Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003799.1 Kokia drynarioides strain JFW-HI SEQ_116783, 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: 57870
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:946 original size:16 final size:16
Alignment explanation
Indices: 904--946 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
894 TTAAAATGTA
*
904 TAAAAACTTAAATTTT
1 TAAAAAATTAAATTTT
* **
920 TAATATTTTAAATTTT
1 TAAAAAATTAAATTTT
936 TAAAAAATTAA
1 TAAAAAATTAA
947 TTAATTACAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAAAAATTAAATTTT
Found at i:4867 original size:21 final size:21
Alignment explanation
Indices: 4843--4885 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4833 TATAGCATTT
4843 CATTTCAAATAAAAATT-TTAA
1 CATTTCAAAT-AAAATTATTAA
* *
4864 CATTTGAGATAAAATTATTAA
1 CATTTCAAATAAAATTATTAA
4885 C
1 C
4886 GTGACATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (21 bp):
CATTTCAAATAAAATTATTAA
Found at i:11218 original size:42 final size:42
Alignment explanation
Indices: 11141--11225 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
11131 AATAATCGAT
*
11141 TTTTAAATATATAAATAATTGATTCAAAAGAAAAAAA-AAATA
1 TTTTAAATATATAAATAATCGATT-AAAAGAAAAAAAGAAATA
*
11183 TTTTAAATATATAAATAATCGATT-TAAGCATAAAAAAGAAATA
1 TTTTAAATATATAAATAATCGATTAAAAG-A-AAAAAAGAAATA
11226 AAAAAAAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
40 3 0.08
41 1 0.03
42 29 0.76
43 5 0.13
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.32
Consensus pattern (42 bp):
TTTTAAATATATAAATAATCGATTAAAAGAAAAAAAGAAATA
Found at i:21692 original size:549 final size:548
Alignment explanation
Indices: 20632--22280 Score: 2412
Period size: 549 Copynumber: 3.0 Consensus size: 548
20622 AAACCCACTA
* ** *
20632 TTTCCTCCCTCAATTGACCATCCTCTTCGATTTTAGTTCTCAGGTCCTCTTCCAGTTCACCTTTC
1 TTTCCACCCTCAGCTGACCATTCTCTTCGATTTTAGTTCTCAGGTCCTCTTCCAGTTCACCTTTC
* *
20697 TGGTTCTTTAGAGAGATGACCTCCAATTCTAGTTCCTTCATTTGTGCCAACAAACTCTCTTTCTC
66 TGGTTCTTTAGAGAAATGACCTCCAATTCTAGTTCCTTCATTTGTGCCAACAAACCCTCTTTCTC
* * * *
20762 CTGCAGAACTCTCCGTTGATCCTCAGTCTTGCTTACGATCTCTTCTTTTGCCTTTTCTATCTCGA
131 CTGCAGAACTCTCTGTTGATCCTCGGTCTTGCTTACTATCTCTTCTTTTGCC-TTTCTATCTCAA
* ** *
20827 TCATATGATCTAAAATAGCTTGAGTTTTACTCTCAAGCTGAACTTCAAGTTCAGCTTTCTGGCTA
195 TCACATGATCGGAAATAGCTTGAGTTTTACTCTCAAGCTGAACTTCAAGTTCTGCTTTCTGGCTA
* * * * * *
20892 TGCATGGATTCCAGTTTCTGCTGCAATGTATTTATTTGATCCATCAAGCTCTTGACTTGA-TTCG
260 TGCAGGGACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACTTGAGTT-G
* * *
20956 ATGCTTCATCGCCTTTAACTACAATATGTTCTTCCAACTGAGCTTTCTCGGTCCGCAGCGACTCC
324 ATGCTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCTCGGTGCGTAGCGACTCC
* * * * * *
21021 ATGTCTCCTAGCAGATTGTTAATCTGCACAGTCAAATTATCCACTCTAGATAATAATTCTGTCTC
389 ATGTCTGCTAGCAGATTGTTGATCTGCACTGTCAAATTCTCCACTCTAGATAATGATTCTTTCTC
* *
21086 ATTATCCTCAAACTTCTTTCTGAGAGTCAAAAGTTCTTCTTGTCT-TGTCTTTGATATCATTTCG
