Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009754.1 Kokia drynarioides strain JFW-HI SEQ_124473, 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: 21600
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Found at i:304 original size:17 final size:17
Alignment explanation
Indices: 273--305 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
263 CAAACACTTA
273 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
290 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
306 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:6502 original size:21 final size:21
Alignment explanation
Indices: 6477--6557 Score: 72
Period size: 21 Copynumber: 3.6 Consensus size: 21
6467 TGGACAAGCT
6477 ACCACATAATTGTCGATAACA
1 ACCACATAATTGTCGATAACA
* *
6498 ACCACATAATTGCATTTTGGATAAACC
1 ACCACATAATTG-----TCGAT-AACA
*
6525 ACCACATAATTGCCGATAACA
1 ACCACATAATTGTCGATAACA
*
6546 GCCACATAATTG
1 ACCACATAATTG
6558 CATTTTGGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 26 0.54
22 3 0.06
26 4 0.08
27 15 0.31
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.25
Consensus pattern (21 bp):
ACCACATAATTGTCGATAACA
Found at i:6529 original size:48 final size:48
Alignment explanation
Indices: 6477--6603 Score: 218
Period size: 48 Copynumber: 2.6 Consensus size: 48
6467 TGGACAAGCT
*
6477 ACCACATAATTGTCGATAACAACCACATAATTGCATTTTGGATAAACC
1 ACCACATAATTGTCGATAACAGCCACATAATTGCATTTTGGATAAACC
*
6525 ACCACATAATTGCCGATAACAGCCACATAATTGCATTTTGGATAAACC
1 ACCACATAATTGTCGATAACAGCCACATAATTGCATTTTGGATAAACC
* *
6573 ACCACATAATTGTTGATAACGGCCACATAAT
1 ACCACATAATTGTCGATAACAGCCACATAAT
6604 CACAGTTAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 74 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.26
Consensus pattern (48 bp):
ACCACATAATTGTCGATAACAGCCACATAATTGCATTTTGGATAAACC
Found at i:6530 original size:27 final size:27
Alignment explanation
Indices: 6498--6584 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 27
6488 GTCGATAACA
6498 ACCACATAATTGCATTTTGGATAAACC
1 ACCACATAATTGCATTTTGGATAAACC
*
6525 ACCACATAATTGC-----CGAT-AA-C
1 ACCACATAATTGCATTTTGGATAAACC
6545 AGCCACATAATTGCATTTTGGATAAACC
1 A-CCACATAATTGCATTTTGGATAAACC
6573 ACCACATAATTG
1 ACCACATAATTG
6585 TTGATAACGG
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
20 2 0.04
21 14 0.28
22 3 0.06
26 3 0.06
27 26 0.52
28 2 0.04
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.26
Consensus pattern (27 bp):
ACCACATAATTGCATTTTGGATAAACC
Found at i:8891 original size:51 final size:51
Alignment explanation
Indices: 8829--8952 Score: 167
Period size: 51 Copynumber: 2.4 Consensus size: 51
8819 ACACCATTTA
* *
8829 TGGACATGCCACCACTGATTTGTAGAGAAACTGCCACTGATAACAATTTTG
1 TGGACAAGCCACCACTGATTTGAAGAGAAACTGCCACTGATAACAATTTTG
* * * ***
8880 TGGACAAGCCACCAGTGATTTGAAGATAAACTGTCACTGATAATTCTTTTG
1 TGGACAAGCCACCACTGATTTGAAGAGAAACTGCCACTGATAACAATTTTG
*
8931 TGGACAAGCCACCACTAATTTG
1 TGGACAAGCCACCACTGATTTG
8953 CAACTATACT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (51 bp):
TGGACAAGCCACCACTGATTTGAAGAGAAACTGCCACTGATAACAATTTTG
Found at i:8969 original size:51 final size:51
Alignment explanation
Indices: 8829--8969 Score: 158
Period size: 51 Copynumber: 2.8 Consensus size: 51
8819 ACACCATTTA
* * * *
8829 TGGACATGCCACCACTGATTTGTAGAGAAACTGCCACTGATAACAATTTTG
1 TGGACAAGCCACCACTAATTTGAAGATAAACTGCCACTGATAACAATTTTG
* * * ***
8880 TGGACAAGCCACCAGTGATTTGAAGATAAACTGTCACTGATAATTCTTTTG
1 TGGACAAGCCACCACTAATTTGAAGATAAACTGCCACTGATAACAATTTTG
* *
8931 TGGACAAGCCACCACTAATTTGCAA-CTATACTGCCACTG
1 TGGACAAGCCACCACTAATTTG-AAGATAAACTGCCACTG
8970 CTTCTACCTT
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
51 74 0.97
52 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (51 bp):
TGGACAAGCCACCACTAATTTGAAGATAAACTGCCACTGATAACAATTTTG
Found at i:9801 original size:39 final size:39
Alignment explanation
Indices: 9755--9853 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 39
9745 TTAAATAGGG
