Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013155.1 Kokia drynarioides strain JFW-HI SEQ_128174, 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, 730
Length: 1218
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:254 original size:30 final size:30
Alignment explanation
Indices: 160--654 Score: 482
Period size: 30 Copynumber: 16.6 Consensus size: 30
150 GGTCCCTAAA
* * *
160 CTTCCAAAAATCTCATTTTTAA-CCCTAAA
1 CTTCCAAAAATCCCATTTTTAACCCCGAAC
*
189 CTTCCAAAAATTACCA-TTTTAACCCCGAA-
1 CTTCCAAAAA-TCCCATTTTTAACCCCGAAC
218 CTTCCAAAAATCCCATTTTTAACCCCGAAC
1 CTTCCAAAAATCCCATTTTTAACCCCGAAC
* * *
248 CTTCCAAAAATAACCA-TTTT-ACCCCCAAA
1 CTTCCAAAAAT-CCCATTTTTAACCCCGAAC
* *
277 CTTCCAAAAATCTCATTTTTAACCTCGAAC
1 CTTCCAAAAATCCCATTTTTAACCCCGAAC
* **
307 CTTCCTAAAATTAC-TATTTTAACCCCGAAC
1 CTTCCAAAAATCCCAT-TTTTAACCCCGAAC
*
337 CTTCCAAAAATCCCATTTTTTACCCCCGAA-
1 CTTCCAAAAATCCCA-TTTTTAACCCCGAAC
* *
367 CTTCCAAAAATCCCAATTTTAACCCCAAAC
1 CTTCCAAAAATCCCATTTTTAACCCCGAAC
*
397 CTTCCAAAAATTACCA-TTTT-ACCCTCGAAC
1 CTTCCAAAAA-TCCCATTTTTAACCC-CGAAC
* * *
427 C-TCCAAAAGTCCCATTTTTTATCCCGAAC
1 CTTCCAAAAATCCCATTTTTAACCCCGAAC
* *
456 CTTTCCAAGAATTACCA-TTTT-ACCCTCGAA-
1 C-TTCCAA-AAATCCCATTTTTAACCC-CGAAC
*
486 CTTCCAAAAATCCCATTTTTAAACCCGAAC
1 CTTCCAAAAATCCCATTTTTAACCCCGAAC
* * *
516 CTTCCAAAAATTGCCA-TTTT-ACCCCTAAA
1 CTTCCAAAAA-TCCCATTTTTAACCCCGAAC
*
545 CTTCCAAAAATCCCAATTTTAACCCCGAAC
1 CTTCCAAAAATCCCATTTTTAACCCCGAAC
** *
575 CTTCCAAAAATTAC-TATTTAAACCCCGAAC
1 CTTCCAAAAATCCCAT-TTTTAACCCCGAAC
*
605 CTTCCAAAACTCCCATTTTTAACCCCGAAC
1 CTTCCAAAAATCCCATTTTTAACCCCGAAC
* *
635 CTTTCAAAAATTACCATTTT
1 CTTCCAAAAA-TCCCATTTT
655 ACCNNNNNNN
Statistics
Matches: 386, Mismatches: 52, Indels: 54
0.78 0.11 0.11
Matches are distributed among these distances:
28 20 0.05
29 128 0.33
30 186 0.48
31 45 0.12
32 7 0.02
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.29
Consensus pattern (30 bp):
CTTCCAAAAATCCCATTTTTAACCCCGAAC
Found at i:281 original size:59 final size:58
Alignment explanation
Indices: 157--654 Score: 399
Period size: 59 Copynumber: 8.4 Consensus size: 58
147 GAAGGTCCCT
* * * *
157 AAACTTCCAAAAATCTCATTTTTAA-CCCTAAACTTCCAAAAATTACCATTTTAACCCCG
1 AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAA-TCCCATTTTAA-CCCG
* * *
216 -AACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATAACCATTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAAT-CCCATTTTAACCCG
* * * * *
274 AAACTTCCAAAAATCTCATTTTTAACCTCGAACCTTCCTAAAATTACTATTTTAACCCCG
