Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009123.1 Kokia drynarioides strain JFW-HI SEQ_123826, 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: 12781
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:53 original size:27 final size:27
Alignment explanation
Indices: 4--81 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 27
1 AAA
* *
4 AATAAAAATCAATAAAAATATTAAATTTT
1 AATAAAAAT--ATAAAAAAATTAAAATTT
33 AATAAAAATATAAAAAAATTAAAATTT
1 AATAAAAATATAAAAAAATTAAAATTT
* *
60 ATTAAAAATTAGAAAAAAATTA
1 AATAAAAA-TATAAAAAAATTA
82 TAAAATGTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 23 0.52
28 12 0.27
29 9 0.20
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (27 bp):
AATAAAAATATAAAAAAATTAAAATTT
Found at i:78 original size:28 final size:27
Alignment explanation
Indices: 4--81 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 27
1 AAA
*
4 AATAAAAATCA-ATAAAAATATTAAATTTT
1 AATAAAAAT-AGA-AAAAA-ATTAAAATTT
*
33 AATAAAAATATAAAAAAATTAAAATTT
1 AATAAAAATAGAAAAAAATTAAAATTT
*
60 ATTAAAAATTAGAAAAAAATTA
1 AATAAAAA-TAGAAAAAAATTA
82 TAAAATGTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
27 16 0.36
28 18 0.41
29 10 0.23
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (27 bp):
AATAAAAATAGAAAAAAATTAAAATTT
Found at i:338 original size:89 final size:89
Alignment explanation
Indices: 236--398 Score: 211
Period size: 89 Copynumber: 1.8 Consensus size: 89
226 TTTGAGGGCC
* * * * * * **
236 TTTTGATGCATTTTGAAAGTTTAAATACCCAATTGAATGCAAAATAAAAAGAGAGGCT-TAATTA
1 TTTTAATGCATTTTAAAAATTCAAATACCCAAGTGAATGCAAAATAAAAACA-AGAATGTAATTA
300 TTATTTTTTTAAATTTAAGGTTTTT
65 TTATTTTTTTAAATTTAAGGTTTTT
* **
325 TTTTAATGCATTTTAAAAATTCAAGTATTCAAGTGAATGCAAAATAAAAACAAGAATGTAATTAT
1 TTTTAATGCATTTTAAAAATTCAAATACCCAAGTGAATGCAAAATAAAAACAAGAATGTAATTAT
390 TATTTTTTT
66 TATTTTTTT
399 GAAAACAATT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
88 3 0.05
89 59 0.95
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (89 bp):
TTTTAATGCATTTTAAAAATTCAAATACCCAAGTGAATGCAAAATAAAAACAAGAATGTAATTAT
TATTTTTTTAAATTTAAGGTTTTT
Found at i:423 original size:23 final size:25
Alignment explanation
Indices: 386--435 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
376 AAGAATGTAA
* *
386 TTATTATTTTTTTGAAAACA-ATTT
1 TTATTATTTTATTGAAAAAACATTT
410 TTATT-TTTTATTGAAAAAACATTT
1 TTATTATTTTATTGAAAAAACATTT
434 TT
1 TT
436 TTAAAATAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (25 bp):
TTATTATTTTATTGAAAAAACATTT
Found at i:427 original size:24 final size:25
Alignment explanation
Indices: 386--436 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
376 AAGAATGTAA
*
386 TTATTATTTTTTTG-AAAACAATTT
