Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001694.1 Kokia drynarioides strain JFW-HI SEQ_113373, 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: 43220
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 146 characters in sequence are not A, C, G, or T
Found at i:2411 original size:21 final size:22
Alignment explanation
Indices: 2387--2433 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
2377 CGATCTGAGG
*
2387 AAAAATAAAAG-AAATGGAATT
1 AAAAATAAAAGAAAATAGAATT
2408 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
2430 AAAA
1 AAAA
2434 GAAATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:2444 original size:22 final size:21
Alignment explanation
Indices: 2387--2448 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
2377 CGATCTGAGG
*
2387 AAAAATAAAAGAAATGGAATTAA
1 AAAAAT-AAA-AAATAGAATTAA
2410 AAATAA-AAGAAAATAGAATTAA
1 AAA-AATAA-AAAATAGAATTAA
2432 AAGAAATAAAAAATAGA
1 AA-AAATAAAAAATAGA
2449 GGTTTCGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
22 25 0.74
23 7 0.21
24 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (21 bp):
AAAAATAAAAAATAGAATTAA
Found at i:3312 original size:29 final size:29
Alignment explanation
Indices: 3230--3312 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 29
3220 TAAACATAAA
3230 TTAAATA-AAAATTTAAATAATAAATAATATC
1 TTAAATATAAAA--TAAATAA-AAATAATATC
* *
3261 TTAAATATTAAATCCTAATAAAAATAATATC
1 TTAAATATAAAAT--AAATAAAAATAATATC
3292 TTAAA-ATAAAATAAAGTAAAA
1 TTAAATATAAAATAAA-TAAAA
3313 CCAAGTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
28 2 0.05
29 5 0.11
30 7 0.16
31 22 0.50
32 8 0.18
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (29 bp):
TTAAATATAAAATAAATAAAAATAATATC
Found at i:13607 original size:6 final size:6
Alignment explanation
Indices: 13598--13635 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
13588 AAGCTAAAGC
13598 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AG
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AG
13636 AAAGACAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:14106 original size:22 final size:22
Alignment explanation
Indices: 14065--14106 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
14055 TAAATTAAAC
*
14065 AAATTAAACACATACTACTTTT
1 AAATTAAACACATACAACTTTT
14087 AAATTAAACA-AGTACAACTT
1 AAATTAAACACA-TACAACTT
14107 AAAATTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATTAAACACATACAACTTTT
Found at i:19743 original size:15 final size:15
Alignment explanation
Indices: 19723--19753 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19713 CTTATTTATT
19723 TTCTATTTCTTTTTA
1 TTCTATTTCTTTTTA
*
19738 TTCTATTTTTTTTTA
1 TTCTATTTCTTTTTA
19753 T
1 T
19754 CTTTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTATTTCTTTTTA
Found at i:23141 original size:18 final size:18
Alignment explanation
Indices: 23114--23148 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23104 CCTTGTTTTC
* *
23114 TATAATTCAATTACCTAT
1 TATAAATCAAATACCTAT
23132 TATAAATCAAATACCTA
1 TATAAATCAAATACCTA
23149 GGTTTCTTGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAAATCAAATACCTAT
