Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012935.1 Kokia drynarioides strain JFW-HI SEQ_127953, 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: 15992
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:2438 original size:20 final size:21
Alignment explanation
Indices: 2406--2445 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2396 ATTATTTTTT
2406 ATGAGAAAAT-AAATTTTAAA
1 ATGAGAAAATAAAATTTTAAA
2426 ATGA-AAAAGTAAAATTTTAA
1 ATGAGAAAA-TAAAATTTTAA
2446 GAAAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (21 bp):
ATGAGAAAATAAAATTTTAAA
Found at i:2824 original size:28 final size:30
Alignment explanation
Indices: 2777--2836 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 30
2767 TTAATGTTAT
*
2777 TTTAATGATTGTTTTAAAATAATATTATATA
1 TTTAATGA-TGTTTTAAAATAATATAATATA
*
2808 TTTAATG-TGTTTT-AAATTATATAATATA
1 TTTAATGATGTTTTAAAATAATATAATATA
2836 T
1 T
2837 AAATTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 14 0.52
29 6 0.22
31 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (30 bp):
TTTAATGATGTTTTAAAATAATATAATATA
Found at i:4262 original size:17 final size:17
Alignment explanation
Indices: 4233--4281 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 17
4223 TTTTTTTGGT
4233 GATATCAATATTTAATG
1 GATATCAATATTTAATG
* *
4250 GATGTCAAAATTTTTAATG
1 GATATC--AATATTTAATG
4269 GATATCAATATTT
1 GATATCAATATTT
4282 CTAACATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 11 0.42
19 15 0.58
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (17 bp):
GATATCAATATTTAATG
Found at i:4267 original size:19 final size:19
Alignment explanation
Indices: 4243--4303 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
4233 GATATCAATA
*
4243 TTTAATGGATGTCAAAATT
1 TTTAATGGATATCAAAATT
*
4262 TTTAATGGATATCAATATT
1 TTTAATGGATATCAAAATT
*
4281 TCTAACAT-GATATCCAAAATT
1 T-TTA-ATGGATAT-CAAAATT
4302 TT
1 TT
4304 AATAGATGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 18 0.51
20 8 0.23
21 9 0.26
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (19 bp):
TTTAATGGATATCAAAATT
Found at i:4491 original size:47 final size:48
Alignment explanation
Indices: 4398--4492 Score: 113
Period size: 47 Copynumber: 2.0 Consensus size: 48
4388 AAATGCTCTC
* * **
4398 AAAAATTCTGACACTTGATTAGAAATTTTGGTATCGCACTCGAAATAA
1 AAAAATTCTGACACTTAATTAGAAATTTTGGTATCGCAATAAAAATAA
* *
4446 AAAAATT-TGATACTTAATTA-AGAATTTTGGTATCGTAATAAAAATAA
1 AAAAATTCTGACACTTAATTAGA-AATTTTGGTATCGCAATAAAAATAA
4493 TATCTAACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
46 1 0.03
47 32 0.80
48 7 0.17
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (48 bp):
AAAAATTCTGACACTTAATTAGAAATTTTGGTATCGCAATAAAAATAA
Found at i:6892 original size:6 final size:6
Alignment explanation
Indices: 6872--6978 Score: 75
Period size: 6 Copynumber: 18.5 Consensus size: 6
6862 ATATTTAAGA
** *
6872 TTAAAT TTATTT TTAAAT TTAAAT TT--AT TCTAAAT TTAAAT TT--GT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT TTAAAT
* * *
6917 TATAAAT TTAAAT TTAAA- TTAAGT TTAAAT TT-ACT TGTAAAT TTAAAA
1 T-TAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT
*
6965 TT-ATT TTAAAT TTA
1 TTAAAT TTAAAT TTA
6979 TTAAAAGTCC
Statistics
Matches: 77, Mismatches: 14, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
4 5 0.06
5 12 0.16
6 52 0.68
7 8 0.10
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:6907 original size:17 final size:16
Alignment explanation
Indices: 6855--6978 Score: 115
Period size: 17 Copynumber: 7.2 Consensus size: 16
6845 ACCAAACCTT
*
6855 TTTAAATATATTTAAGA
1 TTTAAATTTATTTAA-A
6872 -TTAAATTTATTTTTAAA
1 TTTAAATTTA--TTTAAA
6889 TTTAAATTTATTCTAAA
1 TTTAAATTTATT-TAAA
*
6906 TTTAAATTTGTTATAAA
1 TTTAAATTTATT-TAAA
* *
6923 TTTAAATTTAAATTAAG
1 TTTAAATTT-ATTTAAA
6940 TTTAAATTTACTTGTAAA
1 TTTAAATTTA-TT-TAAA
*
6958 TTTAAAATTATTTTAAA
1 TTTAAATTTA-TTTAAA
6975 TTTA
1 TTTA
6979 TTAAAAGTCC
Statistics
Matches: 90, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
16 11 0.12
17 50 0.56
18 29 0.32
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:6928 original size:23 final size:23
Alignment explanation
Indices: 6866--6949 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
6856 TTAAATATAT
* **
6866 TTAAGATTAAATTTATTTTTAAA
1 TTAAGTTTAAATTTAAATTTAAA
*
6889 TTTAAATTT--ATTCTAAATTTAAA
1 -TTAAGTTTAAATT-TAAATTTAAA
*
6912 TT-TGTTATAAATTTAAATTTAAA
1 TTAAGTT-TAAATTTAAATTTAAA
6935 TTAAGTTTAAATTTA
1 TTAAGTTTAAATTTA
6950 CTTGTAAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
21 2 0.04
22 6 0.12
23 28 0.58
24 12 0.25
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (23 bp):
TTAAGTTTAAATTTAAATTTAAA
Found at i:7596 original size:3 final size:3
Alignment explanation
Indices: 7588--7617 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
7578 TTATTGAGTT
7588 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7618 AAATAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:10464 original size:17 final size:18
Alignment explanation
Indices: 10418--10465 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
10408 AGGAGGGATT
10418 TTGGGCAGAGGAGCAGTC
1 TTGGGCAGAGGAGCAGTC
*
10436 TCAGGG-AGAGGAGCA-TC
1 T-TGGGCAGAGGAGCAGTC
10453 TTGGGCAGAGGAG
1 TTGGGCAGAGGAG
10466 ATGTAACACC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.12
17 10 0.38
18 10 0.38
19 3 0.12
ACGTcount: A:0.25, C:0.15, G:0.46, T:0.15
Consensus pattern (18 bp):
TTGGGCAGAGGAGCAGTC
Found at i:11745 original size:12 final size:12
Alignment explanation
Indices: 11728--11757 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
11718 TAAAATTAAA
11728 CACATAATATTT
1 CACATAATATTT
11740 CACATAATATTT
1 CACATAATATTT
11752 CACATA
1 CACATA
11758 TACCTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (12 bp):
CACATAATATTT
Found at i:13291 original size:19 final size:20
Alignment explanation
Indices: 13245--13294 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
13235 TTAAAAAATA
13245 TTAATTTTTTT--TTATATT
1 TTAATTTTTTTAATTATATT
**
13263 TTAAACTTTTTAATTAT-TT
1 TTAATTTTTTTAATTATATT
13282 TTAATTTTTTTAA
1 TTAATTTTTTTAA
13295 AATAATGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 9 0.35
19 13 0.50
20 4 0.15
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTAATTTTTTTAATTATATT
Done.