Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005091.1 Kokia drynarioides strain JFW-HI SEQ_118908, 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: 85263
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:2160 original size:120 final size:119
Alignment explanation
Indices: 1939--2178 Score: 453
Period size: 120 Copynumber: 2.0 Consensus size: 119
1929 CGCAAGGATC
1939 TCGTCTTATTCACCAACCGATGTGGGACTGACTCAACATAATATCTTACAGATTTCTATCCTCTT
1 TCGTCTTATTCACCAACCGATGTGGGACTGACTCAACATAATATCTTACAGATTTCTATCCTCTT
*
2004 GGGCACACTTGTGATTGAAAATTTACTAGTTCTTTTGTTGAAGTATGTAACTTT
66 GGGCACACTTGTGATTGAAAATTTACTAGTTATTTTGTTGAAGTATGTAACTTT
2058 TCGTCTTATTCACCAACCGATGTGGGACTGACTCAACATAATATCTTACAAGATTTCTATCCTCT
1 TCGTCTTATTCACCAACCGATGTGGGACTGACTCAACATAATATCTTAC-AGATTTCTATCCTCT
*
2123 TGGGCATACTTGTGATTGAAAATTTACTAGTTATTTTGTTGAAGTATGTAACTTT
65 TGGGCACACTTGTGATTGAAAATTTACTAGTTATTTTGTTGAAGTATGTAACTTT
2178 T
1 T
2179 GGTATTTATT
Statistics
Matches: 118, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
119 49 0.42
120 69 0.58
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (119 bp):
TCGTCTTATTCACCAACCGATGTGGGACTGACTCAACATAATATCTTACAGATTTCTATCCTCTT
GGGCACACTTGTGATTGAAAATTTACTAGTTATTTTGTTGAAGTATGTAACTTT
Found at i:6376 original size:24 final size:24
Alignment explanation
Indices: 6349--6416 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
6339 AGGGGAAGGG
*
6349 ATAAGGTTGTTAATT-TTTTGGAAA
1 ATAAGGTTGTT-ATTCATTTGGAAA
*
6373 ATAAGGTTGTTCTTCATTTGGAAA
1 ATAAGGTTGTTATTCATTTGGAAA
*
6397 ATAAGGTTGTTCTTCATTTG
1 ATAAGGTTGTTATTCATTTG
6417 CTCAATTTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
23 2 0.05
24 39 0.95
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.46
Consensus pattern (24 bp):
ATAAGGTTGTTATTCATTTGGAAA
Found at i:6435 original size:13 final size:13
Alignment explanation
Indices: 6417--6442 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6407 TCTTCATTTG
6417 CTCAATTTTGTAT
1 CTCAATTTTGTAT
6430 CTCAATTTTGTAT
1 CTCAATTTTGTAT
6443 GTTTGGTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
CTCAATTTTGTAT
Found at i:9916 original size:36 final size:36
Alignment explanation
Indices: 9843--9916 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
9833 TTCATGTTCT
* **
9843 AATGCTTAATAGAACACTTGAGAGCAAAAAGTGCGA
1 AATGCTTAATAGAACACTTGAGAACAAAAAGAACGA
* *
9879 AATGCTTAATAGAGCACTTGAGAACAAAAGGAACGA
1 AATGCTTAATAGAACACTTGAGAACAAAAAGAACGA
9915 AA
1 AA
9917 ATCAGAGCGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.18
Consensus pattern (36 bp):
AATGCTTAATAGAACACTTGAGAACAAAAAGAACGA
Found at i:12865 original size:43 final size:41
Alignment explanation
Indices: 12799--12896 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 41
12789 GGGGGCTTGT
* * **
12799 ATCAGCTAGCTCACAATCATGCAGCAAGGAAGCATGAAAAAAA
1 ATCAGCTTGCTCACAAACATGCAGCAAACAAGCATG--AAAAA
* *
12842 ATCAGCTTGCTCACAAACGTGCAGCAAACAAGCATGAAACA
1 ATCAGCTTGCTCACAAACATGCAGCAAACAAGCATGAAAAA
*
12883 ATCTGCTTGCTCAC
1 ATCAGCTTGCTCAC
12897 TCAACTACGA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 17 0.35
43 31 0.65
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (41 bp):
ATCAGCTTGCTCACAAACATGCAGCAAACAAGCATGAAAAA
Found at i:13018 original size:20 final size:21
Alignment explanation
Indices: 12985--13028 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
12975 CTTATCAGCT
12985 AAATCATCACCTAAACAAATC
1 AAATCATCACCTAAACAAATC
*
13006 AAATCAT-ACCTAAACACATC
1 AAATCATCACCTAAACAAATC
13026 AAA
1 AAA
13029 AAACATGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (21 bp):
AAATCATCACCTAAACAAATC
Found at i:13280 original size:28 final size:28
Alignment explanation
Indices: 13210--13283 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
13200 GAGTCGGCTA
* * *
13210 GCACCTTGGCACTTCACGTGGTTAGCTC
