Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000505.1 Kokia drynarioides strain JFW-HI SEQ_111384, 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: 16688
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:549 original size:98 final size:97
Alignment explanation
Indices: 376--953 Score: 743
Period size: 98 Copynumber: 5.9 Consensus size: 97
366 CAGGTTTCAT
* *
376 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAA-CTCTGTACCTTAGAAACATG
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGAGAACCT-TGTACCTCAGAAACATG
*
440 AAGGGAAAGATTTAAACCGCAACAGCGAATCTAG
65 AAGGGAAAGATTTAAGCCGCAAC-GCGAATCTAG
* *
474 TACCACGAAGATATGGAGGGAAAGGTTTAAATCGCAATGGAGAACCTTGTACCTCAGAAACATGA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGAGAACCTTGTACCTCAGAAACATGA
* * *
539 AGGGAGAGATTTAAGTCGCAACGGTGAATCTAG
66 AGGGAAAGATTTAAGCCGCAAC-GCGAATCTAG
* * * *
572 TACCACGAAGATTTGAAGGGAAAGGTTTAAGTCGCAAC-GACGAACCTTATACCTCAGAAACATA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGA-GAACCTTGTACCTCAGAAACATG
*
636 AAGGGAAAGATTTAAGCCGCAACGACGAATCCAG
65 AAGGGAAAGATTTAAGCCGCAACG-CGAATCTAG
* * * *
670 TACCATGAAGATATGGAGGGAAAGGTTTAAGTCGCAATGAAGAACCTTGTACCTCAGAAGCATGA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGAGAACCTTGTACCTCAGAAACATGA
*
735 AGGGAAAGATTTAAGCCGTAACGACGAATCTAG
66 AGGGAAAGATTTAAGCCGCAACG-CGAATCTAG
* * * *
768 TACCACGAAGATATGGAGGGAAAGATTTAAGTCGTAACAGG-GAACCTTGTACGTCAGAAACATA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAAC-GGAGAACCTTGTACCTCAGAAACATG
** * * *
832 AAGGGAAAGATGGAA-CACGCAATGGTGAATCTGG
65 AAGGGAAAGATTTAAGC-CGCAA-CGCGAATCTAG
** *
866 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGTGACGGTA-AACCTTGTACCTCAAAAACATG
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGG-AGAACCTTGTACCTCAGAAACATG
* *
930 AAGGGAAAGATTAAAGCCGTAACG
65 AAGGGAAAGATTTAAGCCGCAACG
954 GTGAATCTTC
Statistics
Matches: 418, Mismatches: 52, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
97 7 0.02
98 405 0.97
99 6 0.01
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (97 bp):
TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGAGAACCTTGTACCTCAGAAACATGA
AGGGAAAGATTTAAGCCGCAACGCGAATCTAG
Found at i:935 original size:49 final size:48
Alignment explanation
Indices: 392--969 Score: 307
Period size: 49 Copynumber: 11.8 Consensus size: 48
382 GAAGATATGG
* * *
392 AGGGAAAGGTTTAAGTCGCAACGGCGAA-CTCTGTACCTTAGAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGG-GAACCT-TGTACCTCAAAAACATGA
** * * * * * * * *
441 AGGGAAAGATTTAAACCGCAACAGCGAATCTAGTACCACGAAGATATGG
1 AGGGAAAGATTTAAGTCGCAAC-GGGAACCTTGTACCTCAAAAACATGA
* * * *
490 AGGGAAAGGTTTAAATCGCAATGGAGAACCTTGTACCTCAGAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGG-GAACCTTGTACCTCAAAAACATGA
* * * * * * **
539 AGGGAGAGATTTAAGTCGCAACGGTGAATCTAGTACCACGAAGATTTGA
1 AGGGAAAGATTTAAGTCGCAACGG-GAACCTTGTACCTCAAAAACATGA
* * * * *
588 AGGGAAAGGTTTAAGTCGCAACGACGAACCTTATACCTCAGAAACATAA
1 AGGGAAAGATTTAAGTCGCAACG-GGAACCTTGTACCTCAAAAACATGA
* * * * * * *
637 AGGGAAAGATTTAAGCCGCAACGACGAATCC-AGTACCAT-GAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACG-GGAA-CCTTGTACC-TCAAAAACATGA
* * * * *
686 AGGGAAAGGTTTAAGTCGCAATGAAGAACCTTGTACCTCAGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACG-GGAACCTTGTACCTCAAAAACATGA
* * * * * * * * * *
735 AGGGAAAGATTTAAGCCGTAACGACGAATCTAGTACCACGAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACG-GGAACCTTGTACCTCAAAAACATGA