Found at i:25895 original size:10 final size:10
Alignment explanation
Indices: 25880--25928 Score: 80
Period size: 10 Copynumber: 4.9 Consensus size: 10
25870 TAATCTAATG
25880 AAAAAAAGAA
1 AAAAAAAGAA
25890 AAAAAAAGAA
1 AAAAAAAGAA
25900 AAAAAAAGAA
1 AAAAAAAGAA
*
25910 AGAAAAAGAA
1 AAAAAAAGAA
*
25920 AAGAAAAGA
1 AAAAAAAGA
25929 TGATTTGGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:25896 original size:11 final size:11
Alignment explanation
Indices: 25880--25926 Score: 58
Period size: 12 Copynumber: 4.1 Consensus size: 11
25870 TAATCTAATG
25880 AAAAAAAGAAA
1 AAAAAAAGAAA
*
25891 AAAAAAGAAAAA
1 AAAAAA-AGAAA
25903 AAAAGAAAGAAA
1 AAAA-AAAGAAA
*
25915 AAGAAAAGAAA
1 AAAAAAAGAAA
25926 A
1 A
25927 GATGATTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 14 0.45
12 15 0.48
13 2 0.06
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:34824 original size:20 final size:20
Alignment explanation
Indices: 34799--34836 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
34789 AGGGTGGATC
34799 GAAAACTCTTTTACGCTATT
1 GAAAACTCTTTTACGCTATT
34819 GAAAACTCTTTTACGCTA
1 GAAAACTCTTTTACGCTA
34837 CTGTTAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (20 bp):
GAAAACTCTTTTACGCTATT
Found at i:37816 original size:24 final size:24
Alignment explanation
Indices: 37784--37840 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
37774 GAGACTTGTT
37784 TGACATGGACAATGGAAGTAGAGA
1 TGACATGGACAATGGAAGTAGAGA
37808 TGACATGGACAATGGAAGTAGAGA
1 TGACATGGACAATGGAAGTAGAGA
37832 TGACATGGA
1 TGACATGGA
37841 TGAAAGATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.40, C:0.09, G:0.33, T:0.18
Consensus pattern (24 bp):
TGACATGGACAATGGAAGTAGAGA
Found at i:40079 original size:43 final size:43
Alignment explanation
Indices: 40032--40301 Score: 226
Period size: 43 Copynumber: 6.3 Consensus size: 43
40022 TGTTAGTGGT
* *
40032 GTTTGTGAGAAAAACGCCACTAAAAAACATGTTATATAGCGGC
1 GTTTGTGGGAAAAACGCCACTAAAAACCATGTTATATAGCGGC
* ** * *
40075 GTTTGT-GGTAAAACTGCCGTTAAAGACCATGTTCTATTA-CGGC
1 GTTTGTGGGAAAAAC-GCCACTAAAAACCATGTTATA-TAGCGGC
* * * * * *
40118 GTTTGTGGGAAAAATGTCGCTAAAGA-CATGTTATATGGCGAC
1 GTTTGTGGGAAAAACGCCACTAAAAACCATGTTATATAGCGGC
* * * *
40160 GTTTGTGAGAAAAGCGCCACTAAAAACCATGTTCTATAGAGGC
1 GTTTGTGGGAAAAACGCCACTAAAAACCATGTTATATAGCGGC
* * *
40203 GTTTGCGGGAAAAGCACCACTAAAAACCATGCTT-TATAGCGGC
1 GTTTGTGGGAAAAACGCCACTAAAAACCATG-TTATATAGCGGC
* * * * * **
40246 ATTTGTGGGAAAAGA-GCCGCTAAAGATCATGTTTTATAGCAAC
1 GTTTGTGGGAAAA-ACGCCACTAAAAACCATGTTATATAGCGGC
40289 GTTTGTGGGAAAA
1 GTTTGTGGGAAAA
40302 GCACCGCCAA
Statistics
Matches: 181, Mismatches: 38, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
41 1 0.01
42 39 0.22
43 131 0.72
44 10 0.06
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (43 bp):
GTTTGTGGGAAAAACGCCACTAAAAACCATGTTATATAGCGGC
Found at i:40189 original size:85 final size:85
Alignment explanation
Indices: 40058--40215 Score: 205
Period size: 85 Copynumber: 1.9 Consensus size: 85
40048 CCACTAAAAA
* ** * *
40058 ACATGTTATATAGCGGCGTTTGTGGTAAAACTGCCGTTAAAGACCATGTTCTATTA-CGGCGTTT