9755 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
*
9794 TTTTAATGTGTCTTATTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
9833 TTTTAAGGTGTCTAAGTTTGA
1 TTTTAATGTGTCTTAGTTTGA
9854 GACAAATTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.54
Consensus pattern (39 bp):
TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
Found at i:9935 original size:32 final size:32
Alignment explanation
Indices: 9899--9960 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
9889 TGCCGAAATT
* * *
9899 AATTAGCTAATTAATGTGTTTTAGGTACATGC
1 AATTAGCTAATTAATATATTTCAGGTACATGC
*
9931 AATTAGCTGATTAATATATTTCAGGTACAT
1 AATTAGCTAATTAATATATTTCAGGTACAT
9961 TTATGGATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (32 bp):
AATTAGCTAATTAATATATTTCAGGTACATGC
Found at i:13230 original size:21 final size:20
Alignment explanation
Indices: 13183--13221 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13173 AGTGAGAATG
*
13183 AAAAAGAAAAGAAAATTGAA
1 AAAAAGAAAAGAAAAATGAA
*
13203 AAAAAGAAAGGAAAAATGA
1 AAAAAGAAAAGAAAAATGA
13222 GAGAAAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (20 bp):
AAAAAGAAAAGAAAAATGAA
Found at i:13268 original size:31 final size:27
Alignment explanation
Indices: 13203--13268 Score: 69
Period size: 31 Copynumber: 2.3 Consensus size: 27
13193 GAAAATTGAA
*
13203 AAAAAGAAAGGAAAAATGAGAGAAAAG
1 AAAAAGAAAGGAAAAAAGAGAGAAAAG
*
13230 AGCAAAGAAAGTGAGAAGAAAGAGAGAAAAAG
1 A-AAAAGAAAG-GA-AA-AAAGAGAG-AAAAG
13262 AAAAAGA
1 AAAAAGA
13269 TGAAATGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.03
28 8 0.26
29 2 0.06
30 2 0.06
31 12 0.39
32 6 0.19
ACGTcount: A:0.68, C:0.02, G:0.27, T:0.03
Consensus pattern (27 bp):
AAAAAGAAAGGAAAAAAGAGAGAAAAG
Found at i:16410 original size:39 final size:39
Alignment explanation
Indices: 16364--16462 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 39
16354 TTAAATAGGG
16364 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
*
16403 TTTTAATGTGTCTTATTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
16442 TTTTAAGGTGTCTAAGTTTGA
1 TTTTAATGTGTCTTAGTTTGA
16463 GACAAATTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.54
Consensus pattern (39 bp):
TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
Found at i:16543 original size:32 final size:32
Alignment explanation
Indices: 16507--16572 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
16497 CAGCCGAAAT
* *
16507 TAATTAGCTAATTAATGTGTTTCAAGTACATG
1 TAATTAGCTAATTAATATATTTCAAGTACATG
* * *
16539 TAATTAGGTGATTAATATATTTCAGGTACATG
1 TAATTAGCTAATTAATATATTTCAAGTACATG
16571 TA
1 TA
16573 TGGATGGCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.41
Consensus pattern (32 bp):
TAATTAGCTAATTAATATATTTCAAGTACATG
Found at i:17939 original size:34 final size:34
Alignment explanation
Indices: 17890--17959 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
17880 TTATGTTGAC
17890 ACTATGGCACTATACCATTC-GACCAAGATATGAA
1 ACTATGGCACTATACCATTCAG-CCAAGATATGAA
17924 ACTATGGCA-TAATACCATTCAGCCAAGATATGAA
1 ACTATGGCACT-ATACCATTCAGCCAAGATATGAA
17958 AC
1 AC
17960 CTCCGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 1 0.03
34 32 0.94
35 1 0.03
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (34 bp):
ACTATGGCACTATACCATTCAGCCAAGATATGAA
Found at i:21495 original size:50 final size:51
Alignment explanation
Indices: 21434--21557 Score: 137
Period size: 50 Copynumber: 2.4 Consensus size: 51
21424 TTTAATGATG
* *
21434 TATTTAACTAACATGGGAGTTAGATAATGCATGAT-AGGA-TTTGTGATGCA
1 TATTTAACTAACATGAGAGTTACATAATGCATG-TCAGGATTTTGTGATGCA
* **
21484 TATTTAACTAACATGTA-AGTTACTTAATGCATGTCATTATTTTGTGATGCA
1 TATTTAACTAACATG-AGAGTTACATAATGCATGTCAGGATTTTGTGATGCA
* *
21535 AACTTAACTAATCATGAGAGTTA
1 TATTTAACTAA-CATGAGAGTTA
21558 ATGGATGTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
49 1 0.02
50 31 0.50
51 21 0.34
52 9 0.15
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (51 bp):
TATTTAACTAACATGAGAGTTACATAATGCATGTCAGGATTTTGTGATGCA
Done.