Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013303.1 Kokia drynarioides strain JFW-HI SEQ_128325, 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: 15191
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:177 original size:22 final size:22
Alignment explanation
Indices: 91--234 Score: 107
Period size: 22 Copynumber: 6.5 Consensus size: 22
81 AAAAATGATA
* *
91 TTGTTGTTTTG-GTGTTTTTTT
1 TTGTTGTTTTGATTGTTATTTT
* *
112 TTATTGTTTTGGTTGATT-TTTT
1 TTGTTGTTTTGATTG-TTATTTT
* *
134 TTGCTGTTTTGAGTTATT-TTTT
1 TTGTTGTTTTGA-TTGTTATTTT
*
156 TTATTGTTTTGATTGTTATTTT
1 TTGTTGTTTTGATTGTTATTTT
* *
178 TGTGTTATTTTTG-CTGTTATTTTT
1 T-TGTT-GTTTTGATTGTTA-TTTT
* *
202 ATTGTTGTTTTTATTGCTATTTT
1 -TTGTTGTTTTGATTGTTATTTT
225 TTGTTGTTTT
1 TTGTTGTTTT
235 TAATGTTGTT
Statistics
Matches: 98, Mismatches: 16, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
21 14 0.14
22 46 0.47
23 20 0.20
24 17 0.17
25 1 0.01
ACGTcount: A:0.08, C:0.02, G:0.17, T:0.72
Consensus pattern (22 bp):
TTGTTGTTTTGATTGTTATTTT
Found at i:242 original size:34 final size:33
Alignment explanation
Indices: 152--246 Score: 100
Period size: 34 Copynumber: 2.8 Consensus size: 33
142 TTGAGTTATT
* * * *
152 TTTTTTATTGTTTTGATTGTTATTTTTGTGTTA
1 TTTTTTGTTGTTTTTATTGTTGTTTTTGTGCTA
* *
185 TTTTTGCTGTTATTTTTATTGTTGTTTTTATTGCTA
1 TTTTT--TGTTGTTTTTATTGTTGTTTTT-GTGCTA
*
221 TTTTTTGTTGTTTTTAATGTTGTTTT
1 TTTTTTGTTGTTTTTATTGTTGTTTT
247 GCTGTTATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
33 5 0.10
34 19 0.37
35 18 0.35
36 9 0.18
ACGTcount: A:0.11, C:0.02, G:0.15, T:0.73
Consensus pattern (33 bp):
TTTTTTGTTGTTTTTATTGTTGTTTTTGTGCTA
Found at i:282 original size:69 final size:69
Alignment explanation
Indices: 152--282 Score: 156
Period size: 69 Copynumber: 1.9 Consensus size: 69
142 TTGAGTTATT
* * * * * *
152 TTTTTTATTGTTTTGATTGTTATTTTTGTGTTATTTTTGCTGTTATTTTTATTGTTGTTTTTATT
1 TTTTTTATTGTTTTGAATGTTAGTTTTGTGTTATTTTTGCTGCTATTTTGATTGCTATTTTTATT
217 GCTA
66 GCTA
* * * *
221 TTTTTTGTTGTTTTTAATGTT-GTTTTGCTGTTATTTTTGCTGCTGTTTTGGTTGCTATTTTT
1 TTTTTTATTGTTTTGAATGTTAGTTTTG-TGTTATTTTTGCTGCTATTTTGATTGCTATTTTT
283 GTTGTTTGGA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
68 5 0.10
69 46 0.90
ACGTcount: A:0.09, C:0.05, G:0.17, T:0.69
Consensus pattern (69 bp):
TTTTTTATTGTTTTGAATGTTAGTTTTGTGTTATTTTTGCTGCTATTTTGATTGCTATTTTTATT
GCTA
Found at i:286 original size:12 final size:12
Alignment explanation
Indices: 162--288 Score: 82
Period size: 12 Copynumber: 10.8 Consensus size: 12
152 TTTTTTATTG
162 TTTTGATTGTTAT
1 TTTTG-TTGTTAT
175 TTTTG-TGTTAT
1 TTTTGTTGTTAT
*
186 TTTTGCTGTTAT
1 TTTTGTTGTTAT
* *
198 TTTTATTGTTGT
1 TTTTGTTGTTAT
* *
210 TTTTATTGCTA-
1 TTTTGTTGTTAT
*
221 TTTT-TTGTTGT
1 TTTTGTTGTTAT
** *
232 TTTTAATGTT-G
1 TTTTGTTGTTAT
*
243 TTTTGCTGTTAT
1 TTTTGTTGTTAT
* * *
255 TTTTGCTGCTGT
