Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013851.1 Kokia drynarioides strain JFW-HI SEQ_128879, 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: 25642
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Warning! 63 characters in sequence are not A, C, G, or T
Found at i:355 original size:59 final size:59
Alignment explanation
Indices: 263--904 Score: 882
Period size: 59 Copynumber: 10.9 Consensus size: 59
253 GGAGTCGGCT
* * *
263 AAAAATGGGATTTTTGAAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTC
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTC
* *
322 AAAAATGGGATTTTT-AAAGGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTC
1 AAAAATGGGATTTTTGGAA-GTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTC
* * ** *
381 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTATTTTTTTTAAGGTTCGAGG-C
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTC
* * **
439 TAAAAATGGGATTTTTAGAAGTT-TAGGGGTAAAATGGTAATTTTTAGAAGGTTTAGGGT-
1 -AAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTC
* * *
498 AAAAATGGGATTTTTGGAGGTTCGAGGGTAAAATGGTAATTTTTAGAAGTTTTGGGGTC
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTC
* * *
557 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAATGTTCGGGGTA
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTC
* * * *
616 AAAAATGGAATTTTTGGAAGTTTG-GGAGTAAAATGGTAATTTTTAGAATGTTCGGGGTT
1 AAAAATGGGATTTTTGGAAGTTCGAGG-GTAAAATGGTAATTTTTAGAAGGTTCGGGGTC
* *
675 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTC
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTC
* *
734 AAAAATGGGATTTTTAGAAGTTCGAGGGTAAAATGGTAATATTTAGAAGGTTCGGGGTC
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTC
* * * *
793 AAAAATGGGATTTTTGGAAGTT-TAGGGGTAAAAGGGTAATTTTTTGAAGGTTCGAGGTC
1 AAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTC
* *
852 AAAAATTGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTTTGAAGGTT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAA-TTTTTAGAAGGTT
905 TAGGGATCTC
Statistics
Matches: 523, Mismatches: 48, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
58 59 0.11
59 446 0.85
60 18 0.03
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.35
Consensus pattern (59 bp):
AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTC
Found at i:3449 original size:37 final size:37
Alignment explanation
Indices: 3406--3495 Score: 139
Period size: 37 Copynumber: 2.4 Consensus size: 37
3396 CCGCTTCTCT
3406 GTATCTCATCAAGAAGACGAATTTGGTTCACTTCTCCA
1 GTATCTCATCAAGAAGACGAATTTGGTTCACTT-TCCA
3444 -TATCTCATC-AGAAAGACGAATTTGGTTCACTTTCCA
1 GTATCTCATCAAG-AAGACGAATTTGGTTCACTTTCCA
*
3480 GTATCTCATCAGGAAG
1 GTATCTCATCAAGAAG
3496 CTAACCATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
36 6 0.12
37 41 0.85
38 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (37 bp):
GTATCTCATCAAGAAGACGAATTTGGTTCACTTTCCA
Found at i:4454 original size:201 final size:200
Alignment explanation
Indices: 4049--4502 Score: 721
Period size: 201 Copynumber: 2.3 Consensus size: 200
4039 NNNNNNNNNN
* *
4049 TTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTC
1 TTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCGCTTTGAGCCTCATTTGGGTC
* *
4114 TTCTCCTCAGTGTCTCATCAGGAAGATGGTCCCATCATCGTTTCAATTCGCTTCTCTGTATCTCA
66 TTCTCCTCAGTGTCTCATCAGGAAGATGCTCCCATCATCGTTTCAACTCGCTTCTCTGTATCTCA
* *
4179 TCAGGAAGACGAATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCA
131 TCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTATTGCTTCCA
*
4244 CCTGC
196 CCCGC
*
4249 TTCTCAGTGTCTCATCAGGAAGCTAGGGTTCAAAGATTTTGCTCGCTTTGAGCCTCATTTGGGTC
1 TTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCGCTTTGAGCCTCATTTGGGTC
* * *
4314 TTCTCCTCAGTGTCTCATCAGGAAGATGACT-GCATCGTTTGTTTCAACTCGCTTCTCTGTATCT
66 TTCTCCTCAGTGTCTCATCAGGAAGATG-CTCCCATC-ATCGTTTCAACTCGCTTCTCTGTATCT
*
4378 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTC
129 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTATTGCTTC
**
4443 GGCCCGC
194 CACCCGC
* ** *
4450 TTCTCAGTGTCTCATCAAGAAGCTGGGGTTTGAAGATTTTGCTTGCTTTGAGC
1 TTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCGCTTTGAGC
4503 GTAGGCTTGA
Statistics
Matches: 233, Mismatches: 19, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
200 94 0.40
201 139 0.60
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (200 bp):
TTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCGCTTTGAGCCTCATTTGGGTC
TTCTCCTCAGTGTCTCATCAGGAAGATGCTCCCATCATCGTTTCAACTCGCTTCTCTGTATCTCA
TCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTATTGCTTCCA
CCCGC
Found at i:5042 original size:27 final size:27
Alignment explanation
Indices: 5012--5072 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
5002 CCAAGAATTC
*
5012 TATTAAAAAGAGGATCGAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
** *
5039 TATTAAAGGGAGGGTCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
5066 TCATTAA
1 T-ATTAA
5073 TTGAAAATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 24 0.83
28 5 0.17
ACGTcount: A:0.51, C:0.08, G:0.23, T:0.18
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAGGAAACAA
Found at i:17997 original size:59 final size:59
Alignment explanation
Indices: 17837--18567 Score: 924
Period size: 59 Copynumber: 12.4 Consensus size: 59
17827 GCACGGGAGC
* **
17837 AAAATGGTAATTTTTAGAAGGTTCGG-GTC-AAAATGGGATTTTTGGAAGTTCAAGGGT
1 AAAATGGTAATTTTTAGAAGGTTTGGAGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * * *
17894 AAAATGATAATTTTTTTGAAGGTTCGG-GGCTAAAAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAATGGTAA-TTTTTAGAAGGTTTGGAGTC-AAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * *
17954 AAAATGGTAATTTTTAGAAGATTTGGAGTCAAAAATGGGATTTTCGGAGGTTCGAGGGT
1 AAAATGGTAATTTTTAGAAGGTTTGGAGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
*
18013 AAAATGGTAATTTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTTGGAGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * *
18072 -AAATGGTAATTTTTTTGAAGG-TTCGAGGCTAAAAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAATGGTAA-TTTTTAGAAGGTTTGGAGTC-AAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * * **
18131 AAAATAGTAATTTTTAGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAGGTTCAAGGGT
1 AAAATGGTAATTTTTAGAAGGTTTGGAGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
18190 AAAATGGTAATTTTTAGAAGG-TTCGAGGTCAAAAATGGGATTTTTTGAAGTTCGAGGGT
1 AAAATGGTAATTTTTAGAAGGTTTGGA-GTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * * * *
18249 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGAATATTTGGAAGTTCGAGAGT
1 AAAATGGTAATTTTTAGAAGGTTTGGAGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * * *
18308 AAAATGGTAATTTTTAGAATGTTAGGGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGC
1 AAAATGGTAATTTTTAGAAGGTTTGGAGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
18367 AAAATGATAATTTTTAGAAGG-TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTTGGA-GTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
*
18426 AAAATGGTAATTTTTAGAAGGTTCGG-GATCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTTGGAG-TCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
18485 AAAAGGGTAATTTTTAGAAGG-TTCGAGGTC-AAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTTGGA-GTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
*
18543 AAAATGGTAATTTTTTTGAAGGTTT
1 AAAATGGTAA-TTTTTAGAAGGTTT
18568 AGGTACCTCC
Statistics
Matches: 585, Mismatches: 72, Indels: 31
0.85 0.10 0.05
Matches are distributed among these distances:
57 9 0.02
58 76 0.13
59 445 0.76
60 55 0.09
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTAGAAGGTTTGGAGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:18558 original size:118 final size:117
Alignment explanation
Indices: 17837--18566 Score: 1029
