Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009849.1 Kokia drynarioides strain JFW-HI SEQ_124578, 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: 52734
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:2766 original size:53 final size:53
Alignment explanation
Indices: 2686--2793 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
2676 TTAATTGAAT
2686 TTCAAGTCTGATGTACCCAACAACCATGCCAACATTTTAGGATAAAAGATAAA
1 TTCAAGTCTGATGTACCCAACAACCATGCCAACATTTTAGGATAAAAGATAAA
2739 TTCAAGTCTGATGTACCCAACAACCATGCCAACATTTTAGGATAAAAGATAAA
1 TTCAAGTCTGATGTACCCAACAACCATGCCAACATTTTAGGATAAAAGATAAA
2792 TT
1 TT
2794 ATGGCAGCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (53 bp):
TTCAAGTCTGATGTACCCAACAACCATGCCAACATTTTAGGATAAAAGATAAA
Found at i:10523 original size:21 final size:22
Alignment explanation
Indices: 10499--10539 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10489 TGATAAATGA
*
10499 TAAAAT-TATATATTTACTTTC
1 TAAAATATAAATATTTACTTTC
*
10520 TAAAATATAAATTTTTACTT
1 TAAAATATAAATATTTACTT
10540 AAATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAAATATAAATATTTACTTTC
Found at i:10581 original size:24 final size:24
Alignment explanation
Indices: 10539--10587 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
10529 AATTTTTACT
* *
10539 TAAATTTTTAAAAATATAAATATA
1 TAAATTATTAAAAATATAAAAATA
10563 TAAATTATT-AAAATGATAAAAATA
1 TAAATTATTAAAAAT-ATAAAAATA
10587 T
1 T
10588 GTATAACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
TAAATTATTAAAAATATAAAAATA
Found at i:17026 original size:23 final size:22
Alignment explanation
Indices: 16976--17035 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
16966 TTATATTCAT
* *
16976 AAAT-TTAATTATTAAAATATTA
1 AAATATTAATTA-TAAAAAATAA
16998 AAATATTAATTATAAAAAATAA
1 AAATATTAATTATAAAAAATAA
*
17020 AATATATAAAATTATA
1 AA-ATAT-TAATTATA
17036 TTAATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 14 0.44
23 11 0.34
24 7 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATATTAATTATAAAAAATAA
Found at i:22354 original size:6 final size:6
Alignment explanation
Indices: 22343--22385 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
22333 CCCAACCGAT
* *
22343 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCATTC CCATTC C
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC C
22386 AATGCCAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.05, C:0.63, G:0.00, T:0.33
Consensus pattern (6 bp):
CCCTTC
Found at i:23865 original size:2 final size:2
Alignment explanation
Indices: 23852--23886 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
23842 AAGCAGGTGT
*
23852 GA GA GT GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
23887 GCTGTGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.51, T:0.03
Consensus pattern (2 bp):
GA
Found at i:29882 original size:8 final size:8
Alignment explanation
Indices: 29869--29893 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29859 ACATTATAAT
29869 AATAATTC
1 AATAATTC
29877 AATAATTC
1 AATAATTC
29885 AATAATTC
1 AATAATTC
29893 A
1 A
29894 TTTAATTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (8 bp):
AATAATTC
Found at i:34436 original size:51 final size:51
Alignment explanation
Indices: 34360--34461 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
34350 AGTTCGGTTA
*
34360 TGGAATCTATTAACCGATAACTGATCGACAAAACTGATTTAACCAAAGGAG
1 TGGAATCTATTAACCGATAACTGATCGAAAAAACTGATTTAACCAAAGGAG
34411 TGGAATCTATTAACCGATAACTGATCGAAAAAACTGATTTAACCAAAGGAG
1 TGGAATCTATTAACCGATAACTGATCGAAAAAACTGATTTAACCAAAGGAG
34462 AATGGAGAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.24
Consensus pattern (51 bp):
TGGAATCTATTAACCGATAACTGATCGAAAAAACTGATTTAACCAAAGGAG
Found at i:37827 original size:16 final size:17
Alignment explanation
Indices: 37806--37839 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
37796 CAAAAAATAA
*
37806 ATTTAAAATTAA-AATT
1 ATTTAAAAATAATAATT
37822 ATTTAAAAATAATAATT
1 ATTTAAAAATAATAATT
37839 A
1 A
37840 ATATATACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAAAAATAATAATT
Found at i:38836 original size:23 final size:22
Alignment explanation
Indices: 38806--38849 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
38796 TACATATGTT
38806 ATTAATAATTTAGATCTCGAATG
1 ATTAATAATTTAGAT-TCGAATG
38829 ATTAATAATTTAGATTCGAAT
1 ATTAATAATTTAGATTCGAAT
38850 AATCATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (22 bp):
ATTAATAATTTAGATTCGAATG
Found at i:39616 original size:1 final size:1
Alignment explanation
Indices: 39612--39636 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
39602 NNNNNNNNNN
39612 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
39637 CTTACCCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:45613 original size:18 final size:19
Alignment explanation
Indices: 45590--45628 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
45580 TAAAAATATT
* *
45590 TTTTTATAATATT-ATTAA
1 TTTTTAAAAAATTAATTAA
45608 TTTTTAAAAAATTAATTAA
1 TTTTTAAAAAATTAATTAA
45627 TT
1 TT
45629 GTTAGATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTAAAAAATTAATTAA
Found at i:47834 original size:4 final size:4
Alignment explanation
Indices: 47825--47850 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
47815 TTCAGATTTG
47825 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
47851 TTTTTTTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Done.