Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001958.1 Kokia drynarioides strain JFW-HI SEQ_113783, 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: 64853
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Found at i:1963 original size:82 final size:82
Alignment explanation
Indices: 1826--2033 Score: 206
Period size: 82 Copynumber: 2.5 Consensus size: 82
1816 TTTTTAAGAA
* * ** *** **
1826 AAACGCCACTAATGCTCTTATTTTTAACGGCGCTTTTTAATAAACGTC-GTTAATGCTCTAA-CT
1 AAACGCCGCTAATGCTCTGACCTTTAACGGCGCTTTCCCATAAACG-CAACTAATGCTCTAATC-
*
1889 TTTAACAACG-TTTACTCAT
64 TTTAACAACGCTTT-CCCAT
*
1908 AAACGCCGCTAATGCTCTGACCTTTAACGGTGCTTTCCCATAAACGCAACTAATGCTCTAATCTT
1 AAACGCCGCTAATGCTCTGACCTTTAACGGCGCTTTCCCATAAACGCAACTAATGCTCTAATCTT
****
1973 TAGTGGCGCTTTCCCAT
66 TAACAACGCTTTCCCAT
* * *
1990 AAACGCCGCTAATGCTTTGACCTTTAGCGGCGCTTTCTCATAAA
1 AAACGCCGCTAATGCTCTGACCTTTAACGGCGCTTTCCCATAAA
2034 TGCCGCTATT
Statistics
Matches: 104, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
81 1 0.01
82 99 0.95
83 4 0.04
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (82 bp):
AAACGCCGCTAATGCTCTGACCTTTAACGGCGCTTTCCCATAAACGCAACTAATGCTCTAATCTT
TAACAACGCTTTCCCAT
Found at i:2047 original size:41 final size:41
Alignment explanation
Indices: 1905--2046 Score: 185
Period size: 41 Copynumber: 3.5 Consensus size: 41
1895 AACGTTTACT
* *
1905 CATAAACGCCGCTAATGCTCTGACCTTTAACGGTGCTTTCC
1 CATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCC
** * * *
1946 CATAAACGCAACTAATGCTCTAATCTTTAGTGGCGCTTTCC
1 CATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCC
* *
1987 CATAAACGCCGCTAATGCTTTGACCTTTAGCGGCGCTTTCT
1 CATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCC
* *
2028 CATAAATGCCGCTATTGCT
1 CATAAACGCCGCTAATGCT
2047 TAACTTTTTG
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 85 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (41 bp):
CATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCC
Found at i:3786 original size:17 final size:17
Alignment explanation
Indices: 3766--3798 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3756 AAAAGTAAAC
3766 AAATT-AGTAAAGATTAG
1 AAATTAAGTAAA-ATTAG
3783 AAATTAAGTAAAATTA
1 AAATTAAGTAAAATTA
3799 ATTGCAACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (17 bp):
AAATTAAGTAAAATTAG
Found at i:7497 original size:2 final size:2
Alignment explanation
Indices: 7490--7519 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7480 AATGTCATTA
7490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7520 GAAATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11694 original size:16 final size:16
Alignment explanation
Indices: 11673--11703 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11663 ATAATGTGAA
*
11673 AATAAAGATAAAATGT
1 AATAAACATAAAATGT
11689 AATAAACATAAAATG
1 AATAAACATAAAATG
11704 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.10, T:0.23
Consensus pattern (16 bp):
AATAAACATAAAATGT
Found at i:13193 original size:17 final size:17
Alignment explanation
Indices: 13147--13193 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
