Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008934.1 Kokia drynarioides strain JFW-HI SEQ_123626, 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: 39685
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:301 original size:27 final size:25
Alignment explanation
Indices: 254--306 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 25
244 AATTATTTAT
254 ATTTTTATAATTAAATTTAAATATA
1 ATTTTTATAATTAAATTTAAATATA
*
279 ATTTTTATTATTTAAAATTTAAATATA
1 ATTTTTA-TAATT-AAATTTAAATATA
306 A
1 A
307 AATTCATGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.28
26 4 0.16
27 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTTTTATAATTAAATTTAAATATA
Found at i:8047 original size:148 final size:141
Alignment explanation
Indices: 7664--8243 Score: 765
Period size: 148 Copynumber: 4.1 Consensus size: 141
7654 AGTTTTAATT
* * *
7664 TTTATTTTATATATTTTAGGTAAAAAACTCGTAACAAATTGAAAGAATT-AAATTTATTTTTATT
1 TTTATTTTATATATTTTAGGTAAAAAACCCATAACAAATTGAAAGAATTAAAATTTTTTTTTATT
* * *
7728 TTTTCTGTTTTATTTTTATTCAAATTA--T--TTA-TTGAAAATTTATTACTTATTGTTAAATCA
66 TTTTCTGTTTTATTTTTATTCAAATTATTTAATTATTTTAAAATTTATTATTTATTGTTAAATTA
7788 CAATTTTAGTA
131 CAATTTTAGTA
* *
7799 TTTATTTTATATATTTTAGGTAAAAAACCCATAACAAATTGAAAGAATTAAAATATTTTATT-TT
1 TTTATTTTATATATTTTAGGTAAAAAACCCATAACAAATTGAAAGAATTAAAATTTTTTTTTATT
*
7863 TTTTCTGTTTTATTTTTATTCAAATTATTTAGTTATTCTTATAAATATTTATTATTTATTGTTAA
66 TTTTCTGTTTTATTTTTATTCAAATTATTTAATTA-T-TT-TAAA-ATTTATTATTTATTGTTAA
7928 ATTACAATTTTAGTA
127 ATTACAATTTTAGTA
* *
7943 TTTATTTTATATATTTTAGGTAAAAAAAAAACCCACAACAAATTGAAAGAATT-AATTTTTTTTT
1 TTTATTTTATATATTTTAGGT----AAAAAACCCATAACAAATTGAAAGAATTAAAATTTTTTTT
* *
8007 TATTTTTTCTATTTTATTTTTATTCAAATTATTTAATTA--TT----TTTATAATTTATTGTTAA
62 TATTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTATTTTAAAATTTATTATTTATTGTTAA
8066 ATTACAATTTTAGTA
127 ATTACAATTTTAGTA
*
8081 TTTATTTTATATATTTTAGGTAAAAAAAACCCATAAAAAATTGAAAGAATTAAATATTTTTTTTT
1 TTTATTTTATATATTTTAGGT--AAAAAACCCATAACAAATTGAAAGAATTAAA-ATTTTTTTTT
8146 ATTTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTATTTATTGAAAATTTATTATTTATTGT
63 A-TTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTA-TT-TT-AAAATTTATTATTTATTGT
* *
8211 TAAATTACAAATTCAGTA
124 TAAATTACAATTTTAGTA
*
8229 TTTATTATTTTATAT
1 TTTATT-TTATATAT
8244 CTTGAAGGAA
Statistics
Matches: 394, Mismatches: 23, Indels: 42
0.86 0.05 0.09
Matches are distributed among these distances:
135 76 0.19
136 37 0.09
137 3 0.01
138 63 0.16
139 39 0.10
142 2 0.01
143 6 0.02
144 54 0.14
147 9 0.02
148 98 0.25
149 7 0.02
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (141 bp):
