Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013160.1 Kokia drynarioides strain JFW-HI SEQ_128179, 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: 78670
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:8479 original size:21 final size:21
Alignment explanation
Indices: 8450--8502 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
8440 TTGTGCTAGC
*
8450 TCTATCGATACAAG-TATG-A
1 TCTACCGATACAAGTTATGCA
8469 TTTCTACCGATACAAGTTATGCA
1 --TCTACCGATACAAGTTATGCA
8492 TCTACCGATAC
1 TCTACCGATAC
8503 CAAAAACTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 24 0.83
22 4 0.14
23 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (21 bp):
TCTACCGATACAAGTTATGCA
Found at i:15096 original size:43 final size:43
Alignment explanation
Indices: 15035--15162 Score: 145
Period size: 43 Copynumber: 3.0 Consensus size: 43
15025 ATCATTTGGC
*
15035 GTATAAATGGAATACTCATGTCTCGAAATGAACATGAGATTAT
1 GTATAAATGGAAGACTCATGTCTCGAAATGAACATGAGATTAT
* *
15078 GTATAAATGGAAGACTCATGTCTC-AGGATGAGCATGATG-TTAT
1 GTATAAATGGAAGACTCATGTCTCGA-AATGAACATGA-GATTAT
* * * *
15121 GTAAAAATGAAAGACTCGTGACTCGAAATGAGA-ATGAGATTA
1 GTATAAATGGAAGACTCATGTCTCGAAATGA-ACATGAGATTA
15163 CATAAGAAAG
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
42 2 0.03
43 67 0.94
44 2 0.03
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (43 bp):
GTATAAATGGAAGACTCATGTCTCGAAATGAACATGAGATTAT
Found at i:15217 original size:43 final size:41
Alignment explanation
Indices: 15043--15245 Score: 138
Period size: 43 Copynumber: 4.8 Consensus size: 41
15033 GCGTATAAAT
* * * * *
15043 GGAATACTCATGTCTCGAAATGAACATGAGATTATGTATAAAT
1 GGAAAACTCATGTCTCG-GATGAGCATGAGGTTATGTA-AAAA
* *
15086 GGAAGACTCATGTCTCAGGATGAGCATGATGTTATGTAAAAA
1 GGAAAACTCATGTCTC-GGATGAGCATGAGGTTATGTAAAAA
* * * * * * **
15128 TGAAAGACTCGTGACTCGAAATGAGAATGAGATTACATAAGAAA
1 GGAAA-ACTCATGTCTCG-GATGAGCATGAGGTTATGTAA-AAA
* *
15172 GGAAAACTCATGTCTCAGGATGAGCATGAGGTTATGATTATAA
1 GGAAAACTCATGTCTC-GGATGAGCATGAGGTTATG-TAAAAA
* * *
15215 GGAAGAC-CTATGTCTCGGTTGAGCATAAGGT
1 GGAAAACTC-ATGTCTCGGATGAGCATGAGGT
15246 GGTTTAAAAG
Statistics
Matches: 124, Mismatches: 29, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
42 21 0.17
43 92 0.74
44 11 0.09
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (41 bp):
GGAAAACTCATGTCTCGGATGAGCATGAGGTTATGTAAAAA
Found at i:23392 original size:9 final size:9
Alignment explanation
Indices: 23378--23436 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
23368 AAAATTACAA
23378 TTTTATAAT
1 TTTTATAAT
23387 TTTTATAAT
1 TTTTATAAT
23396 TTTTATAAT
1 TTTTATAAT
* *
23405 TTTTTTTAT
1 TTTTATAAT
23414 TTTTAAAGTAAT
1 TTTT--A-TAAT
23426 TTTTA-AAT
1 TTTTATAAT
23434 TTT
1 TTT
23437 AAAAGGGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
8 6 0.14
9 29 0.67
10 1 0.02
12 7 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTATAAT
Found at i:23974 original size:104 final size:104
Alignment explanation
Indices: 23788--24205 Score: 631
Period size: 104 Copynumber: 4.0 Consensus size: 104
23778 AAAGCTTTGT
* * *
23788 GTCGTGACTTCCTCATTGCAGTTGACACTTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTC
1 GTCGCGACTTCCTCATTGCACTTGGCACTTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTC
* *
23853 CCTGCAGTCCATAATTTCAGTCACAACTCAGTAGCAACG
66 CCTGCAATCCATAATTTCAGTCTCAACTCAGTAGCAACG
* * **
23892 GTTGCAACTTCCTCATTATACTTGGCACTTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTC
1 GTCGCGACTTCCTCATTGCACTTGGCACTTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTC
*
23957 CCTGTAATCCATAATTTCAGTCTCAACTCAGTAGCAACG
66 CCTGCAATCCATAATTTCAGTCTCAACTCAGTAGCAACG
* * *
23996 ATCGCGACTTCCTCATTTCACTTGGCACTTTCAAGTCCAACCCAGTAAAGGTGGACGTTATTCTC