13137 GACAATGTAG
*
13147 ATGCAGCGACAATAAAA
1 ATGCAGGGACAATAAAA
* *
13164 ATGTAGTGACAATAAAA
1 ATGCAGGGACAATAAAA
*
13181 ATGCAGGGGCAAT
1 ATGCAGGGACAAT
13194 TATACTATAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.17
Consensus pattern (17 bp):
ATGCAGGGACAATAAAA
Found at i:22798 original size:42 final size:43
Alignment explanation
Indices: 22594--22823 Score: 225
Period size: 42 Copynumber: 5.4 Consensus size: 43
22584 GAAACACTTG
* * * *
22594 ATGTATAAAACGAAAACTCATGTCTCGGAATGAGCATGAGAAT
1 ATGTTTAAAAGGAAGACTCATGTCTCGAAATGAGCATGAGAAT
* * * * *
22637 AAGTTT-AAAGGAAGACTCGTGACTGGGAATGAGCATGAG-AT
1 ATGTTTAAAAGGAAGACTCATGTCTCGAAATGAGCATGAGAAT
* * *
22678 ATGTTTAAAAAGGATGACTCATGACTCGTAATGAGCATGAGAAT
1 ATGTTT-AAAAGGAAGACTCATGTCTCGAAATGAGCATGAGAAT
* * *
22722 ATGTTTAAAAGGGAAGACTCATGTCTC-AGGATGAGAATGAGATT
1 ATGTTTAAAA-GGAAGACTCATGTCTCGA-AATGAGCATGAGAAT
* * * *
22766 ATGTTT-AAAGGAAGATTCATGTCTTGAAATGAGCGTGAGATT
1 ATGTTTAAAAGGAAGACTCATGTCTCGAAATGAGCATGAGAAT
*
22808 ATGTTTGAAAGGAAGA
1 ATGTTTAAAAGGAAGA
22824 TTTATGCCTC
Statistics
Matches: 157, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
41 7 0.04
42 60 0.38
43 50 0.32
44 40 0.25
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.27
Consensus pattern (43 bp):
ATGTTTAAAAGGAAGACTCATGTCTCGAAATGAGCATGAGAAT
Found at i:29906 original size:44 final size:44
Alignment explanation
Indices: 29802--29946 Score: 179
Period size: 44 Copynumber: 3.3 Consensus size: 44
29792 CTTGATGTAT
* * *
29802 AAAAGGAAGAATCATGTCTC-GAAATGAGCATGAGAATACGTTT-
1 AAAAGGAAGACTCATGACTCGGAAA-GAGCATGAGAATATGTTTA
* * *
29845 -AAAGGAAGACTCGTGACTCGGAAAGAACATCAGAATATGTTTA
1 AAAAGGAAGACTCATGACTCGGAAAGAGCATGAGAATATGTTTA
* *
29888 AAAAGGAAGACTCATGACTTGGAATGAGCATGAGAATATGTTTA
1 AAAAGGAAGACTCATGACTCGGAAAGAGCATGAGAATATGTTTA
*
29932 AAAAGGAAGATTCAT
1 AAAAGGAAGACTCAT
29947 TTGTCGAGAT
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
42 31 0.36
43 4 0.05
44 52 0.60
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (44 bp):
AAAAGGAAGACTCATGACTCGGAAAGAGCATGAGAATATGTTTA
Found at i:35485 original size:11 final size:11
Alignment explanation
Indices: 35465--35497 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
35455 ATCACACGAG
*
35465 AGGTGGACAAA
1 AGGTGAACAAA
35476 AGGTGAACAAA
1 AGGTGAACAAA
35487 AGGTGAACAAA
1 AGGTGAACAAA
35498 GTTGGATCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.52, C:0.09, G:0.30, T:0.09
Consensus pattern (11 bp):
AGGTGAACAAA
Found at i:44040 original size:12 final size:12
Alignment explanation
Indices: 44023--44054 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
44013 ATTTATTTAT
44023 TTTTAATTAATG
1 TTTTAATTAATG
44035 TTTTAATTAATG
1 TTTTAATTAATG
44047 TTTTAATT
1 TTTTAATT
44055 TTTTAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (12 bp):
TTTTAATTAATG
Found at i:44064 original size:12 final size:12
Alignment explanation
Indices: 43995--44054 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
43985 AAGTTTTTTT
43995 ATTTTTTAATTAA
1 ATTTTTTAATT-A
* *
