Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007044.1 Kokia drynarioides strain JFW-HI SEQ_121652, 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: 51811
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:4078 original size:39 final size:39
Alignment explanation
Indices: 4024--4103 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
4014 TGAACAATTC
*
4024 AAGAAGAAGATAATGAACCAAATCTCAGAAAATAAAAAT
1 AAGAAGAAAATAATGAACCAAATCTCAGAAAATAAAAAT
4063 AAGAAGAAAATAATGAACCAAATCTCAGAAAATAAAAAT
1 AAGAAGAAAATAATGAACCAAATCTCAGAAAATAAAAAT
4102 AA
1 AA
4104 AAATAATAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.64, C:0.10, G:0.11, T:0.15
Consensus pattern (39 bp):
AAGAAGAAAATAATGAACCAAATCTCAGAAAATAAAAAT
Found at i:4108 original size:12 final size:12
Alignment explanation
Indices: 4091--4128 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
4081 CAAATCTCAG
*
4091 AAAATAAAAATA
1 AAAATAATAATA
4103 AAAATAATAATA
1 AAAATAATAATA
*
4115 ATAATAATAATA
1 AAAATAATAATA
4127 AA
1 AA
4129 CCTTCCAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:4113 original size:3 final size:3
Alignment explanation
Indices: 4093--4127 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
4083 AATCTCAGAA
* *
4093 AAT AAA AAT AAA AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4128 ACCTTCCAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:6730 original size:18 final size:17
Alignment explanation
Indices: 6691--6730 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
6681 CATTCCTTAT
*
6691 CAAAAATACTTTTGGGA
1 CAAAAATACTTTTGAGA
6708 CAAAAAGTACTTTTGAGA
1 CAAAAA-TACTTTTGAGA
*
6726 TAAAA
1 CAAAA
6731 GCATTGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (17 bp):
CAAAAATACTTTTGAGA
Found at i:14915 original size:20 final size:22
Alignment explanation
Indices: 14875--14919 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
14865 AAATACTTTT
*
14875 TTTTTTAATATTTGTTATTATA
1 TTTTTTAATATTTATTATTATA
14897 TTTTTTAAT-TTTATT-TTATA
1 TTTTTTAATATTTATTATTATA
14917 TTT
1 TTT
14920 ATATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 5 0.23
22 9 0.41
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTTTAATATTTATTATTATA
Found at i:23335 original size:45 final size:45
Alignment explanation
Indices: 23255--23350 Score: 106
Period size: 45 Copynumber: 2.1 Consensus size: 45
23245 TTAAGATTCA
* *
23255 ATTTAATTACTTAATTTAATAATAAAACTAGAGCTTCCTT-AATAC
1 ATTTAATTACATAATTTAACAATAAAACTAGAGCTT-CTTCAATAC
** *
23300 ATTTAATTACATAATTTAACGCTAAGAATTA-AGCTTCTTCAATAC
1 ATTTAATTACATAATTTAACAATAA-AACTAGAGCTTCTTCAATAC
*
23345 TTTTAA
1 ATTTAA
23351 GTTAAATCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
44 3 0.07
45 36 0.84
46 4 0.09
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (45 bp):
ATTTAATTACATAATTTAACAATAAAACTAGAGCTTCTTCAATAC
Found at i:29509 original size:20 final size:20
Alignment explanation
Indices: 29486--29526 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
29476 ATTTATTAAC
*
29486 ATAATAATTTTATAAATAAA
1 ATAATAATCTTATAAATAAA
*
29506 ATAATAATCTTATGAATAAA
1 ATAATAATCTTATAAATAAA
29526 A
1 A
29527 CAATTTAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
ATAATAATCTTATAAATAAA
Found at i:44588 original size:2 final size:2
Alignment explanation
Indices: 44581--44646 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
44571 CATATACTTT
44581 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44623 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
