Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007554.1 Kokia drynarioides strain JFW-HI SEQ_122182, 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: 41893
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:2951 original size:15 final size:15
Alignment explanation
Indices: 2931--2970 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2921 TAAAGGATCC
2931 ATTAAATCAAATTGA
1 ATTAAATCAAATTGA
* *
2946 ATTAAATTAAGTTGA
1 ATTAAATCAAATTGA
*
2961 ATCAAATCAA
1 ATTAAATCAA
2971 TTAAATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
ATTAAATCAAATTGA
Found at i:4716 original size:27 final size:28
Alignment explanation
Indices: 4642--4719 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 28
4632 AAATTTTAAT
*
4642 TTTTTATATATATTTTTAAAATTTTGAAAA
1 TTTTTATAAATA-TTTT-AAATTTTGAAAA
* *
4672 TTGTTTTTAAA-A-TATAAATTTTGAAAA
1 TT-TTTATAAATATTTTAAATTTTGAAAA
4699 -TTTTATAAATATTTTAAATTT
1 TTTTTATAAATATTTTAAATTT
4720 AAAAAGTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
25 7 0.17
26 2 0.05
27 20 0.50
28 2 0.05
30 3 0.08
31 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (28 bp):
TTTTTATAAATATTTTAAATTTTGAAAA
Found at i:4750 original size:9 final size:9
Alignment explanation
Indices: 4729--4772 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 9
4719 TAAAAAGTTA
4729 TTTTGAA-T
1 TTTTGAATT
4737 TTTTGAATT
1 TTTTGAATT
4746 TTTTGAATTT
1 TTTTGAA-TT
4756 TTTTGTAATT
1 TTTTG-AATT
4766 TTGTTGA
1 TT-TTGA
4773 GAGAGGCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 7 0.22
9 8 0.25
10 12 0.38
11 5 0.16
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (9 bp):
TTTTGAATT
Found at i:7926 original size:9 final size:9
Alignment explanation
Indices: 7912--7993 Score: 54
Period size: 9 Copynumber: 9.7 Consensus size: 9
7902 ATAATCACCC
7912 ATTAAAATT
1 ATTAAAATT
7921 ATTAAAATT
1 ATTAAAATT
7930 ATT----TT
1 ATTAAAATT
7935 -TTAAAATT
1 ATTAAAATT
7943 A-TAAAATTCT
1 ATTAAAA-T-T
*
7953 TTTAAATATT
1 ATTAAA-ATT
* *
7963 TTTTAAA-T
1 ATTAAAATT
7971 A-TAAAATT
1 ATTAAAATT
7979 ATTAAAATT
1 ATTAAAATT
7988 ATTAAA
1 ATTAAA
7994 TAATTTTAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 22
0.69 0.05 0.26
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
7 4 0.07
8 10 0.17
9 27 0.47
10 7 0.12
11 5 0.09
12 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (9 bp):
ATTAAAATT
Found at i:7948 original size:30 final size:28
Alignment explanation
Indices: 7914--7990 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 28
7904 AATCACCCAT
7914 TAAAATTATTAAAATTATTTTTTAAAATTA
1 TAAAATTATTAAAATTATTTTTT-AAA-TA
* *
7944 TAAAATTCTTTTAAA-TATTTTTTAAATA
1 TAAAATT-ATTAAAATTATTTTTTAAATA
7972 TAAAATTATTAAAATTATT
1 TAAAATTATTAAAATTATT
7991 AAATAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.12
28 13 0.32
29 3 0.07
30 15 0.37
31 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTTAAATA
Found at i:7949 original size:21 final size:22
Alignment explanation
Indices: 7913--7955 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
7903 TAATCACCCA
