Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011734.1 Kokia drynarioides strain JFW-HI SEQ_126728, 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: 46926
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:313 original size:10 final size:10
Alignment explanation
Indices: 298--323 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
288 AAGAAACTGA
298 AATGGAGCTG
1 AATGGAGCTG
308 AATGGAGCTG
1 AATGGAGCTG
318 AATGGA
1 AATGGA
324 CTAGGCTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.08, G:0.38, T:0.19
Consensus pattern (10 bp):
AATGGAGCTG
Found at i:368 original size:10 final size:10
Alignment explanation
Indices: 345--378 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
335 TCAAACAAGA
345 GGAGCTGAAAT
1 GGAGCTG-AAT
356 GGAGCTGAAT
1 GGAGCTGAAT
366 GGAGCTGAAT
1 GGAGCTGAAT
376 GGA
1 GGA
379 CTAGGCTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.32, C:0.09, G:0.41, T:0.18
Consensus pattern (10 bp):
GGAGCTGAAT
Found at i:378 original size:55 final size:55
Alignment explanation
Indices: 294--401 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 55
284 AAGTAAGAAA
294 CTGAAATGGAGCTGAATGGAGCTGAATGGACTAGGCTAGATTCAAACAAGAGGAG
1 CTGAAATGGAGCTGAATGGAGCTGAATGGACTAGGCTAGATTCAAACAAGAGGAG
**
349 CTGAAATGGAGCTGAATGGAGCTGAATGGACTAGGCTAGATTCAGCCAAGAGG
1 CTGAAATGGAGCTGAATGGAGCTGAATGGACTAGGCTAGATTCAAACAAGAGG
402 TGTGAAAGGC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.19
Consensus pattern (55 bp):
CTGAAATGGAGCTGAATGGAGCTGAATGGACTAGGCTAGATTCAAACAAGAGGAG
Found at i:706 original size:32 final size:32
Alignment explanation
Indices: 670--732 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
660 GCCATCCATA
* * *
670 CATGTACCTGAAATATATTAATCAGCTAATTG
1 CATGTACCTGAAACACATTAATCAACTAATTG
702 CATGTACCTGAAACACATTAATCAACTAATT
1 CATGTACCTGAAACACATTAATCAACTAATT
733 AATTTCGGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.32
Consensus pattern (32 bp):
CATGTACCTGAAACACATTAATCAACTAATTG
Found at i:821 original size:39 final size:39
Alignment explanation
Indices: 778--876 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
768 TTAATTTGTC
* * * *
778 TCAAACTTAGACACCTTAAAAATAACTATTAAATATGTA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGAA
*
817 TCAAAATAAGACACATTAAAAACAACTATTAAATATGAA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGAA
856 TCAAACTAAGACACATTAAAA
1 TCAAACTAAGACACATTAAAA
877 CCTTATTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (39 bp):
TCAAACTAAGACACATTAAAAACAACTATTAAATATGAA
Found at i:9916 original size:15 final size:15
Alignment explanation
Indices: 9861--9928 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
9851 CCTTCATCCA
*
9861 TGCTCGTAACATGAG
1 TGCTCGCAACATGAG
* *
9876 TGTTCGCAACATCAG
1 TGCTCGCAACATGAG
* *
9891 TGTTCACAACATGAG
1 TGCTCGCAACATGAG
*
9906 TGCTCGTAACACT-AG
1 TGCTCGCAACA-TGAG
9921 TGCTCGCA
1 TGCTCGCA
9929 TCTTCTAAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
15 42 0.98
