Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013706.1 Kokia drynarioides strain JFW-HI SEQ_128734, 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: 22517
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:3471 original size:30 final size:29
Alignment explanation
Indices: 3422--3603 Score: 147
Period size: 30 Copynumber: 6.1 Consensus size: 29
3412 TGGACATCCA
** *
3422 GGGGTAAATTTGTAA-TTTTGGAAAGTTTT
1 GGGGTAAAAATGTAATTTTTGG-AAGTTTC
*
3451 GGGGTAAAAAATGGAA-TTTTGGAAAG-TTC
1 GGGGT-AAAAATGTAATTTTTGG-AAGTTTC
*
3480 GAGGGT-AAAATGTAATTTTTGGAAGTTTA
1 G-GGGTAAAAATGTAATTTTTGGAAGTTTC
* *
3509 GGGGTAAAATTGTAATTTTTTTTGAAGTTTC
1 GGGGTAAAAATGTAA--TTTTTGGAAGTTTC
* *
3540 GGGGTCAAAAATGGAATTTTTGGAAGTTTTA
1 GGGGT-AAAAATGTAATTTTTGGAAG-TTTC
* * * *
3571 GGGTTATAAATGTAATTTTTAGAAGTTTA
1 GGGGTAAAAATGTAATTTTTGGAAGTTTC
3600 GGGG
1 GGGG
3604 CCTCATTGGC
Statistics
Matches: 126, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
28 15 0.12
29 32 0.25
30 47 0.37
31 24 0.19
32 8 0.06
ACGTcount: A:0.31, C:0.02, G:0.28, T:0.39
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTTGGAAGTTTC
Found at i:3498 original size:28 final size:27
Alignment explanation
Indices: 3423--3527 Score: 88
Period size: 28 Copynumber: 3.6 Consensus size: 27
3413 GGACATCCAG
*
3423 GGGTAAATTTGTAATTTTGGAAAGTTTTG-
1 GGGTAAA-ATGTAATTTTGGAAAG--TTGA
*
3452 GGGTAAAAAATGGAATTTTGGAAAGTTCGA
1 GGGT--AAAATGTAATTTTGGAAAGTT-GA
*
3482 GGGTAAAATGTAATTTTTGG-AAGTTTA
1 GGGTAAAATGTAA-TTTTGGAAAGTTGA
3509 GGGGTAAAATTGTAATTTT
1 -GGGTAAAA-TGTAATTTT
3528 TTTTGAAGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
27 1 0.02
28 27 0.42
29 16 0.25
30 18 0.28
31 3 0.05
ACGTcount: A:0.33, C:0.01, G:0.28, T:0.38
Consensus pattern (27 bp):
GGGTAAAATGTAATTTTGGAAAGTTGA
Found at i:4662 original size:18 final size:18
Alignment explanation
Indices: 4639--4676 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4629 TTTAAAAATT
4639 TATTATGAATGATGATAA
1 TATTATGAATGATGATAA
4657 TATTATGAATGATGATAA
1 TATTATGAATGATGATAA
4675 TA
1 TA
4677 ATGACATGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (18 bp):
TATTATGAATGATGATAA
Found at i:5388 original size:17 final size:17
Alignment explanation
Indices: 5352--5432 Score: 72
Period size: 17 Copynumber: 4.7 Consensus size: 17
5342 CATTTAATTT
*
5352 AATTTTAATTTAAAAATA
1 AATTTAAATTT-AAAATA
*
5370 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAATA
** * * *
5387 AATCCAAACTCAAAATG
1 AATTTAAATTTAAAATA
*
5404 AATTTGAATTTAAAATA
1 AATTTAAATTTAAAATA
*
5421 AATTCAAATTTA
1 AATTTAAATTTA
5433 TTTGAAAATT
Statistics
Matches: 47, Mismatches: 16, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
17 37 0.79
18 10 0.21
