Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007103.1 Kokia drynarioides strain JFW-HI SEQ_121713, 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: 35957
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:7355 original size:19 final size:19
Alignment explanation
Indices: 7331--7373 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
7321 TCAATTGGGT
7331 GCGAAGTGAGGCGGGCCTC
1 GCGAAGTGAGGCGGGCCTC
7350 GCGAAGTGAGGCGGGCCTC
1 GCGAAGTGAGGCGGGCCTC
7369 GCGAA
1 GCGAA
7374 ACCCGCCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.19, C:0.26, G:0.47, T:0.09
Consensus pattern (19 bp):
GCGAAGTGAGGCGGGCCTC
Found at i:19131 original size:99 final size:99
Alignment explanation
Indices: 18990--19197 Score: 220
Period size: 99 Copynumber: 2.1 Consensus size: 99
18980 GATGAATATG
* * * * * * * *
18990 GTACCACGAAGTTATGAAAGGAAAGGTTGAGGCCGCAGCGGCGAACTCGGTACCTCAAAAGATAT
1 GTACCATGAAGATATGAAAGGAAAGGTTAAAGCCACAACGGCGAACCCAGTACCTCAAAAGATAT
* * * *
19055 GATGGGAAGGATTGAAGTCGCAACGGCGAATCC-
66 AATGGGAAAGATTGAAGTCGCAAAGGCAAATCCA
* * * * * *
19088 GATACCATGAAGATATGAAAGGAGAGGTTAAAGTCACAACGGCGAACCCAGTACGTTAGAAGGTA
1 G-TACCATGAAGATATGAAAGGAAAGGTTAAAGCCACAACGGCGAACCCAGTACCTCAAAAGATA
* *
19153 TAATGGGAAAGATTGAGGTCGTAAAGGCAAATCCA
65 TAATGGGAAAGATTGAAGTCGCAAAGGCAAATCCA
19188 GTACCATGAA
1 GTACCATGAA
19198 AGTTAATGGT
Statistics
Matches: 88, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
98 1 0.01
99 86 0.98
100 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (99 bp):
GTACCATGAAGATATGAAAGGAAAGGTTAAAGCCACAACGGCGAACCCAGTACCTCAAAAGATAT
AATGGGAAAGATTGAAGTCGCAAAGGCAAATCCA
Found at i:19318 original size:50 final size:50
Alignment explanation
Indices: 19012--19823 Score: 276
Period size: 49 Copynumber: 16.5 Consensus size: 50
19002 TATGAAAGGA
* * * * *
19012 AAGG-TTGAGGCCGCAGCGGCGAA-CTCGGTACCTCAAAAGATATGATGGG
1 AAGGATTGAAGCCGCAACGGCGAACCT-AGTACCTTAGAAGATATGATGGG
* * * **
19061 AAGGATTGAAGTCGCAACGGCGAATCCGA-TACCAT-GAAGATATGAAAGG
1 AAGGATTGAAGCCGCAACGGCGAA-CCTAGTACCTTAGAAGATATGATGGG
* * * * * * *
19110 AGAGG-TTAAAGTCACAACGGCGAACCCAGTACGTTAGAAGGTATAATGGG
1 A-AGGATTGAAGCCGCAACGGCGAACCTAGTACCTTAGAAGATATGATGGG
* * * * * * * *
19160 AAAGATTGAGGTCGTAAAGGCAAATCC-AGTACCAT-GAA-AGT-TAATGGTG
1 AAGGATTGAAGCCGCAACGGCGAA-CCTAGTACCTTAGAAGA-TATGATGG-G
* * * * * *
19209 AA-GATT-AAGGTCGTAAAGACGAATCTAGTACCTTAG-AGATTTGGA-GGG
1 AAGGATTGAA-GCCGCAACGGCGAACCTAGTACCTTAGAAGATAT-GATGGG
* *
19257 AAACG-TTGAAGCCGGAACGGCGAACCTAGTACCTTAGAAGATATGATGGG
1 -AAGGATTGAAGCCGCAACGGCGAACCTAGTACCTTAGAAGATATGATGGG
* * * * *
19307 AAGGGTTGAAGCCACAACGACGAATCTGGTACC--ACGAAGATATGGA-GGG
1 AAGGATTGAAGCCGCAACGGCGAACCTAGTACCTTA-GAAGATAT-GATGGG
* * ** * * *
19356 AA-AATT-AAGACCGCAATGATGAACC-CGATACCTCAGAAGATGTGATGGG
1 AAGGATTGAAG-CCGCAACGGCGAACCTAG-TACCTTAGAAGATATGATGGG
