Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008717.1 Kokia drynarioides strain JFW-HI SEQ_123399, 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: 15737
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:679 original size:23 final size:24
Alignment explanation
Indices: 638--682 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
628 GTGATAATGC
638 TTAAATATGACATATTTTTAGATA
1 TTAAATATGACATATTTTTAGATA
*
662 TTAAATAT-ATATATTTTTAGA
1 TTAAATATGACATATTTTTAGA
683 GTATGATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
TTAAATATGACATATTTTTAGATA
Found at i:910 original size:19 final size:19
Alignment explanation
Indices: 888--932 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
878 TTATATTAGG
888 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
907 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
926 ATTTAAT
1 ATTTAAT
933 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:1761 original size:22 final size:22
Alignment explanation
Indices: 1734--1794 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
1724 TTCGACTTCC
1734 CTATTTTCTGTTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
1756 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
* *
1778 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTACTTTT
1795 CTTTAGATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.13, C:0.11, G:0.03, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:1784 original size:21 final size:22
Alignment explanation
Indices: 1748--1794 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1738 TTTCTGTTTC
*
1748 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
1770 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
1791 TTTT
1 TTTT
1795 CTTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:3087 original size:43 final size:43
Alignment explanation
Indices: 2867--3087 Score: 210
Period size: 43 Copynumber: 5.1 Consensus size: 43
2857 ATGTTAGTGA
* * * *
2867 CGTTTGTGGGAAAAACGCCGCTAAAGAACAT-GTTTTATAGAGG
1 CGTTTATGGGAAAAGCGCCGCTAAAGAACATGGTCTT-TAGCGG
* * * *
2910 CGTTTTTGGGAAAAGTGCAGCTAAAGATCATGGTCTTTAGCGG
1 CGTTTATGGGAAAAGCGCCGCTAAAGAACATGGTCTTTAGCGG
* * * * * * * *
2953 CGTTTGTGGGAGAAGCGTCGTTAAAGATCAAGGTATTTAGCGA
1 CGTTTATGGGAAAAGCGCCGCTAAAGAACATGGTCTTTAGCGG
* ** * * *
2996 CATTTATGGGTGAAGCGCCACTAAAGAACATGGTCTTTAACAG
1 CGTTTATGGGAAAAGCGCCGCTAAAGAACATGGTCTTTAGCGG
* *
3039 TGTTTATGGGAAAAGCGCCGCTAAAGAACATGATCTTTAGCGG
1 CGTTTATGGGAAAAGCGCCGCTAAAGAACATGGTCTTTAGCGG
3082 CGTTTA
1 CGTTTA
3088 CATGATCTTT
Statistics
Matches: 140, Mismatches: 37, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
43 136 0.97
44 4 0.03
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (43 bp):
CGTTTATGGGAAAAGCGCCGCTAAAGAACATGGTCTTTAGCGG
Found at i:3092 original size:21 final size:21
Alignment explanation
Indices: 3066--3107 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3056 CCGCTAAAGA
3066 ACATGATCTTTAGCGGCGTTT
1 ACATGATCTTTAGCGGCGTTT
3087 ACATGATCTTTAGCGGCGTTT
1 ACATGATCTTTAGCGGCGTTT
3108 TTGGGAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (21 bp):
ACATGATCTTTAGCGGCGTTT
Found at i:3149 original size:43 final size:43
Alignment explanation
Indices: 3088--3170 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
3078 GCGGCGTTTA
*
3088 CATGATCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTATAAAC
1 CATGATCTTTAGAGGCGTTTTTGGGAAAAGCGCCGCTATAAAC
*
3131 CATGATCTTTAGAGGCGTTTTTGGGAAAAGCGTCGCTATA
1 CATGATCTTTAGAGGCGTTTTTGGGAAAAGCGCCGCTATA
3171 GGCCCAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (43 bp):
CATGATCTTTAGAGGCGTTTTTGGGAAAAGCGCCGCTATAAAC
Found at i:13657 original size:2 final size:2
Alignment explanation
Indices: 13650--13690 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
13640 TTGAAAAATA
13650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13691 AAGTAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.