Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001742.1 Kokia drynarioides strain JFW-HI SEQ_113453, 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: 25552
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:948 original size:2 final size:2
Alignment explanation
Indices: 909--938 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
899 AAAAAAAATC
909 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
939 TCTTATATAT
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:1175 original size:23 final size:23
Alignment explanation
Indices: 1138--1181 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1128 TAAATGATTT
* *
1138 TTGCTTTAACTTATTTTATCATA
1 TTGCTTTAACATATTGTATCATA
*
1161 TTGCTTTAGCATATTGTATCA
1 TTGCTTTAACATATTGTATCA
1182 CATGTTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (23 bp):
TTGCTTTAACATATTGTATCATA
Found at i:2302 original size:61 final size:59
Alignment explanation
Indices: 2108--2302 Score: 160
Period size: 61 Copynumber: 3.2 Consensus size: 59
2098 TTAATATAAC
* * * *
2108 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTCA-CTTAA
1 ATTTGGTACCTAAACTTGACATTTTTTCCTAATTTGGTACCTAAA-TTTTTTTAGATTAA
* ** * * * * ***
2167 A-TTGGCAGTTGAACTTGACATTTTTTTTTCTTAATTTGGTACCTAAACTTTTTTGGACCCA
1 ATTTGGTACCTAAACTTGACA---TTTTTTCCTAATTTGGTACCTAAATTTTTTTAGATTAA
* * * *
2228 ATTCGATACCTAAACTTGACATTTTTTCCTAATTCGGTACCTAAGTTTTTTTTTAGATTAA
1 ATTTGGTACCTAAACTTGACATTTTTTCCTAATTTGGTACCTAA--ATTTTTTTAGATTAA
2289 ATTTGGTACCTAAA
1 ATTTGGTACCTAAA
2303 TTTATTAAAT
Statistics
Matches: 101, Mismatches: 28, Indels: 12
0.72 0.20 0.09
Matches are distributed among these distances:
58 16 0.16
59 22 0.22
60 5 0.05
61 45 0.45
62 13 0.13
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (59 bp):
ATTTGGTACCTAAACTTGACATTTTTTCCTAATTTGGTACCTAAATTTTTTTAGATTAA
Found at i:2467 original size:65 final size:65
Alignment explanation
Indices: 2391--2525 Score: 216
Period size: 65 Copynumber: 2.1 Consensus size: 65
2381 ATTTTAGAGA
* * *
2391 AAATTCATGTTAATAATAGGTATTGAGCGATGCTTAACGAATTAATATTGAAAAGATTAGATACC
1 AAATTCATGTTAAAAATAGGTATTGAGCGATGCTTAACGAATTAATAATAAAAAGATTAGATACC
* * *
2456 AAATTCATGTTAAAAATAGGTATTGAGCGTTGCTTAATGAATTAATAATAAAAAGATTAGATACT
1 AAATTCATGTTAAAAATAGGTATTGAGCGATGCTTAACGAATTAATAATAAAAAGATTAGATACC
2521 AAATT
1 AAATT
2526 AGGAAAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (65 bp):
AAATTCATGTTAAAAATAGGTATTGAGCGATGCTTAACGAATTAATAATAAAAAGATTAGATACC
Found at i:3754 original size:8 final size:8
Alignment explanation
Indices: 3737--3766 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3727 CTACGTTGCC
*
3737 TATTAGAT
1 TATTATAT
3745 TATTATAT
1 TATTATAT
3753 TATTATAT
1 TATTATAT
3761 TATTAT
1 TATTAT
3767 TTTTGACACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (8 bp):
TATTATAT
Found at i:8349 original size:17 final size:17
Alignment explanation
Indices: 8329--8365 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
8319 CTCTCTTGAC
*
8329 CTTTAACCTTTCATTTT
1 CTTTAACCTTTCATATT
8346 CTTTAACCTTTCATATT
1 CTTTAACCTTTCATATT
8363 CTT
1 CTT
8366 GTAATTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (17 bp):
CTTTAACCTTTCATATT
Found at i:8879 original size:19 final size:19
Alignment explanation