* * * * * *
19405 AAGGATT-AAGGCTGCAACGACGAA-TTCGGTACCATA-AAGATATGAAATGAG
1 AAGGATTGAA-GCCGCAACGGCGAACCT-AGTACCTTAGAAGATATG--ATGGG
* * * *
19456 -AGG-TTGAAGCTGCAACGGCGAA-CTCAGAACCTTAGAAGATATAATAGG
1 AAGGATTGAAGCCGCAACGGCGAACCT-AGTACCTTAGAAGATATGATGGG
** * * * *
19504 AAGGATTGTGGTCGCAACGGCAAATCCGA-TACCAT-GAA-AGT-TGATGGGG
1 AAGGATTGAAGCCGCAACGGCGAA-CCTAGTACCTTAGAAGA-TATGAT-GGG
** * * * * * * *
19553 AA-GATTGGGGCTGCAACGGCAAATCTAGTACCCTAG-AGATTTGAAAGGA
1 AAGGATTGAAGCCGCAACGGCGAACCTAGTACCTTAGAAGATATG-ATGGG
* ** * *
19602 AAGG-TTGAACCCGCAACGGTAAACCCAGTACCTTAAAAGATATGATGGG
1 AAGGATTGAAGCCGCAACGGCGAACCTAGTACCTTAGAAGATATGATGGG
* * * ** * * * * *
19651 AAGGGTTGAGGTCAAAATGGTGAACCCAATACCTTAGAAGATATGATAGG
1 AAGGATTGAAGCCGCAACGGCGAACCTAGTACCTTAGAAGATATGATGGG
* * * * * *
19701 AAGGATTGAGGCCGCAACGACAAATCCT-GCACCAT-GAAGATATGAAGGG
1 AAGGATTGAAGCCGCAACGGCGAA-CCTAGTACCTTAGAAGATATGATGGG
* ** *
19750 AAAGG-TTGAGGCCGCAATAGCGAACCTAGTACCTTAGAA-ACATGATGGG
1 -AAGGATTGAAGCCGCAACGGCGAACCTAGTACCTTAGAAGATATGATGGG
*
19799 AAAGATTGAAGACCGCAACGGCGAA
1 AAGGATTGAAG-CCGCAACGGCGAA
19824 TCTTATACCC
Statistics
Matches: 567, Mismatches: 139, Indels: 113
0.69 0.17 0.14
Matches are distributed among these distances:
47 8 0.01
48 93 0.16
49 231 0.41
50 222 0.39
51 11 0.02
52 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.18
Consensus pattern (50 bp):
AAGGATTGAAGCCGCAACGGCGAACCTAGTACCTTAGAAGATATGATGGG
Found at i:19544 original size:344 final size:344
Alignment explanation
Indices: 19040--19659 Score: 843
Period size: 344 Copynumber: 1.8 Consensus size: 344
19030 GCGAACTCGG
* * *
19040 TACCTCAAAAGATATGATGGGAAGGATTGAAGTCGCAACGGCGAATCCGATACCATGAAGATATG
1 TACCTCAAAAGATATGATGGGAAGGATTGAAGGCGCAACGACGAATCCGATACCATAAAGATATG
* * * *
19105 AAAGGAGAGGTTAAAGTCACAACGGCGAACCCAGTACGTTAGAAGGTATAATGGGAAAGATTGAG
66 AAAGGAGAGGTTAAAGTCACAACGGCGAACCCAGAACCTTAGAAGATATAATAGGAAAGATTGAG
* * * * *
19170 GTCGTAAAGGCAAATCCAGTACCATGAAAGTTAATGGTGAAGATTAAGG-TCGTAAAGACGAATC
131 GTCGCAAAGGCAAATCCAGTACCATGAAAGTTAATGGGGAAGATTAGGGCT-GCAAAGACAAATC
* * * * * * * *
19234 TAGTACCTTAGAGATTTGGAGGGAAACGTTGAAGCCGGAACGGCGAACCTAGTACCTTAGAAGAT
195 TAGTACCCTAGAGATTTGAAAGGAAACGTTGAACCCGCAACGGCAAACCCAGTACCTTAAAAGAT
19299 ATGATGGGAAGGGTTGAAGCCACAACGACGAATCTGGTACCACGAAGATATGGAGGGAAAATTAA
260 ATGATGGGAAGGGTTGAAGCCACAACGACGAATCTGGTACCACGAAGATATGGAGGGAAAATTAA
19364 GACCGCAATGATGAACCCGA
325 GACCGCAATGATGAACCCGA
* * * *
19384 TACCTCAGAAGATGTGATGGGAAGGATT-AAGGCTGCAACGACGAATTCGGTACCATAAAGATAT
1 TACCTCAAAAGATATGATGGGAAGGATTGAAGGC-GCAACGACGAATCCGATACCATAAAGATAT
* * * * *
19448 GAAATGAGAGGTTGAAG-CTGCAACGGCGAACTCAGAACCTTAGAAGATATAATAGGAAGGATTG
65 GAAAGGAGAGGTTAAAGTC-ACAACGGCGAACCCAGAACCTTAGAAGATATAATAGGAAAGATTG
* * * * * *
19512 TGGTCGCAACGGCAAATCC-GATACCATGAAAGTTGATGGGGAAGATTGGGGCTGCAACGGCAAA
