Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014479.1 Kokia drynarioides strain JFW-HI SEQ_129518, 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: 56064
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:3034 original size:3 final size:3
Alignment explanation
Indices: 3026--3066 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
3016 CTTAGCTCCT
*
3026 TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3067 TGAGTTCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:5303 original size:37 final size:37
Alignment explanation
Indices: 5259--5457 Score: 202
Period size: 37 Copynumber: 5.4 Consensus size: 37
5249 TCGGGTAATA
*
5259 TGCCTAGCAGGCTTCGTGCCGATGTATTCGGGCTATG
1 TGCCTAGCAGGCTTCGTGCCGGTGTATTCGGGCTATG
* *
5296 TGTCTAGCAGGCATT-GTGCCGGTATATTCGGGCTATG
1 TGCCTAGCAGGC-TTCGTGCCGGTGTATTCGGGCTATG
* * * **
5333 TGCCTAGCAGGTTTTGTGCTGGTGTATTTAGGCTATG
1 TGCCTAGCAGGCTTCGTGCCGGTGTATTCGGGCTATG
* * * **
5370 TGCTTAGCAGGATTTGTGCCGGTGTATTCTAGCTATG
1 TGCCTAGCAGGCTTCGTGCCGGTGTATTCGGGCTATG
** * * * *
5407 TGCCTAGTTGGCTTCGTGCTGGTGTACTCGGCCTATA
1 TGCCTAGCAGGCTTCGTGCCGGTGTATTCGGGCTATG
*
5444 TGCCTAGGAGGCTT
1 TGCCTAGCAGGCTT
5458 TTTTGCCGGT
Statistics
Matches: 132, Mismatches: 28, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
36 2 0.02
37 128 0.97
38 2 0.02
ACGTcount: A:0.14, C:0.20, G:0.32, T:0.35
Consensus pattern (37 bp):
TGCCTAGCAGGCTTCGTGCCGGTGTATTCGGGCTATG
Found at i:8084 original size:40 final size:39
Alignment explanation
Indices: 8032--8129 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 39
8022 GAGACAAGTC
8032 TCTTCCAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGACT
1 TCTT-CAAAAGGTGTCCATCCAATATG-AAAGGGTTGTGA-T
* * *
8074 T-TTCAGAAGGTATTCATCCAATATGAAAGGGTTGTGAT
1 TCTTCAAAAGGTGTCCATCCAATATGAAAGGGTTGTGAT
8112 TCTTCAAAAGGTGTCCAT
1 TCTTCAAAAGGTGTCCAT
8130 TTAGTGCATA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.04
39 25 0.51
40 19 0.39
41 2 0.04
42 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (39 bp):
TCTTCAAAAGGTGTCCATCCAATATGAAAGGGTTGTGAT
Found at i:13025 original size:40 final size:39
Alignment explanation
Indices: 12975--13069 Score: 154
Period size: 39 Copynumber: 2.4 Consensus size: 39
12965 TGGGACAAGT
12975 CTCTTCCAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGA
1 CTCTT-CAAAAGGTGTCCATCCAATATG-AAAGGGTTGTGA
* *
13016 CTTTTCAAAAGGTATCCATCCAATATGAAAGGGTTGTGA
1 CTCTTCAAAAGGTGTCCATCCAATATGAAAGGGTTGTGA
13055 CTCTTCAAAAGGTGT
1 CTCTTCAAAAGGTGT
13070 TCATTGAGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 25 0.50
40 21 0.42
41 4 0.08
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (39 bp):
CTCTTCAAAAGGTGTCCATCCAATATGAAAGGGTTGTGA
Found at i:17324 original size:14 final size:14
Alignment explanation
Indices: 17302--17340 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
17292 AAATAGTTAA
*
17302 TTAAATTATTTTAT
1 TTAATTTATTTTAT
*
17316 TTAATTTATATTAT
1 TTAATTTATTTTAT
17330 TTAATTATATT
1 TTAATT-TATT
17341 GTACATTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 18 0.86
15 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTAATTTATTTTAT
Found at i:18583 original size:12 final size:12
Alignment explanation
Indices: 18566--18591 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18556 AAATACATCT
18566 ATAGATAAATGA
1 ATAGATAAATGA
18578 ATAGATAAATGA
1 ATAGATAAATGA
18590 AT
1 AT
18592 GGAGTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (12 bp):
ATAGATAAATGA
Found at i:21283 original size:11 final size:11
Alignment explanation
Indices: 21269--21314 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
21259 TTTTATGTTG
*
21269 TTTTGTTACTA
1 TTTTGTTGCTA
*
21280 TTTTGTTGTTA
1 TTTTGTTGCTA
*
21291 TATTGTTGCTA
1 TTTTGTTGCTA
*
21302 TTTTGTTGTTA
1 TTTTGTTGCTA
21313 TT
1 TT
21315 GTTTGGATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.13, C:0.04, G:0.15, T:0.67
