Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006839.1 Kokia drynarioides strain JFW-HI SEQ_121438, 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: 25185
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1813 original size:12 final size:12
Alignment explanation
Indices: 1796--1838 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
1786 GCGACATACC
1796 TGGGCTCATGCT
1 TGGGCTCATGCT
*
1808 TGGGCTCATACT
1 TGGGCTCATGCT
1820 TGGGCTCATGCT
1 TGGGCTCATGCT
1832 TGGGCTC
1 TGGGCTC
1839 TCTTCCCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.09, C:0.26, G:0.33, T:0.33
Consensus pattern (12 bp):
TGGGCTCATGCT
Found at i:1823 original size:24 final size:24
Alignment explanation
Indices: 1790--1838 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1780 TGAAAGGCGA
1790 CATACCTGGGCTCATGCTTGGGCT
1 CATACCTGGGCTCATGCTTGGGCT
*
1814 CATACTTGGGCTCATGCTTGGGCT
1 CATACCTGGGCTCATGCTTGGGCT
1838 C
1 C
1839 TCTTCCCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.29, G:0.29, T:0.31
Consensus pattern (24 bp):
CATACCTGGGCTCATGCTTGGGCT
Found at i:2288 original size:21 final size:21
Alignment explanation
Indices: 2245--2288 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2235 AGAAACTGTC
* *
2245 AGAACTAGTCCAAAAATGCAA
1 AGAACTACTCCAAAAATGAAA
*
2266 AGAACTACTCCAAAAGTGAAA
1 AGAACTACTCCAAAAATGAAA
2287 AG
1 AG
2289 CATAAAATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.18, G:0.16, T:0.14
Consensus pattern (21 bp):
AGAACTACTCCAAAAATGAAA
Found at i:6909 original size:35 final size:35
Alignment explanation
Indices: 6869--6946 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 35
6859 ATTACGTCCC
* * *
6869 GCCACAACGCCAGAACTTCTTTTATCAATCATCTCA
1 GCCACAACGCCAGAACTTCATCTATCAATAATCT-A
6905 -CCACAACGCCAGAACTTCATCTATCAATAATCTA
1 GCCACAACGCCAGAACTTCATCTATCAATAATCTA
6939 GCCACAAC
1 GCCACAAC
6947 ACGCCAATAC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 1 0.03
35 37 0.97
ACGTcount: A:0.35, C:0.35, G:0.08, T:0.23
Consensus pattern (35 bp):
GCCACAACGCCAGAACTTCATCTATCAATAATCTA
Found at i:7019 original size:16 final size:17
Alignment explanation
Indices: 6990--7024 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
6980 AACATCGATA
6990 CTTCATTCAATCAACAT
1 CTTCATTCAATCAACAT
*
7007 CTTCATT-AATCAATAT
1 CTTCATTCAATCAACAT
7023 CT
1 CT
7025 CTCCACCACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (17 bp):
CTTCATTCAATCAACAT
Found at i:8708 original size:130 final size:130
Alignment explanation
Indices: 8421--8696 Score: 329
Period size: 130 Copynumber: 2.1 Consensus size: 130
8411 GAGGAGGATT
* * * ** * * * *
8421 CATTCTGAACTTTGCAATATTAACACGGTTAGATGAACTTTTGCAACTCCAATATGGTGAGAGAA