44647 CTTGTTAAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46458 original size:17 final size:17
Alignment explanation
Indices: 46436--46497 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
46426 AACTTTTAAT
46436 TTTTAAATTTTAATTTA
1 TTTTAAATTTTAATTTA
* *
46453 TTTTAAATTTAAATTCA
1 TTTTAAATTTTAATTTA
*
46470 TGTTAAATTTATGAATTTA
1 TTTTAAATTT-T-AATTTA
*
46489 TTTTGAATT
1 TTTTAAATT
46498 AAAAATTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 24 0.67
19 12 0.33
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTTAAATTTTAATTTA
Found at i:48358 original size:58 final size:57
Alignment explanation
Indices: 48295--48492 Score: 182
Period size: 58 Copynumber: 3.4 Consensus size: 57
48285 CCCAAACTTC
*
48295 CCAAAATTCCATTCTTAACCTCGATTTTTCCAAAAATTACATTTGACCCCTAAAATTT
1 CCAAAATTCCATT-TTGACCTCGATTTTTCCAAAAATTACATTTGACCCCTAAAATTT
* * * * * * *** *
48353 CCAAAATTCCATTTTGGACCCCAATTTTTTCGAAAATTACATTTTA-CTCTCGGACTT
1 CCAAAATTCCATTTT-GACCTCGATTTTTCCAAAAATTACATTTGACCCCTAAAATTT
* *** *
48410 CCAAAAATTCCATTTTTGACCTTGAAACTTCCAAAAATTACATTTGACCCCTAAACTTT
1 CC-AAAATTCCA-TTTTGACCTCGATTTTTCCAAAAATTACATTTGACCCCTAAAATTT
* *
48469 CCAAAACTCCATTTTTGATCTCGA
1 CCAAAATTCCA-TTTTGACCTCGA
48493 AACTTTCAAA
Statistics
Matches: 107, Mismatches: 29, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
57 10 0.09
58 86 0.80
59 11 0.10
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (57 bp):
CCAAAATTCCATTTTGACCTCGATTTTTCCAAAAATTACATTTGACCCCTAAAATTT
Found at i:48365 original size:28 final size:29
Alignment explanation
Indices: 48321--48474 Score: 100
Period size: 30 Copynumber: 5.3 Consensus size: 29
48311 AACCTCGATT
48321 TTTCCAAAAATTACATTTGACCCCTAAAA
1 TTTCCAAAAATTACATTTGACCCCTAAAA
* **
48350 TTTCC-AAAATTCCATTTTGGACCCC-AATT
1 TTTCCAAAAATTACA-TTT-GACCCCTAAAA
* * * * ***
48379 TTTTCGAAAATTACATTTTA-CTCTCGGA
1 TTTCCAAAAATTACATTTGACCCCTAAAA
* * * *
48407 CTTCCAAAAATTCCATTTTTGA-CCTTGAAA
1 TTTCCAAAAATTACA--TTTGACCCCTAAAA
* *
48437 CTTCCAAAAATTACATTTGACCCCTAAAC
1 TTTCCAAAAATTACATTTGACCCCTAAAA
48466 TTTCCAAAA
1 TTTCCAAAA
48475 CTCCATTTTT
Statistics
Matches: 92, Mismatches: 26, Indels: 14
0.70 0.20 0.11
Matches are distributed among these distances:
27 2 0.02
28 25 0.27
29 30 0.33
30 35 0.38
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (29 bp):
TTTCCAAAAATTACATTTGACCCCTAAAA
Found at i:48440 original size:30 final size:30
Alignment explanation
Indices: 48406--48503 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
48396 TTACTCTCGG
48406 ACTTCCAAAAATTCCATTTTTGACCTTGAA
1 ACTTCCAAAAATTCCATTTTTGACCTTGAA
* *
48436 ACTTCCAAAAATTACA--TTTGACCCCT-AA
1 ACTTCCAAAAATTCCATTTTTGA-CCTTGAA
* * *
48464 ACTTTCC-AAAACTCCATTTTTGATCTCGAA
1 AC-TTCCAAAAATTCCATTTTTGACCTTGAA
*
48494 ACTTTCAAAA
1 ACTTCCAAAA
48504 TTCACCATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
28 16 0.30
29 11 0.20
30 27 0.50
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.34
Consensus pattern (30 bp):
ACTTCCAAAAATTCCATTTTTGACCTTGAA
Found at i:48495 original size:58 final size:58
Alignment explanation
Indices: 48322--48578 Score: 170
Period size: 58 Copynumber: 4.4 Consensus size: 58
48312 ACCTCGATTT
* * * * * **
48322 TTCCAAAAATTACATTTGACCCCTAAAATTTCC-AAAATTCCATTTTGGACCCCAATTT
1 TTCCAAAAATTACATTTGACCCCTAAACTTTCCAAAAACTCCATTTTTGACTCGAA-AC
* * * * ** * *
48380 TTTCGAAAATTACATTTTA-CTCTCGGAC-TTCCAAAAATTCCATTTTTGACCTTGAAAC