7913 TTAAAATTATTAAAATTATTTT
1 TTAAAATTATTAAAATTATTTT
*
7935 TTAAAATTA-TAAAATTCTTTT
1 TTAAAATTATTAAAATTATTTT
7956 AAATATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAATTATTAAAATTATTTT
Found at i:8078 original size:35 final size:35
Alignment explanation
Indices: 8039--8107 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
8029 TATTTTTTCT
8039 CCATTTTTCCATCTAACACCACTTCTTATTCTCAC
1 CCATTTTTCCATCTAACACCACTTCTTATTCTCAC
* *
8074 CCATTTTTCCATCTAGCACCACTTCTTCTTCTCA
1 CCATTTTTCCATCTAACACCACTTCTTATTCTCA
8108 TCATCCAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.20, C:0.38, G:0.01, T:0.41
Consensus pattern (35 bp):
CCATTTTTCCATCTAACACCACTTCTTATTCTCAC
Found at i:8997 original size:51 final size:51
Alignment explanation
Indices: 8926--9025 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 51
8916 GATGATGATG
8926 ATTTTAATAATTTTATA-TTTTAAAAAATAATTTTAAGTTAATTTTAAAATAA
1 ATTTTAATAATTTTATATTTTTAAAAAATAATTTTAA--TAATTTTAAAATAA
*
8978 ATTTT-ATATTTTTATATTTTTAAAAAATAATTTTAATAATTTTAAAAT
1 ATTTTAATAATTTTATATTTTTAAAAAATAATTTTAATAATTTTAAAAT
9026 CATTTGTTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
50 12 0.26
51 10 0.22
52 24 0.52
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (51 bp):
ATTTTAATAATTTTATATTTTTAAAAAATAATTTTAATAATTTTAAAATAA
Found at i:9683 original size:3 final size:3
Alignment explanation
Indices: 9671--9718 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
9661 GTATCTCTAT
*
9671 TTC TTC -TC TTC TTC TT- TTC -TC TTT TTC TTC TTC TTC -TC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
9715 TTC T
1 TTC T
9719 ACTGCCCAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 8 0.21
3 31 0.79
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:9684 original size:8 final size:8
Alignment explanation
Indices: 9671--9715 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
9661 GTATCTCTAT
9671 TTCTTCTC
1 TTCTTCTC
9679 TTC-T-TC
1 TTCTTCTC
9685 TT-TTCTC
1 TTCTTCTC
*
9692 TTTTTCTTC
1 TTCTTC-TC
9701 TTCTTCTC
1 TTCTTCTC
9709 TTCTTCT
1 TTCTTCT
9716 TCTACTGCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
6 5 0.16
7 5 0.16
8 15 0.47
9 7 0.22
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (8 bp):
TTCTTCTC
Found at i:9685 original size:11 final size:11
Alignment explanation
Indices: 9671--9718 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
9661 GTATCTCTAT
9671 TTCTTCTCTTC
1 TTCTTCTCTTC
*
9682 TTCTTTTC-TC
1 TTCTTCTCTTC
9692 TT-TT-TCTTC
1 TTCTTCTCTTC
9701 TTCTTCTCTTC
1 TTCTTCTCTTC
9712 TTCTTCT
1 TTCTTCT
9719 ACTGCCCAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 2 0.06
9 6 0.18
10 6 0.18
11 19 0.58
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (11 bp):
TTCTTCTCTTC
Found at i:14519 original size:6 final size:6
Alignment explanation
Indices: 14508--14592 Score: 65
Period size: 6 Copynumber: 14.7 Consensus size: 6
14498 GGGCCCAACA
* * * *
14508 AAATTT AAATTT -ATTTT AAAATT AAATTT -ATTTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
14554 --ATTT AAAATTT AAATTT --ATTAT AAATTT AAAGTTT AAAT
