Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007387.1 Kokia drynarioides strain JFW-HI SEQ_122005, 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: 48283
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:2942 original size:15 final size:14
Alignment explanation
Indices: 2911--2939 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2901 TAATATTTAA
2911 TATTTAATAATTTT
1 TATTTAATAATTTT
2925 TATTTAATAATTTT
1 TATTTAATAATTTT
2939 T
1 T
2940 TATATAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTTAATAATTTT
Found at i:3507 original size:22 final size:22
Alignment explanation
Indices: 3474--3524 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
3464 TTCTCACAAC
*
3474 TTTTAATAAATT-TTTTTACATT
1 TTTTAATAAATTATTTGTA-ATT
3496 TTTTGAAT-AATTATTTGTAA-T
1 TTTT-AATAAATTATTTGTAATT
3517 TTTTAATA
1 TTTTAATA
3525 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 9 0.36
23 8 0.32
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (22 bp):
TTTTAATAAATTATTTGTAATT
Found at i:5237 original size:95 final size:96
Alignment explanation
Indices: 5054--5244 Score: 246
Period size: 95 Copynumber: 2.0 Consensus size: 96
5044 AATTTTGGAA
* ** * *
5054 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTCA
* *
5119 GAATCGGAGATAAGGAAACATTGCCTCGATT
66 GAATCGGAAATAAAGAAACATTGCCTCGATT
*
5150 AAGG-TATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTC-
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTCA
*
5213 GAAACTC-GAAATAAA-AGAATATTGCCTCGATT
66 G-AA-TCGGAAATAAAGA-AACATTGCCTCGATT
5245 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
94 2 0.02
95 75 0.90
96 6 0.07
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTCA
GAATCGGAAATAAAGAAACATTGCCTCGATT
Found at i:5638 original size:30 final size:29
Alignment explanation
Indices: 5550--5776 Score: 216
Period size: 29 Copynumber: 7.8 Consensus size: 29
5540 AAAAATGTAA
*
5550 TTTTGGGGTCAAAAATGGAATTTTTGGAAG
1 TTTTAGGGT-AAAAATGGAATTTTTGGAAG
***
5580 TTCGGGGGT--AAAT-GATATTTTT-GAAG
1 TTTTAGGGTAAAAATGGA-ATTTTTGGAAG
*
5606 TTTTAGGGTTGAAAATGGAATTTTTGGAAG
1 TTTTAGGG-TAAAAATGGAATTTTTGGAAG
*
5636 -TTTAGGGGTAAAAATGGAATTTTTAGAAG
1 TTTTA-GGGTAAAAATGGAATTTTTGGAAG
5665 TTTT-GAGGTCAAAAATGGAATTTTTGGAAG
1 TTTTAG-GGT-AAAAATGGAATTTTTGGAAG
* * * * *
5695 TTTGAGGGTAAAAATGTAAATCTTGAAAG
1 TTTTAGGGTAAAAATGGAATTTTTGGAAG
*
5724 TTTTATGGTAAAAATTGGAATTTTTGGAAG
1 TTTTAGGGTAAAAA-TGGAATTTTTGGAAG
*
5754 -TTTAGGGGTAAAAATGTAATTTT
1 TTTTA-GGGTAAAAATGGAATTTT
5777 ATAACAATTT
Statistics
Matches: 163, Mismatches: 21, Indels: 27
0.77 0.10 0.13
Matches are distributed among these distances:
26 11 0.07
27 11 0.07
28 1 0.01
29 76 0.47
30 63 0.39
31 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38
Consensus pattern (29 bp):
TTTTAGGGTAAAAATGGAATTTTTGGAAG
Found at i:5693 original size:59 final size:58
Alignment explanation
Indices: 5550--5776 Score: 268
Period size: 59 Copynumber: 3.9 Consensus size: 58
5540 AAAAATGTAA
* **
5550 TTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGT--AAAT-GATATTTTTGAAG
1 TTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGA-ATTTTTGAAG
**
5606 TTTTAGGGTTGAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTAGAAG
1 TTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTT-GAAG
* * *
5665 TTTT-GAGGTCAAAAATGGAATTTTTGGAAGTTT-GAGGGTAAAAATGTAAATCTTGAAAG
1 TTTTAG-GGTCAAAAATGGAATTTTTGGAAGTTTAG-GGGTAAAAATGGAATTTTTG-AAG
* *
5724 TTTTATGGT-AAAAATTGGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTT
1 TTTTAGGGTCAAAAA-TGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTT
5777 ATAACAATTT
Statistics
Matches: 148, Mismatches: 13, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
56 34 0.23
58 18 0.12
59 95 0.64
60 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38
Consensus pattern (58 bp):
TTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGAAG
Found at i:7747 original size:6 final size:6
Alignment explanation
Indices: 7736--7785 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
7726 TGTAATTGAT
* * * *
7736 TTTAAA TTTAAA -ATGAA TTTAAA TTTAAA TTTAAA -GTAAA TTTAAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
7782 TTTA
1 TTTA
7786 GAAATAAATC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
5 7 0.20
6 28 0.80
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:7762 original size:23 final size:23
Alignment explanation
Indices: 7736--7785 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
7726 TGTAATTGAT
*
7736 TTTAAATTTAAAATGAATTTAAA
1 TTTAAATTTAAAATAAATTTAAA
* *
7759 TTTAAATTTAAAGTAAATTTAAT
1 TTTAAATTTAAAATAAATTTAAA
7782 TTTA
1 TTTA
7786 GAAATAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
TTTAAATTTAAAATAAATTTAAA
Found at i:7775 original size:11 final size:11
Alignment explanation
Indices: 7738--7780 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
7728 TAATTGATTT
7738 TAAATTTAAAA
1 TAAATTTAAAA
* *
7749 TGAATTTAAATT
1 TAAATTTAAA-A
*
7761 TAAATTTAAAG
1 TAAATTTAAAA
7772 TAAATTTAA
1 TAAATTTAA
7781 TTTTAGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:7775 original size:17 final size:18
Alignment explanation
Indices: 7755--7799 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
7745 AAAATGAATT
*
7755 TAAATTTAAATTTA-AAG
1 TAAATTTAAATTTAGAAA
*
7772 TAAATTTAATTTTAGAAA
1 TAAATTTAAATTTAGAAA
*
7790 TAAATCTAAA
1 TAAATTTAAA
7800 ACCCATCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
TAAATTTAAATTTAGAAA
Found at i:8353 original size:14 final size:13
Alignment explanation
Indices: 8327--8399 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
8317 TTAAATTTGA
8327 AATTTAA-TTTTT
1 AATTTAATTTTTT
8339 ATATTTAATTTTTT
1 A-ATTTAATTTTTT
*
8353 AATATAATTTTATT
1 AATTTAATTTT-TT
* *
8367 -TTTATAATTTTAT
1 AATT-TAATTTTTT
* **
8380 AATTTTATTAATT
1 AATTTAATTTTTT
8393 AATTTAA
1 AATTTAA
8400 ATAGTTAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
12 1 0.02
13 28 0.61
14 17 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
AATTTAATTTTTT
Found at i:8391 original size:9 final size:8
Alignment explanation
Indices: 8355--8392 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
8345 AATTTTTTAA
8355 TATAATTT
1 TATAATTT
8363 TAT--TTT
1 TATAATTT
8369 TATAATTT
1 TATAATTT
8377 TATAATTT
1 TATAATTT
8385 TATTAATT
1 TA-TAATT
8393 AATTTAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
6 6 0.22
8 16 0.59
9 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATAATTT
Found at i:15155 original size:18 final size:17
Alignment explanation
Indices: 15128--15161 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
15118 AAAAAATTAT
*
15128 GATAATTATATATTTAAA
1 GATAAGTATA-ATTTAAA
15146 GATAAGTATAATTTAA
1 GATAAGTATAATTTAA
15162 TTTATTACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (17 bp):
GATAAGTATAATTTAAA
Found at i:19471 original size:9 final size:8
Alignment explanation
Indices: 19449--19474 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
19439 TATATATTTT
19449 TTAAAAAA
1 TTAAAAAA
19457 TTAAAAAA
1 TTAAAAAA
19465 TTAAAAAA
1 TTAAAAAA
19473 TT
1 TT
19475 TCTAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
TTAAAAAA
Found at i:30230 original size:124 final size:123
Alignment explanation
Indices: 30005--30238 Score: 321
Period size: 124 Copynumber: 1.9 Consensus size: 123
29995 CGCATAAATC
* * * * *
30005 ATTAAGGCAATAATATATTATGAATCTGTTATAATTTGTAATATCTATTTGAGATCTAATATTAT
1 ATTAAGGCAATAATATACTATGAATATGTTATAATTTGTAATATCGATCTGAGAGCTAATATTAT
* *
30070 GATTTTAGGTTCTTGAGCATACATGAATGGCTCATTTATGAACTTTATCCCCTAGAAT
66 GATGTTAGGTTCTTGAGAATACATGAATGGCTCATTTATGAACTTTATCCCCTAGAAT
* *
30128 ATTAAGGCAATCATATACTATGAATATGTTAT-ATGTTGGTAATGTCGATCTGAGAGCTAATATT
1 ATTAAGGCAATAATATACTATGAATATGTTATAAT-TT-GTAATATCGATCTGAGAGCTAATATT
*