1 CATTCTGAACTTTGCACTATCAACATGGCAAAAAGAATTTTTGCAACTCCAACATGGTGAGAGAA
* * * * *
8486 GTTGTTTTGCAACATCAACATAACGGGAAGGACCCTTGCAATTTCAACATGGCGAAAGGAGGACC
66 GTTGTTTTGCAACATCAACACAACGGGAAGAACCCTTGCAAATTCAACATGGCAAAACGAGGACC
* * *
8551 CATTTTGGACTTTGCACTATCAACATGGCAAAAAGAATTTTTGCAACTCCAGCATGGTGAGATG-
1 CATTCTGAACTTTGCACTATCAACATGGCAAAAAGAATTTTTGCAACTCCAACATGGTGAGA-GA
**** * *
8615 AGTTGTTTTGCAACATCAACACGGTTGGAAGAACCCTTGCAAATTCAACTTGGTAAAACGAGGAC
65 AGTTGTTTTGCAACATCAACACAACGGGAAGAACCCTTGCAAATTCAACATGGCAAAACGAGGAC
8680 C
130 C
8681 CATTCTGAACTTTGCA
1 CATTCTGAACTTTGCA
8697 TCCTCAACAT
Statistics
Matches: 120, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
130 119 0.99
131 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (130 bp):
CATTCTGAACTTTGCACTATCAACATGGCAAAAAGAATTTTTGCAACTCCAACATGGTGAGAGAA
GTTGTTTTGCAACATCAACACAACGGGAAGAACCCTTGCAAATTCAACATGGCAAAACGAGGACC
Found at i:8723 original size:130 final size:130
Alignment explanation
Indices: 8421--8742 Score: 326
Period size: 130 Copynumber: 2.5 Consensus size: 130
8411 GAGGAGGATT
* * * ** * * * *
8421 CATTCTGAACTTTGCAATATTAACACGGTTAGATGAACTTTTGCAACTCCAATATGGTGAGAGAA
1 CATTCTGAACTTTGCACTATCAACATGGCAAAAAGAAGTTTTGCAACTCCAACATGGTGAGAGAA
* * * * *
8486 GTTGTTTTGCAACATCAACATAACGGGAAGGACCCTTGCAATTTCAACATGGCGAAAGGAGGACC
66 GTTGTTTTGCAACATCAACACAACGGGAAGAACCCTTGCAAATTCAACATGGCAAAACGAGGACC
* * * *
8551 CATTTTGGACTTTGCACTATCAACATGGCAAAAAGAATTTTTGCAACTCCAGCATGGTGAGATG-
1 CATTCTGAACTTTGCACTATCAACATGGCAAAAAGAAGTTTTGCAACTCCAACATGGTGAGA-GA
**** * *
8615 AGTTGTTTTGCAACATCAACACGGTTGGAAGAACCCTTGCAAATTCAACTTGGTAAAACGAGGAC
65 AGTTGTTTTGCAACATCAACACAACGGGAAGAACCCTTGCAAATTCAACATGGCAAAACGAGGAC
8680 C
130 C
* ** * * *
8681 CATTCTGAACTTTGCA-TCCTCAACATGGTGAGAAGTAGTTTTGC-ACCCTCAACATGGTGAGA
1 CATTCTGAACTTTGCACT-ATCAACATGGCAAAAAGAAGTTTTGCAACTC-CAACATGGTGAGA
8743 AGATGACCTA
Statistics
Matches: 156, Mismatches: 33, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
129 4 0.03
130 151 0.97
131 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (130 bp):
CATTCTGAACTTTGCACTATCAACATGGCAAAAAGAAGTTTTGCAACTCCAACATGGTGAGAGAA
GTTGTTTTGCAACATCAACACAACGGGAAGAACCCTTGCAAATTCAACATGGCAAAACGAGGACC
Found at i:8760 original size:70 final size:70
Alignment explanation
Indices: 8677--8808 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 70
8667 GTAAAACGAG
** **
8677 GACCCATTCTGAACTTTGCATCCTCAACATGGTGAGAAGT-AGTTTTGCACCCTCAACATGGTGA
1 GACCCATTCTGAACTTCACATAATCAACATGGTGAGAA-TAAGTTTTGCACCCTCAACATGGTGA
8741 GAAGAT
65 GAAGAT
* * * *
8747 GACCTATTTTGAACTTCACATAATCAACATGGTGAGGATAAGTTTTGCATCCTCAACATGGT
1 GACCCATTCTGAACTTCACATAATCAACATGGTGAGAATAAGTTTTGCACCCTCAACATGGT
8809 AAGAGAAGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