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAA-TTT AAAT
14593 ATATTTAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
4 7 0.11
5 9 0.14
6 34 0.54
7 13 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:14554 original size:34 final size:34
Alignment explanation
Indices: 14508--14589 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
14498 GGGCCCAACA
*
14508 AAATTTAAATTTATTTTAAAA-TTAAATTTATTTT
1 AAATTTAAATTTA-TTTAAAATTTAAATTTATTAT
*
14542 AAGTTTAAATTTATTTAAAATTTAAATTTATTAT
1 AAATTTAAATTTATTTAAAATTTAAATTTATTAT
14576 AAATTTAAAGTTTA
1 AAATTTAAA-TTTA
14590 AATATATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 7 0.16
34 32 0.74
35 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (34 bp):
AAATTTAAATTTATTTAAAATTTAAATTTATTAT
Found at i:14581 original size:24 final size:23
Alignment explanation
Indices: 14554--14602 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
14544 GTTTAAATTT
*
14554 ATTTAAAATTTAAATTTATTATAA
1 ATTTAAAATTTAAATATATT-TAA
*
14578 ATTTAAAGTTTAAATATATTTAA
1 ATTTAAAATTTAAATATATTTAA
14601 AT
1 AT
14603 CAAAGTCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTTAAAATTTAAATATATTTAA
Found at i:14599 original size:34 final size:34
Alignment explanation
Indices: 14508--14602 Score: 95
Period size: 34 Copynumber: 2.8 Consensus size: 34
14498 GGGCCCAACA
** *
14508 AAATTTAAATTTATTTTAAAA-TTAAATTTATTTT
1 AAATTTAAATTTA-AATAAAATTTAAATTTATTAT
* **
14542 AAGTTTAAATTTATTTAAAATTTAAATTTATTAT
1 AAATTTAAATTTAAATAAAATTTAAATTTATTAT
*
14576 AAATTTAAAGTTTAAAT-ATATTTAAAT
1 AAATTTAAA-TTTAAATAAAATTTAAAT
14603 CAAAGTCCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
33 7 0.13
34 41 0.77
35 5 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (34 bp):
AAATTTAAATTTAAATAAAATTTAAATTTATTAT
Found at i:14601 original size:17 final size:16
Alignment explanation
Indices: 14508--14589 Score: 101
Period size: 17 Copynumber: 4.8 Consensus size: 16
14498 GGGCCCAACA
14508 AAATTTAAATTTATTTT
1 AAATTTAAATTTA-TTT
*
14525 AAAATTAAATTTATTTT
1 AAATTTAAATTTA-TTT
*
14542 AAGTTTAAATTTATTT
1 AAATTTAAATTTATTT
14558 AAAATTTAAATTTATTAT
1 -AAATTTAAATTTATT-T
14576 AAATTTAAAGTTTA
1 AAATTTAAA-TTTA
14590 AATATATTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
16 3 0.05
17 50 0.86
18 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AAATTTAAATTTATTT
Found at i:14665 original size:17 final size:17
Alignment explanation
Indices: 14643--14675 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
14633 CAAGCCCAAT
*
14643 TAAATGACCCTAATACC
1 TAAATGACCCAAATACC
14660 TAAATGACCCAAATAC
1 TAAATGACCCAAATAC
14676 TAATGGACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.27, G:0.06, T:0.21
Consensus pattern (17 bp):
TAAATGACCCAAATACC
Found at i:15428 original size:16 final size:16
Alignment explanation
Indices: 15368--15418 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
15358 TTCAACAAAT
15368 AATAATATCT-ATAATA
1 AATAATAT-TAATAATA
*
15384 ATGATAACATTAATAATA
1 A--ATAATATTAATAATA
15402 AATAATATTAATAATA
1 AATAATATTAATAATA