1 GCACCTTGACATTTCGCGTGGTTAGCTC
*
13238 GCACCTTGACTTTTCGCGTGGTTAGCTC
1 GCACCTTGACATTTCGCGTGGTTAGCTC
** *
13266 GCAGTTTGTCATTTCGCG
1 GCACCTTGACATTTCGCG
13284 AGACAGCTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.12, C:0.28, G:0.26, T:0.34
Consensus pattern (28 bp):
GCACCTTGACATTTCGCGTGGTTAGCTC
Found at i:13314 original size:27 final size:27
Alignment explanation
Indices: 13261--13315 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
13251 TCGCGTGGTT
* *
13261 AGCTCGCAGTTTGTCATTTCGCGAGAC
1 AGCTCGCACTTTGTCATTTCGCAAGAC
*
13288 AGCTTGCACTTTGTCACTTT-GCAAGAC
1 AGCTCGCACTTTGTCA-TTTCGCAAGAC
13315 A
1 A
13316 CGCAGTTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (27 bp):
AGCTCGCACTTTGTCATTTCGCAAGAC
Found at i:17794 original size:7 final size:7
Alignment explanation
Indices: 17782--17809 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
17772 TGTTGCCATG
17782 CTGCTGC
1 CTGCTGC
17789 CTGCTGC
1 CTGCTGC
17796 CTGCTGC
1 CTGCTGC
17803 CTGCTGC
1 CTGCTGC
17810 ATTGCCACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.43, G:0.29, T:0.29
Consensus pattern (7 bp):
CTGCTGC
Found at i:18363 original size:18 final size:17
Alignment explanation
Indices: 18328--18366 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
18318 AGTCAAGTTA
*
18328 AATTTTATAATTCGAAT
1 AATTTTATAATTCAAAT
*
18345 AATTTTAATAATTTAAAT
1 AATTTT-ATAATTCAAAT
18363 AATT
1 AATT
18367 CGAATAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
AATTTTATAATTCAAAT
Found at i:18509 original size:17 final size:19
Alignment explanation
Indices: 18487--18530 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
18477 TTATAAAAAA
*
18487 TAAAAAATT-T-ATACTTT
1 TAAAAAATTATAAAACTTT
18504 TAAAAAAATTATAAAACTTT
1 T-AAAAAATTATAAAACTTT
18524 TAAAAAA
1 TAAAAAA
18531 ATCTAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 8 0.35
19 7 0.30
20 7 0.30
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAAATTATAAAACTTT
Found at i:33272 original size:23 final size:22
Alignment explanation
Indices: 33224--33283 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
33214 TAGGCCGCCA
* *
33224 ATATTTTTTTTTTTAAAAATTC
1 ATATTATTTTATTTAAAAATTC
*
33246 ATATTATTTTATTTAATAATT-
1 ATATTATTTTATTTAAAAATTC
*
33267 TTATATATTTTTATTTA
1 ATAT-TA-TTTTATTTA
33284 TTGAAAGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.09
22 20 0.62
23 9 0.28
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
ATATTATTTTATTTAAAAATTC
Found at i:37965 original size:2 final size:2
Alignment explanation
Indices: 37958--37982 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37948 GCAGCTTCAT
37958 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
37983 TATGATTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59389 original size:18 final size:19
Alignment explanation
Indices: 59362--59397 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
59352 TAATATTAAA
*
59362 TTTTGTAATTTTTAAAATT
1 TTTTGTAATTATTAAAATT
59381 TTTTG-AATTATTAAAAT
1 TTTTGTAATTATTAAAAT
59398 ATTGAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TTTTGTAATTATTAAAATT
Found at i:60370 original size:17 final size:17
Alignment explanation
Indices: 60348--60387 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
60338 ATTTTCATTC
60348 TATTTTAAGTTTAAATA
1 TATTTTAAGTTTAAATA
* *
60365 TATTTTAATTTTCAATA
1 TATTTTAAGTTTAAATA
*
60382 AATTTT
1 TATTTT
60388 TTGAATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TATTTTAAGTTTAAATA
Found at i:72549 original size:23 final size:22
Alignment explanation
Indices: 72523--72589 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 22
72513 TTTTAAAATA
72523 TATATGATAATAAATTAAAATTT
1 TATATGATAATAAA-TAAAATTT
* * *
72546 TATATTATATTAAATAAATTTAAT
1 TATATGATAATAAATAAAATT--T
72570 TATATTGAT-ATAAATAAAAT
1 TATA-TGATAATAAATAAAAT