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:5402 original size:34 final size:34
Alignment explanation
Indices: 5364--5428 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
5354 TTTTAATTTA
*
5364 AAAATAAATTTAAATTTAAAGTAAATCCAAACTC
1 AAAATAAATTTAAATTTAAAATAAATCCAAACTC
* * *
5398 AAAATGAATTTGAATTTAAAATAAATTCAAA
1 AAAATAAATTTAAATTTAAAATAAATCCAAA
5429 TTTATTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.31
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAATAAATCCAAACTC
Found at i:6189 original size:11 final size:10
Alignment explanation
Indices: 6156--6288 Score: 67
Period size: 10 Copynumber: 14.3 Consensus size: 10
6146 TATTTAACCC
*
6156 TAATATTTTA
1 TAATTTTTTA
*
6166 TAAGTTTTTA
1 TAATTTTTTA
6176 TAATTTTTTAA
1 TAATTTTTT-A
*
6187 TAA-TTTTAA
1 TAATTTTTTA
* *
6196 TAAGTTTATA
1 TAATTTTTTA
*
6206 TAA--GTTT-
1 TAATTTTTTA
6213 TAATTTTTTA
1 TAATTTTTTA
6223 T-A---TTTA
1 TAATTTTTTA
6229 TAATTTTTT-
1 TAATTTTTTA
* *
6238 TACTTTTTTC
1 TAATTTTTTA
*
6248 TGA-TTTTTA
1 TAATTTTTTA
6257 -AATTTGTTTA
1 TAATTT-TTTA
6267 TAA--TTTTA
1 TAATTTTTTA
6275 TAATATTTTTA
1 TAAT-TTTTTA
6286 TAA
1 TAA
6289 GAAAAATATT
Statistics
Matches: 93, Mismatches: 14, Indels: 31
0.67 0.10 0.22
Matches are distributed among these distances:
6 5 0.05
7 4 0.04
8 10 0.11
9 24 0.26
10 36 0.39
11 14 0.15
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:6200 original size:30 final size:28
Alignment explanation
Indices: 6156--6224 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 28
6146 TATTTAACCC
* *
6156 TAATATTTTATAAGTTTTTATAATTTTT
1 TAATATTTTATAAGTTTATATAAGTTTT
6184 TAATAATTTTAATAAGTTTATATAAG-TTT
1 TAAT-ATTTT-ATAAGTTTATATAAGTTTT
*
6213 TAATTTTTTATA
1 TAATATTTTATA
6225 TTTATAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.08
28 8 0.22
29 12 0.33
30 13 0.36
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.59
Consensus pattern (28 bp):
TAATATTTTATAAGTTTATATAAGTTTT
Found at i:6285 original size:19 final size:19
Alignment explanation
Indices: 6160--6288 Score: 60
Period size: 19 Copynumber: 7.1 Consensus size: 19
6150 TAACCCTAAT
*
6160 ATTTTATAA-GTTTTTATA
1 ATTTTATAATATTTTTATA
* *
6178 ATTTTTTAATAATTTTAATA
1 ATTTTATAAT-ATTTTTATA
* **
6198 AGTTTAT-ATAAGTTT-TA
1 ATTTTATAATATTTTTATA
*
6215 ATTTT-T--TATATTTATA
1 ATTTTATAATATTTTTATA
* * * *
6231 ATTTTTTTACT-TTTTTCTG
1 A-TTTTATAATATTTTTATA
6250 ATTTT-TAA-ATTTGTTTATA
1 ATTTTATAATA-TT-TTTATA
6269 ATTTTATAATATTTTTATA
1 ATTTTATAATATTTTTATA
6288 A
1 A
6289 GAAAAATATT
Statistics
Matches: 82, Mismatches: 17, Indels: 23
0.67 0.14 0.19
Matches are distributed among these distances:
15 5 0.06
16 4 0.05
17 12 0.15
18 18 0.22
19 24 0.29
20 18 0.22
21 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (19 bp):
ATTTTATAATATTTTTATA