44008 ATTTTATTTATTT
1 ATTTT-TTAATTA
44021 A-TTTTTAATTA
1 ATTTTTTAATTA
*
44032 ATGTTTTAATTA
1 ATTTTTTAATTA
*
44044 ATGTTTTAATT
1 ATTTTTTAATT
44055 TTTTAATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 6 0.15
12 23 0.57
13 6 0.15
14 5 0.12
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (12 bp):
ATTTTTTAATTA
Found at i:45956 original size:47 final size:46
Alignment explanation
Indices: 45852--45957 Score: 108
Period size: 47 Copynumber: 2.3 Consensus size: 46
45842 TCATTTGTGA
* *
45852 TGAT-GATTTTTACTACAATAACTTACAATCCCAGTTACTTGATTT
1 TGATGGATTTTTACTACAATAACTTACAATCCCAGTTACCTGAGTT
* * * *
45897 TGATGGCTTTTTTACTACAATAACTTAGCCATCTCAGTTGTCCTG-GTT
1 TGATGG-ATTTTTACTACAATAACTTA-CAATCCCAGTT-ACCTGAGTT
*
45945 TGGTGGATTTTTA
1 TGATGGATTTTTA
45958 GCCTACCATC
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
45 4 0.08
46 1 0.02
47 25 0.51
48 16 0.33
49 3 0.06
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (46 bp):
TGATGGATTTTTACTACAATAACTTACAATCCCAGTTACCTGAGTT
Found at i:47871 original size:45 final size:44
Alignment explanation
Indices: 47797--47971 Score: 169
Period size: 45 Copynumber: 3.9 Consensus size: 44
47787 TATACGCCTA
* * *
47797 AAAT-GAGTAAGATCATTA-TTGAAAA-ATGTTATGACATCATAAT
1 AAATAGAGTAAGACCA-TAGTT-AAAAGATGCTATGACATCATGAT
* *
47840 AAATATGAGTAAGACCATAGCTAAAAGATGTTATGACATCATGAT
1 AAATA-GAGTAAGACCATAGTTAAAAGATGCTATGACATCATGAT
* * *
47885 GATAATA-AGTAAGACCATAGTTGAAAGATGCTATGATATCATGGT
1 -A-AATAGAGTAAGACCATAGTTAAAAGATGCTATGACATCATGAT
* * *
47930 AAATGAGATTAAGACCATAGTTGAAAGATGCTATTACATCAT
1 AAAT-AGAGTAAGACCATAGTTAAAAGATGCTATGACATCAT
47972 TCGATAAGTT
Statistics
Matches: 113, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 7 0.06
44 8 0.07
45 93 0.82
46 1 0.01
47 4 0.04
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (44 bp):
AAATAGAGTAAGACCATAGTTAAAAGATGCTATGACATCATGAT
Found at i:50860 original size:60 final size:64
Alignment explanation
Indices: 50720--50864 Score: 183
Period size: 60 Copynumber: 2.3 Consensus size: 64
50710 AAGCTATATA
* *
50720 TTATTTTTATTTCTATT-AATTCATATTTTAATAATAAATATATTAAGAATATTATTAAATTAT
1 TTATTTTTATTTCTATTAAATTCACATTTTAATAATAAATATATTAAGAATATGATTAAATTAT
* * * *
50783 ATATTTTTATTTGTATTAAATTC-CA-TTTAATAATAATTATATTTA-AA-ATGATTAAATTAT
1 TTATTTTTATTTCTATTAAATTCACATTTTAATAATAAATATATTAAGAATATGATTAAATTAT
* *
50843 TTATTATTATTTTTATTAAATT
1 TTATTTTTATTTCTATTAAATT
50865 AATAACAATA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
60 31 0.43
61 2 0.03
62 18 0.25
63 16 0.22
64 5 0.07
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (64 bp):
TTATTTTTATTTCTATTAAATTCACATTTTAATAATAAATATATTAAGAATATGATTAAATTAT
Found at i:56886 original size:16 final size:16
Alignment explanation
Indices: 56864--56901 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
56854 TTTTTTAGTC
56864 ATTTTCAAATTCTAAA
1 ATTTTCAAATTCTAAA
* *
56880 CTTTTCAAATTTTAAA
1 ATTTTCAAATTCTAAA
56896 ATTTTC
1 ATTTTC
56902 GTTCTCACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTCAAATTCTAAA
Found at i:58708 original size:39 final size:39
