Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011371.1 Kokia drynarioides strain JFW-HI SEQ_126352, 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: 22421
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:4773 original size:30 final size:29
Alignment explanation
Indices: 4711--5024 Score: 216
Period size: 29 Copynumber: 10.8 Consensus size: 29
4701 TTCGAGGTCG
* * *
4711 AAAATGGAGTTTTTGGATA-TCTGGGGGTA
1 AAAATGGAATTTTTGGA-AGTTTTGGGGTA
4740 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGT-A
* * *
4770 AAAAT-GAGATTTTTAGAAGTTTCGGGATCA
1 AAAATGGA-ATTTTTGGAAGTTTTGGGGT-A
*
4800 AAAAT-GAGATTTTTAGAAG-TTTGAGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTTG-GGGTA
*
4829 AAAATGGAATTATTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTGGGG-TA
* **
4859 AAAAT-GAGATTTTTAGAAGTTCGGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTTGGGGTA
* * * *
4888 AATATGAAATGTTTAGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGT-A
* * * *
4918 AAAATGGGATTTTTAGAAG-TTCGGAGATA
1 AAAATGGAATTTTTGGAAGTTTTGG-GGTA
** *
4947 AAAACAGAA-TTTTGGAAGTTTCGGGG-A
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
** *
4974 TAAAATGGGTTTTTTGGAAGTTTAGGGGT-
1 -AAAATGGAATTTTTGGAAGTTTTGGGGTA
*
5003 -AAACGGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
5025 AGGGACCTCC
Statistics
Matches: 231, Mismatches: 38, Indels: 33
0.76 0.13 0.11
Matches are distributed among these distances:
27 14 0.06
28 20 0.09
29 103 0.45
30 94 0.41
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTA
Found at i:4804 original size:89 final size:88
Alignment explanation
Indices: 4690--4883 Score: 261
Period size: 89 Copynumber: 2.2 Consensus size: 88
4680 TGAAAGGGTA
* * * * *
4690 ATTTTGAG-AGTTTCGAGGTCGAAAATG-GAGTTTTTGGATA-TCTGGGGGTAAAAATGGAATTT
1 ATTTTTAGAAGTTTCG-GGTCAAAAATGAGA-TTTTTAGA-AGTCTGAGGGTAAAAATGGAATTA
4752 TTGGAAGTTTTGGGGTCAAAAATGAG
63 TTGGAAGTTTTGGGGTCAAAAATGAG
*
4778 ATTTTTAGAAGTTTCGGGATCAAAAATGAGATTTTTAGAAGTTTGAGGGTAAAAATGGAATTATT
1 ATTTTTAGAAGTTTCGGG-TCAAAAATGAGATTTTTAGAAGTCTGAGGGTAAAAATGGAATTATT
*
4843 GGAAGTTTTGGGGTTAAAAATGAG
65 GGAAGTTTTGGGGTCAAAAATGAG
4867 ATTTTTAGAAG-TTCGGG
1 ATTTTTAGAAGTTTCGGG
4884 GGTAAATATG
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
88 16 0.17
89 77 0.81
90 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (88 bp):
ATTTTTAGAAGTTTCGGGTCAAAAATGAGATTTTTAGAAGTCTGAGGGTAAAAATGGAATTATTG
GAAGTTTTGGGGTCAAAAATGAG
Found at i:4862 original size:59 final size:57
Alignment explanation
Indices: 4732--5005 Score: 246
Period size: 59 Copynumber: 4.7 Consensus size: 57
4722 TTTGGATATC
* * *
4732 TGGGGGTAAAAATG-GAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTAGAAGTTT
1 TGGGGTTAAAAATGAG-ATTTTTAGAAG-TTTGGGGT-AAAAATG-GAATTTTAGAAGTTT
* * * *
4792 CGGGATCAAAAATGAGATTTTTAGAAGTTTGAGGGTAAAAATGGAATTATTGGAAGTTT
1 TGGGGTTAAAAATGAGATTTTTAGAAGTTTG-GGGTAAAAATGGAATT-TTAGAAGTTT
* * *
4851 TGGGGTTAAAAATGAGATTTTTAGAAGTTCGGGGGTAAATATGAAATGTTTAGAAGTTT
1 TGGGGTTAAAAATGAGATTTTTAGAAGTT-TGGGGTAAAAATGGAAT-TTTAGAAGTTT
* * * * ** *
4910 TGGGGTCAAAAATGGGATTTTTAGAAGTTCGGAGATAAAAACAGAATTTTGGAAGTTT
1 TGGGGTTAAAAATGAGATTTTTAGAAGTTTGG-GGTAAAAATGGAATTTTAGAAGTTT
* * * * *
4968 CGGGGAT-AAAATGGGTTTTTTGGAAGTTTAGGGGTAAA
1 TGGGGTTAAAAATGAGATTTTTAGAAGTTT-GGGGTAAA
5006 CGGAATTTTT
Statistics
Matches: 177, Mismatches: 30, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
57 24 0.14
58 22 0.12
59 104 0.59
60 26 0.15
61 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (57 bp):
TGGGGTTAAAAATGAGATTTTTAGAAGTTTGGGGTAAAAATGGAATTTTAGAAGTTT