1 AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCC-AAAAATCCCATTTTAA-CCCG
* * *
334 AACCTTCCAAAAATCCCATTTTTTACCCCCGAA-CTTCCAAAAATCCCAATTTTAACCCC
1 AAACTTCCAAAAATCCCA-TTTTTAACCCCGAACCTTCCAAAAATCCC-ATTTTAACCCG
* * *
393 AAACCTTCCAAAAATTACCA-TTTT-ACCCTCGAACC-TCCAAAAGTCCCATTTTTTATCCCG
1 AAA-CTTCCAAAAA-TCCCATTTTTAACCC-CGAACCTTCCAAAAATCCCA--TTTTAACCCG
* * *
453 AACCTTTCCAAGAATTACCA-TTTT-ACCCTCGAA-CTTCCAAAAATCCCATTTTTAAACCCG
1 AAAC-TTCCAA-AAATCCCATTTTTAACCC-CGAACCTTCCAAAAATCCCA-TTTT-AACCCG
* * * *
513 AACCTTCCAAAAATTGCCA-TTTT-ACCCCTAAACTTCCAAAAATCCCAATTTTAACCCCG
1 AAACTTCCAAAAA-TCCCATTTTTAACCCCGAACCTTCCAAAAATCCC-ATTTTAA-CCCG
* ** * *
572 AACCTTCCAAAAATTAC-TATTTAAACCCCGAACCTTCCAAAACTCCCATTTTTAACCCCG
1 AAACTTCCAAAAATCCCAT-TTTTAACCCCGAACCTTCCAAAAATCCCA-TTTTAA-CCCG
* * *
632 AACCTTTCAAAAATTACCATTTT
1 AAACTTCCAAAAA-TCCCATTTT
655 ACCNNNNNNN
Statistics
Matches: 371, Mismatches: 41, Indels: 52
0.80 0.09 0.11
Matches are distributed among these distances:
58 40 0.11
59 161 0.43
60 146 0.39
61 23 0.06
62 1 0.00
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.29
Consensus pattern (58 bp):
AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATCCCATTTTAACCCG
Found at i:609 original size:119 final size:117
Alignment explanation
Indices: 160--657 Score: 503
Period size: 119 Copynumber: 4.2 Consensus size: 117
150 GGTCCCTAAA
* *
160 CTTCCAAAAA-TCTCATTTTTAACCCTAAACTTCCAAAAATTACC-ATTTTAACCCCGAA-CTTC
1 CTTCCAAAAATTC-CA-TTTTACCCCTAAACTTCCAAAAA-TCCCAATTTTAACCCCGAACCTTC
* * * *
222 CAAAAA-TCCCATTTTTAACCCCGAACCTTCCAAAAATAACCA-TTTT-ACCCCCAAA
63 CAAAAATTACCA-TTTTAACCCCGAA-CTTCCAAAAAT-CCCATTTTTAACCCCGAAC
* * * * ** *
277 CTTCCAAAAA-TCTCATTTTTAACCTCGAACCTTCCTAAAATTACTATTTTAACCCCGAACCTTC
1 CTTCCAAAAATTC-CA-TTTT-ACCCCTAAACTTCCAAAAATCCCAATTTTAACCCCGAACCTTC
* * * *
341 CAAAAA-TCCCATTTTTTACCCCCGAACTTCCAAAAATCCCAATTTTAACCCCAAAC
63 CAAAAATTACCA--TTTTAACCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAC
* * * * * *
397 CTTCCAAAAATTACCATTTTA-CCCTCGAACCTCCAAAAGTCCCATTTTTTATCCCGAACCTTTC
1 CTTCCAAAAATT-CCATTTTACCCCT-AAACTTCCAAAAATCCCAATTTTAACCCCGAACC-TTC
* *
461 CAAGAATTACCATTTT-ACCCTCGAACTTCCAAAAATCCCATTTTTAAACCCGAAC
63 CAAAAATTACCATTTTAACCC-CGAACTTCCAAAAATCCCATTTTTAACCCCGAAC
516 CTTCCAAAAATTGCCATTTTACCCCTAAACTTCCAAAAATCCCAATTTTAACCCCGAACCTTCCA
1 CTTCCAAAAATT-CCATTTTACCCCTAAACTTCCAAAAATCCCAATTTTAACCCCGAACCTTCCA
* * *
581 AAAATTACTATTTAAACCCCGAACCTTCCAAAACTCCCATTTTTAACCCCGAAC