30192 ATGATGTTAGGTTCTTGAGAATGCAT-ACATGG-TACATTTATGAACTT
64 ATGATGTTAGGTTCTTGAGAATACATGA-ATGGCT-CATTTATGAACTT
30239 AAACCCCAAG
Statistics
Matches: 97, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
122 2 0.02
123 33 0.34
124 62 0.64
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (123 bp):
ATTAAGGCAATAATATACTATGAATATGTTATAATTTGTAATATCGATCTGAGAGCTAATATTAT
GATGTTAGGTTCTTGAGAATACATGAATGGCTCATTTATGAACTTTATCCCCTAGAAT
Found at i:32788 original size:25 final size:24
Alignment explanation
Indices: 32760--32807 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
32750 TTCAACAAGT
*
32760 GAATTGCATTAGCATACACAAATAA
1 GAATTGCATTAGCAAACA-AAATAA
* *
32785 GAATTGTATTTGCAAACAAAATA
1 GAATTGCATTAGCAAACAAAATA
32808 GCAGCCAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (24 bp):
GAATTGCATTAGCAAACAAAATAA
Found at i:38019 original size:15 final size:15
Alignment explanation
Indices: 37987--38019 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
37977 CACATCTTTT
*
37987 AAAATAAAAACTCAA
1 AAAATAAAAACTAAA
38002 AAAAT-AAAACTAAA
1 AAAATAAAAACTAAA
38016 AAAA
1 AAAA
38020 GAAAGTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAATAAAAACTAAA
Found at i:42209 original size:10 final size:10
Alignment explanation
Indices: 42194--42243 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
42184 ATTATTATTA
42194 TTTTAAATTT
1 TTTTAAATTT
*
42204 TTTTAAAATT
1 TTTTAAATTT
*
42214 ATTTAAATTAT
1 TTTTAAATT-T
* *
42225 TTATATATTT
1 TTTTAAATTT
42235 TTTTAAATT
1 TTTTAAATT
42244 ATAATTTTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
10 24 0.77
11 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:42241 original size:21 final size:21
Alignment explanation
Indices: 42185--42245 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
42175 TAAACTTGAA
*
42185 TTAT-TATTATTTTAAATT-T
1 TTATATATTTTTTTAAATTAT
* * * *
42204 TTTTAAAATTATTTAAATTAT
1 TTATATATTTTTTTAAATTAT
42225 TTATATATTTTTTTAAATTAT
1 TTATATATTTTTTTAAATTAT
42246 AATTTTTAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 3 0.10
20 10 0.32
21 18 0.58
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATATATTTTTTTAAATTAT
Found at i:42253 original size:14 final size:15
Alignment explanation
Indices: 42234--42266 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
42224 TTTATATATT
*
42234 TTTTTAAATTAT-AA
1 TTTTTAAAATATAAA
42248 TTTTTAAAATATAAA
1 TTTTTAAAATATAAA
42263 TTTT
1 TTTT
42267 GGAATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTTAAAATATAAA
Found at i:42294 original size:20 final size:18
Alignment explanation
Indices: 42256--42300 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
42246 AATTTTTAAA
42256 ATATAAATTTTGGAATTT
1 ATATAAATTTTGGAATTT
*
42274 ATATAAATATTTTGAATTT
1 ATATAAAT-TTTGGAATTT
42293 -TA-AAATTT
1 ATATAAATTT
42301 ATTTTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 4 0.16
18 10 0.40
19 9 0.36
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (18 bp):
ATATAAATTTTGGAATTT
Found at i:42313 original size:27 final size:29
Alignment explanation
Indices: 42269--42322 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 29
42259 TAAATTTTGG
42269 AATTTATATAAA-TATTTTG-AATTTTAA
1 AATTTATATAAATTATTTTGTAATTTTAA
* * *
42296 AATTTATTTTAATTTTTTTGTAATTTT
1 AATTTATATAAATTATTTTGTAATTTT
42323 TGTTGAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 10 0.45
28 6 0.27
29 6 0.27
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (29 bp):
AATTTATATAAATTATTTTGTAATTTTAA
Found at i:47418 original size:22 final size:23
Alignment explanation
Indices: 47379--47427 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
47369 TTTTGTAATT
* * *
47379 TTTTTACAATAATAAAATTATAA
1 TTTTTAAAATAATAAAATCAAAA
*
47402 TTTTTAAAAT-ATTAAATCAAAA
1 TTTTTAAAATAATAAAATCAAAA
47424 TTTT
1 TTTT
47428 ATCATTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTTAAAATAATAAAATCAAAA
Done.