Found at i:6605 original size:45 final size:44
Alignment explanation
Indices: 6546--7104 Score: 448
Period size: 45 Copynumber: 12.8 Consensus size: 44
6536 ACCATCAAGT
* * *
6546 CTTTTACCCTTAATCCAGAGGGGCAGATTGAAGCAGCCATCCAAC
1 CTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCA-TCATCCAAC
* * * *
6591 CTTTTACCCCTAATCTAGAGGGGTAGGTTGATGCCATCATCTAAC
1 CTTTTACCCCTAATCTAGAGGGGCAGATTGAAG-CATCATCCAAC
* * *
6636 CTTTTACCCCTAATCCAGAGGGGTAGGTTGAAG--TCATCCAAC
1 CTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCATCATCCAAC
* ** *
6678 CTTTTACCCCTAGTCTAGAGGAACA-AGTTGAAG--TCATCTAAC
1 CTTTTACCCCTAATCTAGAGGGGCAGA-TTGAAGCATCATCCAAC
* * * *
6720 CTTTTACCCCTAATCCAAAGGGGCAGGTTGAAGCCATCATCTAAC
1 CTTTTACCCCTAATCTAGAGGGGCAGATTGAAG-CATCATCCAAC
* *
6765 CTTTTACCCCTAATCTAAAGGGGCA-AGTTGAAGC--CATTCAAC
1 CTTTTACCCCTAATCTAGAGGGGCAGA-TTGAAGCATCATCCAAC
* * * * *
6807 CTTTTACCCTTAATCTAAAGAGGCAGGTTGAAGCTATCATCCAAT
1 CTTTTACCCCTAATCTAGAGGGGCAGATTGAAGC-ATCATCCAAC
* * * * *
6852 CTTTTACCCCTAAT-TCAGAAGGGCAGGTTAAAAC-TACTATCCAAT
1 CTTTTACCCCTAATCT-AGAGGGGCAGATTGAAGCAT-C-ATCCAAC
* **
6897 CTTTTACCCCTAATCTAGA-GGGCAGATTGAAGACATCATTCAGT
1 CTTTTACCCCTAATCTAGAGGGGCAGATTGAAG-CATCATCCAAC
* * * * *
6941 CTTTTACCCCTAACCCAAAGGGGCAGATTGAAGTAGTCATCCAAT
1 CTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCA-TCATCCAAC
* * *
6986 CTTTTACCCCTAATCCAGAGGGGCATG-TTGAAGTCACCATCCAAT
1 CTTTTACCCCTAATCTAGAGGGGCA-GATTGAAG-CATCATCCAAC
* * * **
7031 CTTTTA---C-AATTTAGAGGGGCAGATTGAAACCATCATCTAGT
1 CTTTTACCCCTAATCTAGAGGGGCAGATTG-AAGCATCATCCAAC
* *
7072 TTTTTACCCCTAATTTAGAGGGGCAGATTGAAG
1 CTTTTACCCCTAATCTAGAGGGGCAGATTGAAG
7105 TTACAACACC
Statistics
Matches: 426, Mismatches: 61, Indels: 55
0.79 0.11 0.10
Matches are distributed among these distances:
40 1 0.00
41 28 0.07
42 107 0.25
43 1 0.00
44 38 0.09
45 245 0.58
46 6 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (44 bp):
CTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCATCATCCAAC
Found at i:6695 original size:87 final size:88
Alignment explanation
Indices: 6546--7104 Score: 414
Period size: 87 Copynumber: 6.4 Consensus size: 88
6536 ACCATCAAGT
* * * *
6546 CTTTTACCCTTAATCCAGAGGGGCAGATTGAAGCAGCCATCCAACCTTTTACCCCTAATCTAGAG
1 CTTTTACCCCTAATCCAAAGGGGCAGGTTGAAGC--TCATCCAACCTTTTACCCCTAATCTAGAG
* * *
6611 GGGTAGGTTGATGCCATCATCTAAC
64 GGGCAAGTTGAAGCCATCATCTAAC
* * * *
6636 CTTTTACCCCTAATCCAGAGGGGTAGGTTGAAG-TCATCCAACCTTTTACCCCTAGTCTAGAGGA
1 CTTTTACCCCTAATCCAAAGGGGCAGGTTGAAGCTCATCCAACCTTTTACCCCTAATCTAGAGGG
*
6700 ACAAGTTGAAG---TCATCTAAC
66 GCAAGTTGAAGCCATCATCTAAC
* *
6720 CTTTTACCCCTAATCCAAAGGGGCAGGTTGAAGCCATCATCTAACCTTTTACCCCTAATCTAAAG
1 CTTTTACCCCTAATCCAAAGGGGCAGGTTGAAG-C-TCATCCAACCTTTTACCCCTAATCTAGAG