* * * *
784 AGGGAAAGATTTAAGTCGTAACAGGGAACCTTGTACGTCAGAAACATAA
1 AGGGAAAGATTTAAGTCGCAAC-GGGAACCTTGTACCTCAAAAACATGA
** ** * * * * * * * *
833 AGGGAAAGATGGAACACGCAATGGTGAATCTGGTACCACGAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGG-GAACCTTGTACCTCAAAAACATGA
* ** *
882 AGGGAAAGGTTTAAGTCGTGACGGTAAACCTTGTACCTCAAAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGG-GAACCTTGTACCTCAAAAACATGA
* * * * *
931 AGGGAAAGATTAAAGCCGTAACGGTGAATCTTCTACCTC
1 AGGGAAAGATTTAAGTCGCAACGG-GAACCTTGTACCTC
970 GAAGTTACAG
Statistics
Matches: 383, Mismatches: 136, Indels: 20
0.71 0.25 0.04
Matches are distributed among these distances:
48 6 0.02
49 370 0.97
50 7 0.02
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.20
Consensus pattern (48 bp):
AGGGAAAGATTTAAGTCGCAACGGGAACCTTGTACCTCAAAAACATGA
Found at i:3223 original size:35 final size:35
Alignment explanation
Indices: 3182--3262 Score: 155
Period size: 34 Copynumber: 2.3 Consensus size: 35
3172 ATCTAATTCT
3182 TTTATTTTTTTATTTATTTCTTTTAAAATAATCCC
1 TTTATTTTTTTATTTATTTCTTTTAAAATAATCCC
3217 TTTA-TTTTTTATTTATTTCTTTTAAAATAATCCC
1 TTTATTTTTTTATTTATTTCTTTTAAAATAATCCC
3251 TTTATTTTTTTA
1 TTTATTTTTTTA
3263 GATTTTAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
34 34 0.76
35 11 0.24
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (35 bp):
TTTATTTTTTTATTTATTTCTTTTAAAATAATCCC
Found at i:3397 original size:21 final size:22
Alignment explanation
Indices: 3356--3397 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3346 TTAATTTTGT
* *
3356 TTTTTTTAAATTCTTTTATTTC
1 TTTTTTTAAACTCTTTCATTTC
3378 TTTTTTTAAACTC-TTCATTT
1 TTTTTTTAAACTCTTTCATTT
3398 TATGTGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTTTTAAACTCTTTCATTTC
Found at i:3472 original size:12 final size:11
Alignment explanation
Indices: 3450--3476 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3440 TTTCATTACA
3450 TTTTATTTTTT
1 TTTTATTTTTT
3461 TTTTATTTTTT
1 TTTTATTTTTT
3472 TTTTA
1 TTTTA
3477 AAAATTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:8285 original size:39 final size:39
Alignment explanation
Indices: 8158--8360 Score: 153
Period size: 39 Copynumber: 5.2 Consensus size: 39
8148 ACAGTCATCA
* * *
8158 AATCTTTTACCCCGAGCCT-GGGAAGATCACCATTAGAC-
1 AATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAG-CT
* * ** * * *
8196 AATCTCTTACCCCAAGCCTAGGGCAGATTGCAACCATCT
1 AATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCT
* * *
8235 GATCTTTTACCCCGAGCCTGGGGCAGATCACTATCAGCT
1 AATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCT
* * * *
8274 AATCTCCTACCCCGAACCTGGGGCAGA-CTA-CAGTCATCC
1 AATCTCTTACCCCGAGCCTGGGGCAGATC-ACCA-TCAGCT
* * * * *
8313 GATTTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCA
1 AATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCT
8352 AATCTCTTA
1 AATCTCTTA
8361 TATTGAGCTT
Statistics
Matches: 123, Mismatches: 36, Indels: 11
0.72 0.21 0.06
Matches are distributed among these distances:
38 20 0.16
39 100 0.81
40 3 0.02
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.24
Consensus pattern (39 bp):
AATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCT
Found at i:8298 original size:78 final size:77
Alignment explanation
Indices: 8159--8357 Score: 240
Period size: 78 Copynumber: 2.6 Consensus size: 77
8149 CAGTCATCAA
* * *
8159 ATCTTTTACCCCGAGCCT-GGGAAGATCACCATTAGACAATCTCTTACCCCAAGCCTAGGGCAGA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAG-CAATCTCCTACCCCAAGCCTAGGGCAGA
