Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004316.1 Kokia drynarioides strain JFW-HI SEQ_117632, 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: 7618
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:1206 original size:34 final size:32
Alignment explanation
Indices: 1168--1230 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1158 TTAATATAAT
*
1168 ATTTGATACTTGAATATTTGACAATTTTTTTCTA
1 ATTTGATACCT-AA-ATTTGACAATTTTTTTCTA
* *
1202 ATTTGGTACCTAAATTTGACACTTTTTTT
1 ATTTGATACCTAAATTTGACAATTTTTTT
1231 TACGTTGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 15 0.58
33 2 0.08
34 9 0.35
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.52
Consensus pattern (32 bp):
ATTTGATACCTAAATTTGACAATTTTTTTCTA
Found at i:1239 original size:31 final size:32
Alignment explanation
Indices: 1183--1249 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
1173 ATACTTGAAT
* *
1183 ATTTGACAATTTTTTTCTAATTTGGTACCTAA
1 ATTTGACAATTTTTTTCTAAGTTGGTAACTAA
* * *
1215 ATTTGACACTTTTTTT-TACGTTGGTAATTAA
1 ATTTGACAATTTTTTTCTAAGTTGGTAACTAA
1246 ATTT
1 ATTT
1250 TGTGAGGGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 15 0.50
32 15 0.50
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.52
Consensus pattern (32 bp):
ATTTGACAATTTTTTTCTAAGTTGGTAACTAA
Found at i:1813 original size:26 final size:28
Alignment explanation
Indices: 1760--1813 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
1750 ATTCAATTTT
* *
1760 ATTAAATATATTATTAAAAAATCATAATA
1 ATTAAAAATATTATAAAAAAAT-ATAATA
1789 ATTAAAAATATTA-AAAAAAAT-TAAT
1 ATTAAAAATATTATAAAAAAATATAAT
1814 TCAATTGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 4 0.17
28 7 0.30
29 12 0.52
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (28 bp):
ATTAAAAATATTATAAAAAAATATAATA
Found at i:2708 original size:28 final size:28
Alignment explanation
Indices: 2677--2752 Score: 143
Period size: 28 Copynumber: 2.7 Consensus size: 28
2667 GGATACTTGG
*
2677 GGGCAAAATGGTAATTTTGGACTTATGA
1 GGGCAAAATGGGAATTTTGGACTTATGA
2705 GGGCAAAATGGGAATTTTGGACTTATGA
1 GGGCAAAATGGGAATTTTGGACTTATGA
2733 GGGCAAAATGGGAATTTTGG
1 GGGCAAAATGGGAATTTTGG
2753 GAAAGTTCGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.32, C:0.07, G:0.33, T:0.29
Consensus pattern (28 bp):
GGGCAAAATGGGAATTTTGGACTTATGA
Found at i:2887 original size:29 final size:29
Alignment explanation
Indices: 2850--3091 Score: 146
Period size: 30 Copynumber: 8.3 Consensus size: 29
2840 TGGATATTCG
*
2850 GGGGT-AAAAGGGTAATTTTTGAAAGTTT
1 GGGGTCAAAATGGTAATTTTTGAAAGTTT
* * *
2878 TGGGTCAAAAAT-ATAA-TTTTGGAAGTTT
1 GGGGTC-AAAATGGTAATTTTTGAAAGTTT
* * *
2906 AGGGGT-AAAATAGTAA-TTTTGAGAGTCTC
1 -GGGGTCAAAATGGTAATTTTTGAAAGT-TT
* * * *
2935 GGGGTTAAAAATGG-AATTTTTGGAGGTTCA
1 GGGG-TCAAAATGGTAATTTTTGAAAGTT-T
2965 GGGGT-AAAATGGTAATTTTT-AGAAGTTT
1 GGGGTCAAAATGGTAATTTTTGA-AAGTTT
* *
2993 CGGGGTCAAAATTG-AGATTTTTGGAAGTTT
1 -GGGGTCAAAATGGTA-ATTTTTGAAAGTTT
* *
3023 AGTGGTCAAAAT-GTAATTTTTGGAAGTTTT
