Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001192.1 Kokia drynarioides strain JFW-HI SEQ_112535, 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: 61513
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:1598 original size:23 final size:24
Alignment explanation
Indices: 1554--1598 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1544 AGTGTCATTG
* *
1554 TAACATAAACTAAATTAAAGTTTA
1 TAACATAAAATAAAATAAAGTTTA
*
1578 TAAC-TAAAATAAAATAGAGTT
1 TAACATAAAATAAAATAAAGTT
1599 AAATATCAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (24 bp):
TAACATAAAATAAAATAAAGTTTA
Found at i:11504 original size:22 final size:22
Alignment explanation
Indices: 11461--11504 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
11451 GATTGAGAGT
* **
11461 TTTTAAGACTTTTTGTTATTTA
1 TTTTAAGACTTGTAATTATTTA
*
11483 TTTTAAGACTTGTAATTTTTTA
1 TTTTAAGACTTGTAATTATTTA
11505 ACAATTTTGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTTAAGACTTGTAATTATTTA
Found at i:28417 original size:24 final size:23
Alignment explanation
Indices: 28360--28417 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
28350 GATTAAGAAA
28360 ATATAAAT-ATATACTAAAATAT
1 ATATAAATAATATACTAAAATAT
* *
28382 A-ATCACACTAATATATTAAAATAT
1 ATAT-A-AATAATATACTAAAATAT
28406 ATATATAATAAT
1 ATATA-AATAAT
28418 CATGAGTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 2 0.07
22 2 0.07
23 2 0.07
24 20 0.71
25 2 0.07
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (23 bp):
ATATAAATAATATACTAAAATAT
Found at i:29515 original size:3 final size:3
Alignment explanation
Indices: 29507--29548 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
29497 ATTACTAACC
29507 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29549 GATGAGGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:48652 original size:68 final size:68
Alignment explanation
Indices: 48535--48738 Score: 356
Period size: 67 Copynumber: 3.0 Consensus size: 68
48525 AATGTGAAAA
* *
48535 TGCATTTCCGATTGGGTTATAAATTTAATGCTTAACATAATGTTTGGCCTCTGAAATTGGTAATT
1 TGCATTTCAGATTGGGTTATAAATTTAATGCTTAACATACTGTTTGGCCTCTGAAATTGGTAATT
48600 TTT
66 TTT
* * *
48603 TGCATTTCAGATTGGGTTATAAATTTAATGCTTAACGTACTATTCGGCCTCTGAAATTGGTAA-T
1 TGCATTTCAGATTGGGTTATAAATTTAATGCTTAACATACTGTTTGGCCTCTGAAATTGGTAATT
48667 TTT
66 TTT
48670 TGCATTTCAGATTGGGTTATAAATTTAATGCTTAACATACTGTTTGGCCTCTGAAATTGGTAATT
1 TGCATTTCAGATTGGGTTATAAATTTAATGCTTAACATACTGTTTGGCCTCTGAAATTGGTAATT
48735 TTT
66 TTT
48738 T
1 T
48739 TATATTGGTG
Statistics
Matches: 127, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
67 64 0.50
68 63 0.50
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (68 bp):
TGCATTTCAGATTGGGTTATAAATTTAATGCTTAACATACTGTTTGGCCTCTGAAATTGGTAATT
TTT
Found at i:54376 original size:18 final size:18
Alignment explanation
Indices: 54353--54389 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
54343 GAAAACAACA
54353 ACCAAAACAATAAAAAAT
1 ACCAAAACAATAAAAAAT
*
54371 ACCAAAATAATAAAAAAT
1 ACCAAAACAATAAAAAAT
54389 A
1 A
54390 ACACCAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.73, C:0.14, G:0.00, T:0.14
Consensus pattern (18 bp):
ACCAAAACAATAAAAAAT
Found at i:54397 original size:21 final size:21
Alignment explanation
Indices: 54344--54398 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 21
54334 AAACAGCATG
*
54344 AAAACAACAACCAAAACAATAA
1 AAAATAAC-ACCAAAACAATAA
*
54366 AAAAT---ACCAAAATAATAA
1 AAAATAACACCAAAACAATAA
54384 AAAATAACACCAAAA
1 AAAATAACACCAAAA
54399 ACAACCGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 17 0.61
21 7 0.25
22 4 0.14
ACGTcount: A:0.73, C:0.18, G:0.00, T:0.09
Consensus pattern (21 bp):
AAAATAACACCAAAACAATAA
Found at i:54779 original size:3 final size:3
Alignment explanation
Indices: 54773--54800 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54763 CTACTACTAC
54773 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54801 TATTTTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:55494 original size:20 final size:19
Alignment explanation
Indices: 55464--55507 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
55454 ATTCCCATTG
*
55464 TTTTATTTTTTAAAAATAA
1 TTTTATATTTTAAAAATAA
*
55483 TATTTATATTTTAAAATTAA
1 T-TTTATATTTTAAAAATAA
55503 TTTTA
1 TTTTA
55508 GTATACAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATATTTTAAAAATAA
Found at i:59049 original size:76 final size:76
Alignment explanation
Indices: 58923--59074 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
58913 ATTGTATGAA
58923 TGGAAAATCCAACAAGGCACGCACACGAGTGCCCTGCCTGGCCTGCCTTCCATTCATCACTATCA
1 TGGAAAATCCAACAAGGCACGCACACGAGTGCCCTGCCTGGCCTGCCTTCCATTCATCACTATCA
58988 ATAGAGATGGG
66 ATAGAGATGGG
58999 TGGAAAATCCAACAAGGCACGCACACGAGTGCCCTGCCTGGCCTGCCTTCCATTCATCACTATCA
1 TGGAAAATCCAACAAGGCACGCACACGAGTGCCCTGCCTGGCCTGCCTTCCATTCATCACTATCA
*
59064 ATAGGGATGGG
66 ATAGAGATGGG
59075 GGTTTTGGAG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (76 bp):
TGGAAAATCCAACAAGGCACGCACACGAGTGCCCTGCCTGGCCTGCCTTCCATTCATCACTATCA
ATAGAGATGGG
Found at i:60257 original size:16 final size:16
Alignment explanation
Indices: 60236--60271 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
60226 TTATCATTAA
60236 AATTTTAGGATGCTTT
1 AATTTTAGGATGCTTT
60252 AATTTTAGGATGCTTT
1 AATTTTAGGATGCTTT
60268 AATT
1 AATT
60272 AAATTATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.50
Consensus pattern (16 bp):
AATTTTAGGATGCTTT
Found at i:60814 original size:22 final size:22
Alignment explanation
Indices: 60774--60833 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
60764 CGATCTGAGG
* *
60774 AAAAATAGAAG-AAACATAATT
1 AAAAATAAAAGAAAATATAATT
60795 AAAAATAAAAGAAAATATAATT
1 AAAAATAAAAGAAAATATAATT
*
60817 AAAAGA-AATAGAAAATA
1 AAAA-ATAAAAGAAAATA
60834 AAGAAGTCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.29
22 23 0.68
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.18
Consensus pattern (22 bp):
AAAAATAAAAGAAAATATAATT
Found at i:60835 original size:16 final size:16
Alignment explanation
Indices: 60794--60835 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
60784 GAAACATAAT
60794 TAAAAATAAAAGAAAA
1 TAAAAATAAAAGAAAA
* *
60810 TATAATTAAAAG-AAA
1 TAAAAATAAAAGAAAA
60825 TAGAAAATAAA
1 TA-AAAATAAA
60836 GAAGTCGAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (16 bp):
TAAAAATAAAAGAAAA
Done.