16 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (15 bp):
TGCTCGCAACATGAG
Found at i:10481 original size:17 final size:17
Alignment explanation
Indices: 10452--10484 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
10442 CATTAAACTC
10452 AACTTCAGCTTATTTTT
1 AACTTCAGCTTATTTTT
10469 AACTT-AGCATTATTTT
1 AACTTCAGC-TTATTTT
10485 GCTGGGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (17 bp):
AACTTCAGCTTATTTTT
Found at i:10719 original size:32 final size:32
Alignment explanation
Indices: 10683--10745 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
10673 AGCTGAAATT
* *
10683 AATTAGCTGATTAATGTGTTTCAGGTACATGC
1 AATTAGCTGATTAATATATTTCAGGTACATGC
10715 AATTAGCTGATTAATATATTTCAGGTACATG
1 AATTAGCTGATTAATATATTTCAGGTACATG
10746 TATGGATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTCAGGTACATGC
Found at i:22570 original size:18 final size:18
Alignment explanation
Indices: 22547--22585 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
22537 ATTAGGTACC
*
22547 TTTTGATA-CTTTGATGAA
1 TTTTGATATCTTAG-TGAA
22565 TTTTGATATCTTAGTGAA
1 TTTTGATATCTTAGTGAA
22583 TTT
1 TTT
22586 ATTCAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (18 bp):
TTTTGATATCTTAGTGAA
Found at i:25226 original size:18 final size:19
Alignment explanation
Indices: 25203--25238 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25193 AGAGTGAGAA
25203 TGAAAAA-GAAAAGAAAAT
1 TGAAAAAGGAAAAGAAAAT
*
25221 TGAAAAAGGAAAGGAAAA
1 TGAAAAAGGAAAAGAAAA
25239 ATGAGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.08
Consensus pattern (19 bp):
TGAAAAAGGAAAAGAAAAT
Found at i:30617 original size:24 final size:24
Alignment explanation
Indices: 30584--30633 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
30574 GTGTTCCGAC
*
30584 GATCTGGGATCGCCAAAATGGAGA
1 GATCTAGGATCGCCAAAATGGAGA
30608 GATCTAGGATCGCCAAAATGGAGA
1 GATCTAGGATCGCCAAAATGGAGA
30632 GA
1 GA
30634 ACTGGGGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (24 bp):
GATCTAGGATCGCCAAAATGGAGA
Found at i:30921 original size:20 final size:20
Alignment explanation
Indices: 30899--30978 Score: 76
Period size: 20 Copynumber: 4.0 Consensus size: 20
30889 AATCAAGTTA
30899 AAAAT-ATTTTAAACAAGTC
1 AAAATCATTTTAAACAAGTC
* * *
30918 AAAATGATTTCAACCAAGTC
1 AAAATCATTTTAAACAAGTC
*
30938 AAAATCATTTT-AACTCA-TC
1 AAAATCATTTTAAAC-AAGTC
*
30957 AAAATGATTTTCAAACAAGTC
1 AAAATCATTTT-AAACAAGTC
30978 A
1 A
30979 GAATTGCTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
19 19 0.40
20 23 0.48
21 6 0.12
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.30
Consensus pattern (20 bp):
AAAATCATTTTAAACAAGTC
Found at i:30948 original size:40 final size:39
Alignment explanation
Indices: 30899--30978 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 39
30889 AATCAAGTTA
*
30899 AAAATATTTTAAAC-AAGTCAAAATGA-TTTCAACCAAGTC
1 AAAATATTTT-AACTAA-TCAAAATGATTTTCAAACAAGTC
*
30938 AAAATCATTTTAACTCATCAAAATGATTTTCAAACAAGTC
1 AAAAT-ATTTTAACTAATCAAAATGATTTTCAAACAAGTC