129 AGGTCGCAAAGGCAAATCCAG-TACCATGAAAGTTAATGGGGAAGATTAGGGCTGCAAAGACAAA
* *
19576 TCTAGTACCCTAGAGATTTGAAAGGAAAGGTTGAACCCGCAACGGTAAACCCAGTACCTTAAAAG
193 TCTAGTACCCTAGAGATTTGAAAGGAAACGTTGAACCCGCAACGGCAAACCCAGTACCTTAAAAG
19641 ATATGATGGGAAGGGTTGA
258 ATATGATGGGAAGGGTTGA
19660 GGTCAAAATG
Statistics
Matches: 235, Mismatches: 37, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
343 6 0.03
344 228 0.97
345 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.19
Consensus pattern (344 bp):
TACCTCAAAAGATATGATGGGAAGGATTGAAGGCGCAACGACGAATCCGATACCATAAAGATATG
AAAGGAGAGGTTAAAGTCACAACGGCGAACCCAGAACCTTAGAAGATATAATAGGAAAGATTGAG
GTCGCAAAGGCAAATCCAGTACCATGAAAGTTAATGGGGAAGATTAGGGCTGCAAAGACAAATCT
AGTACCCTAGAGATTTGAAAGGAAACGTTGAACCCGCAACGGCAAACCCAGTACCTTAAAAGATA
TGATGGGAAGGGTTGAAGCCACAACGACGAATCTGGTACCACGAAGATATGGAGGGAAAATTAAG
ACCGCAATGATGAACCCGA
Found at i:19743 original size:99 final size:99
Alignment explanation
Indices: 19638--19818 Score: 229
Period size: 99 Copynumber: 1.8 Consensus size: 99
19628 AGTACCTTAA
* * * * * *
19638 AAGATATGATGGGAAGGGTTGAGGTCAAAATGGTGAACCCAATACCTTAGAAGATATGATAGGAA
1 AAGATATGAAGGGAAAGGTTGAGGCCAAAATAGCGAACCCAATACCTTAGAA-ACATGATAGGAA
* *
19703 GGATTG-AGGCCGCAACGACAAATCCTGCACCATG
65 AGATTGAAGACCGCAACGACAAATCCTGCACCATG
** * * *
19737 AAGATATGAAGGGAAAGGTTGAGGCCGCAATAGCGAACCTAGTACCTTAGAAACATGATGGGAAA
1 AAGATATGAAGGGAAAGGTTGAGGCCAAAATAGCGAACCCAATACCTTAGAAACATGATAGGAAA
19802 GATTGAAGACCGCAACG
66 GATTGAAGACCGCAACG
19819 GCGAATCTTA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
98 15 0.22
99 53 0.78
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.18
Consensus pattern (99 bp):
AAGATATGAAGGGAAAGGTTGAGGCCAAAATAGCGAACCCAATACCTTAGAAACATGATAGGAAA
GATTGAAGACCGCAACGACAAATCCTGCACCATG
Found at i:25661 original size:93 final size:92
Alignment explanation
Indices: 25558--25890 Score: 497
Period size: 93 Copynumber: 3.5 Consensus size: 92
25548 TTTATCCTAC
25558 AGATAAATATTGTATTATTTTAATAAGAATTAATATTAAATTTAAAATTAAATCTTATTAAAATA
1 AGATAAATATTGTATTATTTTAATAAGAATTAATATTAAA-TTAAAATTAAATCTTATTAAAATA
*
25623 ATATTATTTTTGAAATAGTTAAAATTGT
65 ATATTATTTTTGAAATAGTTAATATTGT
* *
25651 AGATAAATATTGTATTATTTTAATAAG-ATAAATATTTAAATTTAATATTAAATCTTATTAAAAT
1 AGATAAATATTGTATTATTTTAATAAGAATTAATA-TTAAA-TTAAAATTAAATCTTATTAAAAT
*
25715 AATATTATTTTTGAAATAGTTAATATTAT
64 AATATTATTTTTGAAATAGTTAATATTGT
* *
25744 AGATAAATATTGTATTATTTTAATAAGATTTAATATTAAATTAAATTTAATATTTATCTTATTAA
1 AGATAAATATTGTATTATTTTAATAAGAATTAATATTAAATTAAAATT-A-A---ATCTTATTAA
*
25809 AATAATATTATTTTTGAAATAGTTAATCTTGT
61 AATAATATTATTTTTGAAATAGTTAATATTGT
* * *
25841 AGATAAATATTGTATTATTTTAATAGGATTTAATATTAAATTAAATTTAA
1 AGATAAATATTGTATTATTTTAATAAGAATTAATATTAAATTAAAATTAA
25891 TATTTATCTT
Statistics