Period size: 118 Copynumber: 6.2 Consensus size: 117
17827 GCACGGGAGC
* *
17837 AAAATGGTAATTTTTAGAAGGTTCGGGTC-AAAATGGGATTTTTGGAAGTTCAAGGGTAAAATGA
1 AAAATGGTAATTTTTAGAAGGTTCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGG
* *
17901 TAATTTTTTTGAAGGTTCGGGG-CTAAAAATGGGATTTTTGGAAGTTTGGGGGT
66 TAA-TTTTTAGAAGGTTCGGGGTC-AAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * *
17954 AAAATGGTAATTTTTAGAAGATTTGGAGTCAAAAATGGGATTTTCGGAGGTTCGAGGGTAAAATG
1 AAAATGGTAATTTTTAGAAGGTTCGG-GTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATG
*
18019 GTAATTTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
65 GTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
18072 -AAATGGTAATTTTTTTGAAGGTTCGAGG-CTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAA
1 AAAATGGTAA-TTTTTAGAAGGTTCG-GGTC-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAA
* * * * **
18135 TAGTAATTTTTAGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAGGTTCAAGGGT
63 TGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
*
18190 AAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTTGAAGTTCGAGGGTAAAATG
1 AAAATGGTAATTTTTAGAAGGTTCG-GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATG
* * * *
18255 GTAATTTTTAGAAGGTTCGGGGTCAAAAATGGAATATTTGGAAGTTCGAGAGT
65 GTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * * *
18308 AAAATGGTAATTTTTAGAATGTTAGGGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGCAAAATG
1 AAAATGGTAATTTTTAGAAGGTT-CGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATG
* *
18373 ATAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
65 GTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
18426 AAAATGGTAATTTTTAGAAGGTTCGGGATCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAGG
1 AAAATGGTAATTTTTAGAAGGTTCGGG-TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATG
*
18491 GTAATTTTTAGAAGGTTCGAGGTC-AAAATGGGATTTTTGGAAGTTCGGGGGT
65 GTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
*
18543 AAAATGGTAATTTTTTTGAAGGTT
1 AAAATGGTAA-TTTTTAGAAGGTT
18567 TAGGTACCTC
Statistics
Matches: 550, Mismatches: 52, Indels: 21
0.88 0.08 0.03
Matches are distributed among these distances:
117 75 0.14
118 428 0.78
119 47 0.09
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (117 bp):
AAAATGGTAATTTTTAGAAGGTTCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGG
TAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:19799 original size:18 final size:19
Alignment explanation
Indices: 19788--19829 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
19778 ATTAATATTA
19788 TTATTAATATTAA-AACAG
1 TTATTAATATTAATAACAG
*
19806 TTATTAATATTAATAAAAG
1 TTATTAATATTAATAACAG
19825 TTATT
1 TTATT
19830 GAAACATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (19 bp):
TTATTAATATTAATAACAG
Found at i:21240 original size:29 final size:29
Alignment explanation
Indices: 21180--21305 Score: 84
Period size: 29 Copynumber: 4.3 Consensus size: 29
21170 ACGTGAAGTC
* **
21180 TTTTTACCTCCGAACTTTTAAAAATTTTA
1 TTTTTACCTCCGAACTTCTAAAAATTCCA
21209 TTTTTACC-CCTGAACTTCTAAAAATTCCA
1 TTTTTACCTCC-GAACTTCTAAAAATTCCA
* **
21238 TTTTCGACCT-CGAAAC-TCTCGAAATTAGCC-
1 TTTT-TACCTCCG-AACTTCTAAAAATT--CCA
*
21268 -TTTTACCCCCGAA-TGTCTAAAAATTCCA
1 TTTTTACCTCCGAACT-TCTAAAAATTCCA
*
21296 TTTTAACCTC
1 TTTTTACCTC
21306 GAATTTTCTC
Statistics
Matches: 74, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
27 2 0.03
28 7 0.09
29 56 0.76
30 7 0.09
31 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.38
Consensus pattern (29 bp):
TTTTTACCTCCGAACTTCTAAAAATTCCA
Found at i:24715 original size:16 final size:15
Alignment explanation
Indices: 24680--24712 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
24670 AAACCAAGAG
24680 TTTT-ACAACATTCA
1 TTTTCACAACATTCA
*
24694 TTTTCACAATATTCA
1 TTTTCACAACATTCA
24709 TTTT
1 TTTT
24713 TCATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTCACAACATTCA
Done.