Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012500.1 Kokia drynarioides strain JFW-HI SEQ_127504, 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: 38474
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Found at i:5493 original size:17 final size:18
Alignment explanation
Indices: 5471--5519 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
5461 TTACAAGATA
5471 AATATTAAATTAT-ATTT
1 AATATTAAATTATCATTT
* *
5488 AATATTAAGATAATCCCTTT
1 AATATTAA-ATTAT-CATTT
5508 AATATTAAATTA
1 AATATTAAATTA
5520 ATAAAACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 8 0.31
18 4 0.15
19 3 0.12
20 11 0.42
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (18 bp):
AATATTAAATTATCATTT
Found at i:7079 original size:22 final size:21
Alignment explanation
Indices: 6999--7118 Score: 98
Period size: 22 Copynumber: 5.6 Consensus size: 21
6989 CTCAGAAAAA
* * *
6999 GTCAACGGTCAAAGGTCAACG
1 GTCAACAGTCAACGATCAACG
** *
7020 GTCAATGGTCAACGATAAACG
1 GTCAACAGTCAACGATCAACG
* * *
7041 GTCAA-AGTCATCTATCAATG
1 GTCAACAGTCAACGATCAACG
*
7061 GTCAACATGTCAACGATCACCG
1 GTCAACA-GTCAACGATCAACG
* *
7083 GTCAACCGGTCAATCGGTCAACG
1 GTCAA-CAGTCAA-CGATCAACG
7106 GTCAACAGTCAAC
1 GTCAACAGTCAAC
7119 AGTCAATGGG
Statistics
Matches: 78, Mismatches: 17, Indels: 8
0.76 0.17 0.08
Matches are distributed among these distances:
20 15 0.19
21 24 0.31
22 26 0.33
23 13 0.17
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (21 bp):
GTCAACAGTCAACGATCAACG
Found at i:7090 original size:8 final size:8
Alignment explanation
Indices: 7079--7111 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
7069 GTCAACGATC
7079 ACCGGTCA
1 ACCGGTCA
7087 ACCGGTCA
1 ACCGGTCA
*
7095 ATCGGTCA
1 ACCGGTCA
7103 A-CGGTCA
1 ACCGGTCA
7110 AC
1 AC
7112 AGTCAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.15
Consensus pattern (8 bp):
ACCGGTCA
Found at i:7137 original size:8 final size:7
Alignment explanation
Indices: 6999--7148 Score: 104
Period size: 7 Copynumber: 20.9 Consensus size: 7
6989 CTCAGAAAAA
6999 GTCAACG
1 GTCAACG
*
7006 GTCAAAG
1 GTCAACG
7013 GTCAACG
1 GTCAACG
*
7020 GTCAATG
1 GTCAACG
7027 GTCAACG
1 GTCAACG
* *
7034 ATAAACG
1 GTCAACG
*
7041 GTCAA-A
1 GTCAACG
* *
7047 GTCATCT
1 GTCAACG
* *
7054 ATCAATG
1 GTCAACG
*
7061 GTCAACAT
1 GTCAAC-G
7069 GTCAACG
1 GTCAACG
* *
7076 ATCACCG
1 GTCAACG
7083 GTCAACCG
1 GTCAA-CG
7091 GTCAATCG
1 GTCAA-CG
7099 GTCAACG
1 GTCAACG
*
7106 GTCAACA
1 GTCAACG
*
7113 GTCAACA
1 GTCAACG
*
7120 GTCAATGG
1 GTCAA-CG
7128 GTCAACGG
1 GTCAAC-G
*
7136 GTCAAAG
1 GTCAACG
7143 GTCAAC
1 GTCAAC
7149 AGGCCTAGTC
Statistics
Matches: 108, Mismatches: 30, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
6 4 0.04
7 73 0.68
8 31 0.29
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:13417 original size:35 final size:35
Alignment explanation
Indices: 13371--13441 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
13361 CTTCCACTGT
13371 ACAATCCCACCCTATGGTCACACAATGGTATGATA
1 ACAATCCCACCCTATGGTCACACAATGGTATGATA
13406 ACAATCCCACCCTATGGTCACACAATGGTATGATA
1 ACAATCCCACCCTATGGTCACACAATGGTATGATA
13441 A
1 A
13442 AATAATTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (35 bp):
ACAATCCCACCCTATGGTCACACAATGGTATGATA
Found at i:14138 original size:13 final size:13
Alignment explanation
Indices: 14120--14161 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
14110 TTTCTCGGAA
14120 AAAGTCAATGATC
1 AAAGTCAATGATC
*
14133 AAAGTCAACGATC
1 AAAGTCAATGATC
*
14146 AACAGTCAATGGTC
1 AA-AGTCAATGATC
14160 AA
1 AA
14162 CGGGTTGGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (13 bp):
AAAGTCAATGATC