TTTATTTTATATATTTTAGGTAAAAAACCCATAACAAATTGAAAGAATTAAAATTTTTTTTTATT
TTTTCTGTTTTATTTTTATTCAAATTATTTAATTATTTTAAAATTTATTATTTATTGTTAAATTA
CAATTTTAGTA
Found at i:8204 original size:18 final size:19
Alignment explanation
Indices: 8158--8209 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
8148 TTTTTTCTGT
*
8158 TTTATT-TTTATTCAAATTA
1 TTTATTATTTATTGAAA-TA
8177 TTTAATTATTTATTGAAA-A
1 TTT-ATTATTTATTGAAATA
8196 TTTATTATTTATTG
1 TTTATTATTTATTG
8210 TTAAATTACA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.37
19 7 0.23
20 3 0.10
21 9 0.30
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTATTATTTATTGAAATA
Found at i:9370 original size:55 final size:55
Alignment explanation
Indices: 9310--9429 Score: 163
Period size: 55 Copynumber: 2.2 Consensus size: 55
9300 ATTTAAAAGA
*
9310 AAAAT-AGAAAATATTCCAACGTAATAATCGATTTAAACATA-AAATCAATCGATTC
1 AAAATAAGAAAAT-TTCCAACGTAATAATCGATTTAAACATATAAA-CAATAGATTC
* * *
9365 AAAATAAGCAGATTTCCAACGTAGTAATCGATTTAAACATATAAACAATAGATTC
1 AAAATAAGAAAATTTCCAACGTAATAATCGATTTAAACATATAAACAATAGATTC
*
9420 AAAAGAAGAA
1 AAAATAAGAA
9430 TAAGTAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
55 49 0.86
56 8 0.14
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.25
Consensus pattern (55 bp):
AAAATAAGAAAATTTCCAACGTAATAATCGATTTAAACATATAAACAATAGATTC
Found at i:11029 original size:233 final size:233
Alignment explanation
Indices: 10615--11088 Score: 912
Period size: 233 Copynumber: 2.0 Consensus size: 233
10605 AGTGAGTCAA
*
10615 AGTAATAATTGAATGATATGTAATTTAGGACAATTACTGCACTAAAGGGTTTCTGAAAAATAGTA
1 AGTAATTATTGAATGATATGTAATTTAGGACAATTACTGCACTAAAGGGTTTCTGAAAAATAGTA
10680 ACTTGTCAAGATATCACAAGTCAAATGCAGTTAAAGAAGTTGAAAGAATTGCTATACCTCATCAA
66 ACTTGTCAAGATATCACAAGTCAAATGCAGTTAAAGAAGTTGAAAGAATTGCTATACCTCATCAA
*
10745 CAGCTCCATTGTAGCAATACTGCAGATAACGATTGTTCAGTAAATTAAAAGAATCAGGCAGGTAA
131 CAGCTCCATTGTAGCAATACTGCAGATAAAGATTGTTCAGTAAATTAAAAGAATCAGGCAGGTAA
10810 ATGAGATTGAAATCAATGTTCCCCTTCAAAGATTTTAC
196 ATGAGATTGAAATCAATGTTCCCCTTCAAAGATTTTAC
10848 AGTAATTATTGAATGATATGTAATTTAGGACAATTACTGCACTAAAGGGTTTCTGAAAAATAGTA
1 AGTAATTATTGAATGATATGTAATTTAGGACAATTACTGCACTAAAGGGTTTCTGAAAAATAGTA
10913 ACTTGTCAAGATATCACAAGTCAAATGCAGTTAAAGAAGTTGAAAGAATTGCTATACCTCATCAA
66 ACTTGTCAAGATATCACAAGTCAAATGCAGTTAAAGAAGTTGAAAGAATTGCTATACCTCATCAA
* *
10978 CAGCTCCATTGTAGCAATACTGCAGATAAAGATTGTTCTGTAAATTAAAAGAATCGGGCAGGTAA
131 CAGCTCCATTGTAGCAATACTGCAGATAAAGATTGTTCAGTAAATTAAAAGAATCAGGCAGGTAA
11043 ATGAGATTGAAATCAATGTTCCCCTTCAAAGATTTTAC
196 ATGAGATTGAAATCAATGTTCCCCTTCAAAGATTTTAC
11081 AGTAATTA
1 AGTAATTA
11089 GTCAAAGATT
Statistics
Matches: 237, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
