAAATCCCAT
*
273 TTTTAACCCCGAACCTTCCAAAAAATACCATTTT-ACCCTCGAACNCA
1 TTTTAACCCCGAAACTTCCAAAAAATACCATTTTAACCC-CGAAC-CA
* *
320 TTTT-ACCCCTAAACTTCC-AAAAATCCCATTTTTAACCCCGAACC
1 TTTTAACCCCGAAACTTCCAAAAAATACCA-TTTTAACCCCGAACC
364 TTCCAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
45 10 0.26
46 21 0.54
47 8 0.21
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.27
Consensus pattern (46 bp):
TTTTAACCCCGAAACTTCCAAAAAATACCATTTTAACCCCGAACCA
Found at i:368 original size:76 final size:75
Alignment explanation
Indices: 240--392 Score: 288
Period size: 76 Copynumber: 2.0 Consensus size: 75
230 TCCAAAAATT
240 ACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAAATACCATT
1 ACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAAATACCATT
*
305 TTACCCTCGA
66 TTACCCCCGA
315 ACNCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAAATACCAT
1 AC-CATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAAATACCAT
380 TTTACCCCCGA
65 TTTACCCCCGA
391 AC
1 AC
393 TTCCAAAAGT
Statistics
Matches: 76, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
75 2 0.03
76 74 0.97
ACGTcount: A:0.35, C:0.35, G:0.03, T:0.27
Consensus pattern (75 bp):
ACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAAATACCATT
TTACCCCCGA
Found at i:502 original size:61 final size:59
Alignment explanation
Indices: 318--580 Score: 382
Period size: 59 Copynumber: 4.4 Consensus size: 59
308 CCCTCGAACN
* * * * *
318 CATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAAATAC
1 CATTTTACCCCCAAACTTCCAAAAGTCCCATTTTTTACCCCAAACCTTCCAAAAATTAC
* *
377 CATTTTACCCCCGAACTTCCAAAAGTCCCATTTTTTTACCCTAAACCTTCCAAAAATTAC
1 CATTTTACCCCCAAACTTCCAAAAGTCCCA-TTTTTTACCCCAAACCTTCCAAAAATTAC
437 CATTTTACCCCCAAACTTCCAAAAGTCCCATTTTTTTTACCCCAAACCTTCCAAAAATTAC
1 CATTTTACCCCCAAACTTCCAAAAGTCCCA--TTTTTTACCCCAAACCTTCCAAAAATTAC
* * *
498 CATTTTACCCCCAAACTTCCAAAAGTCCCATTTTTGACCTCGAACCTTCCAAAAATTAC
1 CATTTTACCCCCAAACTTCCAAAAGTCCCATTTTTTACCCCAAACCTTCCAAAAATTAC
* * *
557 CATTTTACCCTCGACCTTCCAAAA
1 CATTTTACCCCCAAACTTCCAAAA
581 ATTACCATTT
Statistics
Matches: 187, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
59 74 0.40
60 54 0.29
61 59 0.32
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.30
Consensus pattern (59 bp):
CATTTTACCCCCAAACTTCCAAAAGTCCCATTTTTTACCCCAAACCTTCCAAAAATTAC
Found at i:598 original size:59 final size:59
Alignment explanation
Indices: 318--639 Score: 363
Period size: 59 Copynumber: 5.4 Consensus size: 59