65 AAAATTACCATTTTAACCCCGAA-CTTCCAAAAATCCCATTTTTAACCCCGAAC
*
635 CTTTCAAAAATTACCATTTTACC
1 CTTCCAAAAATT-CCATTTTACC
658 NNNNNNNNNN
Statistics
Matches: 322, Mismatches: 44, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
117 22 0.07
118 56 0.17
119 190 0.59
120 46 0.14
121 7 0.02
122 1 0.00
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.29
Consensus pattern (117 bp):
CTTCCAAAAATTCCATTTTACCCCTAAACTTCCAAAAATCCCAATTTTAACCCCGAACCTTCCAA
AAATTACCATTTTAACCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAC
Found at i:751 original size:29 final size:30
Alignment explanation
Indices: 708--918 Score: 184
Period size: 30 Copynumber: 7.1 Consensus size: 30
698 NNNNNNNNNN
708 CGAACCTTCCAAAAATTACCATTTTACCCC
1 CGAACCTTCCAAAAATTACCATTTTACCCC
* * *
738 CGAACC-TCCAAAAAGTCCCATTTTTAACCC
1 CGAACCTTCCAAAAATTACCA-TTTTACCCC
*
768 CGAACCTTCCAAAAATTACCATTTTACCCT
1 CGAACCTTCCAAAAATTACCATTTTACCCC
* * * *
798 CGAACC-TCTAAAAAATCCCATTTTTGA-TCC
1 CGAACCTTCCAAAAATTACCA-TTTT-ACCCC
*
828 CGAACCTTCC-AAAATTACCATTCTACCCC
1 CGAACCTTCCAAAAATTACCATTTTACCCC
* * *
857 TGAA-CTTCCAAAAA-TCCCATTTTTGA-CTC
1 CGAACCTTCCAAAAATTACCA-TTTT-ACCCC
* * *
886 CGAACCTTCCCCAAAACTACCATTTTGCCCC
1 CGAACCTT-CCAAAAATTACCATTTTACCCC
917 CG
1 CG
919 TGCATCCGTA
Statistics
Matches: 142, Mismatches: 26, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
28 10 0.07
29 43 0.30
30 56 0.39
31 29 0.20
32 4 0.03
ACGTcount: A:0.31, C:0.36, G:0.06, T:0.27
Consensus pattern (30 bp):
CGAACCTTCCAAAAATTACCATTTTACCCC
Found at i:802 original size:60 final size:58
Alignment explanation
Indices: 708--916 Score: 276
Period size: 60 Copynumber: 3.5 Consensus size: 58
698 NNNNNNNNNN
*
708 CGAACCTTCCAAAAATTACCATTTTACCCCCGAACCTCCAAAAAGTCCCATTTTTAACCC
1 CGAACCTTCCAAAAATTACCATTTTA-CCCCGAACCTCCAAAAA-TCCCATTTTTGACCC
* *
768 CGAACCTTCCAAAAATTACCATTTTACCCTCGAACCTCTAAAAAATCCCATTTTTGATCC
1 CGAACCTTCCAAAAATTACCATTTTACCC-CGAACCTC-CAAAAATCCCATTTTTGACCC
* * *
828 CGAACCTTCC-AAAATTACCATTCTACCCCTGAACTTCCAAAAATCCCATTTTTGACTC
1 CGAACCTTCCAAAAATTACCATTTTACCCC-GAACCTCCAAAAATCCCATTTTTGACCC
* * *
886 CGAACCTTCCCCAAAACTACCATTTTGCCCC
1 CGAACCTT-CCAAAAATTACCATTTTACCCC
917 CGTGCATCCG
Statistics
Matches: 133, Mismatches: 11, Indels: 10
0.86 0.07 0.06
Matches are distributed among these distances:
58 27 0.20
59 28 0.21
60 73 0.55
61 5 0.04
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.27
Consensus pattern (58 bp):
CGAACCTTCCAAAAATTACCATTTTACCCCGAACCTCCAAAAATCCCATTTTTGACCC
Done.