6785 GGGCAAGTTGAAGCCAT--TC-AAC
64 GGGCAAGTTGAAGCCATCATCTAAC
* * * *
6807 CTTTTACCCTTAATCTAAAGAGGCAGGTTGAAGCTATCATCCAATCTTTTACCCCTAAT-TCAGA
1 CTTTTACCCCTAATCCAAAGGGGCAGGTTGAAGC--TCATCCAACCTTTTACCCCTAATCT-AGA
* * * * * * *
6871 AGGGCAGGTTAAAACTA-CTATCCAAT
63 GGGGCAAGTTGAAGCCATC-ATCTAAC
* * * * ** * * *
6897 CTTTTACCCCTAATCTAGA-GGGCAGATTGAAGACATCATTCAGTCTTTTACCCCTAACCCAAAG
1 CTTTTACCCCTAATCCAAAGGGGCAGGTTGAAG-C-TCATCCAACCTTTTACCCCTAATCTAGAG
* * *
6961 GGGC-AGATTGAAG-TAGTCATCCAAT
64 GGGCAAG-TTGAAGCCA-TCATCTAAC
* * * * *
6986 CTTTTACCCCTAATCCAGAGGGGCATGTTGAAGTCACCATCCAATCTTTTA---C-AATTTAGAG
1 CTTTTACCCCTAATCCAAAGGGGCAGGTTGAAG-C-TCATCCAACCTTTTACCCCTAATCTAGAG
* **
7047 GGGC-AGATTGAAACCATCATCTAGT
64 GGGCAAG-TTGAAGCCATCATCTAAC
* ** * *
7072 TTTTTACCCCTAATTTAGAGGGGCAGATTGAAG
1 CTTTTACCCCTAATCCAAAGGGGCAGGTTGAAG
7105 TTACAACACC
Statistics
Matches: 388, Mismatches: 62, Indels: 42
0.79 0.13 0.09
Matches are distributed among these distances:
84 40 0.10
86 54 0.14
87 143 0.37
88 5 0.01
89 69 0.18
90 77 0.20
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (88 bp):
CTTTTACCCCTAATCCAAAGGGGCAGGTTGAAGCTCATCCAACCTTTTACCCCTAATCTAGAGGG
GCAAGTTGAAGCCATCATCTAAC
Found at i:6990 original size:134 final size:134
Alignment explanation
Indices: 6543--7105 Score: 432
Period size: 129 Copynumber: 4.3 Consensus size: 134
6533 ATCACCATCA
* * * * * * *
6543 AGTCTTTTACCCTTAATCCAGAGGGGCAGATTGAAGCAGCCATCCAACCTTTTACCCCTAATCTA
1 AGTCTTTTACCCCTAATCTAAAGGGGCAGATTGAAGTAGTCATCCAATCTTTTACCCCTAATCCA
* * ** * * * * * *
6608 GAGGGGTAGGTTGATGCCA-TCATCTAACCTTTTACCCCTAATCCAGAGGGGTAGGTTGAAG---
66 GAAGGGCAGGTT-AAACTACT-ATCCAATCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGACA
*
6669 TCATCC
129 TCATTC
** * * ** * *
6675 AACCTTTTACCCCTAGTCTAGAGGAACA-AGTTG-A--AGTCATCTAACCTTTTACCCCTAATCC
1 AGTCTTTTACCCCTAATCTAAAGGGGCAGA-TTGAAGTAGTCATCCAATCTTTTACCCCTAATCC
* * * * *
6736 A-AAGGGGCAGGTTGAAGCCA-TCATCTAACCTTTTACCCCTAATCTAAAGGGGCA-AGTTGAAG
65 AGAA-GGGCAGGTT-AAACTACT-ATCCAATCTTTTACCCCTAATCTAGAGGGGCAGA-TTGAAG
6798 -C--CATTC
126 ACATCATTC
** * * * *
6804 AACCTTTTACCCTTAATCTAAAGAGGCAGGTTGAAGCTA-TCATCCAATCTTTTACCCCTAATTC
1 AGTCTTTTACCCCTAATCTAAAGGGGCAGATTGAAG-TAGTCATCCAATCTTTTACCCCTAATCC
6868 AGAAGGGCAGGTTAAAACTACTATCCAATCTTTTACCCCTAATCTAGA-GGGCAGATTGAAGACA
65 AGAAGGGCAGGTT-AAACTACTATCCAATCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGACA
6932 TCATTC
129 TCATTC
* *
6938 AGTCTTTTACCCCTAACCCAAAGGGGCAGATTGAAGTAGTCATCCAATCTTTTACCCCTAATCCA
1 AGTCTTTTACCCCTAATCTAAAGGGGCAGATTGAAGTAGTCATCCAATCTTTTACCCCTAATCCA
* * * * * *
7003 GAGGGGCATGTTGAAGTCACCATCCAATCTTTTA---C-AATTTAGAGGGGCAGATTGAA-ACCA
66 GAAGGGCAGGTTAAACT-ACTATCCAATCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGA-CA
