Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014848.1 Kokia drynarioides strain JFW-HI SEQ_129891, 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: 66205
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 209 characters in sequence are not A, C, G, or T
Found at i:119 original size:21 final size:21
Alignment explanation
Indices: 93--145 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
83 GACTGGTTTC
93 CTTCTCTTTTCACTCTTTGCT
1 CTTCTCTTTTCACTCTTTGCT
114 CTTCTCTTTTCACTCTTTGCT
1 CTTCTCTTTTCACTCTTTGCT
135 CTTCTCTTTTC
1 CTTCTCTTTTC
146 CTTTCTCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.04, C:0.34, G:0.04, T:0.58
Consensus pattern (21 bp):
CTTCTCTTTTCACTCTTTGCT
Found at i:29269 original size:182 final size:181
Alignment explanation
Indices: 28962--29351 Score: 469
Period size: 182 Copynumber: 2.1 Consensus size: 181
28952 AATCAGTTGA
* * ** * * *
28962 AGTAATTCTGAACAAAGAAGCTAAACTGAAAGACTAGTGGAAAACAAGATTTAACCTATTACAAC
1 AGTAATTCAGAAGAAAGAAGCTAAACCAAAAAACTAATGGAAAACAAGATTCAACCTATTACAAC
* * ** *
29027 ACATAGATGATCACAAGATTGTTCCTGGGACAAAGTTCTTGAGTTCGAATTGTGTATAAATAAAG
66 ACATAGATGATCACAAGATTGTTCCAGGCACAAAGTTCGGGAGTTCGAATTGGGTATAAATAAAG
** * ** * * * *
29092 ACCTATTTATGTAAGTAGTCCAACACAACAACTA-CTATCACAATTAATCCAT
131 ACCTATAAACGTAACCAGTCAAACACAACAACAATC-ATCACAATTAAT-AAC
* * * *
29144 AGTAATTCAGAAGAAAGAAGCTAAACCAAAAAACCTAATTGCAAGCAAGATTCAACCTATTTCAA
1 AGTAATTCAGAAGAAAGAAGCTAAACCAAAAAA-CTAATGGAAAACAAGATTCAACCTATTACAA
* *
29209 CACATAGATGATCACAA-ATTGTTTCAGGCACAAAGTTCGGGAGTTCGAATTGGGTATAAATCAA
65 CACATAGATGATCACAAGATTGTTCCAGGCACAAAGTTCGGGAGTTCGAATTGGGTATAAATAAA
*
29273 GACCTATAAACGTAACCAGTCAAACACAACAACAATCATCATAATTAATAAC
130 GACCTATAAACGTAACCAGTCAAACACAACAACAATCATCACAATTAATAAC
*
29325 AGATAATTAAGAAGAAAGAAGCTAAAC
1 AG-TAATTCAGAAGAAAGAAGCTAAAC
29352 AACAACTCAC
Statistics
Matches: 176, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
181 3 0.02
182 130 0.74
183 43 0.24
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (181 bp):
AGTAATTCAGAAGAAAGAAGCTAAACCAAAAAACTAATGGAAAACAAGATTCAACCTATTACAAC
ACATAGATGATCACAAGATTGTTCCAGGCACAAAGTTCGGGAGTTCGAATTGGGTATAAATAAAG
ACCTATAAACGTAACCAGTCAAACACAACAACAATCATCACAATTAATAAC
Found at i:37976 original size:3 final size:3
Alignment explanation
Indices: 37968--38012 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
37958 AAAACAATAC
37968 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
38013 AAGAAGTAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:40578 original size:21 final size:21
Alignment explanation
Indices: 40553--40595 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
40543 CACACAAATC
40553 AAAATCTGAATAAACTGGAGA
1 AAAATCTGAATAAACTGGAGA
* *
40574 AAAATCTGAGTAAATTGGAGA
1 AAAATCTGAATAAACTGGAGA
40595 A
1 A
40596 TAATGATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.21
Consensus pattern (21 bp):
AAAATCTGAATAAACTGGAGA
Found at i:50588 original size:36 final size:32
Alignment explanation
Indices: 50540--50630 Score: 82
Period size: 32 Copynumber: 2.8 Consensus size: 32
50530 AAATTTTTTT
*
50540 ATTTAA-TATTTTAAATTAATAAAGATAAATTTG
1 ATTTAATTCTTTTAAATTAATAAA-A-AAATTTG
*
50573 TACTTTAATTCTTTTAAA--AATATAAAAATTTG
1 -A-TTTAATTCTTTTAAATTAATAAAAAAATTTG
*
50605 ATTTAATTTTTTTAAAATT-ATAAAAA
1 ATTTAATTCTTTT-AAATTAATAAAAA
50631 TTACAATTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
30 11 0.23
31 4 0.08
32 13 0.27
33 1 0.02
34 6 0.12
35 5 0.10
36 8 0.17
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (32 bp):
ATTTAATTCTTTTAAATTAATAAAAAAATTTG
Found at i:50610 original size:30 final size:32
Alignment explanation
Indices: 50566--50632 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 32
50556 TAATAAAGAT
50566 AAATTTGTACTTTAATTCTTTTAAAAATATAA
1 AAATTTGTACTTTAATTCTTTTAAAAATATAA
* *
50598 AAATTTG-A-TTTAATTTTTTTAAAATTATAA
1 AAATTTGTACTTTAATTCTTTTAAAAATATAA
50628 AAATT
1 AAATT
50633 ACAATTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 25 0.76
31 1 0.03
32 7 0.21