1 TTTTGTTGTTAT
* *
267 TTTGGTTGCTAT
1 TTTTGTTGTTAT
279 TTTTGTTGTT
1 TTTTGTTGTT
289 TGGATAATAT
Statistics
Matches: 91, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
10 4 0.04
11 27 0.30
12 55 0.60
13 5 0.05
ACGTcount: A:0.09, C:0.05, G:0.18, T:0.69
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:340 original size:21 final size:21
Alignment explanation
Indices: 294--340 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
284 TTGTTTGGAT
* *
294 AATA-TTTTTACTATTGTTTC
1 AATATTTTTTAATATTATTTC
* *
314 ACTATTTTTTAATATTATTTG
1 AATATTTTTTAATATTATTTC
335 AATATT
1 AATATT
341 GTAGAACTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (21 bp):
AATATTTTTTAATATTATTTC
Found at i:443 original size:11 final size:11
Alignment explanation
Indices: 429--453 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
419 AATTTATTTA
429 TTTTTAATGTT
1 TTTTTAATGTT
440 TTTTTAATGTT
1 TTTTTAATGTT
451 TTT
1 TTT
454 AAGTGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTAATGTT
Found at i:6129 original size:49 final size:49
Alignment explanation
Indices: 6066--6221 Score: 149
Period size: 49 Copynumber: 3.2 Consensus size: 49
6056 TGAAGATATG
*
6066 AAGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCGCGAAGATTCA
1 AAGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCGCAAAGATTCA
* * * * *
6115 AAGGGAAAGGTTTAAGTCACAATGGCAAA-CCTTA-TACCTCAAAAGCA-T-G
1 AAGGGAAAGATTTAAGCCACAACGGCAAATCC--AGTACCGC-AAAG-ATTCA
* ** * *
6164 AACGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCGCAAAGATACA
1 AAGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCGCAAAGATTCA
6213 AAGGGAAAG
1 AAGGGAAAG
6222 GCTTAAGTCG
Statistics
Matches: 82, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
47 1 0.01
48 7 0.09
49 66 0.80
50 7 0.09
51 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCGCAAAGATTCA
Found at i:6248 original size:98 final size:98
Alignment explanation
Indices: 6063--6487 Score: 537
Period size: 98 Copynumber: 4.3 Consensus size: 98
6053 CCATGAAGAT
* * *
6063 ATGAAGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCGCGAAGATTCAAAGGGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGATACAAAGGGAAAGGTTT
* * *
6128 AAGTCACAATGGCAAACCTTATACCTCAAAAGC
66 AAGTCGCAATGACGAACCTTATACCTCAAAAGC
* * * * * *
6161 ATGAACGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCGCAAAGATACAAAGGGAAAGGCTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGATACAAAGGGAAAGGTTT
* * *
6226 AAGTCGTAATGACGAACTTTATACCTCAGAAGC
66 AAGTCGCAATGACGAACCTTATACCTCAAAAGC
* * * *
6259 ATGAAGGGAAAGATTTAAGCCGCAACGACAAATCTAGTATCACGAAGATACAAAGGGAAAGGTCT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGATACAAAGGGAAAGGTTT
*
6324 AAGTCGCAATGACGAACCTTATACCTCAGAAGC
66 AAGTCGCAATGACGAACCTTATACCTCAAAAGC
* * * * * *