72590 AAAAATCCTC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 6 0.17
23 12 0.34
24 14 0.40
25 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (22 bp):
TATATGATAATAAATAAAATTT
Found at i:76494 original size:246 final size:252
Alignment explanation
Indices: 76184--76669 Score: 637
Period size: 257 Copynumber: 1.9 Consensus size: 252
76174 GAAAAAAAGG
*
76184 AAGTAATAAAATGAAAATGAAAAATCTTACTTAAACTCGAATATATCTCAGCCATATTTTCTTAG
1 AAGTAATAAAATGAAAAAGAAAAATCTTACTTAAACTCGAATATATCTCAGCCATATTTTCTTAG
* * * * * **
76249 CAACCAAATAAAATATAAATCTTAA-ACA-A-A-T-GC-ATTTGATAGCTTC-CAAGCATAAATT
66 CAACCAAACAAAAGATAAACCTTAACAAATATATTAACAATTTGATAG-TTCTCAAGCATAAAGC
* * * * * *
76307 GATGAATATCAAGCTAAGTACTAAATTACTTAAGTAACTCATATTTTAGGGGAAAAATAATTCAG
130 GATGAATATCAAACTAAGTACTAAACTACTCAAGTAACTAACATTTTAGAGGAAAAATAATTCAG
*
76372 CAATTAGATTTCAAAATCAAAGAAATCTATCAAACACAAAAACATAATTAAAGGGAAA
195 CAATTAGATTACAAAATCAAAGAAATCTATCAAACACAAAAACATAATTAAAGGGAAA
* * * *
76430 AAGTAATAAATTGAAAAAGAAAAATCTTA-TATAAACTCGGATATATGTTAGCCATATTTTCTTA
1 AAGTAATAAAATGAAAAAGAAAAATCTTACT-TAAACTCGAATATATCTCAGCCATATTTTCTTA
* * * *
76494 GCAACTAAACAGACGATAAACCTTAACCAAATATATTTAAACAAAATTTGGTAGTTCTCAAGCAT
65 GCAACCAAACAAAAGATAAACCTTAA-CAAATATA-TT-AAC--AATTTGATAGTTCTCAAGCAT
*
76559 AAAGCGGTGAATATCAAACTAAGTACTAAACTACTCAAGTAACTAACATTTTAGAGGAAAAATAA
125 AAAGCGATGAATATCAAACTAAGTACTAAACTACTCAAGTAACTAACATTTTAGAGGAAAAATAA
76624 TTCAGCAATTAGATTACAAAATCAAAGAAATCTATCAAACACAAAA
190 TTCAGCAATTAGATTACAAAATCAAAGAAATCTATCAAACACAAAA
76670 CCAAGAATTA
Statistics
Matches: 203, Mismatches: 24, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
245 1 0.00
246 77 0.38
248 2 0.01
249 1 0.00
250 1 0.00
252 1 0.00
254 1 0.00
256 3 0.01
257 116 0.57
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.27
Consensus pattern (252 bp):
AAGTAATAAAATGAAAAAGAAAAATCTTACTTAAACTCGAATATATCTCAGCCATATTTTCTTAG
CAACCAAACAAAAGATAAACCTTAACAAATATATTAACAATTTGATAGTTCTCAAGCATAAAGCG
ATGAATATCAAACTAAGTACTAAACTACTCAAGTAACTAACATTTTAGAGGAAAAATAATTCAGC
AATTAGATTACAAAATCAAAGAAATCTATCAAACACAAAAACATAATTAAAGGGAAA
Found at i:77417 original size:19 final size:19
Alignment explanation
Indices: 77378--77418 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
77368 TCACTTGAAG
* *
77378 ATTTAAAAAAATTATATAA
1 ATTTAAAAAAATTAAAAAA
*
77397 ATTTAAAAATATTAAAAAA
1 ATTTAAAAAAATTAAAAAA
77416 ATT
1 ATT
77419 ATGTTTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTTAAAAAAATTAAAAAA
Found at i:77427 original size:26 final size:27
Alignment explanation
Indices: 77380--77433 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
77370 ACTTGAAGAT
77380 TTAAAAAAATTATATAAATTTAAAAATA
1 TTAAAAAAATTATAT-AATTTAAAAATA
* *
77408 TTAAAAAAATTATGT-TTTTAAAAATA
1 TTAAAAAAATTATATAATTTAAAAATA
77434 GCATAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.42
28 14 0.58
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
TTAAAAAAATTATATAATTTAAAAATA
Found at i:84316 original size:23 final size:22
Alignment explanation
Indices: 84209--84359 Score: 119
Period size: 23 Copynumber: 6.5 Consensus size: 22
84199 TGAAGTACTT
84209 AACAGTAAGCACACAAGTGCTGGGGA
1 AACAGTAAGCACACAAGTGC----GA
84235 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACA-AGTGCGA
* * * *
84257 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACA-AGTGCGA
*
84279 AATCAGTAGGGCACACGAAGTGCGA
1 AA-CAGTA-AGCACAC-AAGTGCGA
84304 AACAGTAAGCACACGAAGTGCGA
1 AACAGTAAGCACAC-AAGTGCGA
*
84327 AACAGTAAGCACACACAATGCTG-
1 AACAGTAAGCACACA-AGTGC-GA
84350 AACAGTAAGC
1 AACAGTAAGC
84360 GCACTAATGT
Statistics
Matches: 108, Mismatches: 10, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
22 20 0.19
23 48 0.44
24 16 0.15
25 4 0.04
26 15 0.14
27 5 0.05
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.11
Consensus pattern (22 bp):
AACAGTAAGCACACAAGTGCGA
Done.