Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004111.1 Kokia drynarioides strain JFW-HI SEQ_117293, 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: 7910
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:4680 original size:98 final size:98
Alignment explanation
Indices: 4511--4687 Score: 345
Period size: 98 Copynumber: 1.8 Consensus size: 98
4501 CATGAGCACC
*
4511 TCCATTAGGAGTGCAATATATTTTACTACTAAATTATTGGTTAATAGAAATATAATTATTAATGT
1 TCCATTAGGAGTGCAATATATTTTACTACTAAATTATTGGTTAATAGAAATATAACTATTAATGT
4576 CGAAACTAATCTTTAAATTTCAAACTTGCATCT
66 CGAAACTAATCTTTAAATTTCAAACTTGCATCT
4609 TCCATTAGGAGTGCAATATATTTTACTACTAAATTATTGGTTAATAGAAATATAACTATTAATGT
1 TCCATTAGGAGTGCAATATATTTTACTACTAAATTATTGGTTAATAGAAATATAACTATTAATGT
4674 CGAAACTAATCTTT
66 CGAAACTAATCTTT
4688 TTTGAAAAAC
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 78 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (98 bp):
TCCATTAGGAGTGCAATATATTTTACTACTAAATTATTGGTTAATAGAAATATAACTATTAATGT
CGAAACTAATCTTTAAATTTCAAACTTGCATCT
Found at i:5303 original size:97 final size:99
Alignment explanation
Indices: 5134--5324 Score: 230
Period size: 97 Copynumber: 1.9 Consensus size: 99
5124 GAAAAAGATG
* ** *
5134 TTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTTAGGTACAAAATTTCAGAATCA
1 TTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGACACAAAATTTCAAAATCA
5199 AAGAT-AAAGAAACATTGCCTCGA-TTTAAGGATA
66 AAGATAAAAG-AACATTGCCTCGACTTTAAGGATA
* ** *
5232 TTCGATTAT-TCCGATTTGAAGAAAAA-TCGTGCCTAGTAAGTTAAGACACAAATTTTCAAAACT
1 TTCGATTATCT-CGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGACACAAAATTTCAAAA-T
* *
5295 CGAA-ATAAAAGAATATTGCCTCGACTTTAA
64 CAAAGATAAAAGAACATTGCCTCGACTTTAA
5325 AGTTTTTATG
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
97 43 0.54
98 36 0.46
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (99 bp):
TTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGACACAAAATTTCAAAATCA
AAGATAAAAGAACATTGCCTCGACTTTAAGGATA
Found at i:5897 original size:174 final size:171
Alignment explanation
Indices: 5556--6040 Score: 473
Period size: 174 Copynumber: 2.8 Consensus size: 171
5546 ACCCGGGGGT
* ** * * * *
5556 AAAATGGTAATTTTGGGAAAGTTCGGGGTTAAAAATGAAATTTTAGACA-TTCGAGGATAAAATG
1 AAAATAGTAATTTT-GGAAAAATCGGGGTTAAAAATGGAATTTTAGA-AGTTTGGGGGTAAAAT-
* * *
5620 GTAATTTTTGGAAAATTTGAGGTCAAAAATGAAATTTTAGAAGTTCGGGGATAAAATGTAATTTT
63 GTAATTTTTGGAAAA-ATGAGGTCAAAAATGGAATTTTAAAAGTTCGGGGATAAAATGTAATTTT
*
5685 TAGAAAAATCGAGGTAAAAAATGGAATTTTGAAAAGTTCAAGGGC
127 TAGAAAAATAGAGGTAAAAAATGGAATTTTGAAAAGTTCAAGGGC
* *
5730 AAAAT-GTAATTTTTGGAAAAAATCGGGGTCACAAATGGAATTTTAGAAGTTTGGGGGTAAAATG