69 1 0.02
70 52 0.98
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (70 bp):
GACCCATTCTGAACTTCACATAATCAACATGGTGAGAATAAGTTTTGCACCCTCAACATGGTGAG
AAGAT
Found at i:8841 original size:28 final size:29
Alignment explanation
Indices: 8769--8841 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
8759 ACTTCACATA
*
8769 ATCAACATGGTGAGGATAAGTTTTGCATCC
1 ATCAACATGGTGA-GAGAAGTTTTGCATCC
*
8799 -TCAACATGGTAAGAGAAGTTTTGCA-CC
1 ATCAACATGGTGAGAGAAGTTTTGCATCC
*
8826 ATCAACATGATGAGAG
1 ATCAACATGGTGAGAG
8842 GATGACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 2 0.05
28 25 0.66
29 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (29 bp):
ATCAACATGGTGAGAGAAGTTTTGCATCC
Found at i:8912 original size:98 final size:98
Alignment explanation
Indices: 8691--8913 Score: 275
Period size: 98 Copynumber: 2.3 Consensus size: 98
8681 CATTCTGAAC
* * * *
8691 TTTGCATCCTCAACATGGTGAGAAGTAGTTTTGCACCCTCAACATGGTGAGAAGATGACCTATTT
1 TTTGCATCCTCAACATGGTGAG-AGAAGTTTTGCACCATCAACATGATGAGAAGATGACCTATTC
* * ** *
8756 TGAACTTCACATAATCAACATGGTGAGGATAAGT
65 TGAACTTCACACAATCAACATGGCGAAAAGAAGT
* *
8790 TTTGCATCCTCAACATGGTAAGAGAAGTTTTGCACCATCAACATGATGAGAGGATGACCTATTCT
1 TTTGCATCCTCAACATGGTGAGAGAAGTTTTGCACCATCAACATGATGAGAAGATGACCTATTCT
** ** *
8855 GAACTTTGCACCCTTAACATGGCGAAAAGAAGT
66 GAACTTCACACAATCAACATGGCGAAAAGAAGT
* *
8888 TTTGCACCCTCAACATGGCGAGAGAA
1 TTTGCATCCTCAACATGGTGAGAGAA
8914 CTTCTCCTAT
Statistics
Matches: 105, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
98 84 0.80
99 21 0.20
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (98 bp):
TTTGCATCCTCAACATGGTGAGAGAAGTTTTGCACCATCAACATGATGAGAAGATGACCTATTCT
GAACTTCACACAATCAACATGGCGAAAAGAAGT
Found at i:13356 original size:16 final size:17
Alignment explanation
Indices: 13335--13366 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13325 CAAAGTTCAG
13335 AAGCATA-TTTGATAGC
1 AAGCATATTTTGATAGC
13351 AAGCATATTTTGATAG
1 AAGCATATTTTGATAG
13367 AAAATGCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (17 bp):
AAGCATATTTTGATAGC
Found at i:18982 original size:58 final size:58
Alignment explanation
Indices: 18881--19000 Score: 179
Period size: 58 Copynumber: 2.1 Consensus size: 58
18871 TATTAAAAAT
* * * *
18881 ATAATTATATTAAAAATGTTATTAAATTATATATTATTTTATTAAATTGTATTTAATA
1 ATAAGTATATTAAAAATATAATTAAATTATATATTATTTTATTAAATTATATTTAATA
*
18939 ATAAGTATATT-AAAATATAATTAAATTATTTATTATTTTTATTAAATTATATTTAATA
1 ATAAGTATATTAAAAATATAATTAAATTATATATTA-TTTTATTAAATTATATTTAATA
18997 ATAA
1 ATAA
19001 ACTTATTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 21 0.38
58 35 0.62
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (58 bp):
ATAAGTATATTAAAAATATAATTAAATTATATATTATTTTATTAAATTATATTTAATA
Done.