* * *
8223 TTGCAACCATCTG
65 CTACAACCATCCG
* *
8236 ATCTTTTACCCCGAGCCTGGGGCAGATCACTATCAGCTAATCTCCTACCCCGAA-CCTGGGGCAG
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGC-AATCTCCTACCCC-AAGCCTAGGGCAG
**
8300 ACTACAGTCATCCG
64 ACTACAACCATCCG
* *
8314 ATTTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCAAATCTC
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGC-AATCTC
8358 TTATATTGAG
Statistics
Matches: 105, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
77 19 0.18
78 84 0.80
79 2 0.02
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (77 bp):
ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCAATCTCCTACCCCAAGCCTAGGGCAGAC
TACAACCATCCG
Found at i:8886 original size:30 final size:29
Alignment explanation
Indices: 8742--9009 Score: 250
Period size: 30 Copynumber: 9.0 Consensus size: 29
8732 GAGAAGCTCG
* * * *
8742 AGGGTCAAAATGTGATTTTGGAAAAGATC
1 AGGGTTAAAATGTAATTTTGGAAAAGTTT
* *
8771 AGCGGTTAAAATGTGATTTTGTAAAAGTTT
1 AG-GGTTAAAATGTAATTTTGGAAAAGTTT
* * *
8801 GGGGTTAAAATATGATTTTGGAAAAGTTT
1 AGGGTTAAAATGTAATTTTGGAAAAGTTT
*
8830 AGGGTTAAAATGTAATTTTTGAAAAGTTT
1 AGGGTTAAAATGTAATTTTGGAAAAGTTT
**
8859 AGTGGTCGAAATGTAATTTTGGAAAAGTTT
1 AG-GGTTAAAATGTAATTTTGGAAAAGTTT
* * *
8889 AAGGTTTAAAATGTTATTTTGGATAAGTTT
1 -AGGGTTAAAATGTAATTTTGGAAAAGTTT
*
8919 AAGGGTTAAAATGTAATTTTAGAAAAGTTT
1 -AGGGTTAAAATGTAATTTTGGAAAAGTTT
* * *
8949 AAGGGTTAAAAT-AAGATTTTAGAAAGGTTT
1 -AGGGTTAAAATGTA-ATTTTGGAAAAGTTT
* * * *
8979 GGGAGTAAAAATATAATTTTAGAAAAAGTTT
1 AGG-GTTAAAATGTAATTTT-GGAAAAGTTT
9010 GGGGACCTTT
Statistics
Matches: 201, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
29 57 0.28
30 134 0.67
31 10 0.05
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.37
Consensus pattern (29 bp):
AGGGTTAAAATGTAATTTTGGAAAAGTTT
Found at i:10613 original size:39 final size:39
Alignment explanation
Indices: 10565--10766 Score: 197
Period size: 39 Copynumber: 5.2 Consensus size: 39
10555 CAACCATTCG
* * * * *
10565 ATCTTTTACCCCGATCATAGGGCTGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
** * * ** * * **
10604 ATCTCTTACCTTGAGCTTGGGGCAAATTGCAACCATTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
*
10643 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
*
10682 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * * * * *
10721 ATCTCTTACCTCGAGCTTGGGGCAGATTACAACCATCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
10760 ATCTCTT
1 ATCTCTT
10767 TAAAAAGAAC
Statistics
Matches: 131, Mismatches: 32, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 131 1.00
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
Found at i:11940 original size:20 final size:17
Alignment explanation
Indices: 11904--11959 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 17
11894 CAAAACATTT
*
11904 ATAATAAATACATAATAA
1 ATAATAAATA-TTAATAA
11922 ATAATTATAATATTAAATAA
1 ATAA-TA-AATATT-AATAA
11942 ATAATAAATATTAATAA
1 ATAATAAATATTAATAA
11959 A
1 A
11960 AAGAAATTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
17 6 0.18
18 10 0.29
19 5 0.15
20 13 0.38
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAAATATTAATAA
Found at i:12921 original size:30 final size:30
Alignment explanation
Indices: 12886--13107 Score: 184
Period size: 30 Copynumber: 7.5 Consensus size: 30
12876 ATAGGCCCCC
* *
12886 AAACTTTTTAAAAATTTCATTTTGACCCTT
1 AAACTTTTCAAAAATTACATTTTGACCCTT