15418 A
1 A
15419 CATTAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 16 0.53
17 1 0.03
18 13 0.43
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (16 bp):
AATAATATTAATAATA
Found at i:16464 original size:29 final size:30
Alignment explanation
Indices: 16417--16519 Score: 129
Period size: 29 Copynumber: 3.5 Consensus size: 30
16407 GAGGTCCCTA
*
16417 AACTGTCCAAAAATTCCATATTTACCCCCG
1 AACTGTCCAAAAATTCCATTTTTACCCCCG
16447 AACT-TCCAAAAATTCCATTTTTACCCCCG
1 AACTGTCCAAAAATTCCATTTTTACCCCCG
* * * *
16476 AA-TGTCTAAAAATTTCATTTTTAACCTCG
1 AACTGTCCAAAAATTCCATTTTTACCCCCG
* *
16505 AACTTTCCCAAAATT
1 AACTGTCCAAAAATT
16520 ACCACTTTGT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 1 0.02
29 49 0.78
30 13 0.21
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (30 bp):
AACTGTCCAAAAATTCCATTTTTACCCCCG
Found at i:21983 original size:158 final size:158
Alignment explanation
Indices: 21675--22010 Score: 415
Period size: 158 Copynumber: 2.1 Consensus size: 158
21665 GTAACCATAT
* * * ** *
21675 ATGCTCACTCGAGCTGTGAAATGGACCTGCTCACACGAGCTATGGGTCGAGATGTGGGGCTACAC
1 ATGCTCACACGAGCTATAAAATGGGTCTGCTCACACGAGCTATGGGTCGAGATGTGAGGCTACAC
* * * * * * *
21740 GATGTTGCTCACACGAGTTGTGGAGAATCCGCAATAAATGTCGAACCTCAGCCATCGGTATGACA
66 GATGCTGCTCACACGAGATGTGAAGAATCCGCAACAAATGTCAAACCTCAGCCATCGGTAGGAAA
* ** *
21805 TCTAAAATTAACACCTATATAACCTGTA
131 TCCAAAACCAACACCTATATAACCTGGA
* * *
21833 ATGCTGACACGAGCTATAAAATGGGTCTGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACAC
1 ATGCTCACACGAGCTATAAAATGGGTCTGCTCACACGAGCTATGGGTCGAGATGTGAGGCTACAC
* *
21898 GATGCTGCTCACACGAGATGTGAAGAATCCGCAACCAATG-CAAGACCTCAGCCATTGGTAGGAA
66 GATGCTGCTCACACGAGATGTGAAGAATCCGCAACAAATGTCAA-ACCTCAGCCATCGGTAGGAA
* *
21962 ATCCAAGACCAGCA-CTCATATAACCTGGA
130 ATCCAAAACCAACACCT-ATATAACCTGGA
*
21991 ATGCTCACACGAGCTGTAAA
1 ATGCTCACACGAGCTATAAA
22011 TATAACATGT
Statistics
Matches: 150, Mismatches: 26, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
157 4 0.03
158 146 0.97
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (158 bp):
ATGCTCACACGAGCTATAAAATGGGTCTGCTCACACGAGCTATGGGTCGAGATGTGAGGCTACAC
GATGCTGCTCACACGAGATGTGAAGAATCCGCAACAAATGTCAAACCTCAGCCATCGGTAGGAAA
TCCAAAACCAACACCTATATAACCTGGA
Found at i:22095 original size:26 final size:26
Alignment explanation
Indices: 22030--22097 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
22020 TAATCATATA
*
22030 TGCTCACACGAGCTGTGAAATGAGTC
1 TGCTCACACGAGCTGTAAAATGAGTC
* *
22056 TGCTCACACAAGCTGTAAAATGGGTC
1 TGCTCACACGAGCTGTAAAATGAGTC
* *
22082 TGCTTACATGAGCTGT
1 TGCTCACACGAGCTGT
22098 GGGTCTAGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (26 bp):
TGCTCACACGAGCTGTAAAATGAGTC
Found at i:38353 original size:19 final size:18
Alignment explanation
Indices: 38324--38360 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
38314 CTAAATTATG
*
38324 TTAAGTAATTAAGATTTA
1 TTAAGTAATTAACATTTA
38342 TTAAGTTAATTAACATTTA
1 TTAAG-TAATTAACATTTA
38361 ATCATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (18 bp):
TTAAGTAATTAACATTTA
Done.