Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006273.1 Kokia drynarioides strain JFW-HI SEQ_120844, 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: 72494
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:13573 original size:14 final size:15
Alignment explanation
Indices: 13556--13588 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
13546 ACGTGATTTT
13556 TTTAATTAAAT-AAA
1 TTTAATTAAATAAAA
*
13570 TTTAATTAATTAAAA
1 TTTAATTAAATAAAA
13585 TTTA
1 TTTA
13589 TAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTAATTAAATAAAA
Found at i:16611 original size:20 final size:21
Alignment explanation
Indices: 16575--16624 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
16565 ATTGGCATGG
*
16575 TTTATATTAAGTGTAAATA-GA
1 TTTA-ATTAAGTGTAAAAATGA
16596 TTTAATTAAGAT-TAAAAATGA
1 TTTAATTAAG-TGTAAAAATGA
16617 -TTAATTAA
1 TTTAATTAA
16625 AGCTTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTAATTAAGTGTAAAAATGA
Found at i:23504 original size:20 final size:21
Alignment explanation
Indices: 23468--23517 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
23458 ATTAGTATGG
*
23468 TTTATATTAAGTGTAAATA-GA
1 TTTA-ATTAAGTGTAAAAATGA
23489 TTTAATTAAGAT-TAAAAATGA
1 TTTAATTAAG-TGTAAAAATGA
23510 -TTAATTAA
1 TTTAATTAA
23518 AGCTTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTAATTAAGTGTAAAAATGA
Found at i:27825 original size:19 final size:18
Alignment explanation
Indices: 27797--27836 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
27787 AATGGATCAC
27797 ACCGCCATCTAAACTTAA
1 ACCGCCATCTAAACTTAA
27815 ACCGTCCATCTAAACTTAA
1 ACCG-CCATCTAAACTTAA
27834 ACC
1 ACC
27837 AAGTGTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.38, C:0.35, G:0.05, T:0.23
Consensus pattern (18 bp):
ACCGCCATCTAAACTTAA
Found at i:36727 original size:15 final size:15
Alignment explanation
Indices: 36707--36757 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
36697 ATAACACGAT
36707 AACGTAAATAATTAA
1 AACGTAAATAATTAA
* *
36722 AACGT-AATATTTCA
1 AACGTAAATAATTAA
**
36736 AATATAAATAATTAA
1 AACGTAAATAATTAA
*
36751 AATGTAA
1 AACGTAA
36758 CTTGAGACAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (15 bp):
AACGTAAATAATTAA
Found at i:40490 original size:111 final size:111
Alignment explanation
Indices: 40289--40582 Score: 367
Period size: 111 Copynumber: 2.6 Consensus size: 111
40279 TGCAGTTGGG
* * * * * * * *
40289 TGATGTCAAG-GTAGTTGGCAATCTAATTTAAACGATCCGTGCAATTT-AAGTCGTTCACTTGAG
1 TGATGTCAAGAG-AGTTAGCAATTTAGTTTAAATGCTCCATGC-ATTTGAAGTTGTTGACTTGAG
* ** * *
40352 CTAGGTTCTTCAAAACAAATTGGTGTGGTTTGATTCGGTCCAGTTATA
64 CCAAATTCTTCAAAACAAATTGATGTGGTTTGATTCGGTCCAGTTACA
* *
40400 TGGTGTCAAGAGAGTTAGCAATTTAGTTTAAATGCTCTATGCATTTGAAGTTGTTGACTTGAGCC
1 TGATGTCAAGAGAGTTAGCAATTTAGTTTAAATGCTCCATGCATTTGAAGTTGTTGACTTGAGCC
* * *
40465 AAATTCTTCAGAACAGATTGATGTGGTTTGATTCGGTGCAGTTACA
66 AAATTCTTCAAAACAAATTGATGTGGTTTGATTCGGTCCAGTTACA
* *
40511 TGATGTCAAGGGAGTTAGTAATTTAGTTTAAATGCTCCATGCATTTGAAGTTGTTGACTTGAGCC
1 TGATGTCAAGAGAGTTAGCAATTTAGTTTAAATGCTCCATGCATTTGAAGTTGTTGACTTGAGCC
*
40576 AAGTTCT
66 AAATTCT
40583 CCTTGTTTGT
Statistics
Matches: 158, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
110 4 0.03
111 153 0.97
112 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (111 bp):
TGATGTCAAGAGAGTTAGCAATTTAGTTTAAATGCTCCATGCATTTGAAGTTGTTGACTTGAGCC
AAATTCTTCAAAACAAATTGATGTGGTTTGATTCGGTCCAGTTACA
Found at i:47961 original size:25 final size:24
Alignment explanation
Indices: 47928--47976 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 24
47918 TGATAGATTT
47928 TTATTTTATTTAATATTAATATAA
1 TTATTTTATTTAATATTAATATAA
47952 TTATATTTATTTAATATTAATATAA
1 TTAT-TTTATTTAATATTAATATAA