Alignment explanation
Indices: 58654--58787 Score: 124
Period size: 39 Copynumber: 3.4 Consensus size: 39
58644 TTTTACAAAT
* *
58654 TATTTAGTTACAAAGTTGGGTTTCCAATAGGACTTTGAA
1 TATTTGGTTAAAAAGTTGGGTTTCCAATAGGACTTTGAA
* * * * *
58693 TATTTGGTTAAAAAGTTGTGTTTTTTCATTAGGAATTTGAG
1 TATTTGGTTAAAAAGTTG-G-GTTTCCAATAGGACTTTGAA
*** * *
58734 TATTTTAATACAAAGTTAGGTTTCCAATAGGACTTTGAA
1 TATTTGGTTAAAAAGTTGGGTTTCCAATAGGACTTTGAA
*
58773 TATTAGGTTATAAAA
1 TATTTGGTTA-AAAA
58788 TTGTACTTTC
Statistics
Matches: 70, Mismatches: 22, Indels: 5
0.72 0.23 0.05
Matches are distributed among these distances:
39 37 0.53
40 5 0.07
41 28 0.40
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (39 bp):
TATTTGGTTAAAAAGTTGGGTTTCCAATAGGACTTTGAA
Found at i:58756 original size:80 final size:78
Alignment explanation
Indices: 58662--58813 Score: 225
Period size: 80 Copynumber: 1.9 Consensus size: 78
58652 ATTATTTAGT
* * ** *
58662 TACAAAGTTGGGTTTCCAATAGGACTTTGAATATTTGGTTA-AAAAGTTGTGTTTTTTCATTAGG
1 TACAAAGTTAGGTTTCCAATAGGACTTTGAATATTAGGTTATAAAA--T-TGTACTTTCACTAGG
58726 AATTTGAGTATTTTAA
63 AATTTGAGTATTTTAA
58742 TACAAAGTTAGGTTTCCAATAGGACTTTGAATATTAGGTTATAAAATTGTACTTTCACTAGGAAT
1 TACAAAGTTAGGTTTCCAATAGGACTTTGAATATTAGGTTATAAAATTGTACTTTCACTAGGAAT
58807 TTGAGTA
66 TTGAGTA
58814 ATAGTTATAG
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
78 22 0.33
79 1 0.02
80 39 0.59
81 4 0.06
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (78 bp):
TACAAAGTTAGGTTTCCAATAGGACTTTGAATATTAGGTTATAAAATTGTACTTTCACTAGGAAT
TTGAGTATTTTAA
Found at i:60973 original size:24 final size:22
Alignment explanation
Indices: 60929--60974 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
60919 TGCTCTTGGC
* *
60929 ATATTAAATGGGCACGTAATTA
1 ATATTAAATGGGCAAGAAATTA
60951 ATATTGAAATGTGGCAAGAAATTA
1 ATATT-AAATG-GGCAAGAAATTA
60975 TCTTAGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 5 0.25
24 10 0.50
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (22 bp):
ATATTAAATGGGCAAGAAATTA
Found at i:62964 original size:58 final size:58
Alignment explanation
Indices: 62874--62989 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
62864 AACTCACGTG
62874 TCACTATCAGAACTTGTGCAGGGCAAGTCCGCACAGGTGGAGAAGGTAACTCGTCATT
1 TCACTATCAGAACTTGTGCAGGGCAAGTCCGCACAGGTGGAGAAGGTAACTCGTCATT
62932 TCACTATCAGAACTTGTGCAGGGCAAGTCCGCACAGGTGGAGAAGGTAACTCGTCATT
1 TCACTATCAGAACTTGTGCAGGGCAAGTCCGCACAGGTGGAGAAGGTAACTCGTCATT
62990 CTCAAAATTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (58 bp):
TCACTATCAGAACTTGTGCAGGGCAAGTCCGCACAGGTGGAGAAGGTAACTCGTCATT
Found at i:63189 original size:8 final size:8
Alignment explanation
Indices: 63162--63204 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
63152 TCAGAAAAAA
63162 AGTCAAC-
1 AGTCAACG
63169 AGTCAA--
1 AGTCAACG
63175 AGTCAACG
1 AGTCAACG
*
63183 GGTCAACG
1 AGTCAACG
63191 AGTCAACG
1 AGTCAACG
63199 AGTCAA
1 AGTCAA
63205 TCAAAAGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 6 0.19
7 6 0.19
8 20 0.62
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (8 bp):
AGTCAACG
Done.