Consensus pattern (11 bp):
TTTTGTTGCTA
Found at i:21283 original size:22 final size:22
Alignment explanation
Indices: 21271--21313 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
21261 TTATGTTGTT
21271 TTGTTACTATTTTGTTGTTATA
1 TTGTTACTATTTTGTTGTTATA
*
21293 TTGTTGCTATTTTGTTGTTAT
1 TTGTTACTATTTTGTTGTTAT
21314 TGTTTGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.05, G:0.16, T:0.65
Consensus pattern (22 bp):
TTGTTACTATTTTGTTGTTATA
Found at i:21935 original size:29 final size:29
Alignment explanation
Indices: 21902--21957 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
21892 TTGTATTAAT
21902 ATACCAA-ATAAATT-TATATTATAAATTGA
1 ATACCAATA-AAATTCTATATTA-AAATTGA
*
21931 ATACCAGTAAAATTCTATATTAAAATT
1 ATACCAATAAAATTCTATATTAAAATT
21958 TTAACATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.38
Consensus pattern (29 bp):
ATACCAATAAAATTCTATATTAAAATTGA
Found at i:24698 original size:26 final size:26
Alignment explanation
Indices: 24661--24714 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
24651 ATTCTGGGCG
*
24661 CAATTCTGGACACGTTCATGCAGCGA
1 CAATTCTAGACACGTTCATGCAGCGA
*
24687 CAATTCTAGACATGTTCATGCAGCGA
1 CAATTCTAGACACGTTCATGCAGCGA
24713 CA
1 CA
24715 TTCCTGGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (26 bp):
CAATTCTAGACACGTTCATGCAGCGA
Found at i:24745 original size:37 final size:38
Alignment explanation
Indices: 24704--24781 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
24694 AGACATGTTC
* *
24704 ATGCAGCGACA-TTCCTGGGTGCAA-TTGAAGAATAGTT
1 ATGCAGCAACAGTT-CTGGATGCAATTTGAAGAATAGTT
* *
24741 ATGCAGCAACAGTTGTGGATGCAATTTGAAGAATATTT
1 ATGCAGCAACAGTTCTGGATGCAATTTGAAGAATAGTT
24779 ATG
1 ATG
24782 TAGAGACAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 18 0.51
38 17 0.49
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (38 bp):
ATGCAGCAACAGTTCTGGATGCAATTTGAAGAATAGTT
Found at i:29312 original size:36 final size:37
Alignment explanation
Indices: 29263--29345 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 37
29253 GAAATATTCC
* * * *
29263 TGCGGTGACAGTTTTGGGTGCAAT-TTGAAGTGCTCA
1 TGCGGCGACAGTTTCGGGCGCAATCTAGAAGTGCTCA
*
29299 TGCGGCGATAGTTTCGGGCGCAATCTAGAAGTGCTCA
1 TGCGGCGACAGTTTCGGGCGCAATCTAGAAGTGCTCA
*
29336 TGCAGCGACA
1 TGCGGCGACA
29346 TTAGTAGTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 20 0.51
37 19 0.49
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.27
Consensus pattern (37 bp):
TGCGGCGACAGTTTCGGGCGCAATCTAGAAGTGCTCA
Found at i:29445 original size:19 final size:19
Alignment explanation
Indices: 29421--29457 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
29411 TGTACTAAAC
29421 TAAAAAATGCTAAAATATT
1 TAAAAAATGCTAAAATATT
29440 TAAAAAATGCTAAAATAT
1 TAAAAAATGCTAAAATAT
29458 GTACTAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (19 bp):
TAAAAAATGCTAAAATATT
Found at i:34186 original size:17 final size:16
Alignment explanation
Indices: 34151--34195 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 16
34141 AAAATTGTCT
34151 TATAAAATATAAT-AATA
1 TATAAAA-A-AATAAATA
34168 TATTAAAAAAATAAATA
1 TA-TAAAAAAATAAATA
34185 TATAAAAAAAT
1 TATAAAAAAAT
34196 GAGACACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 12 0.46
17 9 0.35
18 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TATAAAAAAATAAATA
Found at i:37819 original size:68 final size:67
Alignment explanation
Indices: 37678--37833 Score: 181
Period size: 68 Copynumber: 2.3 Consensus size: 67
37668 TACATTGTTA
* * *
37678 CTGATTTATGTTGTCCAAAGCCACACATATTAATGGTGCTATAACTGTTTCATCCTCTACTTTGT
1 CTGATTTATGTTGTCCAAAGCCAAACATATTAATGGTGCTATAACTGTTTAATCCTCTA-GTTGT
37743 TTG
65 TTG
* ***
37746 CTGATTTATGTTGTCCAAAGCCAAACATATTAATGGTGTTATTGTTGTTTAATGCC-CT-GTTGT
1 CTGATTTATGTTGTCCAAAGCCAAACATATTAATGGTGCTATAACTGTTTAAT-CCTCTAGTTGT
*
37809 ATTT
65 -TTG
*
37813 CTTGATTTATGCTGTCCAAAG