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (32 bp):
AAATTTGTACTTTAATTCTTTTAAAAATATAA
Found at i:50643 original size:31 final size:30
Alignment explanation
Indices: 50576--50644 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
50566 AAATTTGTAC
* **
50576 TTTAATTCTTTTAAAAATATAAAAATTTGA
1 TTTAATTTTTTTAAAAATATAAAAATTCAA
*
50606 TTTAATTTTTTTAAAATTATAAAAATTACAA
1 TTTAATTTTTTTAAAAATATAAAAATT-CAA
50637 TTTAATTT
1 TTTAATTT
50645 CGACCCCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 25 0.74
31 9 0.26
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (30 bp):
TTTAATTTTTTTAAAAATATAAAAATTCAA
Found at i:51103 original size:17 final size:17
Alignment explanation
Indices: 51069--51111 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
51059 ATATTTTAAA
** *
51069 ATATTTTTTGATAGTAT
1 ATATTTTTAAATAATAT
51086 ATATTTTTAAATAATAT
1 ATATTTTTAAATAATAT
*
51103 AAATTTTTA
1 ATATTTTTA
51112 CTTTTAATGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
ATATTTTTAAATAATAT
Found at i:55070 original size:40 final size:40
Alignment explanation
Indices: 55010--55089 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
55000 ACAATTTGGA
*
55010 CCAAGCATGGACAAGGGTTGTTTTTGAATTGAGATTGAGT
1 CCAAACATGGACAAGGGTTGTTTTTGAATTGAGATTGAGT
*
55050 CCAAACATGGACAATGGTTGTTTTTGAATTGAGATTGAGT
1 CCAAACATGGACAAGGGTTGTTTTTGAATTGAGATTGAGT
55090 TAGACTTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.29, C:0.10, G:0.28, T:0.34
Consensus pattern (40 bp):
CCAAACATGGACAAGGGTTGTTTTTGAATTGAGATTGAGT
Found at i:58103 original size:31 final size:31
Alignment explanation
Indices: 58068--58138 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
58058 TCAAATTCAA
58068 GTATCAAATT-GATCAAAAAAAAAAAACTT-AG
1 GTATCAAATTAGA--AAAAAAAAAAAACTTAAG
** *
58099 GTATCAAATTAGAAAAAAAAATCAAGTTAAG
1 GTATCAAATTAGAAAAAAAAAAAAACTTAAG
58130 GTATCAAAT
1 GTATCAAAT
58139 GTTTTATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 12 0.34
31 21 0.60
32 2 0.06
ACGTcount: A:0.56, C:0.08, G:0.11, T:0.24
Consensus pattern (31 bp):
GTATCAAATTAGAAAAAAAAAAAAACTTAAG
Found at i:58117 original size:62 final size:65
Alignment explanation
Indices: 58016--58138 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 65
58006 ACCAAACTGA
*
58016 AAAAAAAAAAAAATTAGATACCACAATTTAGGGAAAAAAAAGTCAAATTCAA-GTATCAAATTGA
1 AAAAAAAAAAAAATTAGATACCACAATTTA-GGAAAAAAAAATCAAATT-AAGGTATCAAATTGA
58080 TC
64 TC
* * * *
58082 AAAAAAAAAAAACTTAGGTATCA-AA-TTA-GAAAAAAAAATCAAGTTAAGGTATCAAAT
1 AAAAAAAAAAAAATTAGATACCACAATTTAGGAAAAAAAAATCAAATTAAGGTATCAAAT
58139 GTTTTATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
61 2 0.04
62 24 0.47
64 3 0.06
65 2 0.04
66 20 0.39
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.21
Consensus pattern (65 bp):
AAAAAAAAAAAAATTAGATACCACAATTTAGGAAAAAAAAATCAAATTAAGGTATCAAATTGATC
Found at i:62025 original size:39 final size:40
Alignment explanation
Indices: 61971--62050 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
61961 TATGCACTCA
*
61971 ATGGACACCTTTTGAAGAGTCACAATCC-TTTCAAATTGG
1 ATGGACACCTATTGAAGAGTCACAATCCTTTTCAAATTGG
*
62010 ATGGACACCTATTGAAGAGTCACAATCCTTTTCATATTGG
1 ATGGACACCTATTGAAGAGTCACAATCCTTTTCAAATTGG
62050 A
1 A
62051 CATACCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 27 0.71
40 11 0.29
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (40 bp):
ATGGACACCTATTGAAGAGTCACAATCCTTTTCAAATTGG
Found at i:62067 original size:39 final size:38
Alignment explanation
Indices: 61975--62063 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 38
61965 CACTCAATGG
*
61975 ACACCTTTTGAAGAGTCACAATCCTTTCAAATTGGATGG
1 ACACCTTTTGAAGAGTCACAATCCTTTCAAATTGGA-GC
* *
62014 ACACCTATTGAAGAGTCACAATCCTTTTCATATTGGA-C
1 ACACCTTTTGAAGAGTCACAATCC-TTTCAAATTGGAGC
*
62052 ATACCTTTTGAA
1 ACACCTTTTGAA
62064 AGAGACTTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
38 10 0.23
39 23 0.52
40 11 0.25
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (38 bp):
ACACCTTTTGAAGAGTCACAATCCTTTCAAATTGGAGC
Done.