Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003488.1 Kokia drynarioides strain JFW-HI SEQ_116307, 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: 47167
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:1229 original size:22 final size:21
Alignment explanation
Indices: 1173--1229 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
1163 AATAATAAAA
* *
1173 TTAAATTTTAATTTTTTTATT
1 TTAAATATTATTTTTTTTATT
*
1194 TAATAAA-ATAATTTTTTTTAATT
1 T--TAAATATTATTTTTTTT-ATT
1217 TTAAATATTATTT
1 TTAAATATTATTT
1230 GATAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
21 5 0.18
22 15 0.54
23 8 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTAAATATTATTTTTTTTATT
Found at i:1259 original size:21 final size:21
Alignment explanation
Indices: 1213--1259 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1203 AATTTTTTTT
*
1213 AATTTTAAATATTATTTGATA
1 AATTTTAAATATTATTTCATA
*
1234 AATTTTAAAT-TTCTTTCATA
1 AATTTTAAATATTATTTCATA
1254 ATATTT
1 A-ATTT
1260 CTAATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (21 bp):
AATTTTAAATATTATTTCATA
Found at i:5895 original size:23 final size:24
Alignment explanation
Indices: 5859--5905 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
5849 AGCTCTCAAC
* *
5859 GTTTATATTTTTTTATTGATTTAA
1 GTTTATATTCTTTTATTGAGTTAA
*
5883 GTTT-TATTCTTTTTTTGAGTTAA
1 GTTTATATTCTTTTATTGAGTTAA
5906 ATCTAACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.21, C:0.02, G:0.11, T:0.66
Consensus pattern (24 bp):
GTTTATATTCTTTTATTGAGTTAA
Found at i:7456 original size:41 final size:41
Alignment explanation
Indices: 7399--7492 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
7389 TATTTAATTC
*
7399 ATTTTTTAAAATTTAAAA-AACTCAAAAAAAT-TATAAAAACT
1 ATTTTTAAAAATTTAAAATAA-T-AAAAAAATATATAAAAACT
* * *
7440 ATTTTTAAAAATTTAAAATAATTAAATAATATATAAAAATT
1 ATTTTTAAAAATTTAAAATAATAAAAAAATATATAAAAACT
*
7481 ATTTTAAAAAAT
1 ATTTTTAAAAAT
7493 AATTATTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 6 0.13
41 38 0.83
42 2 0.04
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (41 bp):
ATTTTTAAAAATTTAAAATAATAAAAAAATATATAAAAACT
Found at i:8909 original size:14 final size:14
Alignment explanation
Indices: 8890--8918 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
8880 CACTGATTCT
8890 ACCAATATTCATCC
1 ACCAATATTCATCC
8904 ACCAATATTCATCC
1 ACCAATATTCATCC
8918 A
1 A
8919 TTCATTACAA
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:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (14 bp):
ACCAATATTCATCC
Found at i:11900 original size:24 final size:23
Alignment explanation
Indices: 11872--11917 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
11862 TCATGAACAA
*
11872 GCTCGTTTAAAGGCTTGTTTATTG
1 GCTCGTTTAAA-GCTCGTTTATTG
*
11896 GCTCGTTTATAGCTCGTTTATT
1 GCTCGTTTAAAGCTCGTTTATT
11918 TATTAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (23 bp):
GCTCGTTTAAAGCTCGTTTATTG
Found at i:12060 original size:23 final size:23
Alignment explanation
Indices: 12013--12077 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
12003 ACATTATTTG
* *
12013 TGAACGTGTTCAATTATATGTTCA
1 TGAACATGTTCGATTA-ATGTTCA
*
12037 TGAACATGTTCGTTTAATGTTCA
1 TGAACATGTTCGATTAATGTTCA
12060 TGAACATGTTCGATTAAT
1 TGAACATGTTCGATTAAT
12078 CAAACGAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 24 0.65