1 TTATTATTTTATTGAAAAACAATTT
*
410 TTATT-TTTTATTGAAAAAACATTTT
1 TTATTATTTTATTG-AAAAACAATTT
435 TT
1 TT
437 TAAAATAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.30
24 5 0.22
25 11 0.48
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (25 bp):
TTATTATTTTATTGAAAAACAATTT
Found at i:1987 original size:115 final size:116
Alignment explanation
Indices: 1785--2014 Score: 336
Period size: 115 Copynumber: 2.0 Consensus size: 116
1775 TCATAAAAAT
* * * *
1785 ATCTGTATTAAGAGTTAGATTGTATTTTGTCCATTCTACTCAAAAAATAAGTAAACTAATTATTA
1 ATCTGTACTAAGAGTTAGATTGTAATTTGGCCATTCTACTCAAAAAATAAGTAAACTAATCATTA
* * *
1850 TACATTAGATTAAAGAGCAAATTGTTCATTATGCTAAAA-TTTGTGTCACA
66 TACATTAAATTAAAAAGCAAATTGATCATTATGCTAAAATTTTGTGTCACA
* * * *
1900 ATCTGTACTAAGAGTTGGATTGTAATTTGGCCATTCTACTCAAAAAATGAGTAAATTAGTCATTA
1 ATCTGTACTAAGAGTTAGATTGTAATTTGGCCATTCTACTCAAAAAATAAGTAAACTAATCATTA
* *
1965 TACATTAAATTAAAAAGCAAATTGATCATTCTGTTAAAATTTTGTGTCAC
66 TACATTAAATTAAAAAGCAAATTGATCATTATGCTAAAATTTTGTGTCAC
2015 TGTCTGATCA
Statistics
Matches: 101, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
115 91 0.90
116 10 0.10
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (116 bp):
ATCTGTACTAAGAGTTAGATTGTAATTTGGCCATTCTACTCAAAAAATAAGTAAACTAATCATTA
TACATTAAATTAAAAAGCAAATTGATCATTATGCTAAAATTTTGTGTCACA
Found at i:2687 original size:116 final size:117
Alignment explanation
Indices: 2476--2707 Score: 349
Period size: 116 Copynumber: 2.0 Consensus size: 117
2466 TCATGAAGGT
* * * *
2476 GTCTGTATTAAGAGTTAGATTGTATTTTATTCATTCTACTCAAAAAAATAAGTAAATTAATTATT
1 GTCTGTACTAAGAGTTAGATTGTAATTTATCCATTCTACTCAAAAAAATAAGTAAATTAATCATT
** *
2541 ATACATTAGATTAAAGAACAAATTTTTCATTCTGTTAAAATTTTGTGTCACA
66 ATACATTAGATTAAAGAACAAATTGATCATTCTGTTAAAATTTTGTATCACA
* * * *
2593 GTCTGTACTAAGAGTTGGATTGTAATTTGTCCATTCTACTC-AAAAAATGAGTAAATTAGTCATT
1 GTCTGTACTAAGAGTTAGATTGTAATTTATCCATTCTACTCAAAAAAATAAGTAAATTAATCATT
*
2657 ATACATTAGATTAAAGAACAAATTGATCATTTTGTTAAAATTTTGTATCAC
66 ATACATTAGATTAAAGAACAAATTGATCATTCTGTTAAAATTTTGTATCAC
2708 TTTCTTATCA
Statistics
Matches: 103, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
116 67 0.65
117 36 0.35
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (117 bp):
GTCTGTACTAAGAGTTAGATTGTAATTTATCCATTCTACTCAAAAAAATAAGTAAATTAATCATT
ATACATTAGATTAAAGAACAAATTGATCATTCTGTTAAAATTTTGTATCACA
Found at i:2819 original size:693 final size:695
Alignment explanation
Indices: 1493--2884 Score: 2135
Period size: 693 Copynumber: 2.0 Consensus size: 695
1483 CTCCCCAATG
*
1493 CTATAGAAAAGATCATGATTTGAGGGATCATTTTTTTTCTAAAATAATAGTAATAATGCTACCAA
1 CTATAGAAAAGATCATGATTTGAGGGATCATTTTTTCTCTAAAATAATAGTAATAATGCTACCAA
* * *
1558 TTTGGAGGATTAAAACGTGAAAGAACTGGGGAACTTTTGAGAAGTTTTTTTAATTTTTTTGTGAA