1 GTCGCGACTTCCTCATTGCACTTGGCACTTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTC
*
24061 CCTGCAATCCATAATTTCAATCTCAACTCAGTAGCAACG
66 CCTGCAATCCATAATTTCAGTCTCAACTCAGTAGCAACG
* * * *
24100 GTCACGACTTCCTCATTGCAC-TGGCACTTTCAAGTCCAACCTAGTAAATGTGGGTGTTATTCTC
1 GTCGCGACTTCCTCATTGCACTTGGCACTTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTC
* * * *
24164 CCTGCAATCCATAATATCAGTCTCAACTTAGTAACAATG
66 CCTGCAATCCATAATTTCAGTCTCAACTCAGTAGCAACG
24203 GTC
1 GTC
24206 ACAACTTACT
Statistics
Matches: 284, Mismatches: 30, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
103 76 0.27
104 208 0.73
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (104 bp):
GTCGCGACTTCCTCATTGCACTTGGCACTTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTC
CCTGCAATCCATAATTTCAGTCTCAACTCAGTAGCAACG
Found at i:27435 original size:48 final size:48
Alignment explanation
Indices: 27364--27459 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
27354 GACTTAATAA
27364 ACACCATTTTCCCTCATTGAGATAGCCATCGATTACACCATTCCTATT
1 ACACCATTTTCCCTCATTGAGATAGCCATCGATTACACCATTCCTATT
27412 ACACCATTTTCCCTCATTGAGATAGCCATCGATTACACCATTCCTATT
1 ACACCATTTTCCCTCATTGAGATAGCCATCGATTACACCATTCCTATT
27460 TTGCCCCTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.33
Consensus pattern (48 bp):
ACACCATTTTCCCTCATTGAGATAGCCATCGATTACACCATTCCTATT
Found at i:32662 original size:20 final size:21
Alignment explanation
Indices: 32620--32662 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
32610 GATAAATATT
*
32620 AATTGTGTGATTAATTGGTGA
1 AATTGTGTGATTAATTGGAGA
* *
32641 AATTGTG-GATTTATTTGAGA
1 AATTGTGTGATTAATTGGAGA
32661 AA
1 AA
32663 ATAAAGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.42
Consensus pattern (21 bp):
AATTGTGTGATTAATTGGAGA
Found at i:34569 original size:22 final size:24
Alignment explanation
Indices: 34516--34582 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 24
34506 GCTCTCCGTT
* *
34516 ATTAGCACTTCGTGTTCTCTTCGTT
1 ATTAGCACTTCGTGTGCTCTTC-TG
34541 ATTAGCACTTCGT-TGCTCTT-TG
1 ATTAGCACTTCGTGTGCTCTTCTG
*
34563 ATTAGCACTTAGTGTGCTCT
1 ATTAGCACTTCGTGTGCTCT
34583 CCATTACCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 13 0.34
23 6 0.16
24 6 0.16
25 13 0.34
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (24 bp):
ATTAGCACTTCGTGTGCTCTTCTG
Found at i:34588 original size:22 final size:22
Alignment explanation
Indices: 34541--34588 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
34531 TCTCTTCGTT
* **
34541 ATTAGCACTTCGTTGCTCTTTG
1 ATTAGCACTTAGTTGCTCTTCC
34563 ATTAGCACTTAGTGTGCTC-TCC
1 ATTAGCACTTAGT-TGCTCTTCC
34585 ATTA
1 ATTA
34589 CCCAGCACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.42
Consensus pattern (22 bp):
ATTAGCACTTAGTTGCTCTTCC
Found at i:35246 original size:20 final size:20
Alignment explanation
Indices: 35223--35272 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
35213 CGTTTTTAAA
35223 GAAAAATATCAATTTTTTAT
1 GAAAAATATCAATTTTTTAT
35243 GAAAAATATCAATTTTTTAT
1 GAAAAATATCAATTTTTTAT
35263 GAAAAATATC
1 GAAAAATATC
35273 GATACCTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (20 bp):
GAAAAATATCAATTTTTTAT
Found at i:38841 original size:20 final size:20
Alignment explanation
Indices: 38803--38841 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38793 AAAGATGGGT
* *
38803 AAATTATACATATTGTCATC
1 AAATTATAAAAATTGTCATC
*
38823 AAATTATAAAAATTTTCAT
1 AAATTATAAAAATTGTCAT
38842 TTTCAGTACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (20 bp):
AAATTATAAAAATTGTCATC
Found at i:39281 original size:25 final size:24
Alignment explanation
Indices: 39248--39301 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
39238 GGGGATTTTT
* *
39248 TTATTTTATTTAATATTAATATAA
1 TTATTTTATATAATATAAATATAA
