Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004927.1 Kokia drynarioides strain JFW-HI SEQ_118629, 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: 6846
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:550 original size:28 final size:28
Alignment explanation
Indices: 510--856 Score: 226
Period size: 28 Copynumber: 12.0 Consensus size: 28
500 GGAGGTCCCG
510 AAACTTCCAAAAATTCCATTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTACCCCT
* *
538 AAACTTCCAAAAATTCCATTTTTTGACCTCG
1 AAACTTCCAAAAATTCCA--TTTT-ACCCCT
*
569 AAACTTCCAAAAATTCCATTTTTACCTC-
1 AAACTTCCAAAAATTCCA-TTTTACCCCT
* *
597 GAACTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCA-TTTT-ACCCCT
*
627 AAACTTCCAAAAATTACATTTTTA-CCCT
1 AAACTTCCAAAAATTCCA-TTTTACCCCT
* * *
655 CAAACCTT-CAAAATTTCCATTTTGACCTCG
1 -AAA-CTTCCAAAAATTCCATTTT-ACCCCT
** * *
685 AAACTTTTAAAAATTACCATTTTGCCCCC
1 AAACTTCCAAAAATT-CCATTTTACCCCT
* * *
714 AAA-TATCCAAAAACTCCATTTTCAACCTCG
1 AAACT-TCCAAAAATTCCATTTT--ACCCCT
* *
744 AAAC-TCTC-AAAATTACCCTTTTACCCCC
1 AAACTTC-CAAAAATT-CCATTTTACCCCT
* * *
772 GAA-TGT-CTAAAATTCCATTTTTAACCCT
1 AAACT-TCCAAAAATTCCA-TTTTACCCCT
* *
800 AAACTTCCCAAAATTACCATTTTGCCCCT
1 AAACTTCCAAAAATT-CCATTTTACCCCT
**
829 AAAAATCC-AAAATTACCATTTTACCCCT
1 AAACTTCCAAAAATT-CCATTTTACCCCT
857 CGGGTATCCG
Statistics
Matches: 258, Mismatches: 37, Indels: 48
0.75 0.11 0.14
Matches are distributed among these distances:
27 3 0.01
28 100 0.39
29 75 0.29
30 58 0.22
31 22 0.09
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (28 bp):
AAACTTCCAAAAATTCCATTTTACCCCT
Found at i:602 original size:59 final size:58
Alignment explanation
Indices: 508--748 Score: 274
Period size: 59 Copynumber: 4.1 Consensus size: 58
498 TTGGAGGTCC
*
508 CGAAACTTCCAAAAATTCCA-TTTTACCCCTAAACTTCCAAAAATTCCATTTTTTGACCT
1 CGAAACTTCCAAAAATTCCATTTTTACCTC-AAACTTCCAAAAATTCCA-TTTTTGACCT
* *
567 CGAAACTTCCAAAAATTCCATTTTTACCTCGAACTTCCAAAAATTCCATTTTTGACCC
1 CGAAACTTCCAAAAATTCCATTTTTACCTCAAACTTCCAAAAATTCCATTTTTGACCT
* * *
625 CAAAACTTCCAAAAATTACATTTTTACCCTCAAACCTT-CAAAATTTCCA-TTTTGACCT
1 CGAAACTTCCAAAAATTCCATTTTTA-CCTCAAA-CTTCCAAAAATTCCATTTTTGACCT
** ** * * **
683 CGAAACTTTTAAAAATTACCATTTTGCCCCCAAA-TATCCAAAAACTCCATTTTCAACCT
1 CGAAACTTCCAAAAATT-CCATTTTTACCTCAAACT-TCCAAAAATTCCATTTTTGACCT
742 CGAAACT
1 CGAAACT
749 CTCAAAATTA
Statistics
Matches: 156, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
56 1 0.01
57 1 0.01
58 70 0.45
59 73 0.47
60 11 0.07
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (58 bp):