30978 A
1 A
30979 GAATTGCTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
39 17 0.47
40 19 0.53
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.30
Consensus pattern (39 bp):
AAAATATTTTAACTAATCAAAATGATTTTCAAACAAGTC
Found at i:32575 original size:3 final size:3
Alignment explanation
Indices: 32560--32600 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
32550 ATCGCTTCTC
*
32560 TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
32601 CACTTCCATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:33770 original size:305 final size:305
Alignment explanation
Indices: 33219--33831 Score: 1208
Period size: 305 Copynumber: 2.0 Consensus size: 305
33209 TTATTATAGG
33219 GATTATAGTTATTATAAAAGGCTAAATTCATATTCTCACTTTTCCGAGCATTGTTTATTGCTTCT
1 GATTATAGTTATTATAAAAGGCTAAATTCATATTCTCACTTTTCCGAGCATTGTTTATTGCTTCT
33284 GAGGCATATATAAACCAATGTCTACAGTACGGCATGTATGAAGCTTGAGGAGTATCAAACTGCTA
66 GAGGCATATATAAACCAATGTCTACAGTACGGCATGTATGAAGCTTGAGGAGTATCAAACTGCTA
*
33349 AGGCTGCGTTGGAGATTGGTGCCGCTTTGGCACCGGGAGAGTCGAGATTTTCTAAGTTGATCAAA
131 AGGCTGCGTTGGAGATTGGTGCCACTTTGGCACCGGGAGAGTCGAGATTTTCTAAGTTGATCAAA
*
33414 GAATGTGAAGAGCGTATTGCGGGTACTTAGCTTTAATAAGGGTGTTTAGGAAGGAAGGAGTTTAT
196 GAATGTGAAGAGCGCATTGCGGGTACTTAGCTTTAATAAGGGTGTTTAGGAAGGAAGGAGTTTAT
33479 CTACTGATATTGCTATATATTTAAAATTAACCTATACCGTTTTGA
261 CTACTGATATTGCTATATATTTAAAATTAACCTATACCGTTTTGA
33524 GATTATAGTTATTATAAAAGGCTAAATTCATATTCTCACTTTTCCGAGCATTGTTTATTGCTTCT
1 GATTATAGTTATTATAAAAGGCTAAATTCATATTCTCACTTTTCCGAGCATTGTTTATTGCTTCT
33589 GAGGCATATATAAACCAATGTCTACAGTACGGCATGTATGAAGCTTGAGGAGTATCAAACTGCTA
66 GAGGCATATATAAACCAATGTCTACAGTACGGCATGTATGAAGCTTGAGGAGTATCAAACTGCTA
33654 AGGCTGCGTTGGAGATTGGTGCCACTTTGGCACCGGGAGAGTCGAGATTTTCTAAGTTGATCAAA
131 AGGCTGCGTTGGAGATTGGTGCCACTTTGGCACCGGGAGAGTCGAGATTTTCTAAGTTGATCAAA
33719 GAATGTGAAGAGCGCATTGCGGGTACTTAGCTTTAATAAGGGTGTTTAGGAAGGAAGGAGTTTAT
196 GAATGTGAAGAGCGCATTGCGGGTACTTAGCTTTAATAAGGGTGTTTAGGAAGGAAGGAGTTTAT
33784 CTACTGATATTGCTATATATTTAAAATTAACCTATACCGTTTTGA
261 CTACTGATATTGCTATATATTTAAAATTAACCTATACCGTTTTGA
33829 GAT
1 GAT
33832 CCTTCCTTGT
Statistics
Matches: 306, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
305 306 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.33
Consensus pattern (305 bp):
GATTATAGTTATTATAAAAGGCTAAATTCATATTCTCACTTTTCCGAGCATTGTTTATTGCTTCT
GAGGCATATATAAACCAATGTCTACAGTACGGCATGTATGAAGCTTGAGGAGTATCAAACTGCTA
AGGCTGCGTTGGAGATTGGTGCCACTTTGGCACCGGGAGAGTCGAGATTTTCTAAGTTGATCAAA
GAATGTGAAGAGCGCATTGCGGGTACTTAGCTTTAATAAGGGTGTTTAGGAAGGAAGGAGTTTAT
CTACTGATATTGCTATATATTTAAAATTAACCTATACCGTTTTGA
Found at i:36549 original size:11 final size:10
Alignment explanation
Indices: 36533--36563 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
36523 GCGCCGAGAC
36533 AAAAAAAAAT
1 AAAAAAAAAT
36543 AAAAAAAAAT
1 AAAAAAAAAT
36553 AAAAAATAAAT
1 AAAAAA-AAAT
36564 CAGCCAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (10 bp):
AAAAAAAAAT
Done.