Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011715.1 Kokia drynarioides strain JFW-HI SEQ_126709, 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: 2988
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.34
Warning! 239 characters in sequence are not A, C, G, or T
Found at i:348 original size:59 final size:58
Alignment explanation
Indices: 273--795 Score: 651
Period size: 58 Copynumber: 8.9 Consensus size: 58
263 TCCCTAAACT
* **
273 TTCCAAAAATCTCATTTTAAACCCCGAACCTTCTAAAAATTACCATTTTGCCCCCGAAC
1 TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTT-CCCCCGAAC
*
332 TTCCAAAAATCCCATTTTTGA-CCCGAATCTTCTAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTT-CCCCCGAAC
* * *
390 TTCCAAAAATCCCAATTTTAACCTCGAACCTTCTAAAAATTACCATTTTGCCCCCGAAC
1 TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTT-CCCCCGAAC
* *** *
449 TGCCAAAAATCCCATTTTTGACCTTAAACCTTCTAAAAATTACCATTTTACCCCGAAC
1 TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTCCCCCGAAC
* * *
507 TTCCAAAAATCCCATTTTTGACCTCGAACCTTCTAAAAAGTACCATTTT-ACCCGAAAC
1 TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTCCCCCG-AAC
* * *
565 TTCCAAAAATCTCATTTTTGACCCTGAACCTTCTAAAAATTACCAATTTTCCCCTGAAC
1 TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACC-ATTTTCCCCCGAAC
* * * *
624 TTCCAAATATCCCATTTTTTACCCTGAACCTTCT-AAAATTACCATTTTACCCCCAAAC
1 TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTT-CCCCCGAAC
* * **
682 TTCCAAAAATCCCATTTTTAACCCCGAACCTT-TCGAAAATTACCATTTTACCTTCGAAC
1 TTCCAAAAATCCCATTTTTGACCCCGAACCTTCT-AAAAATTACCATTTT-CCCCCGAAC
*** * *
741 TTCCAAAAATCCCATTTTTGATTTCGAACCTTC-CAAAACTACCATTTTGCCCCCG
1 TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTT-CCCCCG
796 TGCATCCGAA
Statistics
Matches: 409, Mismatches: 47, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
57 10 0.02
58 212 0.52
59 184 0.45
60 3 0.01
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (58 bp):
TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTCCCCCGAAC
Found at i:421 original size:117 final size:117
Alignment explanation
Indices: 273--795 Score: 693
Period size: 117 Copynumber: 4.5 Consensus size: 117
263 TCCCTAAACT
* * *
273 TTCCAAAAATCTCATTTTAAACCCCGAACCTTCTAAAAATTACCATTTTGCCCCCGAACTTCCAA
1 TTCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAATTACCATTTTGCCCCCGAACTTCCAA
*
338 AAATCCCATTTTTGACCCGAATCTTCTAAAAATTACCATTTTACCCCCGAAC
66 AAATCCCATTTTTGACCCGAACCTTCTAAAAATTACCATTTTACCCCCGAAC
* *
390 TTCCAAAAATCCCAATTTTAACCTCGAACCTTCTAAAAATTACCATTTTGCCCCCGAACTGCCAA
1 TTCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAATTACCATTTTGCCCCCGAACTTCCAA
**
455 AAATCCCATTTTTGACCTTAAACCTTCTAAAAATTACCATTTTA-CCCCGAAC
66 AAATCCCATTTTTGACC-CGAACCTTCTAAAAATTACCATTTTACCCCCGAAC
* * *
507 TTCCAAAAATCCCATTTTTGACCTCGAACCTTCTAAAAAGTACCATTTT--ACCCGAAACTTCCA