24 13 0.35
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (23 bp):
TGAACATGTTCGATTAATGTTCA
Found at i:13093 original size:15 final size:16
Alignment explanation
Indices: 13073--13107 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
13063 TCGCACTTGA
13073 TTTTAAG-TTTTTTTT
1 TTTTAAGCTTTTTTTT
13088 TTTTAAGCTTTTTTTT
1 TTTTAAGCTTTTTTTT
13104 TTTT
1 TTTT
13108 CACCTAGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.80
Consensus pattern (16 bp):
TTTTAAGCTTTTTTTT
Found at i:18547 original size:14 final size:14
Alignment explanation
Indices: 18528--18566 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
18518 CTAAAAAAGT
18528 AAATTATTTTCCAA
1 AAATTATTTTCCAA
**
18542 AAATTATTTTCTGA
1 AAATTATTTTCCAA
*
18556 AAATCATTTTC
1 AAATTATTTTC
18567 AATCAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (14 bp):
AAATTATTTTCCAA
Found at i:19016 original size:15 final size:15
Alignment explanation
Indices: 18996--19025 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18986 ATTAATCCCT
18996 AAAAATAAAAAAAAA
1 AAAAATAAAAAAAAA
19011 AAAAATAAAAAAAAA
1 AAAAATAAAAAAAAA
19026 TATGAAGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (15 bp):
AAAAATAAAAAAAAA
Found at i:24225 original size:33 final size:33
Alignment explanation
Indices: 24187--24252 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
24177 AAAAATCTCA
24187 TTAAATAATTTAATACAATGATACATAAAATAT
1 TTAAATAATTTAATACAATGATACATAAAATAT
* * *
24220 TTAAATAATTTAATATAATGATATATGAAATAT
1 TTAAATAATTTAATACAATGATACATAAAATAT
24253 AAATTAATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (33 bp):
TTAAATAATTTAATACAATGATACATAAAATAT
Found at i:26901 original size:6 final size:6
Alignment explanation
Indices: 26890--26916 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
26880 TACTATACAC
26890 ATCCAA ATCCAA ATCCAA ATCCAA ATC
1 ATCCAA ATCCAA ATCCAA ATCCAA ATC
26917 AGTAGTGCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (6 bp):
ATCCAA
Found at i:27200 original size:24 final size:24
Alignment explanation
Indices: 27168--27214 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
27158 TAATCCTTAA
27168 GTTTTTATGCTTTCTACCAATTTG
1 GTTTTTATGCTTTCTACCAATTTG
27192 GTTTTTATGCTTTCTACCAATTT
1 GTTTTTATGCTTTCTACCAATTT
27215 CATCACGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (24 bp):
GTTTTTATGCTTTCTACCAATTTG
Found at i:32921 original size:20 final size:22
Alignment explanation
Indices: 32898--32951 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
32888 TTAATAAGCT
32898 TTAATTAA-TTAA-ACTAAACC
1 TTAATTAACTTAATACTAAACC
*
32918 TTAATTAACTTAATACTAAA-A
1 TTAATTAACTTAATACTAAACC
*
32939 TTACTTAACTTAA
1 TTAATTAACTTAA
32952 AGTTAGTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 8 0.27
21 16 0.53
22 6 0.20
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAATTAACTTAATACTAAACC
Found at i:38385 original size:18 final size:18
Alignment explanation
Indices: 38345--38385 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
38335 AAATGATTGG
38345 TTTTTTTTTTTTTTAATT
1 TTTTTTTTTTTTTTAATT
* *
38363 GTTTTTTTTTTTTTAGTT
1 TTTTTTTTTTTTTTAATT
38381 TTTTT
1 TTTTT
38386 ATGAAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.00, G:0.05, T:0.88
Consensus pattern (18 bp):
TTTTTTTTTTTTTTAATT
Found at i:38476 original size:15 final size:15