1 AAAATAGTAA-TTTTGG-AAAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTGGGGGTAAAATG
**
5794 TAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTAAAAGTTCGGGG-TAAAAATGATTTTTT
64 TAATTTTTGGAAAAAT-GAGGTCAAAAATGGAATTTTAAAAGTTCGGGGAT-AAAATG-TAATTT
* ** * *
5858 TTCGAAAAATTAG-GGTCGAAAATGGAATTTT-AGAAAGTTCGAGGGT
126 TTAGAAAAA-TAGAGGTAAAAAATGGAATTTTGA-AAAGTTCAAGGGC
* * *
5904 AAAATAGTAAATTATGG-AAAATCGAGGTTAAAAATGGAATTTTAAAAAGTTT-GGGGTAAAAAT
1 AAAATAGT-AATTTTGGAAAAATCGGGGTTAAAAATGGAATTTT-AGAAGTTTGGGGGT-AAAAT
** * * * *
5967 GTAATTTTTTTCAAAAATTAGGGTCAAAAATGGAATTTTGGAAAGCTCGAAGG-TAAATATGTAA
63 GTAA-TTTTTGGAAAAATGA-GGTCAAAAATGGAATTTT-AAAAGTTCG-GGGATAAA-ATGTAA
*
6031 TTTTTGGAAA
123 TTTTTAGAAA
6041 GTTTAGGGTT
Statistics
Matches: 261, Mismatches: 33, Indels: 32
0.80 0.10 0.10
Matches are distributed among these distances:
172 2 0.01
173 87 0.33
174 106 0.41
175 38 0.15
176 22 0.08
177 6 0.02
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (171 bp):
AAAATAGTAATTTTGGAAAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTGGGGGTAAAATGTA
ATTTTTGGAAAAATGAGGTCAAAAATGGAATTTTAAAAGTTCGGGGATAAAATGTAATTTTTAGA
AAAATAGAGGTAAAAAATGGAATTTTGAAAAGTTCAAGGGC
Found at i:5953 original size:58 final size:55
Alignment explanation
Indices: 5551--6040 Score: 401
Period size: 58 Copynumber: 8.4 Consensus size: 55
5541 TCGATACCCG
* * * * * *
5551 GGGGTAAAATGGTAATTTTGGGAAAGTTCGGGGTTAAAAATGAAATTTTAGACA-TTC
1 GGGGTAAAAT-GTAATTTTTGGAAA-ATCGAGGTCAAAAATGGAATTTTA-AAAGTTC
* * * *
5608 GAGGATAAAATGGTAATTTTTGGAAAATTTGAGGTCAAAAATGAAATTTTAGAAGTTC
1 G-GGGTAAAAT-GTAATTTTTGGAAAA-TCGAGGTCAAAAATGGAATTTTAAAAGTTC
* *
5666 GGGGATAAAATGTAATTTTTAGAAAAATCGAGGTAAAAAATGGAATTTTGAAAAGTTC
1 GGGG-TAAAATGTAATTTTT-GGAAAATCGAGGTCAAAAATGGAATTTT-AAAAGTTC
* * * * * *
5724 AAGGGCAAAATGTAATTTTTGGAAAAAATCGGGGTCACAAATGGAATTTTAGAAGTTTG
1 -GGGGTAAAATGTAATTTTTGG--AAAATCGAGGTCAAAAATGGAATTTTAAAAG-TTC
5783 GGGGTAAAATGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTAAAAGTTC
1 GGGGTAAAATGTAATTTTTGG-AAAATCGAGGTCAAAAATGGAATTTTAAAAGTTC
** * * *
5839 GGGGTAAAAATGATTTTTTTTCGAAAAAT-TAGGGTCGAAAATGGAATTTTAGAAAGTTC
1 GGGGT-AAAATG-TAATTTTT-GGAAAATCGA-GGTCAAAAATGGAATTTTA-AAAGTTC
* * * *
5898 GAGGGTAAAATAGTAAATTATGGAAAATCGAGGTTAAAAATGGAATTTTAAAAAGTTT
1 G-GGGTAAAAT-GTAATTTTTGGAAAATCGAGGTCAAAAATGGAATTTT-AAAAGTTC
** * * *
5956 GGGGTAAAAATGTAATTTTTTTCAAAAAT-TAGGGTCAAAAATGGAATTTTGGAAAGCTC
1 GGGGT-AAAATGTAA--TTTTTGGAAAATCGA-GGTCAAAAATGGAATTTT-AAAAGTTC
*
6015 GAAGGTAAATATGTAATTTTTGGAAA
1 G-GGGTAAA-ATGTAATTTTTGGAAA
6041 GTTTAGGGTT
Statistics
Matches: 353, Mismatches: 55, Indels: 49
0.77 0.12 0.11
Matches are distributed among these distances:
56 7 0.02
57 77 0.22
58 173 0.49