6357 TTGAAGGGAAAGATTTAAGCTGCGACGGCAAATCCAGTACCACGAAGATATAAAGGAAAAGATTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGATACAAAGGGAAAGGTTT
* * * *
6422 AAGTCGCAACGAAGAACCTTGTACCTC-AGAGAC
66 AAGTCGCAATGACGAACCTTATACCTCAAAAG-C
* * *
6455 ATGAAAGGAAAAATTTAAGCCGCAACGGTAAAT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCAAAT
6488 TTAATAACAT
Statistics
Matches: 280, Mismatches: 46, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
97 2 0.01
98 278 0.99
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (98 bp):
ATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGATACAAAGGGAAAGGTTT
AAGTCGCAATGACGAACCTTATACCTCAAAAGC
Found at i:6266 original size:49 final size:48
Alignment explanation
Indices: 6213--6368 Score: 140
Period size: 49 Copynumber: 3.2 Consensus size: 48
6203 CAAAGATACA
*
6213 AAGGGAAAGGCTTAAGTCGTAATGACGAACTTTATACCTCAGAAGCATG
1 AAGGGAAAGG-TTAAGTCGCAATGACGAACTTTATACCTCAGAAGCATG
* * * * * *
6262 AAGGGAAAGATTTAAGCCGCAACGAC-AAATCTAGTA--TCACGAAG-ATACA
1 AAGGGAAAG-GTTAAGTCGCAATGACGAACTTTA-TACCTCA-GAAGCAT--G
* *
6311 AAGGGAAAGGTCTAAGTCGCAATGACGAACCTTATACCTCAGAAGCTTG
1 AAGGGAAAGGT-TAAGTCGCAATGACGAACTTTATACCTCAGAAGCATG
6360 AAGGGAAAG
1 AAGGGAAAG
6369 ATTTAAGCTG
Statistics
Matches: 82, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
47 5 0.06
48 10 0.12
49 55 0.67
50 8 0.10
51 4 0.05
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (48 bp):
AAGGGAAAGGTTAAGTCGCAATGACGAACTTTATACCTCAGAAGCATG
Found at i:6446 original size:49 final size:48
Alignment explanation
Indices: 6262--6481 Score: 144
Period size: 49 Copynumber: 4.5 Consensus size: 48
6252 CAGAAGCATG
* * *
6262 AAGGGAAAGATTTAAGCCGCAACGACAAATCTAGTATCACGAAGATACA
1 AAGGGAAAGATTTAAGCCGCAACGA-AAACCTAGTACCACGAAGATATA
* * * * * * * *
6311 AAGGGAAAGGTCTAAGTCGCAATGACGAACCTTA-TACCTCAGAAGCT-TG
1 AAGGGAAAGATTTAAGCCGCAACGA-AAACC-TAGTACCAC-GAAGATATA
* * *
6360 AAGGGAAAGATTTAAGCTGCGACGGCAAATCC-AGTACCACGAAGATATA
1 AAGGGAAAGATTTAAGCCGCAAC-G-AAAACCTAGTACCACGAAGATATA
* * * * *
6409 AAGGAAAAGATTTAAGTCGCAACGAAGAACCTTGTACCTC-AGAGACATGA
1 AAGGGAAAGATTTAAGCCGCAACGAA-AACCTAGTACCACGA-AGATAT-A
*
6459 AA-GGAAAAATTTAAGCCGCAACG
1 AAGGGAAAGATTTAAGCCGCAACG
6482 GTAAATTTAA
Statistics
Matches: 128, Mismatches: 33, Indels: 20
0.71 0.18 0.11
Matches are distributed among these distances:
47 2 0.02
48 11 0.09
49 100 0.78
50 14 0.11
51 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (48 bp):
AAGGGAAAGATTTAAGCCGCAACGAAAACCTAGTACCACGAAGATATA
Found at i:9410 original size:13 final size:15
Alignment explanation
Indices: 9392--9427 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
9382 CTAGTGTTCA
9392 TTTTCTTTCTC-T-T
1 TTTTCTTTCTCTTAT
9405 TTTTCTTT-TCTTAT
1 TTTTCTTTCTCTTAT
9419 TTTTCTTTC
1 TTTTCTTTC
9428 GAATAAATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.10
13 9 0.45
14 9 0.45
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTCTTTCTCTTAT
