Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002244.1 Kokia drynarioides strain JFW-HI SEQ_114250, 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, 823
Length: 1373
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Found at i:550 original size:29 final size:28
Alignment explanation
Indices: 503--934 Score: 415
Period size: 29 Copynumber: 14.8 Consensus size: 28
493 GAGGTCCCTA
503 AACTATCCAAAAATTCCATTTTTATCCCCG
1 AACT-TCCAAAAATTCCATTTTTA-CCCCG
* *
533 AACTTCCAAAAATTCCATTTTCGACCTCG
1 AACTTCCAAAAATTCCATTTT-TACCCCG
*
562 AAACTCCCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCC-CG
* *
592 AAC-TCCCAAAATTCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCC-G
621 AACTTCCAAAAATTCCATTTTTACCCCTG
1 AACTTCCAAAAATTCCATTTTTACCCC-G
* * *
650 AACTTCTAAAAATTCC-TTTTCGACCTCG
1 AACTTCCAAAAATTCCATTTT-TACCCCG
678 AAAC-TCCTAAAAATTCCATTTTTACCCTCG
1 -AACTTCC-AAAAATTCCATTTTTACCC-CG
*
708 AGCTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCC-CG
* * **
737 AACTCCCAAAAATTTCATTTTTTACATCG
1 AACTTCCAAAAATTCCA-TTTTTACCCCG
* *
766 AAACTTTCAAAAATTCTATTTTTACCCCCG
1 -AACTTCCAAAAATTCCATTTTTA-CCCCG
* *
796 AACTCCCAAAAATTCCATTTTTAACCCCCA
1 AACTTCCAAAAATTCCATTTTT-A-CCCCG
* *
826 AACTTTCAAAAATTCCATTTTTACCGCCA
1 AACTTCCAAAAATTCCATTTTTACC-CCG
* * *
855 AACTTCCAAAAATTCTATTTTCAACCTCG
1 AACTTCCAAAAATTCCATTTT-TACCCCG
884 AAAC-TCCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCC-CG
*
913 AA-TGTCTAAAAATTCCATTTTT
1 AACT-TCCAAAAATTCCATTTTT
935 TAAACCCTAA
Statistics
Matches: 336, Mismatches: 44, Indels: 45
0.79 0.10 0.11
Matches are distributed among these distances:
28 31 0.09
29 197 0.59
30 108 0.32
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTTACCCCG
Found at i:601 original size:59 final size:58
Alignment explanation
Indices: 509--999 Score: 448
Period size: 58 Copynumber: 8.4 Consensus size: 58
499 CCTAAACTAT
*
509 CCAAAAATTCCATTTTTATCCC-CGAACTTCCAAAAATTCCATTTTCGACCTCGAAACTC
1 CCAAAAATTCCATTTTTA-CCCTCGAACTTCCAAAAATTCCATTTT-TACCTCGAAACTC
* * * *
568 CCAAAAATTCCATTTTTACCCTCGAAC-TCCCAAAATTCCATTTTTGACCCCAAAACTT
1 CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT-ACCTCGAAACTC
* *
626 CCAAAAATTCCATTTTTACCC-CTGAACTTCTAAAAATTCC-TTTTCGACCTCGAAACTC
1 CCAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATTCCATTTT-TACCTCGAAACTC
* *
684 CTAAAAATTCCATTTTTACCCTCGAGCTTCCAAAAATTCCATTTTTACCCTCG-AACTC
1 CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTA-CCTCGAAACTC
* * * * *
742 CCAAAAATTTCATTTTTTA-CATCGAAACTTTCAAAAATTCTATTTTTACCCCCG-AACTC
1 CCAAAAATTCCA-TTTTTACCCTCG-AACTTCCAAAAATTCCATTTTTA-CCTCGAAACTC