233 237 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (233 bp):
AGTAATTATTGAATGATATGTAATTTAGGACAATTACTGCACTAAAGGGTTTCTGAAAAATAGTA
ACTTGTCAAGATATCACAAGTCAAATGCAGTTAAAGAAGTTGAAAGAATTGCTATACCTCATCAA
CAGCTCCATTGTAGCAATACTGCAGATAAAGATTGTTCAGTAAATTAAAAGAATCAGGCAGGTAA
ATGAGATTGAAATCAATGTTCCCCTTCAAAGATTTTAC
Found at i:12301 original size:133 final size:133
Alignment explanation
Indices: 12063--12338 Score: 507
Period size: 133 Copynumber: 2.1 Consensus size: 133
12053 CACTAAAAGA
*
12063 AAAAAAAAAACACTGAGAATGAACTTCCCATCAAGAACCCTTCATGATCCATGGATGCAGAATTT
1 AAAAAAAAAACACTGAGAATGAACTTCCCATCAAGAACCCTCCATGATCCATGGATGCAGAATTT
* * *
12128 GGTATAAGCTCAGCAGATAGATGATCTGCTAACATAACATAATCTAGACACTTGAATGACAATAC
66 GGCATAAGCTCAGCAGATAGATGATCTGCAAACATAACATAATCTAGACACTTGAAGGACAATAC
12193 TTG
131 TTG
12196 AAAAAAAAAACACTGAGAATGAACTTCCCATCAAGAACCCTCCATGATCCATGGATGCAGAATTT
1 AAAAAAAAAACACTGAGAATGAACTTCCCATCAAGAACCCTCCATGATCCATGGATGCAGAATTT
*
12261 GGCATAAGCTCAGCAGATTGATGATCTGCAAACATAACATAATCTAGACACTTGAAGGACAATAC
66 GGCATAAGCTCAGCAGATAGATGATCTGCAAACATAACATAATCTAGACACTTGAAGGACAATAC
12326 TTG
131 TTG
12329 AAAAAAAAAA
1 AAAAAAAAAA
12339 GGTTTGACAA
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 138 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (133 bp):
AAAAAAAAAACACTGAGAATGAACTTCCCATCAAGAACCCTCCATGATCCATGGATGCAGAATTT
GGCATAAGCTCAGCAGATAGATGATCTGCAAACATAACATAATCTAGACACTTGAAGGACAATAC
TTG
Found at i:12552 original size:33 final size:33
Alignment explanation
Indices: 12510--12585 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
12500 TTTAAAGGCT
12510 AAAC-AATCAAACAGGTAATGGTGATTTCAATG
1 AAACAAATCAAACAGGTAATGGTGATTTCAATG
12542 AAACAAATCAAACAGGTAATGGTGATTTCAATG
1 AAACAAATCAAACAGGTAATGGTGATTTCAATG
12575 AAACAAATCAA
1 AAACAAATCAA
12586 CCCGTAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 4 0.09
33 39 0.91
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (33 bp):
AAACAAATCAAACAGGTAATGGTGATTTCAATG
Found at i:19792 original size:144 final size:144
Alignment explanation
Indices: 19530--19809 Score: 472
Period size: 144 Copynumber: 1.9 Consensus size: 144
19520 AGGTGGAGAG
* *
19530 GAGAGTCCAACACTACCAAAACTCTCGCAAGTATATGATAATTTGATGACACAATATGCTTGAAG
1 GAGAGTCCAACACTACCAAAACTCACGCAAGTATATGATAATTTGATGACACAATAAGCTTGAAG
* *
19595 TCATCTTTAGGTGGCAACTTTAACACGTAACTAAGCCGAGTACACAAGGAGTGTAACAAGAACAC
66 TCATCTTTAGGTGGCAACTTTAACACGTAACTAAGCCAAGTACACAAGAAGTGTAACAAGAACAC
19660 AAAAGTATCAGGTA
131 AAAAGTATCAGGTA
* *
19674 GAGAGTCCATCACTACCAAAACTCACGCAATTATATGATAATTTGATGACACAATAAGCTTGAAG
1 GAGAGTCCAACACTACCAAAACTCACGCAAGTATATGATAATTTGATGACACAATAAGCTTGAAG