454 ATTATCCTCAAACTTCTTTGTGAGAGTCAAAAGTTCTTCTTGTCTCTGT-TTTGATATCATCTCG
*
21150 AGTTCTGAAATTTGAGATTGCAGTCCCATAT
518 AGTTCTGAAATTTGAGATTGCAGTCCTATAT
* *
21181 TTTCCACCCTCAGCTGACCGTTCTCTTCGATTTTATTTCTCAGGTCCTCTTCCAGTTCACCTTTC
1 TTTCCACCCTCAGCTGACCATTCTCTTCGATTTTAGTTCTCAGGTCCTCTTCCAGTTCACCTTTC
21246 TGGTTCTTTAGAGAAATGACCTCCAATTCTAGTTCCTTCATTTGTGCCAACAAACCCTCTTTCTC
66 TGGTTCTTTAGAGAAATGACCTCCAATTCTAGTTCCTTCATTTGTGCCAACAAACCCTCTTTCTC
21311 CTGCAGAACTCTCTGTTGATCCTCGGTCTTGCTTACTATCTCTTCTTTTGCCTTCTCTATCTCAA
131 CTGCAGAACTCTCTGTTGATCCTCGGTCTTGCTTACTATCTCTTCTTTTGCCTT-TCTATCTCAA
* * *
21376 TCACATGATCGGAAATAGCTTGAGTTTTTCTCTCAAGCTGAACTTCCAGTTCTGTTTTCTGGCTA
195 TCACATGATCGGAAATAGCTTGAGTTTTACTCTCAAGCTGAACTTCAAGTTCTGCTTTCTGGCTA
*
21441 TGCAGGGACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACCTGAGTTGA
260 TGCAGGGACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACTTGAGTTGA
21506 TGCTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCT-GGATGCGTA-CGGACTC
325 TGCTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCTCGG-TGCGTAGC-GACTC
* *
21569 CATGTCTGCTAGCAAATTGTTGATCTGCACTGTCAAATTCTCTACTCTAGATAGA-GATTCTTTC
388 CATGTCTGCTAGCAGATTGTTGATCTGCACTGTCAAATTCTCCACTCTAGATA-ATGATTCTTTC
* * *
21633 TCGTTGTCCTCAAACTTCTTTGTGAGTGTCAAAAGTTCTTCTTGTCTCTGTTTTGATATCATCTC
452 TCATTATCCTCAAACTTCTTTGTGAGAGTCAAAAGTTCTTCTTGTCTCTGTTTTGATATCATCTC
* *
21698 GAGTTCTGAAATTTGAGATTGCAGTCCTAAAC
517 GAGTTCTGAAATTTGAGATTGCAGTCCTATAT
* * ** **
21730 TTTCCTCCCTCAGCTGACTATTCTCTTCGATTTTAGTTCTCAAATCCTCTTCCAACTCACCTTTC
1 TTTCCACCCTCAGCTGACCATTCTCTTCGATTTTAGTTCTCAGGTCCTCTTCCAGTTCACCTTTC
* * * * * *
21795 TGCTTCTTTA-ACGAATTGACATCAAATTCTAGTTCCTTCATTTGTGCCACCAAGCCCTCTTTCT
66 TGGTTCTTTAGA-GAAATGACCTCCAATTCTAGTTCCTTCATTTGTGCCAACAAACCCTCTTTCT
* * * *
21859 CCTGCAGAACTCTTTGTTGATCCTCGGTCTTGCTTGCTATCTCTTCTTTTGCATTTATGATCTCA
130 CCTGCAGAACTCTCTGTTGATCCTCGGTCTTGCTTACTATCTCTTCTTTTGCCTTTCT-ATCTCA
* *
21924 ATCACATGATCGGAAATCGCTTGAGTTTTACTCTCAAGCTGAACTTCAAGTTCTGCTTTCTGACT
194 ATCACATGATCGGAAATAGCTTGAGTTTTACTCTCAAGCTGAACTTCAAGTTCTGCTTTCTGGCT
** * * *
21989 CCGCAGGGACTCCAGCTCCTGCTGCAAATTATTTATCTGATCCATCAAGCTTTTGACTTGAGTGG
259 ATGCAGGGACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACTTGAGTTG
** * *
22054 ATGCTTCATCATCTTTCACTGCAATATGTTCTTCCAACTGAGCTTTCTCGGTGCGTAGTGACTCC
324 ATGCTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCTCGGTGCGTAGCGACTCC
* * *
22119 ATGTCTGCTAGCAGATTGTTGATCTGCAGTGTCAAGTTCTCCACTCTAGACAATGATTCTTTCTC
389 ATGTCTGCTAGCAGATTGTTGATCTGCACTGTCAAATTCTCCACTCTAGATAATGATTCTTTCTC
** * * * * *
22184 ATTATCCTCAATTTTTTTTGCGAGAGTCAAAAGTTCTTCTTCTCTCT-TTTCTGACATCATCTCA
454 ATTATCCTCAAACTTCTTTGTGAGAGTCAAAAGTTCTTCTTGTCTCTGTTT-TGATATCATCTCG
*
22248 AGTTCTGAAATTTGGGATTGCAGTCCTATAT
518 AGTTCTGAAATTTGAGATTGCAGTCCTATAT
22279 TT
1 TT
22281 ACCTCTCCCA
Statistics
Matches: 992, Mismatches: 96, Indels: 24
0.89 0.09 0.02
Matches are distributed among these distances:
548 12 0.01
549 972 0.98