Alignment explanation
Indices: 38456--38533 Score: 56
Period size: 15 Copynumber: 5.4 Consensus size: 15
38446 AAACTATAAA
38456 ATATTTATTATTAAT
1 ATATTTATTATTAAT
* *
38471 ATATTTATAATT-GT
1 ATATTTATTATTAAT
* *
38485 AAATTT-TTAATAA-
1 ATATTTATTATTAAT
* *
38498 ATATTTATAATTAAA
1 ATATTTATTATTAAT
*
38513 ATA-TTAATATTAAAT
1 ATATTTATTATT-AAT
38528 ATATTT
1 ATATTT
38534 TAATAATATA
Statistics
Matches: 46, Mismatches: 12, Indels: 9
0.69 0.18 0.13
Matches are distributed among these distances:
13 8 0.17
14 17 0.37
15 19 0.41
16 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:38512 original size:25 final size:27
Alignment explanation
Indices: 38461--38521 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
38451 ATAAAATATT
* *
38461 TATTATTAATATATTTATAATTGTAAAT
1 TATTAATAA-ATATTTATAATTGTAAAA
*
38489 TTTTAATAAATATTTATAA-T-TAAAA
1 TATTAATAAATATTTATAATTGTAAAA
38514 TATTAATA
1 TATTAATA
38522 TTAAATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 11 0.38
26 1 0.03
27 10 0.34
28 7 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
TATTAATAAATATTTATAATTGTAAAA
Found at i:38535 original size:42 final size:42
Alignment explanation
Indices: 38454--38544 Score: 105
Period size: 42 Copynumber: 2.1 Consensus size: 42
38444 TTAAACTATA
* * * *
38454 AAATATTTATTATTAATATATTTATAATTGTAAATTTTTAAT
1 AAATATTTATAATTAAAATATTAATAATTGAAAATTTTTAAT
38496 AAATATTTATAATTAAAATATTAAT-ATT-AAATATATTTTAAT
1 AAATATTTATAATTAAAATATTAATAATTGAAA-AT-TTTTAAT
38538 AATATAT
1 AA-ATAT
38545 GAAGAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 2 0.05
41 5 0.12
42 31 0.74
43 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (42 bp):
AAATATTTATAATTAAAATATTAATAATTGAAAATTTTTAAT
Found at i:41488 original size:26 final size:26
Alignment explanation
Indices: 41459--41553 Score: 129
Period size: 26 Copynumber: 3.7 Consensus size: 26
41449 TCTGTTTGGA
41459 CTCGTAAGAGCTAAACTTTGTCTGGG
1 CTCGTAAGAGCTAAACTTTGTCTGGG
* *
41485 CTCGTATGAGTTAAA-TTCTGTCTGGG
1 CTCGTAAGAGCTAAACTT-TGTCTGGG
* *
41511 CTCGTAAAAGCTAAACTCTGTCTGGG
1 CTCGTAAGAGCTAAACTTTGTCTGGG
*
41537 CTCGTGAGAGCTAAACT
1 CTCGTAAGAGCTAAACT
41554 ATATTCTGGA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
25 2 0.03
26 56 0.95
27 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (26 bp):
CTCGTAAGAGCTAAACTTTGTCTGGG
Found at i:42380 original size:55 final size:54
Alignment explanation
Indices: 42287--42393 Score: 160
Period size: 55 Copynumber: 2.0 Consensus size: 54
42277 CACATAGGGG
* * * *
42287 CGTGTGTTGGAATTTGGGTATGCACATGGCCTGTCACACGGTTTGTGACATGGC
1 CGTGTGTTGGAATTCGGGTATGCACATGGCCTGGCACACGGTCTATGACATGGC
*
42341 CGTGTGTTGGTAATTCGGGTATGCACATGGTCTGGCACACGGTCTATGACATG
1 CGTGTGTTGG-AATTCGGGTATGCACATGGCCTGGCACACGGTCTATGACATG
42394 AACGTGTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 10 0.21
55 37 0.79
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.31
Consensus pattern (54 bp):
CGTGTGTTGGAATTCGGGTATGCACATGGCCTGGCACACGGTCTATGACATGGC
Found at i:46943 original size:14 final size:14
Alignment explanation
Indices: 46924--46951 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46914 TTGGCACCAC
46924 CCTGCAGAACACAT
1 CCTGCAGAACACAT
46938 CCTGCAGAACACAT
1 CCTGCAGAACACAT
46952 TCATTAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (14 bp):
CCTGCAGAACACAT
Done.