Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003946.1 Kokia drynarioides strain JFW-HI SEQ_117030, 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: 4059
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Found at i:165 original size:14 final size:13
Alignment explanation
Indices: 119--167 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
109 AAAAACATAG
119 AGACAAAAGCAAA
1 AGACAAAAGCAAA
132 AGA-AAAAGAACAACA
1 AGACAAAAG--CAA-A
147 AGACAAAAGCAAGA
1 AGACAAAAGCAA-A
161 AGACAAA
1 AGACAAA
168 TGTAATAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.16
13 3 0.10
14 14 0.45
15 4 0.13
16 5 0.16
ACGTcount: A:0.69, C:0.14, G:0.16, T:0.00
Consensus pattern (13 bp):
AGACAAAAGCAAA
Found at i:1221 original size:50 final size:49
Alignment explanation
Indices: 1102--1674 Score: 367
Period size: 50 Copynumber: 11.7 Consensus size: 49
1092 ACCAAGGAAA
* * *
1102 CATGAAGATGTAATGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTAC
1 CATGAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
* * * *
1151 CATGAAG--GTGAAGGGAAAGGTTGAAGCCGTAATGGCGAACCCGATAC
1 CATGAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
* * * *
1198 CTTGAAAGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACTCGGTAC
1 CATG-AAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
* * * * * *
1248 CATGAAGA--TGAAGGAAAAGGTTG-AGATCGTAACGGTGAACCCGATAC
1 CATGAAGATGTGATGGGAAAGGTTGAAG-CCGCAACGGCGAACCCGGTAC
* * * * * * * * *
1295 CTTGGAAGATGTGATAGGAAAGGTTGAGGTCGTAATGTCGAACTCGATAC
1 CAT-GAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
* * * * **
1345 CATGAAGA--TGAAGAGAAAGGTT-AAGGCCGTAACGGTGAACCCAATAC
1 CATGAAGATGTGATGGGAAAGGTTGAA-GCCGCAACGGCGAACCCGGTAC
* * * * * *
1392 CTTGGAAGACGTGATGGGAAAGGTTGAGGCCGTAACGGTGAACCCTGTAC
1 CAT-GAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
** * * * *
1442 CATGAAGACATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACTCGGTAC
1 CATGAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
* * * ** * * *
1491 CTTAGAAGATGCGATGGG-AAGGATTGAAGCCACAATAGCAAATCTGGTAC
1 CAT-GAAGATGTGATGGGAAAGG-TTGAAGCCGCAACGGCGAACCCGGTAC
* * * * *
1541 CATGAAGATATGAAGGGAAAGGTTG-AGTCGCAATGGTGAACCCGGTAC
1 CATGAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
* * * * ** * *
1589 CTTAGAAGATGTAATGGG-AAGGATTGAGGCCACAACGAAGAATCTGGTAC
1 CAT-GAAGATGTGATGGGAAAGG-TTGAAGCCGCAACGGCGAACCCGGTAC
* * * *
1639 CATGAAGATATGAAGGGAAAGGTTGAGGCCACAACG
1 CATGAAGATGTGATGGGAAAGGTTGAAGCCGCAACG
1675 AGAACCTTGT
Statistics
Matches: 408, Mismatches: 96, Indels: 40
0.75 0.18 0.07
Matches are distributed among these distances:
46 2 0.00
47 97 0.24
48 35 0.09
49 114 0.28
50 158 0.39
51 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (49 bp):
CATGAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
Found at i:1279 original size:97 final size:98
Alignment explanation
Indices: 1106--1665 Score: 548
Period size: 97 Copynumber: 5.7 Consensus size: 98
1096 AGGAAACATG
* * * *
1106 AAGATGTAATGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCATGAAG-GTGAAGGGAAAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGGTACCATGAAGAATGAAGGGAAAG
*
1170 GTTGA-AGCCGTAATGGCGAACCCGATACCTTGA
66 GTTGAGA-CCGTAATGGTGAACCCGATACCTTGA
* *
1203 AAGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACTCGGTACCATGAAG-ATGAAGGAAAAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGGTACCATGAAGAATGAAGGGAAAG
* * *
1267 GTTGAGATCGTAACGGTGAACCCGATACCTTGG
66 GTTGAGACCGTAATGGTGAACCCGATACCTTGA
* * * * * * *
1300 AAGATGTGATAGGAAAGGTTGAGGTCGTAATGTCGAACTCGATACCATGAAG-ATGAAGAGAAAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGGTACCATGAAGAATGAAGGGAAAG
* * * * *
1364 GTTAAGGCCGTAACGGTGAACCCAATACCTTGG
