Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003749.1 Kokia drynarioides strain JFW-HI SEQ_116712, 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: 27321
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--32 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33 AAATTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1363 original size:23 final size:26
Alignment explanation
Indices: 1326--1378 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 26
1316 ATATTCTTAG
1326 AATAATCAGAATTTAACT-GGA-AAA
1 AATAATCAGAATTTAACTAGGAGAAA
*
1350 AATAA-CAGTATTTAACTAGGAGAAA
1 AATAATCAGAATTTAACTAGGAGAAA
1375 AATA
1 AATA
1379 CAAGGCACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 11 0.42
24 8 0.31
25 7 0.27
ACGTcount: A:0.55, C:0.08, G:0.13, T:0.25
Consensus pattern (26 bp):
AATAATCAGAATTTAACTAGGAGAAA
Found at i:1583 original size:13 final size:14
Alignment explanation
Indices: 1561--1606 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
1551 TGGGGGTTGA
*
1561 GTTTATAATTTAGG
1 GTTTAGAATTTAGG
*
1575 GTTT-GAATTTAGA
1 GTTTAGAATTTAGG
*
1588 GTTTAGGATTTAGG
1 GTTTAGAATTTAGG
1602 GTTTA
1 GTTTA
1607 AGATTTAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (14 bp):
GTTTAGAATTTAGG
Found at i:1589 original size:27 final size:28
Alignment explanation
Indices: 1559--1618 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
1549 TTTGGGGGTT
* *
1559 GAGTTTATAATTTAGGGTTTGA-ATTTA
1 GAGTTTAGAATTTAGGGTTTAAGATTTA
*
1586 GAGTTTAGGATTTAGGGTTTAAGATTTA
1 GAGTTTAGAATTTAGGGTTTAAGATTTA
1614 GAGTT
1 GAGTT
1619 CGAGTTACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (28 bp):
GAGTTTAGAATTTAGGGTTTAAGATTTA
Found at i:1600 original size:14 final size:14
Alignment explanation
Indices: 1568--1618 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
1558 TGAGTTTATA
* *
1568 ATTTAGGGTTT-GA
1 ATTTAGAGTTTAGG
1581 ATTTAGAGTTTAGG
1 ATTTAGAGTTTAGG
* *
1595 ATTTAGGGTTTAAG
1 ATTTAGAGTTTAGG
1609 ATTTAGAGTT
1 ATTTAGAGTT
1619 CGAGTTACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 10 0.31
14 22 0.69
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (14 bp):
ATTTAGAGTTTAGG
Found at i:6007 original size:18 final size:19
Alignment explanation
Indices: 5984--6022 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5974 TTTTTTTTCG
* *
5984 TTTAATTTTCAAACTC-CT
1 TTTAATTATAAAACTCTCT
6002 TTTAATTATAAAACTCTCT
1 TTTAATTATAAAACTCTCT
6021 TT
1 TT
6023 GGTTTTCGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTAATTATAAAACTCTCT
Found at i:20510 original size:24 final size:24
Alignment explanation
Indices: 20477--20525 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
20467 GAGGATGACC
*
20477 CAGAACTAGCAA-TTGCTTTGATAG
1 CAGAACTAGCAACTTG-TTTCATAG
*
20501 CAGAATTAGCAACTTGTTTCATAG
1 CAGAACTAGCAACTTGTTTCATAG
20525 C
1 C
20526 CATATCTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (24 bp):
CAGAACTAGCAACTTGTTTCATAG
Found at i:20811 original size:87 final size:87
Alignment explanation
Indices: 20665--20840 Score: 325
Period size: 87 Copynumber: 2.0 Consensus size: 87
20655 AAACCGAAGA
* * *
20665 AGTCATATTGCAGCTTGGCTTTTGCTTTCTCTGCTATGATTTGTTGACTTTTAGTACGTGGCGAA
1 AGTCACATTGCAGCTTGGCTTTTACTTTCTCTGCTAAGATTTGTTGACTTTTAGTACGTGGCGAA
20730 TTTTAGTTTGTTCTTATCAAGC
66 TTTTAGTTTGTTCTTATCAAGC
20752 AGTCACATTGCAGCTTGGCTTTTACTTTCTCTGCTAAGATTTGTTGACTTTTAGTACGTGGCGAA
1 AGTCACATTGCAGCTTGGCTTTTACTTTCTCTGCTAAGATTTGTTGACTTTTAGTACGTGGCGAA
20817 TTTTAGTTTGTTCTTATCAAGC
66 TTTTAGTTTGTTCTTATCAAGC
20839 AG
1 AG
20841 GCAGCCATTA
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.19, C:0.16, G:0.20, T:0.44
Consensus pattern (87 bp):
AGTCACATTGCAGCTTGGCTTTTACTTTCTCTGCTAAGATTTGTTGACTTTTAGTACGTGGCGAA
TTTTAGTTTGTTCTTATCAAGC
Found at i:21081 original size:19 final size:19
Alignment explanation
Indices: 21057--21095 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21047 AAAATGTTAC
*
21057 ATTAATAATTTATT-AAAAA
1 ATTAAT-ATTAATTCAAAAA
21076 ATTAATATTAATTCAAAAA
1 ATTAATATTAATTCAAAAA
21095 A
1 A
21096 ATTTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTAATATTAATTCAAAAA
Found at i:21204 original size:29 final size:29
Alignment explanation
Indices: 21127--21206 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
21117 AACTTAAATT
* **
21127 TTAAATTTTAAAATTTTAAAAATGGAGTGA
1 TTAAATTTT-AAATTTTAAAAATAGAACGA
** *
21157 TTAAATTTTTAAA-AATAAAAATATAACGA
1 TTAAA-TTTTAAATTTTAAAAATAGAACGA
21186 TTAAATTTTAAATTTTAAAAA
1 TTAAATTTTAAATTTTAAAAA
21207 AAATAGAGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
28 7 0.17
29 21 0.52
30 8 0.20
31 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (29 bp):
TTAAATTTTAAATTTTAAAAATAGAACGA
Done.