550 8 0.01
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.39
Consensus pattern (548 bp):
TTTCCACCCTCAGCTGACCATTCTCTTCGATTTTAGTTCTCAGGTCCTCTTCCAGTTCACCTTTC
TGGTTCTTTAGAGAAATGACCTCCAATTCTAGTTCCTTCATTTGTGCCAACAAACCCTCTTTCTC
CTGCAGAACTCTCTGTTGATCCTCGGTCTTGCTTACTATCTCTTCTTTTGCCTTTCTATCTCAAT
CACATGATCGGAAATAGCTTGAGTTTTACTCTCAAGCTGAACTTCAAGTTCTGCTTTCTGGCTAT
GCAGGGACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACTTGAGTTGAT
GCTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCTCGGTGCGTAGCGACTCCAT
GTCTGCTAGCAGATTGTTGATCTGCACTGTCAAATTCTCCACTCTAGATAATGATTCTTTCTCAT
TATCCTCAAACTTCTTTGTGAGAGTCAAAAGTTCTTCTTGTCTCTGTTTTGATATCATCTCGAGT
TCTGAAATTTGAGATTGCAGTCCTATAT
Found at i:44290 original size:25 final size:26
Alignment explanation
Indices: 44243--44292 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
44233 TAAAGATTTG
*
44243 GGATAATTTTCTTTAATGCATCACAA
1 GGATAACTTTCTTTAATGCATCACAA
* *
44269 GGATAACTTT-TTTAGTGTATCACA
1 GGATAACTTTCTTTAATGCATCACA
44293 TGCTCAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (26 bp):
GGATAACTTTCTTTAATGCATCACAA
Found at i:45364 original size:15 final size:15
Alignment explanation
Indices: 45335--45377 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
45325 AACTTAATAC
* *
45335 TATAAATTATATATT
1 TATAAATAATTTATT
45350 TATAAATAATTTATT
1 TATAAATAATTTATT
*
45365 CATAACATAATTT
1 TATAA-ATAATTT
45378 TCATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
TATAAATAATTTATT
Found at i:50121 original size:26 final size:26
Alignment explanation
Indices: 50091--50171 Score: 71
Period size: 26 Copynumber: 3.1 Consensus size: 26
50081 AACTTTTAAA
50091 TTATTTTCACTATT-T-AAAATAAATAT
1 TTATTTTCA-TATTATAAAAATAAAT-T
*
50117 TTATTTTTATATTATAAAAATAAATT
1 TTATTTTCATATTATAAAAATAAATT
* *
50143 TTA-TAT-ATATATATATAAAATAAAAT
1 TTATTTTCATAT-TATA-AAAATAAATT
50169 TTA
1 TTA
50172 AATCGTTTGC
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.08
25 10 0.21
26 25 0.52
27 9 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
TTATTTTCATATTATAAAAATAAATT
Found at i:50136 original size:27 final size:27
Alignment explanation
Indices: 50105--50171 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 27
50095 TTTCACTATT
* *
50105 TAAAATAAATATTTATTTTTATAT-TA
1 TAAAATAAATATTTATATATATATATA
50131 TAAAAATAAAT-TTTATATATATATATA
1 T-AAAATAAATATTTATATATATATATA
50158 TAAAATAAA-ATTTA
1 TAAAATAAATATTTA
50172 AATCGTTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 24 0.67
27 12 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TAAAATAAATATTTATATATATATATA
Found at i:50845 original size:6 final size:6
Alignment explanation
Indices: 50813--50843 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
50803 AATCCGTTGT
*
50813 CGCTGC CGCTGC CGCTGC CGCTGC CTCTGC C
1 CGCTGC CGCTGC CGCTGC CGCTGC CGCTGC C
50844 TCCACACCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.52, G:0.29, T:0.19
Consensus pattern (6 bp):
CGCTGC
Done.