Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008008.1 Kokia drynarioides strain JFW-HI SEQ_122662, 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, 871
Length: 1453
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Found at i:675 original size:28 final size:28
Alignment explanation
Indices: 656--782 Score: 114
Period size: 28 Copynumber: 4.4 Consensus size: 28
646 TTTTTCTCCC
656 AAATTTACAAAAATTGCATTTTACCCCT
1 AAATTTACAAAAATTGCATTTTACCCCT
* *
684 AAATTTTCAAAAATTACCATTTTACCCCT
1 AAATTTACAAAAATT-GCATTTTACCCCT
* **
713 AAACTTTCCAAAAATCACATTTTTACCCCT
1 AAA-TTTACAAAAATTGCA-TTTTACCCCT
* *
743 AAACTTT-C-AAAATTACCATTTTACCTCT
1 AAA-TTTACAAAAATT-GCATTTTACCCCT
* *
771 AAACTTCCAAAA
1 AAATTTACAAAA
783 TATCATTTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
27 2 0.02
28 32 0.38
29 23 0.27
30 27 0.32
ACGTcount: A:0.39, C:0.25, G:0.01, T:0.35
Consensus pattern (28 bp):
AAATTTACAAAAATTGCATTTTACCCCT
Found at i:706 original size:29 final size:29
Alignment explanation
Indices: 656--855 Score: 162
Period size: 29 Copynumber: 7.0 Consensus size: 29
646 TTTTTCTCCC
* *
656 AAATTTACAAAAATT-GCATTTTACCCCT
1 AAATTTTCAAAAATTACCATTTTACCCCT
684 AAATTTTCAAAAATTACCATTTTACCCCT
1 AAATTTTCAAAAATTACCATTTTACCCCT
* *
713 AAACTTTCCAAAAATCA-CATTTTTACCCCT
1 AAA-TTTTCAAAAATTACCA-TTTTACCCCT
* *
743 AAACTTTC-AAAATTACCATTTTACCTCT
1 AAATTTTCAAAAATTACCATTTTACCCCT
* * * *
771 AAA-CTTCCAAAA-TATCATTTTTGACCTC-
1 AAATTTTCAAAAATTACCA-TTTT-ACCCCT
* * * * *
799 GAATTTTCCAAAATTATCGTTTTGCTCCC-
1 AAATTTTCAAAAATTACCATTTTAC-CCCT
*
828 AAACTTTCAAAAATTACCATTTTACCCC
1 AAATTTTCAAAAATTACCATTTTACCCC
856 ACAAACTTCC
Statistics
Matches: 141, Mismatches: 21, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
27 7 0.05
28 46 0.33
29 60 0.43
30 28 0.20
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
AAATTTTCAAAAATTACCATTTTACCCCT
Found at i:725 original size:58 final size:57
Alignment explanation
Indices: 663--855 Score: 184
Period size: 58 Copynumber: 3.4 Consensus size: 57
653 CCCAAATTTA
663 CAAAAATTGCA-TTTTACCCCTAAATTTTCAAAAATTACCATTTTACCCCTAAACTTTC
1 CAAAAATT-CATTTTTACCCCTAAATTTTC-AAAATTACCATTTTACCCCTAAACTTTC
* * *
721 CAAAAATCACATTTTTACCCCTAAACTTTCAAAATTACCATTTTACCTCTAAAC-TTC
1 CAAAAAT-TCATTTTTACCCCTAAATTTTCAAAATTACCATTTTACCCCTAAACTTTC
* * * * *
778 C-AAAATATCATTTTTGACCTC-GAATTTTCCAAAATTATCGTTTTGCTCCC-AAACTTT-
1 CAAAAAT-TCATTTTT-ACCCCTAAATTTT-CAAAATTACCATTTTAC-CCCTAAACTTTC
835 CAAAAATTACCA-TTTTACCCC
1 CAAAAATT--CATTTTTACCCC
856 ACAAACTTCC
Statistics
Matches: 113, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
56 17 0.15
57 32 0.28
58 45 0.40
59 19 0.17
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (57 bp):
CAAAAATTCATTTTTACCCCTAAATTTTCAAAATTACCATTTTACCCCTAAACTTTC
Found at i:982 original size:28 final size:29
Alignment explanation
Indices: 896--985 Score: 80
Period size: 28 Copynumber: 3.1 Consensus size: 29
886 AGAGTGTTTA
*
896 AAAATTACCATTTTCACCC-CTG-AGTATCC
1 AAAATTACCATTTT-ACCCTC-GAAGCATCC
* * * *
925 AAAAATTACCGTTTTGCCTTCGAA-CCTCC
1 -AAAATTACCATTTTACCCTCGAAGCATCC
954 AAAATTACCATTTTACCCTC-AAGCATCC
1 AAAATTACCATTTTACCCTCGAAGCATCC
982 AAAA
1 AAAA
986 ATCGTATTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
27 2 0.04
28 25 0.52
29 6 0.12
30 15 0.31
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.29
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAAGCATCC
Done.