Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013619.1 Kokia drynarioides strain JFW-HI SEQ_128647, 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: 2075
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Found at i:1716 original size:117 final size:116
Alignment explanation
Indices: 1589--1801 Score: 270
Period size: 117 Copynumber: 1.8 Consensus size: 116
1579 GAAAGTTCAT
* * *
1589 GGTTAAAAATGAAAATTT--AAGCATCCGAGGGTAAAATGGTATTTTTTGGAAAGAATCAAGATC
1 GGTTAAAAATGAAAATTTGAAAG--TCCGAGGGTAAAATGGTAATTTTTGGAAA-AATAAAGATA
*
1652 AAAAATGG-AATTTTTGATAGTTTGGGGGTAAAAAAGTATTTTGGGAGGAATTAG
63 AAAAATGGAAATTTTGGA-AGTTTGGGGGTAAAAAAGTATTTTGGGAGGAATTAG
* ** * * *
1706 GGTTAAAAATGAAATTTTGGAAAGTTTGGGGGTAAAATGTTAATTTTTGGAAAAATAAAGGTAAA
1 GGTTAAAAATGAAAATTT-GAAAGTCCGAGGGTAAAATGGTAATTTTTGGAAAAATAAAGATAAA
1771 AAATGGAAATTTTGGAAGTTTGGGGGTAAAA
65 AAATGGAAATTTTGGAAGTTTGGGGGTAAAA
1802 TGGTAATTGG
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
117 47 0.57
118 32 0.39
120 3 0.04
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.31
Consensus pattern (116 bp):
GGTTAAAAATGAAAATTTGAAAGTCCGAGGGTAAAATGGTAATTTTTGGAAAAATAAAGATAAAA
AATGGAAATTTTGGAAGTTTGGGGGTAAAAAAGTATTTTGGGAGGAATTAG
Found at i:1792 original size:59 final size:58
Alignment explanation
Indices: 1617--1991 Score: 348
Period size: 59 Copynumber: 6.4 Consensus size: 58
1607 AAGCATCCGA
* * * *
1617 GGGTAAAATGGTATTTTTTGGAAAGAATCAAGATCAAAAATGGAATTTTTGATAGTTTGG
1 GGGTAAAATGGTAATTTTTGGAAA-AATCAAGGTAAAAAATGGAATTTTGGA-AGTTTGG
** * ** * * * *
1677 GGGTAAAAAAGT-ATTTTGGGAGGAATTAGGGTTAAAAATGAAATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGAAAAATCAAGGTAAAAAATGGAATTTTGG-AAGTTTGG
* *
1735 GGGTAAAATGTTAATTTTTGGAAAAATAAAGGTAAAAAATGGAAATTTTGGAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGAAAAATCAAGGTAAAAAATGG-AATTTTGGAAGTTTGG
* * * * *
1794 GGGTAAAATGGTAA---TTGGAAAAATCGAGGTCAAAAATGGAATTTTTAGAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGAAAAATCAAGGTAAAAAATGGAA-TTTTGGAAGTTTGG
* * * * * * *
1850 GGGTAAAATGGTTATTTTTTGGAAAAATCGAGGTTAAAAATTGAATTTTGGAAGGTCGA
1 GGGTAAAATGG-TAATTTTTGGAAAAATCAAGGTAAAAAATGGAATTTTGGAAGTTTGG
* ** *
1909 GGGTAAAATGGTAATTTTTGGAAAAATCGACATAAAAAATGGAATTTAGGAATGTTTGG
1 GGGTAAAATGGTAATTTTTGGAAAAATCAAGGTAAAAAATGGAATTTTGGAA-GTTTGG
*
1968 GGGTAAAAAT-GTTATTTTT-GAAAA
1 GGGT-AAAATGGTAATTTTTGGAAAA
1992 GTTTAGGTGT
Statistics
Matches: 261, Mismatches: 44, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
55 2 0.01
56 44 0.17
57 2 0.01
58 76 0.29
59 89 0.34
60 48 0.18
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.32
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGAAAAATCAAGGTAAAAAATGGAATTTTGGAAGTTTGG
Found at i:1799 original size:30 final size:30
Alignment explanation
Indices: 1705--1801 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 30
1695 GGAGGAATTA
*
1705 GGGTTAAAAAT-GAAATTTTGGAAAGTTTGG
1 GGGTAAAAAATGGAAATTTTGG-AAGTTTGG
* * *** **
1735 GGGT--AAAATGTTAATTTTTGGAAAAATAA
1 GGGTAAAAAATG-GAAATTTTGGAAGTTTGG
*
1764 AGGTAAAAAATGGAAATTTTGGAAGTTTGG
1 GGGTAAAAAATGGAAATTTTGGAAGTTTGG
1794 GGGTAAAA
1 GGGTAAAA
1802 TGGTAATTGG
Statistics