1 -GGGGTCAAAATGGTAATTTTTGAAAG-TTT
*
3053 GGGGTCAAAAGTGG-AATTTTGGAGAAGTTT
1 GGGGTCAAAA-TGGTAATTTTTGA-AAGTTT
3083 AGGGGTCAA
1 -GGGGTCAA
3092 TAATATAATT
Statistics
Matches: 169, Mismatches: 24, Indels: 39
0.73 0.10 0.17
Matches are distributed among these distances:
27 5 0.03
28 37 0.22
29 51 0.30
30 64 0.38
31 12 0.07
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (29 bp):
GGGGTCAAAATGGTAATTTTTGAAAGTTT
Found at i:2898 original size:28 final size:28
Alignment explanation
Indices: 2850--3117 Score: 118
Period size: 29 Copynumber: 9.1 Consensus size: 28
2840 TGGATATTCG
**
2850 GGGGTAAAAGGGTAATTTTTGAAAGTTT-
1 GGGGTAAAATAGTAA-TTTTGAAAGTTTA
* *
2878 TGGGTCAAAAATA-TAATTTTGGAAGTTTA
1 GGGGT--AAAATAGTAATTTTGAAAGTTTA
* * *
2907 GGGGTAAAATAGTAATTTTGAGAGTCTC
1 GGGGTAAAATAGTAATTTTGAAAGTTTA
* * * *
2935 GGGGTTAAAA-ATGGAATTTTTGGAGGTTCA
1 GGGG-TAAAATA-GTAA-TTTTGAAAGTTTA
* * *
2965 GGGGTAAAATGGTAATTTTTAGAAGTTTC
1 GGGGTAAAATAGTAATTTTGA-AAGTTTA
* *
2994 GGGGTCAAAATTGAG-ATTTTTGGAAGTTTA
1 GGGGT-AAAA-T-AGTAATTTTGAAAGTTTA
* * *
3024 GTGGTCAAAAT-GTAATTTTTGGAAGTTTT
1 GGGGT-AAAATAGTAA-TTTTGAAAGTTTA
*
3053 GGGGTCAAAAGT-GGAATTTTGGAGAAGTTTA
1 GGGGT-AAAA-TAGTAATTTT-GA-AAGTTTA
*
3084 GGGGTCAATAATA-TAATTTCTAGATAGTTTA
1 GGGGT-AA-AATAGTAATTT-T-GAAAGTTTA
3115 GGG
1 GGG
3118 ACCTTCAGGG
Statistics
Matches: 182, Mismatches: 38, Indels: 37
0.71 0.15 0.14
Matches are distributed among these distances:
27 7 0.04
28 37 0.20
29 58 0.32
30 39 0.21
31 35 0.19
32 6 0.03
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.36
Consensus pattern (28 bp):
GGGGTAAAATAGTAATTTTGAAAGTTTA
Found at i:3013 original size:30 final size:29
Alignment explanation
Indices: 2894--3117 Score: 115
Period size: 30 Copynumber: 7.6 Consensus size: 29
2884 AAAAATATAA
* *
2894 TTTTGGAAGTTTAGGGGT-AAAAT-AGTAA
1 TTTTAGAAGTTTAGGGGTCAAAATGAG-AT
* * *
2922 TTTT-GAGAGTCTCGGGGTTAAAAATG-GAAT
1 TTTTAGA-AGTTTAGGGG-TCAAAATGAG-AT
* * *
2952 TTTTGGAGGTTCAGGGGT-AAAATG-GTAAT
1 TTTTAGAAGTTTAGGGGTCAAAATGAG--AT
*
2981 TTTTAGAAGTTTCGGGGTCAAAATTGAGAT
1 TTTTAGAAGTTTAGGGGTCAAAA-TGAGAT
* *
3011 TTTTGGAAGTTTAGTGGTCAAAATGTA-AT
1 TTTTAGAAGTTTAGGGGTCAAAATG-AGAT
* *
3040 TTTTGGAAGTTTTGGGGTCAAAAGTG-GAAT
1 TTTTAGAAGTTTAGGGGTCAAAA-TGAG-AT
* *
3070 TTTGGAGAAGTTTAGGGGTCAATAAT-ATAAT
1 TTT-TAGAAGTTTAGGGGTCAA-AATGA-GAT
*
3101 TTCTAGATAGTTTAGGG
1 TTTTAGA-AGTTTAGGG
3118 ACCTTCAGGG
Statistics
Matches: 155, Mismatches: 23, Indels: 33
0.73 0.11 0.16
Matches are distributed among these distances:
27 2 0.01
28 19 0.12
29 44 0.28
30 54 0.35
31 33 0.21
32 3 0.02
ACGTcount: A:0.30, C:0.04, G:0.29, T:0.37
Consensus pattern (29 bp):
TTTTAGAAGTTTAGGGGTCAAAATGAGAT
Found at i:3039 original size:59 final size:59
Alignment explanation
Indices: 2826--3113 Score: 259
Period size: 59 Copynumber: 4.9 Consensus size: 59
2816 AATCGGGATA
* ** ** *
2826 AAAAACGGAATTTTTGGATA-TTCGGGGGTAAAAGGGTAATTTTT-GAAAGTTT-TGGGTC
1 AAAAATGGAATTTTTGGA-AGTTTAGGGGTAAAATAGTAATTTTTAG-AAGTTTCGGGGTC
