Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009549.1 Kokia drynarioides strain JFW-HI SEQ_124261, 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: 26623
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:847 original size:16 final size:16
Alignment explanation
Indices: 826--862 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
816 TCCTTTCCTT
*
826 TTTCTTTAATTTGGTC
1 TTTCTTCAATTTGGTC
842 TTTCTTCAATTTGGTC
1 TTTCTTCAATTTGGTC
858 TTTCT
1 TTTCT
863 CCTTCTTCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.16, G:0.11, T:0.62
Consensus pattern (16 bp):
TTTCTTCAATTTGGTC
Found at i:3777 original size:29 final size:29
Alignment explanation
Indices: 3735--3791 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
3725 ATACCAAATC
**
3735 CTTAACTTCTCCTCTTATTAGATTTGATA
1 CTTAACTTCTCCTCGAATTAGATTTGATA
3764 CTTAACTTCTCCTCGAATTAGATTTGAT
1 CTTAACTTCTCCTCGAATTAGATTTGAT
3792 TGTCTCGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.09, T:0.46
Consensus pattern (29 bp):
CTTAACTTCTCCTCGAATTAGATTTGATA
Found at i:16749 original size:97 final size:98
Alignment explanation
Indices: 16556--17029 Score: 534
Period size: 97 Copynumber: 4.9 Consensus size: 98
16546 AGGTTTGATG
* * ** * * *
16556 GGAAAGATTGAAGGCGCAATGGCGAATCATGTACCATGGAAATATG-GAGGGAAAGGTTG-AAGC
1 GGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGG--AGATGCGAGGGAAAGGTCGAAAGC
* * *
16619 CACAACAGTGAACCTTATACCTTAG-AAGAATAATA
64 CGCAACGGTGAACCTTGTACCTTAGAAAG-ATAATA
* * * *** *
16654 GGAAAGATTAAAGCCACAACGGTGAATCTTGTACCACAAAGATGCGAGAGAAAGGTCGAAA-CCG
1 GGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATGCGAGGGAAAGGTCGAAAGCCG
* * *
16718 CAACGGTAAACTTTGTACCTTAGAAAGATAATG
66 CAACGGTGAACCTTGTACCTTAGAAAGATAATA
* *
16751 GGAAGGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATGCGAGGGAAAGGT-TAAAGCCG
1 GGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATGCGAGGGAAAGGTCGAAAGCCG
* *
16815 TAACGGTGAACCTTGTACCTTAGAAAGTTAATA
66 CAACGGTGAACCTTGTACCTTAGAAAGATAATA
* * *
16848 GGAAAGATTGAAGCTGTAACGG-AGAATCTTGTACCATGGAGATGCGAGGGAAAGGTTG-AAGCC
1 GGAAAGATTGAAGCCGCAACGGTA-AATCTTGTACCATGGAGATGCGAGGGAAAGGTCGAAAGCC
* *
16911 GCAACGGCGAACCTTGTACCTTA-AAAGATAATG
65 GCAACGGTGAACCTTGTACCTTAGAAAGATAATA
* * *
16944 GGAAAGATTCAAGCTGCAACGGTAAATCTTGTACCATGGAGATGTGAGGGAAAGGTC-AAAGCCG
1 GGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATGCGAGGGAAAGGTCGAAAGCCG
***
17008 CAACTACGAACCTTGTACCTTA
66 CAACGGTGAACCTTGTACCTTA
17030 AAAAAGATTG
Statistics
Matches: 322, Mismatches: 46, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
96 93 0.29
97 194 0.60
98 35 0.11
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.20
Consensus pattern (98 bp):
GGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATGCGAGGGAAAGGTCGAAAGCCG
CAACGGTGAACCTTGTACCTTAGAAAGATAATA
Found at i:16883 original size:194 final size:192
Alignment explanation
Indices: 16553--17029 Score: 598
Period size: 194 Copynumber: 2.5 Consensus size: 192
16543 TATAGGTTTG
* * ** * * *
16553 ATGGGAAAGATTGAAGGCGCAATGGCGAATCATGTACCATGGAAATATGGAGGGAAAGGTTGAAG
1 ATGGGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGG--AGATGGAGGGAAAGGTTAAAG
* * *
16618 CCACAACAGTGAACCTTATACCTTAGAAGAATAATAGGAAAGATTAAAGCCACAACGGTGAATCT