1 ACATGTTATATAGCGACGTTTGTGGTAAAACTGCCACTAAAAACCATGTTCTA-TAGAGGCGTTT
*
40122 GTGGGAAAAATGTCGCTAAAG
65 GCGGGAAAAATGTCGCTAAAG
*
40143 ACATGTTATATGGCGACGTTTGTGAG-AAAAGC-GCCACTAAAAACCATGTTCTATAGAGGCGTT
1 ACATGTTATATAGCGACGTTTGTG-GTAAAA-CTGCCACTAAAAACCATGTTCTATAGAGGCGTT
40206 TGCGGGAAAA
64 TGCGGGAAAA
40216 GCACCACTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
84 2 0.03
85 59 0.94
86 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (85 bp):
ACATGTTATATAGCGACGTTTGTGGTAAAACTGCCACTAAAAACCATGTTCTATAGAGGCGTTTG
CGGGAAAAATGTCGCTAAAG
Found at i:40191 original size:128 final size:129
Alignment explanation
Indices: 40032--40303 Score: 329
Period size: 128 Copynumber: 2.1 Consensus size: 129
40022 TGTTAGTGGT
* * * * * **
40032 GTTTGTGAGAAAAACGCCACTAAAAAACATGTTATATAGCGGCGTTTGTGGTAAAA-CTGCCGTT
1 GTTTGTGAGAAAAGCGCCACTAAAAAACATGTTATATAGAGGCGTTTGCGGGAAAAGC-ACCACT
* * * *
40096 AAAGACCATG-TTCTATTA-CGGCGTTTGTGGGAAAA-ATGTCGCTAAAGA-CATGTTATATGGC
65 AAAAACCATGCTT-TA-TAGCGGCATTTGTGGGAAAAGA-GCCGCTAAAGATCATGTTATATAGC
*
40157 GAC
127 AAC
* *
40160 GTTTGTGAGAAAAGCGCCACTAAAAACCATGTTCTATAGAGGCGTTTGCGGGAAAAGCACCACTA
1 GTTTGTGAGAAAAGCGCCACTAAAAAACATGTTATATAGAGGCGTTTGCGGGAAAAGCACCACTA
*
40225 AAAACCATGCTTTATAGCGGCATTTGTGGGAAAAGAGCCGCTAAAGATCATGTTTTATAGCAAC
66 AAAACCATGCTTTATAGCGGCATTTGTGGGAAAAGAGCCGCTAAAGATCATGTTATATAGCAAC
*
40289 GTTTGTGGGAAAAGC
1 GTTTGTGAGAAAAGC
40304 ACCGCCAAAG
Statistics
Matches: 123, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
127 2 0.02
128 90 0.73
129 31 0.25
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.26
Consensus pattern (129 bp):
GTTTGTGAGAAAAGCGCCACTAAAAAACATGTTATATAGAGGCGTTTGCGGGAAAAGCACCACTA
AAAACCATGCTTTATAGCGGCATTTGTGGGAAAAGAGCCGCTAAAGATCATGTTATATAGCAAC
Found at i:40306 original size:86 final size:85
Alignment explanation
Indices: 40032--40306 Score: 259
Period size: 86 Copynumber: 3.2 Consensus size: 85
40022 TGTTAGTGGT
* * * ** *
40032 GTTTGTGAGAAAAACGCCACTAAAAAACATGTTATATAGCGGCGTTTGTGGTAAAACTGCCGTTA
1 GTTTGTGGGAAAAACACCACT-AAAAACATGTTATATAGCGGCGTTTGTGGGAAAAGAGCCGCTA
*
40097 AAGACCATGTTCTATTA-CGGC
65 AAGACCATGTTCTA-TAGCAGC
*** * * * * * * *
40118 GTTTGTGGGAAAAATGTCGCTAAAGACATGTTATATGGCGACGTTTGTGAGAAAAGCGCCACTAA
1 GTTTGTGGGAAAAACACCACTAAAAACATGTTATATAGCGGCGTTTGTGGGAAAAGAGCCGCTAA
*
40183 AAACCATGTTCTATAG-AGGC
66 AGACCATGTTCTATAGCA-GC
* * *
40203 GTTTGCGGGAAAAGCACCACTAAAAACCATGCTT-TATAGCGGCATTTGTGGGAAAAGAGCCGCT
1 GTTTGTGGGAAAAACACCACTAAAAA-CATG-TTATATAGCGGCGTTTGTGGGAAAAGAGCCGCT
* * *
40267 AAAGATCATGTTTTATAGCAAC
64 AAAGACCATGTTCTATAGCAGC
*
40289 GTTTGTGGGAAAAGCACC
1 GTTTGTGGGAAAAACACC
40307 GCCAAAGATT
Statistics
Matches: 151, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
84 2 0.01
85 68 0.45
86 78 0.52
87 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (85 bp):
GTTTGTGGGAAAAACACCACTAAAAACATGTTATATAGCGGCGTTTGTGGGAAAAGAGCCGCTAA
AGACCATGTTCTATAGCAGC
Found at i:40692 original size:31 final size:31
Alignment explanation
Indices: 40656--40719 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
40646 GATTTTAAAT