Found at i:4921 original size:89 final size:88
Alignment explanation
Indices: 4734--4938 Score: 288
Period size: 89 Copynumber: 2.3 Consensus size: 88
4724 TGGATATCTG
4734 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTAGAAGTTTCGGGATC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTAGAAGTTTCGGGATC
* *
4799 AAAAATGAGATTTTTAGAAGTTT
66 AAAAATGAAATGTTTAGAAGTTT
* * *
4822 GAGGGTAAAAATGGAATTATTGGAAGTTTTGGGGTTAAAAATGAGATTTTTAGAAG-TTCGGGGG
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTAGAAGTTTC-GGGA
*
4886 T-AAATATGAAATGTTTAGAAGTTTT
64 TCAAAAATGAAATGTTTAGAAG-TTT
* *
4911 GGGGTCAAAAATGGGATTTTTAGAAGTT
1 GGGGT-AAAAATGGAATTTTTGGAAGTT
4939 CGGAGATAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
88 25 0.24
89 79 0.76
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (88 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTAGAAGTTTCGGGATC
AAAAATGAAATGTTTAGAAGTTT
Found at i:5955 original size:3 final size:3
Alignment explanation
Indices: 5949--6027 Score: 54
Period size: 3 Copynumber: 25.7 Consensus size: 3
5939 TTATTAATGG
* * * * *
5949 TAT TATT TAT TAT TAT TAA TA- AAT TCAT TAC TGT TAT AAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
*
5995 TAT CA- TAT TCAT TAT TAT TAT TAT TATT TAT TA
1 TAT TAT TAT T-AT TAT TAT TAT TAT TA-T TAT TA
6028 ATGTTATTAA
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
2 2 0.03
3 45 0.76
4 12 0.20
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:5993 original size:30 final size:31
Alignment explanation
Indices: 5957--6029 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
5947 GGTATTATTT
*
5957 ATTATTATTAAT-AAATTCATTACTGTTATA
1 ATTATTATTAATCAAATTCATTACTATTATA
* * *
5987 ATTATTATT-ATCATATTCATTATTATTATT
1 ATTATTATTAATCAAATTCATTACTATTATA
6017 ATTATTTATTAAT
1 ATTA-TTATTAAT
6030 GTTATTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 2 0.06
30 27 0.75
31 5 0.14
32 2 0.06
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.56
Consensus pattern (31 bp):
ATTATTATTAATCAAATTCATTACTATTATA
Found at i:6242 original size:3 final size:3
Alignment explanation
Indices: 6236--6317 Score: 60
Period size: 3 Copynumber: 26.7 Consensus size: 3
6226 TTATTAATGA
* * * * *
6236 TAT TATT TAT TAT TAT TAA TA- AAT TCAT TAC TGT TAT AAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
*
6282 TAT CA- TAT TCAT TAT TAT TAT TAT TAT TATT TAT TA
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TA-T TAT TA
6318 ATGTTATTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
2 2 0.03
3 48 0.77
4 12 0.19
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:6280 original size:30 final size:30
Alignment explanation
Indices: 6244--6312 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
6234 GATATTATTT
*
6244 ATTATTATTAAT-AAATTCATTACTGTTATA
1 ATTATTATT-ATCAAATTCATTACTATTATA
* * *
6274 ATTATTATTATCATATTCATTATTATTATT
1 ATTATTATTATCAAATTCATTACTATTATA
6304 ATTATTATT
1 ATTATTATT
6313 TATTAATGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 2 0.06
30 32 0.94
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (30 bp):
ATTATTATTATCAAATTCATTACTATTATA
Found at i:7019 original size:17 final size:17
Alignment explanation
Indices: 6997--7070 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 17
6987 TTGGATATTT
*
6997 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
7014 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
*
7031 TAAATTTAGATTTAAAA
1 TAAATTTAAATTTAAAA
* * *
7048 TAAACTGAATTTTAAAA
1 TAAATTTAAATTTAAAA
7065 TAAATT
1 TAAATT
7071 CCAATAAGCC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Done.