Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014286.1 Kokia drynarioides strain JFW-HI SEQ_129319, 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: 23081
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8019 original size:59 final size:57
Alignment explanation
Indices: 7919--8258 Score: 205
Period size: 59 Copynumber: 5.8 Consensus size: 57
7909 TAGACATTCA
7919 GGGGTAAAAGGGTAA-TTTT-GAGAGTTTCGAGGTAAAAAATGGTG-TCTTAGAA-CATCTG
1 GGGGTAAAAGGGTAATTTTTGGA-AGTTTCG-GGTAAAAAATGG-GATCTTAGAAGC-TC-G
* * *
7977 GGGGTAAAAGGGTAATTTTTGGAAGTTTCAGGGTCAAAAATGGGATTTTTGGAAGCTCG
1 GGGGTAAAAGGGTAATTTTTGGAAGTTTC-GGGTAAAAAATGGGA-TCTTAGAAGCTCG
* * * * *
8036 GGGGTAAAATTGG-AATTTTTGGAAGTTTTGGGGTAAAAAATGGGATTTTTGGAAGTTCG
1 GGGGTAAAA-GGGTAATTTTTGGAAG-TTTCGGGTAAAAAATGGGA-TCTTAGAAGCTCG
* * * * * *
8095 AGGGTAAAAATGG-AATTTTTTGGAAGTTTCGAGGTAAAAAATGGGATTTTTGGAAGTTCA
1 GGGGT-AAAAGGGTAA-TTTTTGGAAGTTTCG-GGTAAAAAATGGGA-TCTTAGAAGCTCG
* * * * * * * *
8155 GGAGTAAAAATGG-AATTTTTGGAAGTTTCTGGGT-CAAAATGAGATTTTTGGAAGTTTG
1 GGGGT-AAAAGGGTAATTTTTGGAAGTTTC-GGGTAAAAAATGGGA-TCTTAGAAGCTCG
* * *
8213 GAGGTAAAA--ATAGAGTTTTTGGAAGTTTTGGGGTAAAAAATGGGAT
1 GGGGTAAAAGGGTA-A-TTTTTGGAAG-TTTCGGGTAAAAAATGGGAT
8259 TATTGGAAGT
Statistics
Matches: 243, Mismatches: 22, Indels: 34
0.81 0.07 0.11
Matches are distributed among these distances:
56 1 0.00
57 5 0.02
58 54 0.22
59 111 0.46
60 71 0.29
61 1 0.00
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (57 bp):
GGGGTAAAAGGGTAATTTTTGGAAGTTTCGGGTAAAAAATGGGATCTTAGAAGCTCG
Found at i:8027 original size:30 final size:29
Alignment explanation
Indices: 7991--8304 Score: 293
Period size: 29 Copynumber: 10.7 Consensus size: 29
7981 TAAAAGGGTA
7991 ATTTTTGGAAGTTTCAGGGTCAAAAATGGG
1 ATTTTTGGAAGTTTCAGGGT-AAAAATGGG
* * * *
8021 ATTTTTGGAAG-CTCGGGGGTAAAATTGGA
1 ATTTTTGGAAGTTTC-AGGGTAAAAATGGG
**
8050 ATTTTTGGAAGTTTTGGGGTAAAAAATGGG
1 ATTTTTGGAAGTTTCAGGGT-AAAAATGGG
*
8080 ATTTTTGGAAG-TTCGAGGGTAAAAATGGA
1 ATTTTTGGAAGTTTC-AGGGTAAAAATGGG
8109 ATTTTTTGGAAGTTTC-GAGGTAAAAAATGGG
1 A-TTTTTGGAAGTTTCAG-GGT-AAAAATGGG
*
8140 ATTTTTGGAAG-TTCAGGAGTAAAAATGGA
1 ATTTTTGGAAGTTTCAGG-GTAAAAATGGG
* * *
8169 ATTTTTGGAAGTTTCTGGGTCAAAATGAG
1 ATTTTTGGAAGTTTCAGGGTAAAAATGGG
* *
8198 ATTTTTGGAAGTTT-GGAGGTAAAAAT-AG
1 ATTTTTGGAAGTTTCAG-GGTAAAAATGGG
**
8226 AGTTTTTGGAAGTTTTGGGGTAAAAAATGGG
1 A-TTTTTGGAAGTTTCAGGGT-AAAAATGGG
* * *
8257 ATTATTGGAAG-TTCGAGGGAAAAAATGGA
1 ATTTTTGGAAGTTTC-AGGGTAAAAATGGG
8286 ATTTTTGGACAGTTT-AGGG
1 ATTTTTGGA-AGTTTCAGGG
8305 ACCTCCGGGG
Statistics
Matches: 239, Mismatches: 26, Indels: 39
0.79 0.09 0.13
Matches are distributed among these distances:
28 4 0.02
29 128 0.54
30 91 0.38
31 16 0.07
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.34
Consensus pattern (29 bp):
ATTTTTGGAAGTTTCAGGGTAAAAATGGG
Found at i:8281 original size:59 final size:59
Alignment explanation
Indices: 7990--8300 Score: 414
Period size: 59 Copynumber: 5.3 Consensus size: 59
7980 GTAAAAGGGT
** * * * *
7990 AATTTTTGGAAGTTTCAGGGTCAAAAATGGGATTTTTGGAAGCTCGGGGGTAAAATTGG
1 AATTTTTGGAAGTTTTGGGGTAAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
