Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001936.1 Kokia drynarioides strain JFW-HI SEQ_113747, 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: 2321
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Found at i:611 original size:15 final size:15
Alignment explanation
Indices: 591--636 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
581 AAATGTTTTG
591 ATATTAATAATAATA
1 ATATTAATAATAATA
* *
606 ATATTAATAATTATT
1 ATATTAATAATAATA
621 A-ATTAATAATTAATA
1 ATATTAATAA-TAATA
636 A
1 A
637 AAAAAGGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTAATAATAATA
Found at i:623 original size:7 final size:7
Alignment explanation
Indices: 598--636 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
588 TTGATATTAA
598 TAATAA-
1 TAATAAT
604 TAAT-AT
1 TAATAAT
610 TAATAAT
1 TAATAAT
*
617 TATTAAT
1 TAATAAT
624 TAATAAT
1 TAATAAT
631 TAATAA
1 TAATAA
637 AAAAAGGGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 1 0.03
6 8 0.28
7 20 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATAAT
Found at i:1760 original size:30 final size:29
Alignment explanation
Indices: 1724--2031 Score: 190
Period size: 30 Copynumber: 10.5 Consensus size: 29
1714 CCTAAACTTT
*
1724 CAAAAATCTCATTTTTAACCCCGAATCTTC
1 CAAAAATCTCA-TTTTAACCCCGAACCTTC
*
1754 CAAAAAT-TACCATTTTACCCCCGAA-CTTC
1 CAAAAATCT--CATTTTAACCCCGAACCTTC
*
1783 CAAAAATCCCATTTTAAACCCCGAACCTTC
1 CAAAAATCTCATTTT-AACCCCGAACCTTC
* * *
1813 CAAAATTAC-CATTTT-ACCCCTAAACTTC
1 CAAAAAT-CTCATTTTAACCCCGAACCTTC
* *
1841 CAAAAATCCCATTTTAACCTCGAACCTTC
1 CAAAAATCTCATTTTAACCCCGAACCTTC
*
1870 CAAAAAT-TACCATTTT-ACCCTCAAACC-TC
1 CAAAAATCT--CATTTTAACCC-CGAACCTTC
* *
1899 CAAAAAGTCTCATTTTTTATCCCGAACCTTC
1 CAAAAA-TCTCA-TTTTAACCCCGAACCTTC
* * *
1930 CAAAAATTATCATTTT-ACGCTCGAA-CTTT
1 CAAAAA-TCTCATTTTAAC-CCCGAACCTTC
* * * * * *
1959 CGAAAATCCCATTTTTGATCTCGATCCTTC
1 CAAAAATCTCA-TTTTAACCCCGAACCTTC
* *
1989 CAAAATTAC-CATTCT-ACCCCTGAA-CTTC
1 CAAAAAT-CTCATTTTAACCCC-GAACCTTC
*
2017 CAAAAATCCCATTTT
1 CAAAAATCTCATTTT
2032 TGACTCCAAA
Statistics
Matches: 221, Mismatches: 34, Indels: 48
0.73 0.11 0.16
Matches are distributed among these distances:
27 2 0.01
28 50 0.23
29 73 0.33
30 76 0.34
31 20 0.09
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.31
Consensus pattern (29 bp):
CAAAAATCTCATTTTAACCCCGAACCTTC
Found at i:1774 original size:29 final size:28
Alignment explanation
Indices: 1736--2031 Score: 210
Period size: 29 Copynumber: 10.1 Consensus size: 28
1726 AAAATCTCAT
1736 TTTTAACCCCGAATCTTCCAAAAATTACCA
1 TTTT-ACCCCGAA-CTTCCAAAAATTACCA
*
1766 TTTTACCCCCGAACTTCCAAAAA-TCCCA
1 TTTTA-CCCCGAACTTCCAAAAATTACCA
1794 TTTTAAACCCCGAACCTTCC-AAAATTACCA
1 TTTT--ACCCCGAA-CTTCCAAAAATTACCA
* *
1824 TTTTACCCCTAAACTTCCAAAAA-TCCCA
1 TTTTACCCC-GAACTTCCAAAAATTACCA
*
1852 TTTTAACCTCGAACCTTCCAAAAATTACCA
1 TTTT-ACCCCGAA-CTTCCAAAAATTACCA
* * *
1882 TTTTACCCTCAAACCTCCAAAAAGT-CTCA
1 TTTTACCC-CGAACTTCCAAAAATTAC-CA
* *
1911 TTTTTTATCCCGAACCTTCCAAAAATTATCA
1 --TTTTACCCCGAA-CTTCCAAAAATTACCA
* * * *
1942 TTTTACGCTCGAACTTTCGAAAA-TCCCA
1 TTTTAC-CCCGAACTTCCAAAAATTACCA
* * *
1970 TTTTTGATCTCGATCCTTCC-AAAATTACCA
1 -TTTT-ACCCCGA-ACTTCCAAAAATTACCA
* *
2000 TTCTACCCCTGAACTTCCAAAAA-TCCCA
1 TTTTACCCC-GAACTTCCAAAAATTACCA
2028 TTTT
1 TTTT
2032 TGACTCCAAA
Statistics
Matches: 211, Mismatches: 32, Indels: 48
0.73 0.11 0.16
Matches are distributed among these distances:
28 47 0.22
29 92 0.44
30 53 0.25
31 19 0.09
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (28 bp):
TTTTACCCCGAACTTCCAAAAATTACCA
Found at i:1826 original size:58 final size:59
Alignment explanation
Indices: 1718--2069 Score: 395
Period size: 58 Copynumber: 6.0 Consensus size: 59
1708 GAGGTCCCTA
* * *
1718 AACTTTCAAAAATCTCATTTTTAACCCCGAATCTTCCAAAAATTACCATTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCG
* **
1777 AACTTCCAAAAATCCCATTTTAAACCCCGAACCTTCC-AAAATTACCATTTTACCCCTA
1 AACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCG
* * *
1835 AACTTCCAAAAATCCCA-TTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCTCA
1 AACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCG
* * * * * * *
1893 AACCTCCAAAAAGTCTCATTTTTTATCCCGAACCTTCCAAAAATTATCATTTTACGCTCG
1 AACTTCCAAAAA-TCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCG
* * * * * * * *
1953 AACTTTCGAAAATCCCATTTTTGATCTCGATCCTTCC-AAAATTACCATTCTACCCCTG
1 AACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCG
* * * * * *
2011 AACTTCCAAAAATCCCATTTTTGACTCCAAACCTTCCCCAAAACTACCATTTTGCCCCC
1 AACTTCCAAAAATCCCATTTTTAACCCCGAACCTT-CCAAAAATTACCATTTTACCCCC
2070 ATGCATCCGT
Statistics
Matches: 247, Mismatches: 41, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
57 17 0.07
58 110 0.45
59 60 0.24
60 60 0.24
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.31
Consensus pattern (59 bp):
AACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCG
Done.