*
40656 TTTGAAAAGTAC-AGGAATTAAAATTGATCAA
1 TTTGAAAAGTACAAGG-ACTAAAATTGATCAA
* *
40687 TTTGAATAGTACAATGACTAAAATTGATCAA
1 TTTGAAAAGTACAAGGACTAAAATTGATCAA
40718 TT
1 TT
40720 CGAATTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (31 bp):
TTTGAAAAGTACAAGGACTAAAATTGATCAA
Found at i:41178 original size:31 final size:31
Alignment explanation
Indices: 41119--41193 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
41109 TACAAAATGG
* * *
41119 TCACTGAATTATTTGAAAGATTCCATTTAAG
1 TCACTAAACTATTTGAAAGATTCCATTTAAA
* * **
41150 TCATTAAACTATTTGAAAGTTTTTATTTAAA
1 TCACTAAACTATTTGAAAGATTCCATTTAAA
*
41181 TCACTAAATTATT
1 TCACTAAACTATT
41194 AAGTTTCTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (31 bp):
TCACTAAACTATTTGAAAGATTCCATTTAAA
Found at i:42575 original size:23 final size:23
Alignment explanation
Indices: 42535--42581 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
42525 ATTTGTTTTA
* *
42535 AAATTTAAATTTATTTTAGATTT
1 AAATTTAAATTTAGTTTAAATTT
42558 AAATTT-AATTTGAGTTTAAATTT
1 AAATTTAAATTT-AGTTTAAATTT
42581 A
1 A
42582 CTTTCAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (23 bp):
AAATTTAAATTTAGTTTAAATTT
Found at i:42577 original size:52 final size:52
Alignment explanation
Indices: 42503--42612 Score: 130
Period size: 52 Copynumber: 2.1 Consensus size: 52
42493 CTAAATTCAT
* ** * * *
42503 TTTAAATTTATTTTAAAATTAAATTTGTTTTAAAATTTAAATTTATTTTAGA
1 TTTAAATTTAATTTAAAATTAAATTTACTTTAAAATTTAAAATTATTATAAA
* ** *
42555 TTTAAATTTAATTTGAGTTTAAATTTACTTTCAAATTTAAAATTATTATAAA
1 TTTAAATTTAATTTAAAATTAAATTTACTTTAAAATTTAAAATTATTATAAA
42607 TTTAAA
1 TTTAAA
42613 ATAAATAAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (52 bp):
TTTAAATTTAATTTAAAATTAAATTTACTTTAAAATTTAAAATTATTATAAA
Found at i:42593 original size:35 final size:35
Alignment explanation
Indices: 42503--42612 Score: 109
Period size: 35 Copynumber: 3.2 Consensus size: 35
42493 CTAAATTCAT
* **
42503 TTTAAATTTATTTTAAAATTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAAA
* * *
42538 TTTAAATTTATTTTAGATTTAAATTTAATTT-GAG
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAAA
* *
42572 TTTAAATTTACTTTCAAATTTAAAATT-A-TTATAAA
1 TTTAAATTTA-TTTTAAATTTAAATTTAATTTA-AAA
42607 TTTAAA
1 TTTAAA
42613 ATAAATAAAG
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
33 2 0.03
34 12 0.20
35 47 0.77
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAAA
Found at i:42614 original size:17 final size:17
Alignment explanation
Indices: 42503--42612 Score: 121
Period size: 17 Copynumber: 6.4 Consensus size: 17
42493 CTAAATTCAT
42503 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
42520 ATTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
*
42538 TTTAAATTTATTTTAGA
1 TTTAAATTTATTTTAAA
* * *
42555 TTTAAATTTAATTTGAG
1 TTTAAATTTATTTTAAA
*
42572 TTTAAATTTACTTTCAAA
1 TTTAAATTTA-TTTTAAA
* *
42590 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
42607 TTTAAA
1 TTTAAA
42613 ATAAATAAAG
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
17 48 0.64
18 27 0.36
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Done.