66 TTTGGAGGA-TAAAACGTGAAAGAACTGGGGAACTCTTGAGAAGTTTTTTT-ATTTTTTGGTAAA
* *
1623 TTATAATAGCGATCGCGACTTAAATTCAAATTATATTTGAGGTAATAAATGTCTTTGATTATTAG
129 TTATAATAGCGATCGCGACTTAAATTCAAATTATATTTGAGGTAATAAATATCTTTGATTATCAG
* * *
1688 GTTAATACATAGGTTTAACTTTTGAGAGGTTTTTTGTTGATTTAAGCAACATAACATAATTTATC
194 GTCAATAAATAGGTTCAACTTTTGAGAGGTTTTTTGTTGATTTAAGCAACATAACATAATTTATC
*
1753 ATATAAAAAATAGGTAATAATATCATAAAAATATCTGTATTAAGAGTTAGATTGTATTTTGTCCA
259 ATATAAAAAATAGGTAATAATATCATAAAAATATCTGTATTAAGAGTTAGATTGTATTTTATCCA
*
1818 TTCTACTCAAAAAATAAGTAAACTAATTATTATACATTAGATTAAAGAGCAAATTGTTCATTATG
324 TTCTACTCAAAAAATAAGTAAACTAATTATTATACATTAGATTAAAGAACAAATTGTTCATTATG
1883 CTAAAATTTGTGTCACAATCTGTACTAAGAGTTGGATTGTAATTTGGCCATTCTACTCAAAAAAT
389 CTAAAATTTGTGTCACAATCTGTACTAAGAGTTGGATTGTAATTTGGCCATTCTACTCAAAAAAT
*
1948 GAGTAAATTAGTCATTATACATTAAATTAAAAAGCAAATTGATCATTCTGTTAAAATTTTGTGTC
454 GAGTAAATTAGTCATTATACATTAAATTAAAAAGCAAATTGATCATTCTGTTAAAATTTTGTATC
*
2013 ACTGTCTGATCAATTTACTCTTTCATCAAACATATATGAACTAATTTATCCTTTAAGTAAAGAGG
519 ACTGTCTGATCAATTTACTCTTTCATCAAACATATATGAACTAATTTATCCTTTAAATAAAGAGG
2078 TAAAATACAATTTAACTCCTATTACAAATATCTCAATGATACTTT-TATAAAAAAAA-AA-TT-A
584 TAAAATACAATTTAACTCCTATTACAAATATCTCAATGATACTTTATATAAAAAAAAGAATTTGA
*
2139 CGTTTAAGTTTTGAAATGTTTAATTTATTTTGTATCACACCATCTTT
649 CGTTTAAGTTTTGAAATGGTTAATTTATTTTGTATCACACCATCTTT
*
2186 CTATAGAAAAGATCATGATTTGAGGGATCA-TTTTTCTCTACAATAATAGTAATAATGCTACCAA
1 CTATAGAAAAGATCATGATTTGAGGGATCATTTTTTCTCTAAAATAATAGTAATAATGCTACCAA
* *
2250 TTTGGA-G-TAAAACGTGAAAGAAGTGGGGAACTCTTGAGAGGTTTTTTGT-TTTTTTGGTAAAT
66 TTTGGAGGATAAAACGTGAAAGAACTGGGGAACTCTTGAGAAGTTTTTT-TATTTTTTGGTAAAT
* * * * *
2312 TATAACTGTGCTTAGT-GCGA-TTCGAATTTAAATTATATTT-AGAGTAATAAATATTTTTGATT
130 TATAA-T-AGC-GA-TCGCGACTT-AAATTCAAATTATATTTGAG-GTAATAAATATCTTTGATT
*
2374 ATCAGGTCAATAAATAGGTTCAACTTTTGAGAGGTTTTTTGTTGGTTTAAGCAACATAACATAAT
189 ATCAGGTCAATAAATAGGTTCAACTTTTGAGAGGTTTTTTGTTGATTTAAGCAACATAACATAAT
* * * ** *
2439 TTATCATATAAAAAATGGGTAATAGTATCATGAAGGTGTCTGTATTAAGAGTTAGATTGTATTTT
254 TTATCATATAAAAAATAGGTAATAATATCATAAAAATATCTGTATTAAGAGTTAGATTGTATTTT
* * *
2504 ATTCATTCTACTCAAAAAAATAAGTAAATTAATTATTATACATTAGATTAAAGAACAAATTTTTC
319 ATCCATTCTACTC-AAAAAATAAGTAAACTAATTATTATACATTAGATTAAAGAACAAATTGTTC
* * * *
2569 ATTCTGTTAAAATTTTGTGTCACAGTCTGTACTAAGAGTTGGATTGTAATTTGTCCATTCTACTC
383 ATTATGCTAAAA-TTTGTGTCACAATCTGTACTAAGAGTTGGATTGTAATTTGGCCATTCTACTC
* *
2634 AAAAAATGAGTAAATTAGTCATTATACATTAGATTAAAGAA-CAAATTGATCATTTTGTTAAAAT
447 AAAAAATGAGTAAATTAGTCATTATACATTAAATTAAA-AAGCAAATTGATCATTCTGTTAAAAT
* * * * * *
2698 TTTGTATCACTTTCTTATCAATTTGCTCTTTCATCAACCATATTTGAATTAATTTATCCTTTAAA
