Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010787.1 Kokia drynarioides strain JFW-HI SEQ_125754, 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:0.34, C:0.18, G:0.19, T:0.28
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:5119 original size:9 final size:8
Alignment explanation
Indices: 5092--5153 Score: 56
Period size: 8 Copynumber: 7.8 Consensus size: 8
5082 CAATGAATAA
5092 AAGAAAAG
1 AAGAAAAG
*
5100 AAAAAAAG
1 AAGAAAAG
5108 AAGAAGAAG
1 AAGAA-AAG
5117 AAG-AAA-
1 AAGAAAAG
5123 AAGCAAAAG
1 AAG-AAAAG
* *
5132 AAAAAAAA
1 AAGAAAAG
*
5140 AAGAAAAA
1 AAGAAAAG
5148 AAGAAA
1 AAGAAA
5154 CACAAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
6 3 0.07
7 2 0.04
8 32 0.71
9 8 0.18
ACGTcount: A:0.81, C:0.02, G:0.18, T:0.00
Consensus pattern (8 bp):
AAGAAAAG
Found at i:5132 original size:12 final size:11
Alignment explanation
Indices: 5090--5182 Score: 68
Period size: 11 Copynumber: 8.5 Consensus size: 11
5080 TTCAATGAAT
5090 AAAAGAAAAG-
1 AAAAGAAAAGA
5100 -AAA-AAAAGA
1 AAAAGAAAAGA
*
5109 AGAAGAAGAAGA
1 AAAAGAA-AAGA
5121 AAAAGCAAAAGA
1 AAAAG-AAAAGA
*
5133 AAAAAAAAAGA
1 AAAAGAAAAGA
* *
5144 AAAAAAGAAACA
1 AAAAGA-AAAGA
*
5156 CAAAA-AAAGGA
1 -AAAAGAAAAGA
*
5167 AAAAAAAAAGA
1 AAAAGAAAAGA
5178 AAAAG
1 AAAAG
5183 GAGAGATCGA
Statistics
Matches: 67, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
8 5 0.07
9 3 0.04
10 6 0.09
11 26 0.39
12 21 0.31
13 6 0.09
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:5181 original size:6 final size:6
Alignment explanation
Indices: 5090--5182 Score: 77
Period size: 6 Copynumber: 15.8 Consensus size: 6
5080 TTCAATGAAT
* * * *
5090 AAAAGA AAAGAAA AAAAGA AGAAGA AGAAGA AAAAGC AAAAGA AAAA-A
1 AAAAGA AAA-AGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
* * *
5138 AAAAGA AAAA-A AGAAACA CAAA-A AAAGGA AAAA-A AAAAGA AAAAG
1 AAAAGA AAAAGA A-AAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAG
5183 GAGAGATCGA
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
5 15 0.21
6 50 0.70
7 6 0.08
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:5343 original size:16 final size:16
Alignment explanation
Indices: 5322--5353 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5312 AAGTAGCAAG
5322 GTGGAGAAACTTTATA
1 GTGGAGAAACTTTATA
5338 GTGGAGAAACTTTATA
1 GTGGAGAAACTTTATA
5354 CCTTGAGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (16 bp):
GTGGAGAAACTTTATA
Found at i:6526 original size:49 final size:49
Alignment explanation
Indices: 6343--6641 Score: 167
Period size: 49 Copynumber: 6.1 Consensus size: 49
6333 CTGAGAAAAA
*
6343 CATGAAGATTAGAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTAC
1 CATGAAGATTAGATGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTAC
* * * * * * ** * *
6392 CTTAGCAGA-TATTATAGG-AAGGATTGAGGCAGCAACGATAAATCCGGTTC
1 CAT-GAAGATTA-GATGGGAAAGG-TTAAGGCCGCAACGGCAAACCCGGTAC
* * * * * *
6442 CATGAAGATGAAATGGGAAAGGTTGAGACCACAACGGCGAACCCGGTAC
1 CATGAAGATTAGATGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTAC
* * * *
6491 CATGAAGATTTGACGGGAAAGGTTAAGGTCGCAACGGCAAATCCGGTAC
1 CATGAAGATTAGATGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTAC
* * * * * * * * *
6540 CTTAGCAGA-TATTATGGG-AAGGATTGAGGCCGCAACAGTAGATCCGGTTC
1 CAT-GAAGATTA-GATGGGAAAGG-TTAAGGCCGCAACGGCAAACCCGGTAC
** * * * * * *
6590 TGTG-AGATGAAATGGGAAAGGTTGAGGCCGCATCGGCGAACCCGATAC
1 CATGAAGATTAGATGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTAC
6638 CATG
1 CATG
6642 GAGACATGAA
Statistics
Matches: 181, Mismatches: 59, Indels: 21
0.69 0.23 0.08
Matches are distributed among these distances:
48 29 0.16
49 87 0.48
50 65 0.36
ACGTcount: A:0.33, C:0.19, G:0.30, T:0.18
Consensus pattern (49 bp):
CATGAAGATTAGATGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTAC
Found at i:6665 original size:148 final size:148
Alignment explanation
Indices: 6354--6658 Score: 452
Period size: 148 Copynumber: 2.1 Consensus size: 148
6344 ATGAAGATTA
6354 GAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTACCTTAGCAGATATTATAGGAAGGATTGA
1 GAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTACCTTAGCAGATATTATAGGAAGGATTGA
6419 GGCAGCAACGATAAATCCGGTTCCATGAAGATGAAATGGGAAAGGTTGAGACCACAACGGCGAAC
66 GGCAGCAACGATAAATCCGGTTCCATGAAGATGAAATGGGAAAGGTTGAGACCACAACGGCGAAC
* **
6484 CCGGTACCATGAAGATTT
131 CCGATACCATGAAGACAT
* * * *
6502 GACGGGAAAGGTTAAGGTCGCAACGGCAAATCCGGTACCTTAGCAGATATTATGGGAAGGATTGA
1 GAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTACCTTAGCAGATATTATAGGAAGGATTGA
* * ** * * *
6567 GGCCGCAAC-AGTAGATCCGGTTCTGTG-AGATGAAATGGGAAAGGTTGAGGCCGCATCGGCGAA
66 GGCAGCAACGA-TAAATCCGGTTCCATGAAGATGAAATGGGAAAGGTTGAGACCACAACGGCGAA
*
6630 CCCGATACCATGGAGACAT
130 CCCGATACCATGAAGACAT
6649 GAAGGGAAAG
1 GAAGGGAAAG
6659 ATTTAAGCCG
Statistics
Matches: 140, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
147 58 0.41
148 82 0.59
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.17
Consensus pattern (148 bp):
GAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTACCTTAGCAGATATTATAGGAAGGATTGA
GGCAGCAACGATAAATCCGGTTCCATGAAGATGAAATGGGAAAGGTTGAGACCACAACGGCGAAC
CCGATACCATGAAGACAT
Done.