39272 TTATATTTATATAATATAAATATAA
1 TTAT-TTTATATAATATAAATATAA
*
39297 GTATT
1 TTATT
39302 AATATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TTATTTTATATAATATAAATATAA
Found at i:39311 original size:19 final size:18
Alignment explanation
Indices: 39261--39309 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
39251 TTTTATTTAA
* **
39261 TATTAATATAATTATATT
1 TATTAATATAAATATAAG
39279 TATATAATATAAATATAAG
1 TAT-TAATATAAATATAAG
39298 TATTAATATAAA
1 TATTAATATAAA
39310 ATTTAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TATTAATATAAATATAAG
Found at i:39340 original size:29 final size:28
Alignment explanation
Indices: 39306--39382 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 28
39296 AGTATTAATA
* *
39306 TAAAATTTAAATTTATTATTATATTTTT
1 TAAAATTTATATTTATTATTATATATTT
*
39334 TGAAAATATT-TATTTATTTTTATATATTT
1 T-AAAAT-TTATATTTATTATTATATATTT
39363 TAAAATTTATATATTATTAT
1 TAAAATTTATAT-TTATTAT
39383 CTAAAATTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 2 0.05
28 9 0.22
29 28 0.68
30 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (28 bp):
TAAAATTTATATTTATTATTATATATTT
Found at i:40074 original size:12 final size:13
Alignment explanation
Indices: 40039--40080 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
40029 TTTCTTAAAC
*
40039 GATATGAGATATGA
1 GATATGATATAT-A
40053 GATATGATATATA
1 GATATGATATATA
40066 GATAT-ATATATA
1 GATATGATATATA
40078 GAT
1 GAT
40081 TCATAATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 10 0.37
13 6 0.22
14 11 0.41
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (13 bp):
GATATGATATATA
Found at i:47520 original size:22 final size:23
Alignment explanation
Indices: 47481--47524 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
47471 AGTAATAAAA
*
47481 TAAAACTTATCAATTTGATTAAC
1 TAAAACTTATCAACTTGATTAAC
47504 TAAAAC-TATCAACTTGATTAA
1 TAAAACTTATCAACTTGATTAA
47525 AAAATGCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (23 bp):
TAAAACTTATCAACTTGATTAAC
Found at i:54973 original size:17 final size:17
Alignment explanation
Indices: 54953--54995 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
54943 TCTCCCTTGA
* *
54953 TCTTTAGCCTTCCATCT
1 TCTTTAACCTTCCATAT
*
54970 TCTTTAACCTTTCATAT
1 TCTTTAACCTTCCATAT
54987 TCTTGTAAC
1 TCTT-TAAC
54996 TATTTTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.19, C:0.28, G:0.05, T:0.49
Consensus pattern (17 bp):
TCTTTAACCTTCCATAT
Found at i:62193 original size:21 final size:21
Alignment explanation
Indices: 62162--62226 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
62152 TCCAAAATTT
* *
62162 GAACCTCAAATCTTAAATCTC
1 GAACCTTAAATTTTAAATCTC
62183 -AACACTTAAATTTTAAATC-C
1 GAAC-CTTAAATTTTAAATCTC
*
62203 GAACTTTAAATTTTAAATCTC
1 GAACCTTAAATTTTAAATCTC
62224 GAA
1 GAA
62227 TCCAAACTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
20 18 0.47
21 20 0.53
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.34
Consensus pattern (21 bp):
GAACCTTAAATTTTAAATCTC
Found at i:71484 original size:82 final size:82
Alignment explanation
Indices: 71347--71511 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
71337 TCTTTCATAG
71347 AAGCATAATGAGTATCAAGGGGTGAATGCATAAACTGAAACACTCGATTCACAGCATGTGCAATT
1 AAGCATAATGAGTATCAAGGGGTGAATGCATAAACTGAAACACTCGATTCACAGCATGTGCAATT
71412 TCAGGTTTTGTAATCAC
66 TCAGGTTTTGTAATCAC
*
71429 AAGCATAATGAGTATCAAGGGGTGAATGCATAAACTGAAGCACTCGATTCACAGCATGTGCAATT
1 AAGCATAATGAGTATCAAGGGGTGAATGCATAAACTGAAACACTCGATTCACAGCATGTGCAATT
71494 TCAGGTTTTGTAATCAC
66 TCAGGTTTTGTAATCAC
71511 A
1 A
71512 TCCTTTGGCA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (82 bp):
AAGCATAATGAGTATCAAGGGGTGAATGCATAAACTGAAACACTCGATTCACAGCATGTGCAATT
TCAGGTTTTGTAATCAC
Done.