* * *
12916 AAACTTTCCAAAAATCACATTTT-ACCCCT
1 AAACTTTTCAAAAATTACATTTTGACCCTT
* *
12945 AAACTTTCCAAAAATCACATTTTGA-CCTT
1 AAACTTTTCAAAAATTACATTTTGACCCTT
* * * *
12974 GTAACTTCTCCAAAATTACATTTTGATCCTT
1 -AAACTTTTCAAAAATTACATTTTGACCCTT
* *
13005 AAACTTTTCCAAAATTAAAATTTT-ACCCTT
1 AAACTTTTCAAAAATT-ACATTTTGACCCTT
* ** * *
13035 AAACTTTTCCAAAATTGTATTTTAACCCCT
1 AAACTTTTCAAAAATTACATTTTGACCCTT
* * *
13065 AAACTTCTCCAAAATCACATTTTCGA-CCTT
1 AAACTTTTCAAAAATTACATTTT-GACCCTT
*
13095 AAA-TTTTCCAAAA
1 AAACTTTTCAAAAA
13108 GTTCGATGTG
Statistics
Matches: 161, Mismatches: 25, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
29 45 0.28
30 105 0.65
31 11 0.07
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (30 bp):
AAACTTTTCAAAAATTACATTTTGACCCTT
Found at i:13019 original size:60 final size:58
Alignment explanation
Indices: 12903--13107 Score: 211
Period size: 60 Copynumber: 3.4 Consensus size: 58
12893 TTAAAAATTT
*
12903 CATTTTGACCCTTAAACTTTCCAAAAATCACATTTTACCCCTAAAC-TTTCCAAAAATCA
1 CATTTTGACCCTTAAACTTTCC-AAAATTACATTTTACCCCTAAACTTTTCC-AAAATCA
* * * *
12962 CATTTTGA-CCTTGTAACTTCTCCAAAATTACATTTTGATCCTTAAACTTTTCCAAAATTAA
1 CATTTTGACCCTT-AAACTT-TCCAAAATTACATTTT-ACCCCTAAACTTTTCCAAAA-TCA
* ** *
13023 AATTTT-ACCCTTAAACTTTTCCAAAATTGTATTTTAACCCCTAAACTTCTCCAAAATCA
1 CATTTTGACCCTTAAAC-TTTCCAAAATTACATTTT-ACCCCTAAACTTTTCCAAAATCA
*
13082 CATTTTCGA-CCTTAAATTTTCCAAAA
1 CATTTT-GACCCTTAAACTTTCCAAAA
13108 GTTCGATGTG
Statistics
Matches: 121, Mismatches: 16, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
58 4 0.03
59 41 0.34
60 57 0.47
61 19 0.16
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (58 bp):
CATTTTGACCCTTAAACTTTCCAAAATTACATTTTACCCCTAAACTTTTCCAAAATCA
Found at i:13057 original size:90 final size:89
Alignment explanation
Indices: 12896--13107 Score: 243
Period size: 90 Copynumber: 2.4 Consensus size: 89
12886 AAACTTTTTA
* * *
12896 AAAATTTCATTTTGACCCTTAAAC-TTTCCAAAAATCACATTTTACCCCTAAACTTTCCAAAAAT
1 AAAATTACATTTTGA-CCTTAAACTTTTCCAAAAATAAAATTTTACCCCTAAACTTTCCAAAAAT
* * *
12960 CACATTTTGA-CCTTGTAACTTCTCC
65 CACATTTTAACCCCT-AAACTTCTCC
* *
12985 AAAATTACATTTTGATCCTTAAACTTTTCCAAAATTAAAATTTTACCCTTAAACTTTTCC-AAAA
1 AAAATTACATTTTGA-CCTTAAACTTTTCCAAAAATAAAATTTTACCCCTAAAC-TTTCCAAAAA
***
13049 TTGTATTTTAACCCCTAAACTTCTCC
64 TCACATTTTAACCCCTAAACTTCTCC
*
13075 AAAATCACATTTTCGACCTTAAA-TTTTCCAAAA
1 AAAATTACATTTT-GACCTTAAACTTTTCCAAAA
13108 GTTCGATGTG
Statistics
Matches: 106, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
89 32 0.30
90 64 0.60
91 10 0.09
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (89 bp):
AAAATTACATTTTGACCTTAAACTTTTCCAAAAATAAAATTTTACCCCTAAACTTTCCAAAAATC
ACATTTTAACCCCTAAACTTCTCC
Found at i:14014 original size:21 final size:21
Alignment explanation
Indices: 13988--14028 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13978 GACAACTGTC
13988 TTTTTTAAAAAAAATTTTAAT
1 TTTTTTAAAAAAAATTTTAAT
* *
14009 TTTTTTAAAGATAATTTTAA
1 TTTTTTAAAAAAAATTTTAA
14029 GGTGTCGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTTTAAAAAAAATTTTAAT
Found at i:14417 original size:20 final size:19
Alignment explanation
Indices: 14381--14418 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
14371 AAATAGTATT
*
14381 ATTAAAATTATTCAATATA
1 ATTAAAATTATTAAATATA
14400 ATTAAAATATATTAAATAT
1 ATTAAAAT-TATTAAATAT
14419 TTTGATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTAAAATTATTAAATATA
Done.