1 C-TGATTTATGTTGTCCAAAG
37834 TAGCACATAT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
66 4 0.05
67 3 0.04
68 67 0.88
69 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (67 bp):
CTGATTTATGTTGTCCAAAGCCAAACATATTAATGGTGCTATAACTGTTTAATCCTCTAGTTGTT
TG
Found at i:41157 original size:37 final size:36
Alignment explanation
Indices: 41087--41172 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 36
41077 AAGTAAATTG
* **
41087 GGCTATGTGCCTAGTAGGCTTAGTGTTGATGTATTC
1 GGCTATGTGCCTAGTAAGCTTAGTGCAGATGTATTC
*
41123 GAGCTATGTGCCTAGTAAGCTTCGTGCCAG-TGTATTC
1 G-GCTATGTGCCTAGTAAGCTTAGTG-CAGATGTATTC
*
41160 GGGTATGTGCCTA
1 GGCTATGTGCCTA
41173 TTAGATTTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
36 12 0.28
37 30 0.70
38 1 0.02
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.35
Consensus pattern (36 bp):
GGCTATGTGCCTAGTAAGCTTAGTGCAGATGTATTC
Found at i:42214 original size:19 final size:20
Alignment explanation
Indices: 42177--42214 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42167 TTCACCAATT
42177 CTTTCTAACTTTTTCTTAAG
1 CTTTCTAACTTTTTCTTAAG
42197 CTTTCTAACTTTTT-TTAA
1 CTTTCTAACTTTTTCTTAA
42215 ATTCGTTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.21, C:0.18, G:0.03, T:0.58
Consensus pattern (20 bp):
CTTTCTAACTTTTTCTTAAG
Found at i:43825 original size:26 final size:27
Alignment explanation
Indices: 43780--43831 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
43770 AAACTCATGC
43780 CAGCCCAATTTTTACCTAGTCCTTACT
1 CAGCCCAATTTTTACCTAGTCCTTACT
43807 CAGCCCAA-TTTTACCTAGTCCTTAC
1 CAGCCCAATTTTTACCTAGTCCTTAC
43832 CTAGTCCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.23, C:0.35, G:0.08, T:0.35
Consensus pattern (27 bp):
CAGCCCAATTTTTACCTAGTCCTTACT
Found at i:43833 original size:11 final size:11
Alignment explanation
Indices: 43817--43842 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
43807 CAGCCCAATT
43817 TTACCTAGTCC
1 TTACCTAGTCC
43828 TTACCTAGTCC
1 TTACCTAGTCC
43839 TTAC
1 TTAC
43843 AAAGTTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.35, G:0.08, T:0.38
Consensus pattern (11 bp):
TTACCTAGTCC
Found at i:47239 original size:15 final size:14
Alignment explanation
Indices: 47219--47275 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 14
47209 AAATTCAACG
47219 AAATCAATTTGAATT
1 AAATCAATTT-AATT
*
47234 AAATCAAGTTAAATT
1 AAATCAA-TTTAATT
* *
47249 AAATTAAATTAATT
1 AAATCAATTTAATT
47263 AAATCAATTTAAT
1 AAATCAATTTAAT
47276 ATTTATCATT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
14 16 0.46
15 17 0.49
16 2 0.06
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.39
Consensus pattern (14 bp):
AAATCAATTTAATT
Found at i:51360 original size:36 final size:36
Alignment explanation
Indices: 51320--51388 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
51310 ACTCGTTTTT
51320 CCCTTCCTTTTGCTCTCTTAATATCAAGAATGGTTC
1 CCCTTCCTTTTGCTCTCTTAATATCAAGAATGGTTC
* *
51356 CCCTTCCTTTTGCTCTCTTGATATCAGGAATGG
1 CCCTTCCTTTTGCTCTCTTAATATCAAGAATGG
51389 AAGGTGGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.17, C:0.28, G:0.14, T:0.41
Consensus pattern (36 bp):
CCCTTCCTTTTGCTCTCTTAATATCAAGAATGGTTC
Found at i:51675 original size:3 final size:3
Alignment explanation
Indices: 51667--51693 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
51657 TCTTTGTTTC
51667 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
51694 GTACTGATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:54261 original size:27 final size:26
Alignment explanation
Indices: 54231--54281 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
54221 TTAATTTTAA
54231 TTTTCTAAAATCATAAATGAAATAAAC
1 TTTTCTAAAA-CATAAATGAAATAAAC
* * *
54258 TTTTTTAATAGATAAATGAAATAA
1 TTTTCTAAAACATAAATGAAATAA
54282 TTTTAATTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (26 bp):
TTTTCTAAAACATAAATGAAATAAAC
Done.