* *
19739 TCATCTTTGGGTGGCAACTTTAACACGTAATTAAGCCAAGTACAGC-AGAAGTGTAACAAGAACA
66 TCATCTTTAGGTGGCAACTTTAACACGTAACTAAGCCAAGTACA-CAAGAAGTGTAACAAGAACA
19803 CAAAAGT
130 CAAAAGT
19810 TGACATTAGA
Statistics
Matches: 127, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
144 126 0.99
145 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.23
Consensus pattern (144 bp):
GAGAGTCCAACACTACCAAAACTCACGCAAGTATATGATAATTTGATGACACAATAAGCTTGAAG
TCATCTTTAGGTGGCAACTTTAACACGTAACTAAGCCAAGTACACAAGAAGTGTAACAAGAACAC
AAAAGTATCAGGTA
Found at i:21724 original size:22 final size:21
Alignment explanation
Indices: 21685--21726 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
21675 GTAAATCCAC
*
21685 TATATGCAGACAACTAACAGG
1 TATATGCACACAACTAACAGG
*
21706 TATATAGCACACAAGTAACAG
1 TATAT-GCACACAACTAACAG
21727 AATGCAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (21 bp):
TATATGCACACAACTAACAGG
Found at i:22139 original size:27 final size:27
Alignment explanation
Indices: 22109--22162 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
22099 ACAACGAAGA
** *
22109 CCCTCCACTTGCAGCACCCAACCCACC
1 CCCTCCACCAGCACCACCCAACCCACC
* *
22136 CCCTGCACCAGCACCACTCAACCCACC
1 CCCTCCACCAGCACCACCCAACCCACC
22163 ATAAACAGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.24, C:0.59, G:0.07, T:0.09
Consensus pattern (27 bp):
CCCTCCACCAGCACCACCCAACCCACC
Found at i:22203 original size:24 final size:24
Alignment explanation
Indices: 22158--22237 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
22148 ACCACTCAAC
*
22158 CCACCATAAACAGTTGAACCTGGT
1 CCACCATAACCAGTTGAACCTGGT
* * *
22182 CCGCCATAACCAGCTGATCCTGGT
1 CCACCATAACCAGTTGAACCTGGT
* *
22206 ACACCATAGCCAGTTGAACCTGGT
1 CCACCATAACCAGTTGAACCTGGT
22230 CCACCATA
1 CCACCATA
22238 CCCACCATAC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (24 bp):
CCACCATAACCAGTTGAACCTGGT
Found at i:32819 original size:20 final size:21
Alignment explanation
Indices: 32794--32840 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
32784 TATAAAAAAT
32794 TTATTAAACT-AATC-ATTCAA
1 TTATTAAA-TAAATCAATTCAA
*
32814 TTATTAAATAAATCAATTTAA
1 TTATTAAATAAATCAATTCAA
32835 TTATTA
1 TTATTA
32841 TATTATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 12 0.50
21 11 0.46
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATTAAATAAATCAATTCAA
Found at i:39637 original size:2 final size:2
Alignment explanation
Indices: 39630--39657 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39620 ATTCTGAAGC
39630 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39658 GCTTCAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.