64 CCGCAACAGTGAACCTTGTACCTTAGAAGAATAATAGGAAAGATTAAAGCCACAACGGAGAATCT
* *
16683 TGTACCACAAAGATGCGAGAGAAAGGTCGAAACCGCAACGGTAAACTTTGTACCTTAGAAAGATA
129 TGTACCACAAAGATGCGAGAGAAAGGTCGAAACCGCAACGGCAAACCTTGTACCTTA-AAAGATA
*
16748 ATGGGAAGGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATGCGAGGGAAAGGTTAAAGC
1 ATGGGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATG-GAGGGAAAGGTTAAAGC
* * * * ***
16813 CGTAACGGTGAACCTTGTACCTTAGAA-AGTTAATAGGAAAGATTGAAGCTGTAACGGAGAATCT
65 CGCAACAGTGAACCTTGTACCTTAGAAGA-ATAATAGGAAAGATTAAAGCCACAACGGAGAATCT
*** * * * *
16877 TGTACCATGGAGATGCGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAAAAGATA
129 TGTACCACAAAGATGCGAGAGAAAGGTCGAAACCGCAACGGCAAACCTTGTACCTTAAAAGATA
* * *
16941 ATGGGAAAGATTCAAGCTGCAACGGTAAATCTTGTACCATGGAGATGTGAGGGAAAGGTCAAAGC
1 ATGGGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATG-GAGGGAAAGGTTAAAGC
*
17006 CGCAACTA-CGAACCTTGTACCTTA
65 CGCAAC-AGTGAACCTTGTACCTTA
17030 AAAAAGATTG
Statistics
Matches: 244, Mismatches: 35, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
193 92 0.38
194 116 0.48
195 36 0.15
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.20
Consensus pattern (192 bp):
ATGGGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATGGAGGGAAAGGTTAAAGCC
GCAACAGTGAACCTTGTACCTTAGAAGAATAATAGGAAAGATTAAAGCCACAACGGAGAATCTTG
TACCACAAAGATGCGAGAGAAAGGTCGAAACCGCAACGGCAAACCTTGTACCTTAAAAGATA
Found at i:16947 original size:48 final size:48
Alignment explanation
Indices: 16604--16978 Score: 235
Period size: 48 Copynumber: 7.8 Consensus size: 48
16594 GAAATATGGA
* * * *
16604 GGGAAAGGTTGAAGCCACAACAGTGAACCTTATACCTTAGAAGAATAAT
1 GGGAAAGGTTGAAGCCGCAACGGTGAACCTTGTACCTTAAAAG-ATAAT
* * * * * *
16653 AGGAAAGATTAAAGCCACAACGGTGAATCTTGTACC--ACAAAGATGCGA-
1 GGGAAAGGTTGAAGCCGCAACGGTGAACCTTGTACCTTA-AAAGAT--AAT
* * * * *
16701 GAGAAAGGTCGAAACCGCAACGGTAAACTTTGTACCTTAGAAAGATAAT
1 GGGAAAGGTTGAAGCCGCAACGGTGAACCTTGTACCTTA-AAAGATAAT
* * * ** *
16750 GGG-AAGGATTGAAGCCGCAACGGTAAATCTTGTACCAT-GGAGATGCGA-
1 GGGAAAGG-TTGAAGCCGCAACGGTGAACCTTGTACCTTAAAAGAT--AAT
* * *
16798 GGGAAAGGTTAAAGCCGTAACGGTGAACCTTGTACCTTAGAAAGTTAAT
1 GGGAAAGGTTGAAGCCGCAACGGTGAACCTTGTACCTTA-AAAGATAAT
* * * * * * * ** *
16847 AGGAAAGATTGAAGCTGTAACGGAGAATCTTGTACCAT-GGAGATGCGA-
1 GGGAAAGGTTGAAGCCGCAACGGTGAACCTTGTACCTTAAAAGAT--AAT
*
16895 GGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAAAAGATAAT
1 GGGAAAGGTTGAAGCCGCAACGGTGAACCTTGTACCTTAAAAGATAAT
* * * * *
16943 GGGAAAGATTCAAGCTGCAACGGTAAATCTTGTACC
1 GGGAAAGGTTGAAGCCGCAACGGTGAACCTTGTACC
16979 ATGGAGATGT
Statistics
Matches: 244, Mismatches: 65, Indels: 35
0.71 0.19 0.10
Matches are distributed among these distances:
47 11 0.05
48 124 0.51
49 99 0.41
50 10 0.04
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (48 bp):
GGGAAAGGTTGAAGCCGCAACGGTGAACCTTGTACCTTAAAAGATAAT
Found at i:16995 original size:48 final size:48
Alignment explanation
Indices: 16555--17011 Score: 219
Period size: 48 Copynumber: 9.4 Consensus size: 48
16545 TAGGTTTGAT
* * ** * * *
16555 GGGAAAGATTGAAGGCGCAATGGCGAATCATGTACCATGGAAATATGGA
1 GGGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATGT-GA
* * * * * * * * *
16604 GGGAAAGGTTGAAGCCACAACAGTGAACCTTATACCTTAGAAGAATAAT-A
