Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010231.1 Kokia drynarioides strain JFW-HI SEQ_125061, 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: 6673
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Found at i:1389 original size:201 final size:200
Alignment explanation
Indices: 982--1806 Score: 975
Period size: 206 Copynumber: 4.1 Consensus size: 200
972 AAATGGTTAG
* * ** ***
982 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCGATATGAGCAAATCTTCGAATTTC
1 CTTCCTGATGAGATACAGAGAAGAATACCAACTC-AGGCTCAATGCGAGCAAATCTTCGAACCCC
* *
1047 AATTTCCTGATGAGATACTGAGAAGCAGGGCGAAGTAAT-AAAAGGTTAGCTTCCTGATGAGATA
65 AACTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATA
* * *
1111 CTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAGTAAGGT
130 CTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGT
1176 GGTCAT
195 GGTCAT
* *
1182 CTTCCTGATGAGATACAGAGAAGAATACCAACTCGAGGCTCAATGCGAGCAAATCTTGGACCCCC
1 CTTCCTGATGAGATACAGAGAAGAATACCAACTC-AGGCTCAATGCGAGCAAATCTTCGAACCCC
* *
1247 AACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATA
65 AACTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATA
* * * * * * *
1312 CTGAGAAGTGAACCAAATTCATTTTCCTGATGAGATACAAAGTAGCAGATTGAAACAAGCGATGT
130 CTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGT
*
1377 GGTCAC
195 GGTCAT
* * * * **
1383 CTTCCTGATGAGATA-ATGAGAAGAAGACCAAATCAAACCCACGCTCAATGCGAGTAAATCTTTA
1 CTTCCTGATGAGATACA-GAGAAGAATA-C----C-AACTCAGGCTCAATGCGAGCAAATCTTCG
* *
1447 AACCTCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGAT
59 AACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGAT
* * *
1512 GAGATACTGAGAAGTGGACCAAATTTGTCTCCCTGATGAGATACAGAGAAGCGGATTGAAACAAG
124 GAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAG
*
1577 TGAGGCGGTCAT
189 TGAGGTGGTCAT
* * *
1589 CTTCCTGATGAGATACAAAGAAGTATACC-A---A--CTCAATGCGAACAAATCTTCG-ACCCCA
1 CTTCCTGATGAGATACAGAGAAGAATACCAACTCAGGCTCAATGCGAGCAAATCTTCGAACCCCA
* * *
1647 GCTTCCTGATGAGATACTAAGAAGCAGGGCGAAACAATAAAAAGGTTAGCTTCCTGATGAGATAC
66 ACTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATAC
* * * * * * * * ** * *
1712 GGAGAAGTGAACTAAATCCGTCTTCTTGATAAAACACAGAGAAGTGGATCAAAACAAGTGATGCG
131 TGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGTG
* *
1777 ATCGT
196 GTCAT
* **
1782 CTTCTTGATGAGATATTGAGAAGAA
1 CTTCCTGATGAGATACAGAGAAGAA
1807 GGCCAAGTCA
Statistics
Matches: 537, Mismatches: 79, Indels: 25
0.84 0.12 0.04
Matches are distributed among these distances:
193 142 0.26
194 17 0.03
196 1 0.00
199 1 0.00
200 92 0.17
201 109 0.20
202 1 0.00
205 1 0.00
206 168 0.31
207 5 0.01
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (200 bp):
CTTCCTGATGAGATACAGAGAAGAATACCAACTCAGGCTCAATGCGAGCAAATCTTCGAACCCCA
ACTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATAC
TGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGTG
GTCAT
Found at i:2174 original size:17 final size:17
Alignment explanation
Indices: 2154--2193 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2144 TTAAGTCTAT
2154 TTTAAAATTAAATTTAC
1 TTTAAAATTAAATTTAC
**
2171 TTTAAGTTTAAATTTAC
1 TTTAAAATTAAATTTAC
2188 -TTAAAA
1 TTTAAAA
2194 GTTATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTAAAATTAAATTTAC
Found at i:2979 original size:12 final size:12
Alignment explanation
Indices: 2964--3007 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
2954 TAATGATAGC
2964 ATTAATAATAAT
1 ATTAATAATAAT
* *
2976 ATTAATAAAAAC
1 ATTAATAATAAT
2988 ATTAATAATAAT
1 ATTAATAATAAT
*
3000 AATAATAA
1 ATTAATAA
3008 AGAAATTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
ATTAATAATAAT
Found at i:2979 original size:24 final size:24
Alignment explanation
Indices: 2963--3008 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2953 TTAATGATAG
2963 CATTAATAATAATATTAATAAAAA
1 CATTAATAATAATATTAATAAAAA
*
2987 CATTAATAATAATAATAATAAA
1 CATTAATAATAATATTAATAAA
3009 GAAATTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
CATTAATAATAATATTAATAAAAA
Found at i:3077 original size:20 final size:22
Alignment explanation
Indices: 3048--3089 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
3038 CGACCGAACT
*
3048 GAGCCTGAACC-ACCA-CGTCG
1 GAGCCAGAACCTACCACCGTCG
3068 GAGCCAGAACCTACCACCGTCG
1 GAGCCAGAACCTACCACCGTCG
3090 CCGTTGCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 4 0.21
22 5 0.26
ACGTcount: A:0.26, C:0.40, G:0.24, T:0.10
Consensus pattern (22 bp):
GAGCCAGAACCTACCACCGTCG
Found at i:3492 original size:13 final size:12