1 TTCCAAAAATTACATTTGACCCCT-AAACTTTCCAAAAACTCCATTTTTGA-CTCGAAAC
48438 TTCCAAAAATTACATTTGACCCCTAAACTTTCC-AAAACTCCATTTTTGATCTCGAAAC
1 TTCCAAAAATTACATTTGACCCCTAAACTTTCCAAAAACTCCATTTTTGA-CTCGAAAC
* * ** * * *
48496 TTTC-AAAATTCACCATTTTACCCCTGGA-TGTCCAAAAACTCCATTTTT-ACCCTAAAAC
1 TTCCAAAAATT-A-CATTTGACCCCTAAACTTTCCAAAAACTCCATTTTTGACTC-GAAAC
* *
48554 TTTC-AAAATTACCATTTTACCCCTA
1 TTCCAAAAATTA-CATTTGACCCCTA
48579 GATGTCCAAA
Statistics
Matches: 160, Mismatches: 30, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
57 29 0.18
58 95 0.59
59 36 0.22
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.35
Consensus pattern (58 bp):
TTCCAAAAATTACATTTGACCCCTAAACTTTCCAAAAACTCCATTTTTGACTCGAAAC
Found at i:48531 original size:29 final size:29
Alignment explanation
Indices: 48499--48589 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
48489 TCGAAACTTT
*
48499 CAAAATTCACCATTTTACCCCTGGATGTC
1 CAAAATTCACCATTTTACCCCTAGATGTC
* * * *
48528 CAAAA-ACTCCATTTTTA-CCCTAAAACT-TT
1 CAAAATTCACCA-TTTTACCCCT-AGA-TGTC
48557 CAAAATT-ACCATTTTACCCCTAGATGTC
1 CAAAATTCACCATTTTACCCCTAGATGTC
48585 CAAAA
1 CAAAA
48590 ATTTCGTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 13
0.68 0.13 0.19
Matches are distributed among these distances:
27 1 0.02
28 21 0.45
29 24 0.51
30 1 0.02
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (29 bp):
CAAAATTCACCATTTTACCCCTAGATGTC
Found at i:48554 original size:116 final size:116
Alignment explanation
Indices: 48322--48578 Score: 301
Period size: 116 Copynumber: 2.2 Consensus size: 116
48312 ACCTCGATTT
* **
48322 TTCCAAAAATTACATTTGACCCCTAAAATTTCCAAAATTCCATTTTGGACCCCAATTTTTTCGAA
1 TTCCAAAAATTACATTTGACCCCTAAAATTTCCAAAACTCCATTTTGGACCCCAATACTTTCGAA
* * * *
48387 AATTACATTTTACTCTCGGACTTCCAAAAATTCCATTTTTGACCTTGAAAC
66 AATTACATTTTACCCTCGGACTTCCAAAAACTCCATTTTTGACCCTAAAAC
* * * *
48438 TTCCAAAAATTACATTTGACCCCTAAACTTTCCAAAACTCCATTTTTGATCTCGAA-ACTTTC-A
1 TTCCAAAAATTACATTTGACCCCTAAAATTTCCAAAACTCCATTTTGGA-CCCCAATACTTTCGA
48501 AAATTCACCATTTTACCC-CTGGA-TGTCCAAAAACTCCATTTTT-ACCCTAAAAC
65 AAATT-A-CATTTTACCCTC-GGACT-TCCAAAAACTCCATTTTTGACCCTAAAAC
* *
48554 TTTC-AAAATTACCATTTTACCCCTA
1 TTCCAAAAATTA-CATTTGACCCCTA
48579 GATGTCCAAA
Statistics
Matches: 122, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
115 13 0.11
116 76 0.62
117 33 0.27
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.35
Consensus pattern (116 bp):
TTCCAAAAATTACATTTGACCCCTAAAATTTCCAAAACTCCATTTTGGACCCCAATACTTTCGAA
AATTACATTTTACCCTCGGACTTCCAAAAACTCCATTTTTGACCCTAAAAC
Found at i:48590 original size:29 final size:29
Alignment explanation
Indices: 48500--48592 Score: 86
Period size: 28 Copynumber: 3.2 Consensus size: 29
48490 CGAAACTTTC
*
48500 AAAATTCACCATTTTACCCCTGGATGTCCA
1 AAAATT-ACCATTTTACCCCTAGATGTCCA
* * *
48530 AAAACT-CCATTTTTA-CCCTAAAACT-TTC-
1 AAAATTACCA-TTTTACCCCT-AGA-TGTCCA
48558 AAAATTACCATTTTACCCCTAGATGTCCA
1 AAAATTACCATTTTACCCCTAGATGTCCA
48587 AAAATT
1 AAAATT
48593 TCGTTTTAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
27 1 0.02
28 21 0.43
29 21 0.43
30 6 0.12
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCTAGATGTCCA
Found at i:50753 original size:16 final size:15
Alignment explanation
Indices: 50726--50758 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
50716 TTATCTAGTA
50726 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
50741 AAATATTTAAAAAA-
1 AAATATTTAAAAAAT
50755 AAAT
1 AAAT
50759 GCATGACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Done.