Matches: 47, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
28 5 0.11
29 6 0.13
30 30 0.64
31 6 0.13
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (30 bp):
GGGTAAAAAATGGAAATTTTGGAAGTTTGG
Found at i:1857 original size:28 final size:29
Alignment explanation
Indices: 1735--1931 Score: 106
Period size: 28 Copynumber: 6.8 Consensus size: 29
1725 GAAAGTTTGG
* * *
1735 GGGTAAAATGTTAATTTTTGGAAAAAT-AA
1 GGGTAAAATGGTAATTTTTGG-AAGATCGA
* * * * *
1764 AGGTAAAAAATGG-AAATTTTGGAAGTTTGG
1 GGGT--AAAATGGTAATTTTTGGAAGATCGA
*
1794 GGGTAAAATGGTAA---TTGGAAAAATCGA
1 GGGTAAAATGGTAATTTTTGG-AAGATCGA
* *
1821 -GGTCAAAAATGG-AATTTTTAGAAGTTCGA
1 GGGT--AAAATGGTAATTTTTGGAAGATCGA
* *
1850 GGGTAAAATGGTTATTTTTTGGAAAAATCGA
1 GGGTAAAATGG-TAATTTTTGG-AAGATCGA
* * *
1881 GGTTAAAAATTG-AA-TTTTGGAAGGTCGA
1 GGGT-AAAATGGTAATTTTTGGAAGATCGA
1909 GGGTAAAATGGTAATTTTTGGAA
1 GGGTAAAATGGTAATTTTTGGAA
1932 AAATCGACAT
Statistics
Matches: 125, Mismatches: 26, Indels: 34
0.68 0.14 0.18
Matches are distributed among these distances:
26 7 0.06
27 12 0.10
28 32 0.26
29 28 0.22
30 25 0.20
31 15 0.12
32 6 0.05
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.31
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGGAAGATCGA
Found at i:1867 original size:115 final size:116
Alignment explanation
Indices: 1614--1955 Score: 343
Period size: 115 Copynumber: 2.9 Consensus size: 116
1604 TTTAAGCATC
* * *
1614 CGAGGGTAAAATGG-TATTTTTTGGAAAGAATCAAGATCAAAAATGGAATTTTTGATAGTTTGGG
1 CGAGGGTAAAATGGTTATTTTTTGGAAA-AATCAAGGTAAAAAATGGAATTTTGGA-AGTTTGGG
** * ** * * * *
1678 GGTAAAAAAGTATTTTGGGAGGAAT-TAGGGTTAAAAAT-GAAATTTTGGAAAGTT
64 GGTAAAATGGTA-ATT-GGAAAAATCGA-GGTAAAAAATGGAATTTTTAGAAAGTT
* * * *
1732 TGGGGGTAAAAT-GTTAATTTTTGGAAAAATAAAGGTAAAAAATGGAAATTTTGGAAGTTTGGGG
1 CGAGGGTAAAATGGTTATTTTTTGGAAAAATCAAGGTAAAAAATGG-AATTTTGGAAGTTTGGGG
*
1796 GTAAAATGGTAATTGGAAAAATCGAGGTCAAAAATGGAATTTTTAG-AAGTT
65 GTAAAATGGTAATTGGAAAAATCGAGGTAAAAAATGGAATTTTTAGAAAGTT
* * * * * *
1847 CGAGGGTAAAATGGTTATTTTTTGGAAAAATCGAGGTTAAAAATTGAATTTTGGAAGGTCGAGGG
1 CGAGGGTAAAATGGTTATTTTTTGGAAAAATCAAGGTAAAAAATGGAATTTTGGAAGTTTGGGGG
**
1912 TAAAATGGTAATTTTTGGAAAAATCGACATAAAAAATGGAATTT
66 TAAAATGGTAA---TTGGAAAAATCGAGGTAAAAAATGGAATTT
1956 AGGAATGTTT
Statistics
Matches: 187, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
115 57 0.30
116 39 0.21
117 34 0.18
118 57 0.30
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.31
Consensus pattern (116 bp):
CGAGGGTAAAATGGTTATTTTTTGGAAAAATCAAGGTAAAAAATGGAATTTTGGAAGTTTGGGGG
TAAAATGGTAATTGGAAAAATCGAGGTAAAAAATGGAATTTTTAGAAAGTT
Found at i:2039 original size:30 final size:29
Alignment explanation
Indices: 1962--2044 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
1952 ATTTAGGAAT
* * *
1962 GTTTGGGGGTAAAAATGTTATTTTTGAAAA
1 GTTTGGGGGT-AAAATATAATTTTGGAAAA
* * * *
1992 GTTTAGGTGTTAAATATAATTTTGGAGAA
1 GTTTGGGGGTAAAATATAATTTTGGAAAA
2021 GTTTGGGGGTCAAAATATAATTTT
1 GTTTGGGGGT-AAAATATAATTTT
2045 TGGACTGTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
29 22 0.52
30 20 0.48
ACGTcount: A:0.33, C:0.01, G:0.25, T:0.41
Consensus pattern (29 bp):
GTTTGGGGGTAAAATATAATTTTGGAAAA
Done.