Alignment explanation
Indices: 3471--3495 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3461 TGAAGATTTT
3471 TTTGTAAAAAAA
1 TTTGTAAAAAAA
3483 TTTGTAAAAAAA
1 TTTGTAAAAAAA
3495 T
1 T
3496 GAAAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TTTGTAAAAAAA
Found at i:4092 original size:30 final size:30
Alignment explanation
Indices: 3963--4133 Score: 183
Period size: 29 Copynumber: 5.7 Consensus size: 30
3953 TGGAGGTCCT
**
3963 AAACTGTCCAAAAATT--ATATTTTGACCCTA
1 AAACT-TCCAAAAATTCCAT-TTTTGACCCCG
*
3993 AAACTTCCAAAAATTACATTTTT-ACCCACG
1 AAACTTCCAAAAATTCCATTTTTGACCC-CG
*
4023 -AACTTCCAAAAATTACATTTTT-ACCCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCC-CG
* *
4052 -AACTTTCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
4081 AAACTTCCAAAAATTCCATTTTTGATCCCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
4111 AAACTTGCAAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
4134 GCCTCAAGTA
Statistics
Matches: 125, Mismatches: 10, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
29 64 0.51
30 52 0.42
31 9 0.07
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCG
Found at i:5890 original size:30 final size:29
Alignment explanation
Indices: 5851--6297 Score: 405
Period size: 30 Copynumber: 15.1 Consensus size: 29
5841 AGACATTCGG
5851 GGGGTAAAAATGGAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
5880 GGGGTCAAAAATAGG-ATTTTT-GATAGTTT-
1 GGGGT-AAAAAT-GGAATTTTTGGA-AGTTTC
* *
5909 GGAGGTAAAAATGGAATTTTTGAAAGTTTTA
1 GG-GGTAAAAATGGAATTTTTGGAAG-TTTC
** * *
5940 GGGCCAAAAATGGGATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
* * * *
5969 AGGGTCGAAAATGGGATTTTTGGAAGTTTGG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTT-C
6000 GGGGTAAAAATGGAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
* *
6029 GAGGTCAAAAATGGGATTTTT-GAGAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGA-AGTTTC
* *
6058 GGTGGTAAAAATGGAATTTTTGGAAATTTT
1 GG-GGTAAAAATGGAATTTTTGGAAGTTTC
* * * *
6088 GATGTTAAAAAATAGG-ATTTTTGGGAGTTTA
1 G-GGGT-AAAAAT-GGAATTTTTGGAAGTTTC
*
6119 GGGGTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
*
6148 GGGGTCAAAAAT-GAGATTTTTGGGAG-TTC
1 GGGGT-AAAAATGGA-ATTTTTGGAAGTTTC
6177 GAGGGTAAAAATGGAA-TTTTGGAAGTTTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTC
*
6206 GAGGTCAAAAAT-GAGATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGA-ATTTTTGGAAGTTTC
6235 GAGGGTAAAAATGGAATTTTTGGAAGTTTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTC
** * *
6265 AAGGTCGAAAATGGGATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTC
6294 GGGG
1 GGGG
6298 ACCTCCAAGG
Statistics
Matches: 346, Mismatches: 41, Indels: 62
0.77 0.09 0.14
Matches are distributed among these distances:
28 17 0.05
29 129 0.37
30 171 0.49
31 27 0.08
32 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.34
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTC
Found at i:5923 original size:59 final size:58
Alignment explanation
Indices: 5856--6297 Score: 452
Period size: 59 Copynumber: 7.5 Consensus size: 58
5846 TTCGGGGGGT
*
5856 AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATAGG-ATTTTT-GATAGTTTGGAGGT-
1 AAAAATGGAATTTTTGGAAG-TTCGGGGT-AAAAAT-GGAATTTTTGGA-AGTTTCGAGGTC
* * ** * *
5915 AAAAATGGAATTTTTGAAAGTTTTAGGGCCAAAAATGGGATTTTTGGAAGTTT-TAGGGTC
1 AAAAATGGAATTTTTGGAAG--TTCGGGGTAAAAATGGAATTTTTGGAAGTTTCGA-GGTC
* * *
5975 GAAAATGGGATTTTTGGAAGTTTGGGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC
1 AAAAATGGAATTTTTGGAAG-TT-CGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC
* * * * *
6035 AAAAATGGGATTTTT-GAGAGTTCGGTGGTAAAAATGGAATTTTTGGAAATTTTGATGTTA
1 AAAAATGGAATTTTTGGA-AGTTCGG-GGTAAAAATGGAATTTTTGGAAGTTTCGA-GGTC
* * * *
6095 AAAAATAGG-ATTTTTGGGAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTC
1 AAAAAT-GGAATTTTTGGAAG-TTCGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC
*
6154 AAAAAT-GAGATTTTTGGGAGTTCGAGGGTAAAAATGGAA-TTTTGGAAGTTTCGAGGTC
1 AAAAATGGA-ATTTTTGGAAGTTCG-GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC
*
6212 AAAAAT-GAGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTC
1 AAAAATGGA-ATTTTTGGAAGTTCG-GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC
* *
6271 GAAAATGGGATTTTTGGAAGTTCGGGG
1 AAAAATGGAATTTTTGGAAGTTCGGGG
6298 ACCTCCAAGG
Statistics
Matches: 333, Mismatches: 32, Indels: 37
0.83 0.08 0.09
Matches are distributed among these distances:
57 1 0.00
58 66 0.20
59 144 0.43
60 114 0.34
61 8 0.02
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC
Done.