CGAAACTTCCAAAAATTCCATTTTTACCTCAAACTTCCAAAAATTCCATTTTTGACCT
Found at i:647 original size:58 final size:58
Alignment explanation
Indices: 508--822 Score: 270
Period size: 58 Copynumber: 5.4 Consensus size: 58
498 TTGGAGGTCC
* *
508 CGAAACTTCCAAAAATTCCA-TTTTACCCCTAAACTTCCAAAAATTCCATTTTTTGACCT
1 CGAAACTTCCAAAAATTACATTTTTACCTC-AAACTTCCAAAAATTCCA-TTTTTGACCT
* * *
567 CGAAACTTCCAAAAATTCCATTTTTACCTCGAACTTCCAAAAATTCCATTTTTGACCC
1 CGAAACTTCCAAAAATTACATTTTTACCTCAAACTTCCAAAAATTCCATTTTTGACCT
* *
625 CAAAACTTCCAAAAATTACATTTTTACCCTCAAACCTT-CAAAATTTCCA-TTTTGACCT
1 CGAAACTTCCAAAAATTACATTTTTA-CCTCAAA-CTTCCAAAAATTCCATTTTTGACCT
** ** * * **
683 CGAAACTTTTAAAAATTACCATTTTGCCCCCAAA-TATCCAAAAACTCCATTTTCAACCT
1 CGAAACTTCCAAAAATTA-CATTTTTACCTCAAACT-TCCAAAAATTCCATTTTTGACCT
** * * * *
742 CGAAAC-TCTC-AAAATTACCCTTTTACCCCCGAA-TGT-CTAAAATTCCATTTTTAACC-
1 CGAAACTTC-CAAAAATTACATTTTTA-CCTCAAACT-TCCAAAAATTCCATTTTTGACCT
* *
798 CTAAACTTCCCAAAATTACCATTTT
1 CGAAACTTCCAAAAATTA-CATTTT
823 GCCCCTAAAA
Statistics
Matches: 212, Mismatches: 32, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
56 7 0.03
57 31 0.15
58 91 0.43
59 72 0.34
60 11 0.05
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (58 bp):
CGAAACTTCCAAAAATTACATTTTTACCTCAAACTTCCAAAAATTCCATTTTTGACCT
Found at i:673 original size:87 final size:84
Alignment explanation
Indices: 511--822 Score: 292
Period size: 87 Copynumber: 3.6 Consensus size: 84
501 GAGGTCCCGA
*
511 AACTTCCAAAAATTCCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTTGACCTCGAAACTTC
1 AACTTCCAAAAATTCCATTTTACCCCTAAACTTCCAAAAATTACA-TTTTT-ACCTCGAAACTT-
*
576 CAAAAATTCCATTTTTACCTCG
63 CAAAATTTCCATTTTTACCTCG
*
598 AACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACATTTTTACCCTC-AAACCT
1 AACTTCCAAAAATTCCA-TTTT-ACCCCTAAACTTCCAAAAATTACATTTTTA-CCTCGAAA-CT
*
662 TCAAAATTTCCATTTTGACCTCG
62 TCAAAATTTCCATTTTTACCTCG
** * * * * *
685 AAACTTTTAAAAATTACCATTTTGCCCCCAAA-TATCCAAAAACTCCATTTTCAACCTCGAAACT
1 -AACTTCCAAAAATT-CCATTTTACCCCTAAACT-TCCAAAAATTACATTTT-TACCTCGAAACT
* * *
749 CTCAAAATTACC-CTTTTACCCCCG
62 -TCAAAATTTCCATTTTTA-CCTCG
* * *
773 AA-TGT-CTAAAATTCCATTTTTAACCCTAAACTTCCCAAAATTACCATTTT
1 AACT-TCCAAAAATTCCA-TTTTACCCCTAAACTTCCAAAAATTA-CATTTT
823 GCCCCTAAAA
Statistics
Matches: 187, Mismatches: 23, Indels: 30
0.78 0.10 0.12
Matches are distributed among these distances:
85 3 0.02
86 26 0.14
87 83 0.44
88 50 0.27
89 25 0.13
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (84 bp):
AACTTCCAAAAATTCCATTTTACCCCTAAACTTCCAAAAATTACATTTTTACCTCGAAACTTCAA
AATTTCCATTTTTACCTCG
Done.