8049 AATTTTTGGAAGTTTTGGGGTAAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
1 AATTTTTGGAAGTTTTGGGGTAAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
* *
8108 AATTTTTTGGAAGTTTCGAGGTAAAAAATGGGATTTTTGGAAGTTC-AGGAGTAAAAATGG
1 AA-TTTTTGGAAGTTTTGGGGTAAAAAATGGGATTTTTGGAAGTTCGAGG-GTAAAAATGG
* * * *
8168 AATTTTTGGAAGTTTCT-GGGT-CAAAATGAGATTTTTGGAAGTTTG-GAGGTAAAAATAG
1 AATTTTTGGAAGTTT-TGGGGTAAAAAATGGGATTTTTGGAAGTTCGAG-GGTAAAAATGG
* * *
8226 AGTTTTTGGAAGTTTTGGGGTAAAAAATGGGATTATTGGAAGTTCGAGGGAAAAAATGG
1 AATTTTTGGAAGTTTTGGGGTAAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
8285 AATTTTTGGACAGTTT
1 AATTTTTGGA-AGTTT
8301 AGGGACCTCC
Statistics
Matches: 221, Mismatches: 22, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
57 1 0.00
58 48 0.22
59 113 0.51
60 59 0.27
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (59 bp):
AATTTTTGGAAGTTTTGGGGTAAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
Found at i:9998 original size:17 final size:16
Alignment explanation
Indices: 9964--10017 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
9954 TGGACCTTTT
9964 TTTTAAATTAATTAAA
1 TTTTAAATTAATTAAA
9980 TTTTAAATTCAAATT-AA
1 TTTTAAATT--AATTAAA
9997 TTTTAAACTTAATTTAAA
1 TTTTAAA-TTAA-TTAAA
10015 TTT
1 TTT
10018 AAACTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 11 0.33
17 11 0.33
18 11 0.33
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAATTAATTAAA
Found at i:10018 original size:17 final size:16
Alignment explanation
Indices: 9965--10056 Score: 71
Period size: 17 Copynumber: 5.4 Consensus size: 16
9955 GGACCTTTTT
9965 TTTAAA-TTAATTAAA
1 TTTAAACTTAATTAAA
*
9980 TTTTAAA-TTCAAATTAAT
1 -TTTAAACTT--AATTAAA
9998 TTTAAACTTAATTTAAA
1 TTTAAACTTAA-TTAAA
**
10015 TTTAAACTTAAAAAAA
1 TTTAAACTTAATTAAA
*
10031 GTTAAAACTTTAAATTAAA
1 -TTTAAAC-TT-AATTAAA
10050 TTTAAAC
1 TTTAAAC
10057 CCAAAATGAG
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
16 13 0.21
17 27 0.44
18 16 0.26
19 5 0.08
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (16 bp):
TTTAAACTTAATTAAA
Found at i:10049 original size:35 final size:35
Alignment explanation
Indices: 10001--10078 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
9991 AATTAATTTT
* **
10001 AAAC-TTAATTTAAATTTAAACTTAAAAAAAGTTA
1 AAACTTTAAATTAAATTTAAACCCAAAAAAAGTTA
**
10035 AAACTTTAAATTAAATTTAAACCCAAAATGAGTTA
1 AAACTTTAAATTAAATTTAAACCCAAAAAAAGTTA
10070 AAA-TTTAAA
1 AAACTTTAAA
10079 AACTTAAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
34 10 0.26
35 28 0.74
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (35 bp):
AAACTTTAAATTAAATTTAAACCCAAAAAAAGTTA
Found at i:22462 original size:28 final size:28
Alignment explanation
Indices: 22399--22464 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
22389 GGATGGTCAA
* *
22399 AGTAAT-ATATATTATAAATATTATATT
1 AGTAATAATATATGATAAATAATATATT
**
22426 AGTGTTAATATATGATAAATAATAGTATT
1 AGTAATAATATATGATAAATAATA-TATT
22455 A-TAATAATAT
1 AGTAATAATAT
22465 TCTAATAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 4 0.13
28 22 0.71
29 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (28 bp):
AGTAATAATATATGATAAATAATATATT
Done.