1 TTCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAATTACCATTTTGCCCCCG-AACTTCCA
* *
570 AAAATCTCATTTTTGACCCTGAACCTTCTAAAAATTACCAATTTT-CCCCTGAAC
65 AAAATCCCATTTTTGACCC-GAACCTTCTAAAAATTACC-ATTTTACCCCCGAAC
* * * *
624 TTCCAAATATCCCATTTTTTACC-CTGAACCTTCT-AAAATTACCATTTTACCCCCAAACTTCCA
1 TTCCAAAAATCCCATTTTTAACCTC-GAACCTTCTAAAAATTACCATTTTGCCCCCGAACTTCCA
* * **
687 AAAATCCCATTTTTAACCCCGAACCTT-TCGAAAATTACCATTTTACCTTCGAAC
65 AAAATCCCATTTTTGA-CCCGAACCTTCT-AAAAATTACCATTTTACCCCCGAAC
* ** * *
741 TTCCAAAAATCCCATTTTTGATTTCGAACCTTC-CAAAACTACCATTTTGCCCCCG
1 TTCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAATTACCATTTTGCCCCCG
796 TGCATCCGAA
Statistics
Matches: 358, Mismatches: 35, Indels: 26
0.85 0.08 0.06
Matches are distributed among these distances:
115 4 0.01
116 62 0.17
117 262 0.73
118 30 0.08
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (117 bp):
TTCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAATTACCATTTTGCCCCCGAACTTCCAA
AAATCCCATTTTTGACCCGAACCTTCTAAAAATTACCATTTTACCCCCGAAC
Found at i:789 original size:29 final size:30
Alignment explanation
Indices: 297--789 Score: 252
Period size: 29 Copynumber: 16.8 Consensus size: 30
287 TTTTAAACCC
* **
297 CGAACCTTCTAAAAATTACCATTTTG-CCCC
1 CGAACCTTCCAAAAA-TACCATTTTGACCTT
*
327 CGAA-CTTCCAAAAATCCCATTTTTGACC--
1 CGAACCTTCCAAAAATACCA-TTTTGACCTT
* * **
355 CGAATCTTCTAAAAATTACCATTTT-ACCCC
1 CGAACCTTCCAAAAA-TACCATTTTGACCTT
* *
385 CGAA-CTTCCAAAAATCCCAATTTTAACC-T
1 CGAACCTTCCAAAAATACC-ATTTTGACCTT
* **
414 CGAACCTTCTAAAAATTACCATTTTG-CCCC
1 CGAACCTTCCAAAAA-TACCATTTTGACCTT
* *
444 CGAA-CTGCCAAAAATCCCATTTTTGACCTT
1 CGAACCTTCCAAAAATACCA-TTTTGACCTT
* * *
474 -AAACCTTCTAAAAATTACCATTTT-ACC-C
1 CGAACCTTCCAAAAA-TACCATTTTGACCTT
*
502 CGAA-CTTCCAAAAATCCCATTTTTGACC-T
1 CGAACCTTCCAAAAATACCA-TTTTGACCTT
*
531 CGAACCTTCTAAAAAGTACCATTTT-ACC--
1 CGAACCTTCCAAAAA-TACCATTTTGACCTT
* *
559 CGAAACTTCCAAAAAT-CTCATTTTTGACCCT
1 CGAACCTTCCAAAAATAC-CA-TTTTGACCTT
* * *
590 -GAACCTTCTAAAAATTACCAATTTT-CCCCT
1 CGAACCTTCCAAAAA-TACC-ATTTTGACCTT
* * * *
620 -GAA-CTTCCAAATATCCCATTTTTTACCCT
1 CGAACCTTCCAAAAATACCA-TTTTGACCTT
* * *
649 -GAACCTTCTAAAATTACCATTTT-ACC-C
1 CGAACCTTCCAAAAATACCATTTTGACCTT
* * * * *
676 CCAAACTTCCAAAAATCCCATTTTTAACC-C
1 CGAACCTTCCAAAAATACCA-TTTTGACCTT
* *
706 CGAACCTTTCGAAAATTACCATTTT-ACCTT
1 CGAACC-TTCCAAAAATACCATTTTGACCTT
* *
736 CGAA-CTTCCAAAAATCCCATTTTTGA-TTT
1 CGAACCTTCCAAAAATACCA-TTTTGACCTT
*
765 CGAACCTTCCAAAACTACCATTTTG
1 CGAACCTTCCAAAAATACCATTTTG
790 CCCCCGTGCA
Statistics
Matches: 366, Mismatches: 58, Indels: 79
0.73 0.12 0.16
Matches are distributed among these distances:
26 1 0.00
27 8 0.02
28 83 0.23
29 122 0.33
30 122 0.33
31 28 0.08
32 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (30 bp):
CGAACCTTCCAAAAATACCATTTTGACCTT
Done.