Found at i:16986 original size:13 final size:13
Alignment explanation
Indices: 16919--16995 Score: 54
Period size: 13 Copynumber: 6.0 Consensus size: 13
16909 TTTATAAAAA
16919 AAATTTGATA--T
1 AAATTTGATATTT
16930 AATATTTGATATTT
1 AA-ATTTGATATTT
* **
16944 AATTTTTTTTATTT
1 AA-ATTTGATATTT
* *
16958 -AATTT-ATTACTC
1 AAATTTGA-TATTT
16970 AAATTTGATATTT
1 AAATTTGATATTT
16983 AAATTTGATATTT
1 AAATTTGATATTT
16996 TTTTAAGTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
11 2 0.04
12 14 0.27
13 22 0.43
14 13 0.25
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (13 bp):
AAATTTGATATTT
Found at i:16994 original size:29 final size:29
Alignment explanation
Indices: 16962--17017 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
16952 TTATTTAATT
*
16962 TATTACTCAAATTTGATATTTAAATTTGA
1 TATTACTCAAAGTTGATATTTAAATTTGA
** **
16991 TATTTTTTTAAGTTGATATTTAAATTT
1 TATTACTCAAAGTTGATATTTAAATTT
17018 TTTAGTATTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (29 bp):
TATTACTCAAAGTTGATATTTAAATTTGA
Found at i:21134 original size:3 final size:3
Alignment explanation
Indices: 21126--21163 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
21116 ATCACATGCA
21126 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
21164 AAAAAATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:23251 original size:20 final size:20
Alignment explanation
Indices: 23204--23256 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
23194 CTCTTATGAG
* * *
23204 ACTTCTAACGGTAGAACTCC
1 ACTTCTACCGATACAACTCC
*
23224 ACTTCTACTGATACAACTCC
1 ACTTCTACCGATACAACTCC
23244 ACTTCTACCGATA
1 ACTTCTACCGATA
23257 TATTGAAGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.28
Consensus pattern (20 bp):
ACTTCTACCGATACAACTCC
Found at i:24536 original size:28 final size:28
Alignment explanation
Indices: 24496--24551 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
24486 GTCCAGAATG
24496 CCTCATAGTTCAGCATCAAAGACTGAGC
1 CCTCATAGTTCAGCATCAAAGACTGAGC
*
24524 CCTCATAGTTCAGCATCAAGGACTGAGC
1 CCTCATAGTTCAGCATCAAAGACTGAGC
24552 ACTTTCCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (28 bp):
CCTCATAGTTCAGCATCAAAGACTGAGC
Found at i:27199 original size:19 final size:19
Alignment explanation
Indices: 27170--27213 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
27160 TGGAGTTCCA
27170 AGAATGGCGAGAGGCACCTT
1 AGAA-GGCGAGAGGCACCTT
27190 AGAAGGCGAGAGGCACCTT
1 AGAAGGCGAGAGGCACCTT
27209 AGAAG
1 AGAAG
27214 ACAATTGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.34, C:0.18, G:0.36, T:0.11
Consensus pattern (19 bp):
AGAAGGCGAGAGGCACCTT
Found at i:33069 original size:26 final size:25
Alignment explanation
Indices: 33031--33082 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 25
33021 GGTCTGCTTG
* *
33031 AAAAACGACCTTTGCCTCTTCCTCGAT
1 AAAAACGAACTTT--CTCTGCCTCGAT
33058 AAAAA-GAACTTTCTCTGCCTCGAT
1 AAAAACGAACTTTCTCTGCCTCGAT
33082 A
1 A
33083 TCCACCTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 12 0.52
26 6 0.26
27 5 0.22
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (25 bp):
AAAAACGAACTTTCTCTGCCTCGAT
Found at i:34574 original size:21 final size:21
Alignment explanation
Indices: 34550--34613 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
34540 AAAAAAATAA
34550 GACTAAGTCCTAGGGAGATTT
1 GACTAAGTCCTAGGGAGATTT
*
34571 GACTAAGACCTAAGGG-GATTT
1 GACTAAGTCCT-AGGGAGATTT
*
34592 GACTAAGTCCTAAGGAGATTT
1 GACTAAGTCCTAGGGAGATTT
34613 G
1 G
34614 TTAGCTTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 3 0.08
21 31 0.82
22 4 0.11
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (21 bp):
GACTAAGTCCTAGGGAGATTT
Done.