Found at i:13671 original size:17 final size:18
Alignment explanation
Indices: 13639--13673 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13629 ATCACATTAA
*
13639 AAATTTTTAATGAATATC
1 AAATTTTTAATAAATATC
13657 AAATTTTTAA-AAATATC
1 AAATTTTTAATAAATATC
13674 TTGTTAGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
AAATTTTTAATAAATATC
Found at i:14946 original size:23 final size:24
Alignment explanation
Indices: 14920--14971 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
14910 GTTTTCATTC
14920 TTTTTTTACTG-TTTTG-GTTGATT
1 TTTTTTTACTGTTTTTGAGTT-ATT
*
14943 TTTTTTTGCTGTTTTTGAGTTATT
1 TTTTTTTACTGTTTTTGAGTTATT
14967 TTTTT
1 TTTTT
14972 ATTGTTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.38
24 13 0.50
25 3 0.12
ACGTcount: A:0.08, C:0.04, G:0.15, T:0.73
Consensus pattern (24 bp):
TTTTTTTACTGTTTTTGAGTTATT
Found at i:14989 original size:23 final size:23
Alignment explanation
Indices: 14920--14991 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
14910 GTTTTCATTC
* *
14920 TTTTTTTACTGTTTTGGTTGATT
1 TTTTTTTACTGTTTTGATTGATA
* *
14943 TTTTTTTGCTGTTTTTGA--GTTA
1 TTTTTTTACTG-TTTTGATTGATA
* *
14965 TTTTTTTATTGTTTTGATTGCTA
1 TTTTTTTACTGTTTTGATTGATA
14988 TTTT
1 TTTT
14992 CGTGTTATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
21 6 0.15
22 11 0.28
23 17 0.44
24 5 0.13
ACGTcount: A:0.10, C:0.04, G:0.15, T:0.71
Consensus pattern (23 bp):
TTTTTTTACTGTTTTGATTGATA
Found at i:15026 original size:12 final size:12
Alignment explanation
Indices: 15011--15099 Score: 51
Period size: 12 Copynumber: 7.8 Consensus size: 12
15001 TTTGCTGTTA
15011 TTTTTGTTGCTG
1 TTTTTGTTGCTG
* *
15023 TTTTTATTGCTA
1 TTTTTGTTGCTG
15035 TTTTTG-T--TG
1 TTTTTGTTGCTG
** *
15044 TTTTTAATGTTG
1 TTTTTGTTGCTG
** * *
15056 -TTTTACTGTTA
1 TTTTTGTTGCTG
15067 TTTTTGTTGCTG
1 TTTTTGTTGCTG
* *
15079 TTTTGGTTGCTA
1 TTTTTGTTGCTG
15091 TTTTTGTTG
1 TTTTTGTTG
15100 TTTGGATATT
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
9 6 0.10
10 1 0.02
11 10 0.17
12 42 0.71
ACGTcount: A:0.08, C:0.06, G:0.19, T:0.67
Consensus pattern (12 bp):
TTTTTGTTGCTG
Found at i:15116 original size:56 final size:55
Alignment explanation
Indices: 14996--15118 Score: 158
Period size: 56 Copynumber: 2.2 Consensus size: 55
14986 TATTTTCGTG
* * * **
14996 TTATGTTTGCTGTTATTTTTGTTGCTGTTTTTATTGCTATTTTTGTTGTTTTTAA
1 TTATTTTTACTGTTATTTTTGTTGCTGTTTTGATTGCTATTTTTGTTGTTTGGAA
*
15051 TGT-TGTTTTACTGTTATTTTTGTTGCTGTTTTGGTTGCTATTTTTGTTGTTTGGATA
1 T-TAT-TTTTACTGTTATTTTTGTTGCTGTTTTGATTGCTATTTTTGTTGTTTGGA-A
15108 TTATTTTTACT
1 TTATTTTTACT
15119 ATTGTTTCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
55 2 0.03
56 53 0.91
57 3 0.05
ACGTcount: A:0.11, C:0.06, G:0.18, T:0.66
Consensus pattern (55 bp):
TTATTTTTACTGTTATTTTTGTTGCTGTTTTGATTGCTATTTTTGTTGTTTGGAA
Done.