Indices: 8855--8902 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
8845 TTAAATTTAT
8855 TTAATAAAATATATTAAAA
1 TTAATAAAATATATTAAAA
*** *
8874 TTAATATTTTATATTTAAA
1 TTAATAAAATATATTAAAA
*
8893 TTAATTAAAT
1 TTAATAAAAT
8903 TCATCAATTA
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATAAAATATATTAAAA
Found at i:15461 original size:21 final size:21
Alignment explanation
Indices: 15396--15463 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
15386 AAACATTATG
* *
15396 TTTGTAACTCTCCCCATAATG
1 TTTGTAACTCTCCTCATAATT
* *
15417 TTTGTAACTCTCCTCGTAAGT
1 TTTGTAACTCTCCTCATAATT
* *
15438 TTTGTAACTCTCATCATGATT
1 TTTGTAACTCTCCTCATAATT
15459 TTTGT
1 TTTGT
15464 TTTAAATTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.46
Consensus pattern (21 bp):
TTTGTAACTCTCCTCATAATT
Found at i:18967 original size:36 final size:36
Alignment explanation
Indices: 18920--19090 Score: 265
Period size: 36 Copynumber: 4.8 Consensus size: 36
18910 CGATATTCGA
*
18920 TTTACTCCCTGTTAACCTAAAGGTCATGATGCTCAT
1 TTTACTCCCTGTTGACCTAAAGGTCATGATGCTCAT
*
18956 TTTACTCCCTGTTGACTTAAAGGTCATGATGCTCAT
1 TTTACTCCCTGTTGACCTAAAGGTCATGATGCTCAT
*
18992 TTTACTCCCTGTTGA-CTCAAAGGTCATGATGCTTAT
1 TTTACTCCCTGTTGACCT-AAAGGTCATGATGCTCAT
* *
19028 TTTACTCCTTGTTGACCCAAAGGTCATGATGCTCAT
1 TTTACTCCCTGTTGACCTAAAGGTCATGATGCTCAT
*
19064 TTTACT-CCTGTTGACCCAAAGGTCATG
1 TTTACTCCCTGTTGACCTAAAGGTCATG
19091 CCTGTTACCA
Statistics
Matches: 125, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
35 21 0.17
36 103 0.82
37 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (36 bp):
TTTACTCCCTGTTGACCTAAAGGTCATGATGCTCAT
Found at i:23933 original size:96 final size:96
Alignment explanation
Indices: 23749--23940 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 96
23739 TTTTTAAAAA
** * *
23749 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCA
*
23814 GAACTGAAGATAAGGAAACATTGCCTCGATT
66 GAACTGAAGATAAAGAAACATTGCCTCGATT
* * *
23845 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTACACCTAGTGAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATA-TTTC
*
23909 -GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
65 AG-AACT-GAAGATAAAGA-AACATTGCCTCGATT
23941 TTAAAGCTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
95 3 0.04
96 77 0.93
97 3 0.04
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCA
GAACTGAAGATAAAGAAACATTGCCTCGATT
Found at i:24367 original size:29 final size:29
Alignment explanation
Indices: 24324--24814 Score: 354
Period size: 29 Copynumber: 16.8 Consensus size: 29
24314 ATTCAGGGGC
* *
24324 AAAATGGTAATTTTTAGAGGTTTCGGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTCGGGGT-A
* *
24355 AAAATGGGATTTTTGGAAG-TTCGAGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* * * **
24383 GAAATGGAATTTTAGGAAGTTTTGAGTTTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
* **
24413 AAAATGGGATTTTTTAAAGTTT-GAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
* * *
24442 AATATAGAATTTTTGGAAGTATCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
** *
24472 AAAATGGGGTTTTTGGAAG-TTCGAGGGTG
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
*
24501 AAAAT-GAATTTTTTGNG-AGTTTTGGGGTCA
1 AAAATGGAA-TTTTTG-GAAGTTTCGGGGT-A
* * *
24531 AAAATGGGA--TTTGGAAGTTTAGGGGTG
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* *
24558 AAAATGGAATTTTTGGGAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGGGG-TA
*
24588 AAAATAGG-ATTTTTGGAAGTTTTGGGGTA
1 AAAAT-GGAATTTTTGGAAGTTTCGGGGTA
* *
24617 AAAATGGAATTTTTGGAAGTTTCGAGGTC
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
** * *
24646 AAAATGGGTTTTTTAGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* ** * *
24675 AAAATGGAATTTTT-AAGAGTTTTAGAGTT
1 AAAATGGAATTTTTGGA-AGTTTCGGGGTA
*
24704 AAAATGGGATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
** *
24733 AAAATGGAATTTTTGGAAGTTTTTAGGTTA
1 AAAATGGAATTTTTGGAAG-TTTCGGGGTA
** ** *
24763 AAAATGGGTTTTTTGGAAGTTTAAGGGTG
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* *
24792 AAAACGAAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
24815 AGGGACCTTC
Statistics
Matches: 361, Mismatches: 77, Indels: 45
0.75 0.16 0.09
Matches are distributed among these distances:
27 9 0.02
28 37 0.10
29 193 0.53
30 109 0.30
31 13 0.04
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:24388 original size:59 final size:58
Alignment explanation
Indices: 24324--24783 Score: 403
Period size: 58 Copynumber: 7.9 Consensus size: 58
24314 ATTCAGGGGC
* *
24324 AAAATGGTAATTTTTAGAGGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGTA
1 AAAATGG-AATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGTA
* * * * ** *
24383 GAAATGGAA-TTTTAGGAAGTTTTGAGTTTAAAAATGGGATTTTTTAAAGTTTGAGGGTA
1 AAAATGGAATTTTTA-GAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGTA
* * * * * * *
24442 AATATAGAATTTTTGGAAGTATCGGGGTCAAAAATGGGGTTTTTGGAAGTTCGAGGGTG
1 AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGTA
* * * * *
24501 AAAAT-GAATTTTTTGNGAGTTTTGGGGTCAAAAATGGGA--TTTGGAAGTTTAGGGGTG
1 AAAATGGAATTTTTAG-AAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGTA
* * * * * *
24558 AAAATGGAATTTTTGGGAGTTTTGGGGTTAAAAATAGGATTTTTGGAAGTTTTGGGGTA
1 AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGTA
* * * * * * *
24617 AAAATGGAATTTTTGGAAGTTTCGAGGTC-AAAATGGGTTTTTTAGAAGTTTGGGGGTA
1 AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGTA
* * *
24675 AAAATGGAATTTTTA-AGAGTTTTAGAGT-TAAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTAGA-AGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGTA
* ** * *
24733 AAAATGGAATTTTTGGAAGTTTTTAGGTTAAAAATGGGTTTTTTGGAAGTT
1 AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
24784 TAAGGGTGAA
Statistics
Matches: 329, Mismatches: 59, Indels: 26
0.79 0.14 0.06
Matches are distributed among these distances:
57 47 0.14
58 143 0.43
59 135 0.41
60 4 0.01
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.37
Consensus pattern (58 bp):
AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGTA
Found at i:24404 original size:117 final size:117
Alignment explanation
Indices: 24228--24814 Score: 497
Period size: 117 Copynumber: 5.0 Consensus size: 117
24218 TTGGAAAAAA
* * * * *
24228 TTCGGGGTAAAAAATGGAATTTTTAGACA-TTCGGGGGT-AAAAGGGTAA-TTTT-GAGAGTTTT
1 TTCGGGGTCAAAAATGGGATTTTTGGA-AGTTC-GAGGTAAAAATGG-AATTTTTGGA-AGTTTT
* * * * *
24289 GAGATCGAAAATGGAGTTTTTGGACA-TTCAGGGG-CAAAATGGTAATTTTTAGAG-GT
62 GAGGTCAAAAATGG-GTTTTTAGA-AGTTTAGGGGTAAAAATGG-AATTTTTAGAGAGT
* * *
