Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012831.1 Kokia drynarioides strain JFW-HI SEQ_127844, 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: 9172
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Found at i:7270 original size:201 final size:201
Alignment explanation
Indices: 6925--7716 Score: 1397
Period size: 201 Copynumber: 3.9 Consensus size: 201
6915 TCAGGTCTAC
*
6925 GCTCGAAACGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGGAGC
1 GCTCGAAACGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGC
*
6990 AATAAATGGTTAACTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
66 AATAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
* *
7055 TATAGATGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGAGACACTGAGAAGAAGACCCA
131 TAGAGAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGAGACACTGAGAAGAAGACCCA
7120 AACGAG
196 AACGAG
* * *
7126 GCTCGAAACGAGCGAAATCTTCAAAACCCAGCTTCTTTATGAGACACTGAGAAGCAGGTGGGAGC
1 GCTCGAAACGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGC
7191 AATAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
66 AATAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
7256 TAGAGAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGAGACACTGAGAAGAAGACCCA
131 TAGAGAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGAGACACTGAGAAGAAGACCCA
7321 AACGAG
196 AACGAG
*
7327 GCTCGAAACGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGAAAGC
1 GCTCGAAACGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGC
*
7392 AATAAATGGTTAGCTTCCTGATGACATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
66 AATAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
* *
7457 TAGAGAAGCGGATTGAAACAAGCGATATGGTCATTTTCCTGATGAGACACTGAGGAGAAGA-CCA
131 TAGAGAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGAGACACTGAGAAGAAGACCCA
7521 AACGAG
196 AACGAG
* *
7527 GCTCGAAACGAGCGAAATCTTCAAAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTAGAAGC
1 GCTCGAAACGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGC
*
7592 AATAAATGGTTAGCTTTCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
66 AATAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
* * * * * *
7657 CAGAGAAGCGGATTGAAAGAAGCGACGCGGTCATTTTTCTGATGAGATACTGAGAAGAAG
131 TAGAGAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGAGACACTGAGAAGAAG
7717 GTCAAGTCAA
Statistics
Matches: 566, Mismatches: 25, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
200 186 0.33
201 380 0.67
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (201 bp):
GCTCGAAACGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGC
AATAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
TAGAGAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGAGACACTGAGAAGAAGACCCA
AACGAG
Found at i:8066 original size:35 final size:35
Alignment explanation
Indices: 8027--8124 Score: 103
Period size: 35 Copynumber: 2.9 Consensus size: 35
8017 CAAACTCCCT
*
8027 TTAAATTTATTTTAAAAATTAAATTTGTTTAAAAA
1 TTAAATTTATTTTAAAAATTAAATTTATTTAAAAA
* * * *
8062 TTAAAATTTATTTT-CAATTTAAATTTATTTTAAAT
1 TT-AAATTTATTTTAAAAATTAAATTTATTTAAAAA
* *
8097 TTAAATTTAATTT--AATTTAAATTTATTT
1 TTAAATTTATTTTAAAAATTAAATTTATTT
8125 TCAAATTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
33 15 0.27
34 10 0.18
35 20 0.36
36 11 0.20
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (35 bp):
TTAAATTTATTTTAAAAATTAAATTTATTTAAAAA
Found at i:8082 original size:11 final size:11
Alignment explanation
Indices: 8077--8134 Score: 73
Period size: 11 Copynumber: 5.2 Consensus size: 11
8067 ATTTATTTTC
8077 AATTTAAATTT
1 AATTTAAATTT
*
8088 ATTTTAAATTT
1 AATTTAAATTT
8099 AAATTT-AATTT
1 -AATTTAAATTT
8110 AATTTAAATTT
1 AATTTAAATTT
*
8121 ATTTTCAAATTT
1 AATTT-AAATTT
8133 AA
1 AA
8135 AATTACTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
10 5 0.12
11 24 0.60
12 11 0.28
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:8086 original size:6 final size:6
Alignment explanation
Indices: 8059--8153 Score: 67
Period size: 6 Copynumber: 16.7 Consensus size: 6
8049 ATTTGTTTAA
* * * *
8059 AAATTA AAATTT -ATTTT CAATTT AAATTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * * *
8105 -AATTT -AATTT AAATTT -ATTTT CAAATTT AAAATT -ACTAT AAATTT
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT AAATTT
8150 AAAT
1 AAAT
8154 AAGGCTAAAA
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
5 24 0.35
6 41 0.59
7 4 0.06
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:8149 original size:17 final size:17
Alignment explanation
Indices: 8026--8153 Score: 141
Period size: 17 Copynumber: 7.4 Consensus size: 17
8016 CCAAACTCCC
8026 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
8044 ATTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
* *
8062 TTAAAATTTATTTTCAA
1 TTTAAATTTATTTTAAA
8079 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
8096 TTTAAATTTAATTT-AA
1 TTTAAATTTATTTTAAA
8112 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* * *
8130 TTTAAAATTACTATAAA
1 TTTAAATTTATTTTAAA
8147 TTTAAAT
1 TTTAAAT
8154 AAGGCTAAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
16 15 0.16
17 39 0.43
18 37 0.41
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:8796 original size:16 final size:16
Alignment explanation
Indices: 8771--8830 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 16
8761 CCGTTCATGC
8771 ATATTATTACTATAAT
1 ATATTATTACTATAAT
* **
8787 ATATTGTTAC-AT-GC
1 ATATTATTACTATAAT
8801 ATATTATTACTATAAT
1 ATATTATTACTATAAT
*
8817 ATATTGTTACTATA
1 ATATTATTACTATA
8831 CGCGTTTTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
14 9 0.26
15 4 0.11
16 22 0.63
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.48
Consensus pattern (16 bp):
ATATTATTACTATAAT
Found at i:8800 original size:30 final size:30
Alignment explanation
Indices: 8766--8826 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
8756 AATACCCGTT
8766 CATGCATATTATTACTATAATATATTGTTA
1 CATGCATATTATTACTATAATATATTGTTA
8796 CATGCATATTATTACTATAATATATTGTTA
1 CATGCATATTATTACTATAATATATTGTTA
8826 C
1 C
8827 TATACGCGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (30 bp):
CATGCATATTATTACTATAATATATTGTTA
Found at i:8987 original size:3 final size:3
Alignment explanation
Indices: 8981--9019 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
8971 AAATATTTTT
* *
8981 TAA TAA TAA TAA TAT TAA TAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9020 AACGAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:8987 original size:20 final size:19
Alignment explanation
Indices: 8959--8996 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
8949 TTTCATAATG
*
8959 TTTATTAATAATAAATATTT
1 TTTAATAATAAT-AATATTT
8979 TTTAATAATAATAATATT
1 TTTAATAATAATAATATT
8997 AATAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAATAATAATAATATTT
Done.