59 82 0.23
60 14 0.04
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (55 bp):
GGGGTAAAATGTAATTTTTGGAAAATCGAGGTCAAAAATGGAATTTTAAAAGTTC
Found at i:5997 original size:117 final size:115
Alignment explanation
Indices: 5552--6094 Score: 485
Period size: 116 Copynumber: 4.7 Consensus size: 115
5542 CGATACCCGG
* * * * * * * *
5552 GGGTAAAATGGTAATTTTGGGAAAGTTCGGGGTTAAAAATGAAATTTTAGACA-TTCGAGG-ATA
1 GGGTAAAAT-GTAATTTTTGGAAA-ATCGAGGTTAAAAATGGAATTTTAAAAAGTTTGGGGTA-A
** * *
5615 AAATGGTAA--TTTTTGGAAAATTTGAGGTCAAAAATGAAATTTTAGAAGTTCG-
63 AAAT-GTAATTTTTTTCAAAAATTAG-GGTCAAAAATGGAATTTTAGAAGTTCGA
* * * ** *
5667 GGGATAAAATGTAATTTTTAGAAAAATCGAGGTAAAAAATGGAATTTTGAAAAGTTCAAGGG-CA
1 GGG-TAAAATGTAATTTTT-GGAAAATCGAGGTTAAAAATGGAATTTTAAAAAGTT-TGGGGTAA
*** ** * * *
5731 AAATGTAATTTTTGGAAAAAATCGGGGTCACAAATGGAATTTTAGAAGTTTGG
63 AAATGTAATTTTTTTCAAAAATTAGGGTCAAAAATGGAATTTTAGAAGTTCGA
* *
5784 GGGTAAAATGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTT-AAAAGTTCGGGGTAAAA
1 GGGTAAAATGTAATTTTTGG-AAAATCGAGGTTAAAAATGGAATTTTAAAAAGTTTGGGGTAAAA
* *
5848 ATG-ATTTTTTTTCGAAAAATTAGGGTCGAAAATGGAATTTTAGAAAGTTCGA
65 ATGTAATTTTTTTC-AAAAATTAGGGTCAAAAATGGAATTTTAG-AAGTTCGA
* *
5900 GGGTAAAATAGTAAATTATGGAAAATCGAGGTTAAAAATGGAATTTTAAAAAGTTTGGGGTAAAA
1 GGGTAAAAT-GTAATTTTTGGAAAATCGAGGTTAAAAATGGAATTTTAAAAAGTTTGGGGTAAAA
* *
5965 ATGTAATTTTTTTCAAAAATTAGGGTCAAAAATGGAATTTTGGAAAGCTCGA
65 ATGTAATTTTTTTCAAAAATTAGGGTCAAAAATGGAATTTTAG-AAGTTCGA
* * ** *
6017 AGGTAAATATGTAATTTTTGGAAAGTTTAGGGTTAAAACAT--AATTTTAGAGAAGTTTGGGGAT
1 GGGTAAA-ATGTAATTTTTGGAAAATCGA-GGTTAAAA-ATGGAATTTTA-AAAAGTTTGGGG-T
* *
6080 CAAAATATAATTTTT
61 AAAAATGTAATTTTT
6095 GGATAGTTTA
Statistics
Matches: 355, Mismatches: 54, Indels: 34
0.80 0.12 0.08
Matches are distributed among these distances:
114 9 0.03
115 75 0.21
116 121 0.34
117 104 0.29
118 30 0.08
119 16 0.05
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.32
Consensus pattern (115 bp):
GGGTAAAATGTAATTTTTGGAAAATCGAGGTTAAAAATGGAATTTTAAAAAGTTTGGGGTAAAAA
TGTAATTTTTTTCAAAAATTAGGGTCAAAAATGGAATTTTAGAAGTTCGA
Found at i:6060 original size:29 final size:30
Alignment explanation
Indices: 6028--6108 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
6018 GGTAAATATG
*
6028 TAATTTTTGGAAAGTTTAGGG-TTAAAACA
1 TAATTTTTGGAAAGTTTAGGGATCAAAACA
* * *
6057 TAA-TTTTAGAGAAGTTTGGGGATCAAAATA
1 TAATTTTTGGA-AAGTTTAGGGATCAAAACA
*
6087 TAATTTTTGGATAGTTTAGGGA
1 TAATTTTTGGAAAGTTTAGGGA
6109 CCTTTAAAGC
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
28 6 0.14
29 12 0.29
30 18 0.43
31 6 0.14
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.38
Consensus pattern (30 bp):
TAATTTTTGGAAAGTTTAGGGATCAAAACA
Done.