66 GTTGAGACCGTAATGGTGAACCCGATACCTTGA
* * * * *
1397 AAGACGTGATGGGAAAGGTTGAGGCCGTAACGGTGAACCCTGTACCATGAAGACATGAAGGGAAA
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGGTACCATGAAGA-ATGAAGGGAAA
* * * * *
1462 GGTTGAGGCCGCAATGGCGAACTCGGTACCTT-A
65 GGTTGAGACCGTAATGGTGAACCCGATACCTTGA
* * * ** *
1495 GAAGATGCGATGGG-AAGGATTGAAGCCACAATAGC-AAATCTGGTACCATGAAGATATGAAGGG
1 -AAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGCGAACTC-GGTACCATGAAGA-ATGAAGGG
* * *
1558 AAAGGTTGAG-TCGCAATGGTGAACCCGGTACCTT-A
62 AAAGGTTGAGACCGTAATGGTGAACCCGATACCTTGA
* * **
1593 GAAGATGTAATGGG-AAGGATTGAGGCCACAACGAAGAA-TCTGGTACCATGAAGATATGAAGGG
1 -AAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGCGAACTC-GGTACCATGAAGA-ATGAAGGG
1656 AAAGGTTGAG
62 AAAGGTTGAG
1666 GCCACAACGA
Statistics
Matches: 395, Mismatches: 61, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
97 214 0.54
98 93 0.24
99 88 0.22
ACGTcount: A:0.34, C:0.16, G:0.33, T:0.18
Consensus pattern (98 bp):
AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGGTACCATGAAGAATGAAGGGAAAG
GTTGAGACCGTAATGGTGAACCCGATACCTTGA
Found at i:1687 original size:98 final size:98
Alignment explanation
Indices: 1438--1687 Score: 317
Period size: 98 Copynumber: 2.5 Consensus size: 98
1428 GGTGAACCCT
* * *
1438 GTACCATGAAGACATGAAGGGAAAGGTTGAGGCCGCAATGGCGAA-CTCGGTACCTTAGAAGATG
1 GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCACAA-GGAGAACCT-GGTACCTTAGAAGATG
* *
1502 CGATGGGAAGGATTGAAGCCACAATAGCAAATCTG
64 CAATGGGAAGGATTGAAGCCACAATAGAAAATCTG
* * * * *
1537 GTACCATGAAGATATGAAGGGAAAGGTTGAGTCGCA-ATGGTGAACCCGGTACCTTAGAAGATGT
1 GTACCATGAAGATATGAAGGGAAAGGTTGAGGC-CACAAGGAGAACCTGGTACCTTAGAAGATGC
* *
1601 AATGGGAAGGATTGAGGCCACAA-CGAAGAATCTG
65 AATGGGAAGGATTGAAGCCACAATAGAA-AATCTG
* *
1635 GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCACAACGAGAACCTTGTACC
1 GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCACAAGGAGAACCTGGTACC
1688 CTAAAAATGA
Statistics
Matches: 130, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
97 4 0.03
98 92 0.71
99 33 0.25
100 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (98 bp):
GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCACAAGGAGAACCTGGTACCTTAGAAGATGCA
ATGGGAAGGATTGAAGCCACAATAGAAAATCTG
Found at i:2017 original size:39 final size:39
Alignment explanation
Indices: 1875--2223 Score: 286
Period size: 38 Copynumber: 9.0 Consensus size: 39
1865 GACACCATTT
* *
1875 AATCTCTTACCCCGATCATGGAGCAGATTGAAGACAT-C
1 AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCC
* *
1913 AATCTTTTACC-CGATCATGGGACAGATTGAAG-CATCC
1 AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCC
* * ** * * **
1950 AATCTTTTAACTTAATCA-GAAGGTAGATTGAAGACATGT
1 AATCTCTTACCTCGATCATG-GGGCAGATTGAAGACATCC
*
1989 AATCTCTTACCTTGATCATGGGGCAGATTGAAG-CATCC
1 AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCC
** * *
2027 AATCTCTTACCTTAATCA-GAAGGCAGATTGAAGACATGC
1 AATCTCTTACCTCGATCATG-GGGCAGATTGAAGACATCC
*
2066 AATCTCTTACCCCGATCATGGGGCAGATTGAAG-CATCC
1 AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCC
* * * *
2104 AATCT-TATACC-CTAATTA-GTGGGCAAATTGAAGACACACC
1 AATCTCT-TACCTC-GATCATG-GGGCAGATTGAAGACA-TCC
* *
2144 AATCTCTTACCTCGATCATGGGGTAGATTAAAGACATCAATC
1 AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATC---C
* * * * *
2186 AATCTCTTACCCCAATTATAGGGAAGATTGAAGACATC
1 AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATC
2224 ATCCAATCTT
Statistics
Matches: 250, Mismatches: 42, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
36 3 0.01
37 35 0.14
38 84 0.34
39 63 0.25
40 29 0.12
41 3 0.01
42 33 0.13
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (39 bp):
AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCC
Found at i:2020 original size:77 final size:77
Alignment explanation
Indices: 1897--2185 Score: 377
Period size: 77 Copynumber: 3.8 Consensus size: 77
1887 CGATCATGGA
* * *
1897 GCAGATTGAAGACAT-CAATCTTTTACC-CGATCATGGGACAGATTGAAGCATCCAATCTTTTAA
1 GCAGATTGAAGACATGCAATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTAC
1960 CTTAATCAGAAG
66 CTTAATCAGAAG
* * * *
1972 GTAGATTGAAGACATGTAATCTCTTACCTTGATCATGGGGCAGATTGAAGCATCCAATCTCTTAC
1 GCAGATTGAAGACATGCAATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTAC
2037 CTTAATCAGAAG
66 CTTAATCAGAAG
* *
2049 GCAGATTGAAGACATGCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTATAC
1 GCAGATTGAAGACATGCAATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTAC
* * **
2114 CCTAATTAGTGG
66 CTTAATCAGAAG
* ** * *
2126 GCAAATTGAAGACACACCAATCTCTTACCTCGATCATGGGGTAGATTAAAGACAT-CAATC
1 GCAGATTGAAGACA-TGCAATCTCTTACCTCGATCATGGGGCAGATTGAAG-CATCCAATC
2186 AATCTCTTAC
Statistics
Matches: 187, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
75 14 0.07
76 10 0.05
77 124 0.66
78 36 0.19
79 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (77 bp):
GCAGATTGAAGACATGCAATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTAC
CTTAATCAGAAG
Found at i:2189 original size:42 final size:42
Alignment explanation
Indices: 2022--2232 Score: 115
Period size: 42 Copynumber: 5.2 Consensus size: 42
2012 CAGATTGAAG
** * * * *
2022 CATCCAATCTCTTACCTTAATCAGAAGGCAGATTGAAG--A-
1 CATCCAATCTCTTACCCCAATCATAGGGAAGATTAAAGACAT
* * * * *
2061 CATGCAATCTCTTACCCCGATCATGGGGCAGATT---GA-AG
1 CATCCAATCTCTTACCCCAATCATAGGGAAGATTAAAGACAT
* * *
2099 CATCCAATCT-TATACCCTAATTAGT-GGGCAA-ATTGAAGACA-
1 CATCCAATCTCT-TACCCCAATCA-TAGGG-AAGATTAAAGACAT
* * * *
2140 CA-CCAATCTCTTACCTCGATCATGGGGTAGATTAAAGACAT
1 CATCCAATCTCTTACCCCAATCATAGGGAAGATTAAAGACAT
* *
2181 CAAT-CAATCTCTTACCCCAATTATAGGGAAGATTGAAGACAT
1 C-ATCCAATCTCTTACCCCAATCATAGGGAAGATTAAAGACAT
2223 CATCCAATCT
1 CATCCAATCT
2233 TATACCCTTA
Statistics
Matches: 132, Mismatches: 24, Indels: 29
0.71 0.13 0.16
Matches are distributed among these distances:
36 1 0.01
37 2 0.02
38 23 0.17
39 31 0.23
40 26 0.20
41 8 0.06
42 41 0.31
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (42 bp):
CATCCAATCTCTTACCCCAATCATAGGGAAGATTAAAGACAT
Found at i:2239 original size:42 final size:41
Alignment explanation
Indices: 2065--2232 Score: 129
Period size: 42 Copynumber: 4.1 Consensus size: 41
2055 TGAAGACATG
* * *
2065 CAATCTCTTACCCCGATCATGGGGCAGATTGAAG----CATC
1 CAATCTCTTACCCCAATTAT-GGGAAGATTGAAGACATCATC
*
2103 CAATCT-TATACCCTAATTAGTGGGCAA-ATTGAAGACA-CA-C
1 CAATCTCT-TACCCCAATTA-TGGG-AAGATTGAAGACATCATC
* * * * *
2143 CAATCTCTTACCTCGATCATGGGGTAGATTAAAGACATCAAT-
1 CAATCTCTTACCCCAATTAT-GGGAAGATTGAAGACATC-ATC
2185 CAATCTCTTACCCCAATTATAGGGAAGATTGAAGACATCATC
1 CAATCTCTTACCCCAATTAT-GGGAAGATTGAAGACATCATC
2227 CAATCT
1 CAATCT
2233 TATACCCTTA
Statistics
Matches: 101, Mismatches: 16, Indels: 22
0.73 0.12 0.16
Matches are distributed among these distances:
37 1 0.01
38 24 0.24
39 4 0.04
40 26 0.26
41 6 0.06
42 40 0.40
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (41 bp):
CAATCTCTTACCCCAATTATGGGAAGATTGAAGACATCATC
Found at i:3058 original size:14 final size:13
Alignment explanation
Indices: 3012--3060 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
3002 AAAAACACAG
3012 AGACAAAAGCAAA
1 AGACAAAAGCAAA
* *
3025 AGATAAAGAGTAACA
1 AGACAAA-AGCAA-A
3040 AGACAAAAGCAAGA
1 AGACAAAAGCAA-A
3054 AGACAAA
1 AGACAAA
3061 TGTAATCGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 6 0.21
14 16 0.55
15 7 0.24
ACGTcount: A:0.65, C:0.12, G:0.18, T:0.04
Consensus pattern (13 bp):
AGACAAAAGCAAA
Done.