47977 AATTTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTTTATTTAATATTAATATAA
Found at i:55494 original size:21 final size:21
Alignment explanation
Indices: 55447--55492 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
55437 AGTCCTAAAA
55447 AATTTAAACTCTATACAATCG
1 AATTTAAACTCTATACAATCG
*
55468 AATTTAAACTTTATACAATC-
1 AATTTAAACTCTATACAATCG
55488 AATTT
1 AATTT
55493 TACTATAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTTAAACTCTATACAATCG
Found at i:55960 original size:6 final size:6
Alignment explanation
Indices: 55949--55978 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
55939 TTAAGGCCCA
55949 GACCCC GACCCC GACCCC GACCCC GACCCC
1 GACCCC GACCCC GACCCC GACCCC GACCCC
55979 AGAACTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.67, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCCC
Found at i:61258 original size:28 final size:29
Alignment explanation
Indices: 61222--61276 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
61212 AATAATATTT
*
61222 AAGTTTTAAATTTTAAATT-TTT-TATGTG
1 AAGTCTTAAA-TTTAAATTATTTCTATGTG
61250 AAGTCTTAAATTTAAATTATTTCTATG
1 AAGTCTTAAATTTAAATTATTTCTATG
61277 GACTTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 12 0.50
29 4 0.17
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.53
Consensus pattern (29 bp):
AAGTCTTAAATTTAAATTATTTCTATGTG
Found at i:65487 original size:139 final size:139
Alignment explanation
Indices: 65237--65517 Score: 544
Period size: 139 Copynumber: 2.0 Consensus size: 139
65227 CCAAGTTGAT
*
65237 AATATTAACAATGTTAAAGATTGAATTGAGTTTTTTAAATCATATTAACTTTTAGCTTTTTAAGT
1 AATATTAACAATGTTAAAGATTGAATTGAGTTTTTTAAATCATATTAAATTTTAGCTTTTTAAGT
65302 ATAAGGATGAAATTTTAAATTTTATCTAAATACAGTGACTAACAACACATTTTAACCTTAAAAAC
66 ATAAGGATGAAATTTTAAATTTTATCTAAATACAGTGACTAACAACACATTTTAACCTTAAAAAC
65367 AAATATCAA
131 AAATATCAA
*
65376 AATATTAACAATGTTAAAGATTGAATTGGGTTTTTTAAATCATATTAAATTTTAGCTTTTTAAGT
1 AATATTAACAATGTTAAAGATTGAATTGAGTTTTTTAAATCATATTAAATTTTAGCTTTTTAAGT
65441 ATAAGGATGAAATTTTAAATTTTATCTAAATACAGTGACTAACAACACATTTTAACCTTAAAAAC
66 ATAAGGATGAAATTTTAAATTTTATCTAAATACAGTGACTAACAACACATTTTAACCTTAAAAAC
65506 AAATATCAA
131 AAATATCAA
65515 AAT
1 AAT
65518 TTGGAAATGA
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 140 1.00
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (139 bp):
AATATTAACAATGTTAAAGATTGAATTGAGTTTTTTAAATCATATTAAATTTTAGCTTTTTAAGT
ATAAGGATGAAATTTTAAATTTTATCTAAATACAGTGACTAACAACACATTTTAACCTTAAAAAC
AAATATCAA
Found at i:65891 original size:18 final size:18
Alignment explanation
Indices: 65848--65892 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
65838 CAAAGTGAAT
*
65848 ATTTTGTAATCTTAAAGG
1 ATTTTGTAATCTTAAAGA
** *
65866 ATACTGTAATCTTAGAGA
1 ATTTTGTAATCTTAAAGA
65884 ATTTTGTAA
1 ATTTTGTAA
65893 GTCCTTTAAG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.42
Consensus pattern (18 bp):
ATTTTGTAATCTTAAAGA
Found at i:66747 original size:20 final size:20
Alignment explanation
Indices: 66705--66750 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
66695 TTTAAAAAAT
* **
66705 ATTT-TTAACAATAATTATT
1 ATTTATTAAAAATAATTAAA
66724 ATTTATTAAAAATAATTAAA
1 ATTTATTAAAAATAATTAAA
66744 ATTTATT
1 ATTTATT
66751 TTTAATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTATTAAAAATAATTAAA
Found at i:66772 original size:16 final size:16
Alignment explanation
Indices: 66753--66791 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
66743 AATTTATTTT
*
66753 TAATTATT-TTTAAATA
1 TAATTATTCTTT-AACA
66769 TAATTATTCTTTAACA
1 TAATTATTCTTTAACA
66785 TAATTAT
1 TAATTAT
66792 ATTTGGTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATTATTCTTTAACA
Done.