Matches: 222, Mismatches: 11, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
92 12 0.05
93 115 0.52
94 6 0.03
95 1 0.00
96 1 0.00
97 87 0.39
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.47
Consensus pattern (92 bp):
AGATAAATATTGTATTATTTTAATAAGAATTAATATTAAATTAAAATTAAATCTTATTAAAATAA
TATTATTTTTGAAATAGTTAATATTGT
Found at i:25835 original size:97 final size:97
Alignment explanation
Indices: 25558--25916 Score: 531
Period size: 97 Copynumber: 3.8 Consensus size: 97
25548 TTTATCCTAC
* *
25558 AGATAAATATTGTATTATTTTAATAAGAATTAATATTAAATTTAAAATT-A-A---ATCTTATTA
1 AGATAAATATTGTATTATTTTAATAAGATTTAATATTAAA-TTAAATTTAATATTTATCTTATTA
*
25618 AAATAATATTATTTTTGAAATAGTTAAAATTGT
65 AAATAATATTATTTTTGAAATAGTTAATATTGT
* *
25651 AGATAAATATTGTATTATTTTAATAAGA--TAA-A-T-ATTTAAATTTAATATTAAATCTTATTA
1 AGATAAATATTGTATTATTTTAATAAGATTTAATATTAAATTAAATTTAATATT-TATCTTATTA
*
25711 AAATAATATTATTTTTGAAATAGTTAATATTAT
65 AAATAATATTATTTTTGAAATAGTTAATATTGT
25744 AGATAAATATTGTATTATTTTAATAAGATTTAATATTAAATTAAATTTAATATTTATCTTATTAA
1 AGATAAATATTGTATTATTTTAATAAGATTTAATATTAAATTAAATTTAATATTTATCTTATTAA
*
25809 AATAATATTATTTTTGAAATAGTTAATCTTGT
66 AATAATATTATTTTTGAAATAGTTAATATTGT
* *
25841 AGATAAATATTGTATTATTTTAATAGGATTTAATATTAAATTAAATTTAATATTTATCTTAATAA
1 AGATAAATATTGTATTATTTTAATAAGATTTAATATTAAATTAAATTTAATATTTATCTTATTAA
*
25906 ATATTATATTA
66 A-ATAATATTA
25917 ATCTAATATT
Statistics
Matches: 243, Mismatches: 11, Indels: 19
0.89 0.04 0.07
Matches are distributed among these distances:
87 7 0.03
88 2 0.01
89 2 0.01
90 1 0.00
91 3 0.01
93 96 0.40
95 3 0.01
96 1 0.00
97 105 0.43
98 23 0.09
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (97 bp):
AGATAAATATTGTATTATTTTAATAAGATTTAATATTAAATTAAATTTAATATTTATCTTATTAA
AATAATATTATTTTTGAAATAGTTAATATTGT
Found at i:25940 original size:17 final size:17
Alignment explanation
Indices: 25868--25950 Score: 66
Period size: 17 Copynumber: 5.0 Consensus size: 17
25858 TTTTAATAGG
* *
25868 ATTTAATATTAAATTAA
1 ATTTAATATTTAATTTA
25885 ATTTAATATTT-ATCTTA
1 ATTTAATATTTAAT-TTA
*
25902 A-TAAATA-TT-ATATTA
1 ATTTAATATTTAAT-TTA
*
25917 ATCTAATATTTAATTTA
1 ATTTAATATTTAATTTA
* *
25934 ATTTAATGTTTATTTTA
1 ATTTAATATTTAATTTA
25951 TTGATAAACA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
15 8 0.15
16 11 0.21
17 32 0.60
18 2 0.04
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (17 bp):
ATTTAATATTTAATTTA
Found at i:33415 original size:19 final size:19
Alignment explanation
Indices: 33391--33433 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
33381 TCAATTGGGT
33391 GCGAAGTGAGGCGGGCCTC
1 GCGAAGTGAGGCGGGCCTC
33410 GCGAAGTGAGGCGGGCCTC
1 GCGAAGTGAGGCGGGCCTC
33429 GCGAA
1 GCGAA
33434 ACCCGCCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.19, C:0.26, G:0.47, T:0.09
Consensus pattern (19 bp):
GCGAAGTGAGGCGGGCCTC
Done.