24345 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGTAGAAATGGAATTTTAGGAAGTTTTGAGT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGTAAAAATGGAATTTTTGGAAGTTTTGAGG
* * * *
24410 TTAAAAATGGGATTTTTTA-AAGTTT-GAGGGTAAATATAGAATTTTTGGA-AGT
66 TCAAAAATGGG--TTTTTAGAAGTTTAG-GGGTAAAAATGGAATTTTTAGAGAGT
* * *
24462 ATCGGGGTCAAAAATGGGGTTTTTGGAAGTTCGAGGGTGAAAAT-GAATTTTTTGNG-AGTTTTG
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGTAAAAATGGAA-TTTTTG-GAAGTTTTG
* * * * *
24525 GGGTCAAAAATGGG-ATTTGGAAGTTTAGGGGTGAAAATGGAATTTTT-GGGAGT
63 AGGTCAAAAATGGGTTTTTAGAAGTTTAGGGGTAAAAATGGAATTTTTAGAGAGT
* * * * * *
24578 TTTGGGGTTAAAAATAGGATTTTTGGAAGTTTTGGGGTAAAAATGGAATTTTTGGAAGTTTCGAG
1 TTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGTAAAAATGGAATTTTTGGAAGTTTTGAG
*
24643 GTC-AAAATGGGTTTTTTAGAAGTTTGGGGGTAAAAATGGAATTTTTA-AGAGT
65 GTCAAAAATGGG-TTTTTAGAAGTTTAGGGGTAAAAATGGAATTTTTAGAGAGT
** * * *
24695 TTTAGAGT-TAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTTAG
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGTAAAAATGGAATTTTTGGAAGTTTTGAG
* * * * * * * *
24759 GTTAAAAATGGGTTTTTTGGAAGTTTAAGGGTGAAAACGAAATTTTTGGACAGT
65 GTCAAAAATGGG-TTTTTAGAAGTTTAGGGGTAAAAATGGAATTTTTAGAGAGT
24813 TT
1 TT
24815 AGGGACCTTC
Statistics
Matches: 383, Mismatches: 62, Indels: 49
0.78 0.13 0.10
Matches are distributed among these distances:
115 16 0.04
116 131 0.34
117 187 0.49
118 48 0.13
119 1 0.00
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (117 bp):
TTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGTAAAAATGGAATTTTTGGAAGTTTTGAGG
TCAAAAATGGGTTTTTAGAAGTTTAGGGGTAAAAATGGAATTTTTAGAGAGT
Found at i:24817 original size:58 final size:59
Alignment explanation
Indices: 24324--24814 Score: 482
Period size: 59 Copynumber: 8.4 Consensus size: 59
24314 ATTCAGGGGC
* * * * * *
24324 AAAATGGTAATTTTTAGAGGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGTA
1 AAAATGG-AATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTA
* * * **
24383 GAAATGGAATTTTAGGAAGTTTTGAGTTTAAAAATGGGATTTTTTAAAGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTA
* * * * * * * * *
24442 AATATAGAATTTTTGGAAGTATCGGGGTCAAAAATGGGGTTTTTGGAAGTTCGAGGGTG
1 AAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTA
* * *
24501 AAAAT-GAATTTTTTGNG-AGTTTTGGGGTCAAAAATGGGA--TTTGGAAGTTT-AGGGGTG
1 AAAATGGAA-TTTTTG-GAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTGA-GGGTA
* * *
24558 AAAATGGAATTTTTGGGAGTTTTGGGGTTAAAAATAGGATTTTTGGAAGTTTTG-GGGTA
1 AAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAG-TTTGAGGGTA
* * * * *
24617 AAAATGGAATTTTTGGAAGTTTCGAGG-TCAAAATGGGTTTTTTAGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTA
* *
24675 AAAATGGAATTTTT-AAGAGTTTT-AGAGTT-AAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGA-AGTTTTGAG-GTTAAAAATGGGATTTTTGGAAGTTTGAGGGTA
* * * *
24733 AAAATGGAATTTTTGGAAGTTTTTAGGTTAAAAATGGGTTTTTTGGAAGTTTAAGGGTG
1 AAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTA
* *
24792 AAAACGAAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
24815 AGGGACCTTC
Statistics
Matches: 361, Mismatches: 53, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
56 2 0.01
57 53 0.15
58 133 0.37
59 164 0.45
60 9 0.02
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.36
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTA
Done.