* * * * * *
801 CCAAAAATTCCATTTTTAACCCCCAAACTTTCAAAAATTCCATTTTTACCGCCAAACTT
1 CCAAAAATTCCATTTTT-ACCCTCGAACTTCCAAAAATTCCATTTTTACCTCGAAACTC
* * * **
860 CCAAAAATTCTATTTTCAACCTCGAAAC-TCCAAAAATTCCATTTTTACCCTCGAATGT-
1 CCAAAAATTCCATTTTTACCCTCG-AACTTCCAAAAATTCCATTTTTA-CCTCGAAACTC
* * * * ** *
918 CTAAAAATTCCATTTTTTAAACCCT-AAATTTTCCCAAAATTACCATTTTGCCCTCGAAAAT-
1 CCAAAAATTCCA-TTTTT--ACCCTCGAA-CTTCCAAAAATT-CCATTTTTACCTCGAAACTC
979 CCAAAAATTACCA-TTTTACCC
1 CCAAAAATT-CCATTTTTACCC
1000 CCGAGTATCC
Statistics
Matches: 358, Mismatches: 52, Indels: 45
0.79 0.11 0.10
Matches are distributed among these distances:
57 1 0.00
58 165 0.46
59 147 0.41
60 6 0.02
61 29 0.08
62 10 0.03
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (58 bp):
CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTACCTCGAAACTC
Found at i:1014 original size:29 final size:29
Alignment explanation
Indices: 507--1003 Score: 110
Period size: 29 Copynumber: 16.9 Consensus size: 29
497 TCCCTAAACT
* *
507 ATCCAAAAATT-CCATTTTTATCCCCGAAC
1 ATCCAAAAATTACCA-TTTTACCCCCGAAA
* *
536 TTCCAAAAATT-CCATTTT-CGACCTCGAAA
1 ATCCAAAAATTACCATTTTAC--CCCCGAAA
* *
565 CTCCCAAAAATT-CCATTTTTACCCTCG-AA
1 AT-CCAAAAATTACCA-TTTTACCCCCGAAA
* *
594 CTCCCAAAATT-CCATTTTTGA-CCCC-AAA
1 ATCCAAAAATTACCA-TTTT-ACCCCCGAAA
* *
622 ACTTCCAAAAATT-CCATTTTTACCCCTGAAC
1 A--TCCAAAAATTACCA-TTTTACCCCCGAAA
* * *
653 TTCTAAAAATT-CC-TTTT-CGACCTCGAAA
1 ATCCAAAAATTACCATTTTAC--CCCCGAAA
* * **
681 CTCCTAAAAATT-CCATTTTTACCCTCGAGC
1 ATCC-AAAAATTACCA-TTTTACCCCCGAAA
* *
711 TTCCAAAAATT-CCATTTTTACCCTCG-AA
1 ATCCAAAAATTACCA-TTTTACCCCCGAAA
* * **
739 CTCCCAAAAATT-TCATTTTTTA-CATCGAAA
1 AT-CCAAAAATTACCA--TTTTACCCCCGAAA
* * *
769 CTTTCAAAAATT-CTATTTTTACCCCCG-AA
1 -ATCCAAAAATTACCA-TTTTACCCCCGAAA
*
798 CTCCCAAAAATT-CCATTTTTAACCCCC-AAA
1 AT-CCAAAAATTACCA-TTTT-ACCCCCGAAA
* * *
828 CTTTCAAAAATT-CCATTTTTACCGCC-AAA
1 -ATCCAAAAATTACCA-TTTTACCCCCGAAA
* * * *
857 CTTCCAAAAATT-CTATTTTCAACCTCGAAA
1 -ATCCAAAAATTACCATTTT-ACCCCCGAAA
* * *
887 CTCCAAAAATT-CCATTTTTACCCTCGAAT
1 ATCCAAAAATTACCA-TTTTACCCCCGAAA
* * ** *
916 GTCTAAAAATT-CCATTTTTTAAACCCTAAA
1 ATCCAAAAATTACCA--TTTTACCCCCGAAA
* * * *
946 TTTTCCCAAAATTACCATTTTGCCCTCGAAA
1 --ATCCAAAAATTACCATTTTACCCCCGAAA
977 ATCCAAAAATTACCATTTTACCCCCGA
1 ATCCAAAAATTACCATTTTACCCCCGA
1004 GTATCCGAAA
Statistics
Matches: 369, Mismatches: 66, Indels: 66
0.74 0.13 0.13
Matches are distributed among these distances:
26 1 0.00
27 4 0.01
28 38 0.10
29 185 0.50
30 107 0.29
31 21 0.06
32 10 0.03
33 3 0.01
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
ATCCAAAAATTACCATTTTACCCCCGAAA
Done.