511 TTTGTATCACTGTCTGATCAATTTACTCTTTCATCAAACATATATGAACTAATTTATCCTTTAAA
* *
2763 TAAAGAGGTAAAATACAATTTAACTCCTATTACATGA-ATCTCAATGATTATTTTATATAAAAAA
576 TAAAGAGGTAAAATACAATTTAACTCCTATTACA-AATATCTCAATGA-TACTTTATATAAAAAA
*
2827 AATGAATTTGAGGTTTAAGTTTTGAAATGGTTAATTTATTTTGTATCACACCATCTTT
639 AA-GAATTTGACGTTTAAGTTTTGAAATGGTTAATTTATTTTGTATCACACCATCTTT
2885 GAAATATATA
Statistics
Matches: 635, Mismatches: 47, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
688 16 0.03
689 38 0.06
690 7 0.01
691 168 0.26
692 97 0.15
693 240 0.38
694 8 0.01
695 11 0.02
697 2 0.00
698 2 0.00
699 46 0.07
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (695 bp):
CTATAGAAAAGATCATGATTTGAGGGATCATTTTTTCTCTAAAATAATAGTAATAATGCTACCAA
TTTGGAGGATAAAACGTGAAAGAACTGGGGAACTCTTGAGAAGTTTTTTTATTTTTTGGTAAATT
ATAATAGCGATCGCGACTTAAATTCAAATTATATTTGAGGTAATAAATATCTTTGATTATCAGGT
CAATAAATAGGTTCAACTTTTGAGAGGTTTTTTGTTGATTTAAGCAACATAACATAATTTATCAT
ATAAAAAATAGGTAATAATATCATAAAAATATCTGTATTAAGAGTTAGATTGTATTTTATCCATT
CTACTCAAAAAATAAGTAAACTAATTATTATACATTAGATTAAAGAACAAATTGTTCATTATGCT
AAAATTTGTGTCACAATCTGTACTAAGAGTTGGATTGTAATTTGGCCATTCTACTCAAAAAATGA
GTAAATTAGTCATTATACATTAAATTAAAAAGCAAATTGATCATTCTGTTAAAATTTTGTATCAC
TGTCTGATCAATTTACTCTTTCATCAAACATATATGAACTAATTTATCCTTTAAATAAAGAGGTA
AAATACAATTTAACTCCTATTACAAATATCTCAATGATACTTTATATAAAAAAAAGAATTTGACG
TTTAAGTTTTGAAATGGTTAATTTATTTTGTATCACACCATCTTT
Found at i:3413 original size:17 final size:17
Alignment explanation
Indices: 3391--3425 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3381 TATCCTCCAA
3391 TATATCTCACTCTTCCT
1 TATATCTCACTCTTCCT
3408 TATATCTCACTCTTCCT
1 TATATCTCACTCTTCCT
3425 T
1 T
3426 TCTGTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATCTCACTCTTCCT
Found at i:10086 original size:21 final size:21
Alignment explanation
Indices: 10037--10087 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
10027 ATCCAAGCTC
*
10037 GAATGTTCACTCAAAAATTTG
1 GAATGTTTACTCAAAAATTTG
10058 GAATGTTTACTCAAAAATTTG
1 GAATGTTTACTCAAAAATTTG
10079 GAATGTTTA
1 GAATGTTTA
10088 GATAATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (21 bp):
GAATGTTTACTCAAAAATTTG
Found at i:12028 original size:17 final size:17
Alignment explanation
Indices: 11942--12018 Score: 84
Period size: 17 Copynumber: 4.5 Consensus size: 17
11932 CCTAATCAGC
* *
11942 TTAAATTTATTTTAAAA
1 TTAAATTTATTATAAAT
* *
11959 TTAAGTTTATTCTAAAT
1 TTAAATTTATTATAAAT
* *
11976 TTAAATTTGGTT-GAAAT
1 TTAAATTT-ATTATAAAT
11993 TTAAATTTATTATAAAT
1 TTAAATTTATTATAAAT
12010 TTAAATTTA
1 TTAAATTTA
12019 AAATTTATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 2 0.04
17 46 0.92
18 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTATAAAT
Done.