7063 TCA-TC
129 TCATTC
* * *
7068 TAGTTTTTTACCCCTAATTTAGAGGGGCAGATTGAAGT
1 -AGTCTTTTACCCCTAATCTAAAGGGGCAGATTGAAGT
7106 TACAACACCA
Statistics
Matches: 358, Mismatches: 53, Indels: 41
0.79 0.12 0.09
Matches are distributed among these distances:
128 1 0.00
129 105 0.29
130 11 0.03
131 63 0.18
132 85 0.24
133 9 0.03
134 84 0.23
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (134 bp):
AGTCTTTTACCCCTAATCTAAAGGGGCAGATTGAAGTAGTCATCCAATCTTTTACCCCTAATCCA
GAAGGGCAGGTTAAACTACTATCCAATCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGACATC
ATTC
Found at i:12577 original size:33 final size:33
Alignment explanation
Indices: 12494--12578 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
12484 TATCTTAGTG
* *
12494 TTATTT-ATATA-TATTTTTTAATTTTTTTAAT
1 TTATTTGATATATTATATTTTAATGTTTTTAAT
* *
12525 TTATTGGGA-ATCATT-TATTTTAATGTTTTTATT
1 TTATT-TGATAT-ATTATATTTTAATGTTTTTAAT
12558 TTATTTGATATATTATATTTT
1 TTATTTGATATATTATATTTT
12579 TAAATTTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
31 5 0.12
32 7 0.16
33 30 0.70
34 1 0.02
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (33 bp):
TTATTTGATATATTATATTTTAATGTTTTTAAT
Found at i:15136 original size:31 final size:30
Alignment explanation
Indices: 15095--15238 Score: 146
Period size: 31 Copynumber: 4.7 Consensus size: 30
15085 TGTTTTTTAA
15095 CCCTCAAATTTTCCAAAAATTCTAATTCGAC
1 CCCT-AAATTTTCCAAAAATTCTAATTCGAC
15126 CCCTTAAATTTTCCAAAAAATT-TGAATTCGAC
1 CCC-TAAATTTTCC-AAAAATTCT-AATTCGAC
* * *
15158 CCCTAAATTTTTCAAAAAATTCCAATTTGAC
1 CCCTAAA-TTTTCCAAAAATTCTAATTCGAC
* * * * * *
15189 CTCTAAACTTTCTAGAACTTCTAATTTGAC
1 CCCTAAATTTTCCAAAAATTCTAATTCGAC
*
15219 CCCTAAAATTTCCAAAAATT
1 CCCTAAATTTTCCAAAAATT
15239 TAAATTTGAC
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
30 33 0.35
31 37 0.39
32 24 0.26
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (30 bp):
CCCTAAATTTTCCAAAAATTCTAATTCGAC
Found at i:15245 original size:30 final size:29
Alignment explanation
Indices: 15095--15248 Score: 137
Period size: 30 Copynumber: 5.0 Consensus size: 29
15085 TGTTTTTTAA
*
15095 CCCTCAAATTTTCCAAAAATTCTAATTCGAC
1 CCCT-AAATTTTCCAAAAATT-TAATTTGAC
*
15126 CCCTTAAATTTTCCAAAAAATTTGAATTCGAC
1 CCC-TAAATTTTCC-AAAAATTT-AATTTGAC
* *
15158 CCCTAAATTTTTCAAAAAATTCCAATTTGAC
1 CCCTAAA-TTTTCCAAAAATT-TAATTTGAC
* * * * *
15189 CTCTAAACTTTCTAGAACTTCTAATTTGAC
1 CCCTAAATTTTCCAAAAATT-TAATTTGAC
*
15219 CCCTAAAATTTCCAAAAATTTAAATTTGAC
1 CCCTAAATTTTCCAAAAATTT-AATTTGAC
15249 TCCATTTTAA
Statistics
Matches: 103, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
29 1 0.01
30 41 0.40
31 37 0.36
32 24 0.23
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (29 bp):
CCCTAAATTTTCCAAAAATTTAATTTGAC
Done.