1 GGGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCAT-GGAG-AT-GTGA
* * * *** *
16654 -GGAAAGATTAAAGCCACAACGGTGAATCTTGTACCACAAAGATGCGA
1 GGGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATGTGA
* * * * * * * *
16701 GAGAAAGGTCGAAACCGCAACGGTAAA-CTTTGTACCTTAGA-AAGATAA
1 GGGAAAGATTGAAGCCGCAACGGTAAATC-TTGTACCATGGAGATG-TGA
* *
16749 TGGGAAGGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATGCGA
1 -GGGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATGTGA
* * * * * * * * *
16798 GGGAAAGGTTAAAGCCGTAACGGTGAACCTTGTACCTTAGA-AAGTTAA
1 GGGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATG-TGA
* * * *
16846 TAGGAAAGATTGAAGCTGTAACGG-AGAATCTTGTACCATGGAGATGCGA
1 -GGGAAAGATTGAAGCCGCAACGGTA-AATCTTGTACCATGGAGATGTGA
* ** * * * * *
16895 GGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACC-T-TAAAAGATAA
1 GGGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATG-TGA
* *
16942 TGGGAAAGATTCAAGCTGCAACGGTAAATCTTGTACCATGGAGATGTGA
1 -GGGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATGTGA
* **
16991 GGGAAAGGTCAAAGCCGCAAC
1 GGGAAAGATTGAAGCCGCAAC
17012 TACGAACCTT
Statistics
Matches: 297, Mismatches: 92, Indels: 39
0.69 0.21 0.09
Matches are distributed among these distances:
46 3 0.01
47 10 0.03
48 142 0.48
49 127 0.43
50 11 0.04
51 2 0.01
52 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (48 bp):
GGGAAAGATTGAAGCCGCAACGGTAAATCTTGTACCATGGAGATGTGA
Found at i:19903 original size:37 final size:37
Alignment explanation
Indices: 19862--19943 Score: 164
Period size: 37 Copynumber: 2.2 Consensus size: 37
19852 TTTTATGCGT
19862 CATCGTTTTAGGTTTGATGCCAATAACCTGGAAACGA
1 CATCGTTTTAGGTTTGATGCCAATAACCTGGAAACGA
19899 CATCGTTTTAGGTTTGATGCCAATAACCTGGAAACGA
1 CATCGTTTTAGGTTTGATGCCAATAACCTGGAAACGA
19936 CATCGTTT
1 CATCGTTT
19944 CATTTAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (37 bp):
CATCGTTTTAGGTTTGATGCCAATAACCTGGAAACGA
Found at i:23151 original size:19 final size:19
Alignment explanation
Indices: 23123--23172 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
23113 CCTTTACAAA
* *
23123 AAAAAGTAAAATTAATTTAT
1 AAAAA-TAAAATGAAATTAT
23143 AAAAATAAAA-GAAATTAT
1 AAAAATAAAATGAAATTAT
*
23161 AAAGATAAAATG
1 AAAAATAAAATG
23173 TGGGACCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 15 0.58
19 6 0.23
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (19 bp):
AAAAATAAAATGAAATTAT
Found at i:26574 original size:7 final size:7
Alignment explanation
Indices: 26562--26600 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
26552 CCCCTTTTTT
26562 TTATTAA
1 TTATTAA
26569 TTATTAA
1 TTATTAA
*
26576 TTAATAA
1 TTATTAA
26583 TTATTAA
1 TTATTAA
26590 -TATT-A
1 TTATTAA
26595 TTATTA
1 TTATTA
26601 TTAATATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 1 0.04
6 8 0.29
7 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTATTAA
Found at i:26602 original size:15 final size:15
Alignment explanation
Indices: 26562--26607 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
26552 CCCCTTTTTT
26562 TTATTAATTATTAAT-
1 TTATT-ATTATTAATA
* *
26577 TAATAATTATTAATA
1 TTATTATTATTAATA
26592 TTATTATTATTAATA
1 TTATTATTATTAATA
26607 T
1 T
26608 CAAAACATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATTATTAATA
Done.