** * * *
2884 AAAAATATAA-TTTTGGAAGTTTAGGGGTAAAATAGTAATTTTGAG-AGTCTCGGGGTT
1 AAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATAGTAATTTTTAGAAGTTTCGGGGTC
* * *
2941 AAAAATGGAATTTTTGGAGGTTCAGGGGTAAAATGGTAATTTTTAGAAGTTTCGGGGTC
1 AAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATAGTAATTTTTAGAAGTTTCGGGGTC
* * * *
3000 -AAAATTGAGATTTTTGGAAGTTTAGTGGTCAAAAT-GTAATTTTTGGAAGTTTTGGGGTC
1 AAAAATGGA-ATTTTTGGAAGTTTAGGGGT-AAAATAGTAATTTTTAGAAGTTTCGGGGTC
* * *
3059 AAAAGTGGAATTTTGGAGAAGTTTAGGGGTCAATAATA-TAATTTCTAGATAGTTT
1 AAAAATGGAATTTTTG-GAAGTTTAGGGGT-AA-AATAGTAATTTTTAGA-AGTTT
3114 AGGGACCTTC
Statistics
Matches: 187, Mismatches: 31, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
56 5 0.03
57 38 0.20
58 46 0.25
59 55 0.29
60 26 0.14
61 12 0.06
62 5 0.03
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.36
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATAGTAATTTTTAGAAGTTTCGGGGTC
Found at i:4143 original size:3 final size:3
Alignment explanation
Indices: 4137--4189 Score: 61
Period size: 3 Copynumber: 17.0 Consensus size: 3
4127 TTAAAAAAAG
* * *
4137 TTA TTA TTG TCA TTG TTA ATTA ATTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA
4184 TTA TTA
1 TTA TTA
4190 ACCATTTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 36 0.84
4 7 0.16
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:4878 original size:17 final size:17
Alignment explanation
Indices: 4817--4908 Score: 78
Period size: 17 Copynumber: 5.3 Consensus size: 17
4807 TAAATTTAAG
* *
4817 ATTTAAGTTTAAAAT-C
1 ATTTAAATTTAAAATAA
* *
4833 ATTTCGAATTTAAACTAA
1 ATTT-AAATTTAAAATAA
**
4851 ATTTATTTTTAAAATAA
1 ATTTAAATTTAAAATAA
*
4868 ATTTAAATTTAAAAATTA
1 ATTTAAATTT-AAAATAA
*
4886 ATTTAAATTTAAATTTAA
1 ATTTAAATTTAAA-ATAA
4904 ATTTA
1 ATTTA
4909 TGAATAAATT
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
16 4 0.07
17 28 0.47
18 27 0.46
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:4888 original size:18 final size:18
Alignment explanation
Indices: 4839--4908 Score: 72
Period size: 18 Copynumber: 4.0 Consensus size: 18
4829 AATCATTTCG
*
4839 AATTT-AAACTAAATTT-
1 AATTTAAAAATAAATTTA
* *
4855 ATTTTTAAAATAAATTTA
1 AATTTAAAAATAAATTTA
*
4873 AATTTAAAAATTAATTTA
1 AATTTAAAAATAAATTTA
**
4891 AATTTAAATTTAAATTTA
1 AATTTAAAAATAAATTTA
4909 TGAATAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
16 4 0.09
17 10 0.23
18 30 0.68
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTAAAAATAAATTTA
Found at i:4922 original size:6 final size:6
Alignment explanation
Indices: 4839--4908 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
4829 AATCATTTCG
* ** * *
4839 AATTTA AA-CTA AATTTA TTTTTA AA-ATA AATTTA AATTTAA AAATT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA
4885 AATTTA AATTTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA
4909 TGAATAAATT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
5 12 0.24
6 33 0.66
7 5 0.10
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (6 bp):
AATTTA
Done.