308 CCCTCGAACN
** * *
318 CATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCC-CGAACCTTCCAAAAAATAC
1 CATTTTACCCCCGAACTTCCAAAAGTCCCATTTTT-ACCCTCGAACCTTCCAAAAATTAC
*
377 CATTTTACCCCCGAACTTCCAAAAGTCCCATTTTTTTACCCT-AAACCTTCCAAAAATTAC
1 CATTTTACCCCCGAACTTCCAAAAGTCCCA--TTTTTACCCTCGAACCTTCCAAAAATTAC
* *
437 CATTTTACCCCCAAACTTCCAAAAGTCCCATTTTTTTTACCC-CAAACCTTCCAAAAATTAC
1 CATTTTACCCCCGAACTTCCAAAAGTCCCA---TTTTTACCCTCGAACCTTCCAAAAATTAC
*
498 CATTTTACCCCCAAACTTCCAAAAGTCCCATTTTTGA-CCTCGAACCTTCCAAAAATTAC
1 CATTTTACCCCCGAACTTCCAAAAGTCCCATTTTT-ACCCTCGAACCTTCCAAAAATTAC
* * * * *
557 CATTTTACCCTCGACCTTCCAAAAATTACCA-TTTTACCCTCGAA-CTTCCAAAGA-T-C
1 CATTTTACCCCCGAACTTCC-AAAAGTCCCATTTTTACCCTCGAACCTTCCAAAAATTAC
*
613 CTATTTTTAACCCCGAACCTTCCAAAA
1 C-A-TTTTACCCCCGAA-CTTCCAAAA
640 ATTACCCTTT
Statistics
Matches: 235, Mismatches: 16, Indels: 25
0.85 0.06 0.09
Matches are distributed among these distances:
56 2 0.01
57 2 0.01
58 31 0.13
59 79 0.34
60 57 0.24
61 64 0.27
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.30
Consensus pattern (59 bp):
CATTTTACCCCCGAACTTCCAAAAGTCCCATTTTTACCCTCGAACCTTCCAAAAATTAC
Found at i:651 original size:30 final size:29
Alignment explanation
Indices: 318--655 Score: 280
Period size: 29 Copynumber: 11.4 Consensus size: 29
308 CCCTCGAACN
* * *
318 CATTTTACCCCTAAACTTCCAAAAA-TCC
1 CATTTTACCCCGAACCTTCCAAAAATTAC
*
346 CATTTTTAACCCCGAACCTTCCAAAAAATAC
1 CA-TTTT-ACCCCGAACCTTCCAAAAATTAC
* *
377 CATTTTACCCCCGAA-CTTCC-AAAAGTCC
1 CATTTTA-CCCCGAACCTTCCAAAAATTAC
**
405 CATTTTTTTACCCTAAACCTTCCAAAAATTAC
1 CA---TTTTACCCCGAACCTTCCAAAAATTAC
* * * *
437 CATTTTACCCCCAAACTTCC-AAAAGTCC
1 CATTTTACCCCGAACCTTCCAAAAATTAC
*
465 CATTTTTTTTACCCCAAACCTTCCAAAAATTAC
1 CA----TTTTACCCCGAACCTTCCAAAAATTAC
* * * *
498 CATTTTACCCCCAAACTTCC-AAAAGTCC
1 CATTTTACCCCGAACCTTCCAAAAATTAC
*
526 CATTTTTGACCTCGAACCTTCCAAAAATTAC
1 CA-TTTT-ACCCCGAACCTTCCAAAAATTAC
557 CATTTTACCCTCG-ACCTTCCAAAAATTAC
1 CATTTTACCC-CGAACCTTCCAAAAATTAC
*
586 CATTTTACCCTCGAA-CTTCCAAAGA-T-C
1 CATTTTACCC-CGAACCTTCCAAAAATTAC
613 CTATTTTTAACCCCGAACCTTCCAAAAATTAC
1 C-A-TTTT-ACCCCGAACCTTCCAAAAATTAC
*
645 CCTTTTACCCC
1 CATTTTACCCC
656 CGAATGTTTG
Statistics
Matches: 254, Mismatches: 31, Indels: 49
0.76 0.09 0.15
Matches are distributed among these distances:
27 2 0.01
28 28 0.11
29 99 0.39
30 68 0.27
31 23 0.09
32 26 0.10
33 8 0.03
ACGTcount: A:0.32, C:0.34, G:0.03, T:0.30
Consensus pattern (29 bp):
CATTTTACCCCGAACCTTCCAAAAATTAC
Done.