Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011108.1 Kokia drynarioides strain JFW-HI SEQ_126081, 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: 166255
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 185 characters in sequence are not A, C, G, or T
Found at i:430 original size:23 final size:23
Alignment explanation
Indices: 388--537 Score: 128
Period size: 23 Copynumber: 6.4 Consensus size: 23
378 AGCACGTCTC
*
388 GTGCTCTCTGTTATTAGCACTATGT
1 GTGCTCTCTG--ATTAGCACTTTGT
*
413 GTGCTATCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* * *
436 GTGCTTTCTAATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
459 GTACTCTCTGTTTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
482 GTGCTCTCTG-TTGCCCAGCAC-TTAT
1 GTGCTCTCTGATT----AGCACTTTGT
*
507 GTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATTAGCACTTTGT
*
528 GTACTCTCTG
1 GTGCTCTCTG
538 TTTGTTTCGT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
21 13 0.12
22 4 0.04
23 59 0.56
25 24 0.23
26 5 0.05
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:525 original size:21 final size:20
Alignment explanation
Indices: 367--539 Score: 76
Period size: 23 Copynumber: 7.5 Consensus size: 20
357 AAACTAGCGC
*
367 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTG-TTAGCAC-T-TTGT
390 GCTCTCTGTTATTAGCACTATGTGT
1 GCTCTCTG---TTAGCACT-T-TGT
*
415 GCTATCTGATTAGCACTTTGTGT
1 GCTCTCTG-TTAGCAC-TT-TGT
* * *
438 GCTTTCTAATTAGTACTTTGT
1 GCTCTCT-GTTAGCACTTTGT
459 GTACTCTCTGTTTAGCACTTTGTGT
1 G--CTCTCTG-TTAGCAC-TT-TGT
484 GCTCTCTGTTGCCCAGCACTTATGT
1 GCTCTCTGTT----AGCACTT-TGT
*
509 GCTCTCTGTTAGTACTTTGGT
1 GCTCTCTGTTAGCACTTT-GT
*
530 ACTCTCTGTT
1 GCTCTCTGTT
540 TGTTTCGTAT
Statistics
Matches: 122, Mismatches: 13, Indels: 32
0.73 0.08 0.19
Matches are distributed among these distances:
20 1 0.01
21 21 0.17
22 4 0.03
23 51 0.42
24 5 0.04
25 35 0.29
26 5 0.04
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.45
Consensus pattern (20 bp):
GCTCTCTGTTAGCACTTTGT
Found at i:3221 original size:24 final size:23
Alignment explanation
Indices: 3194--3238 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
3184 GTATTCTCAA
*
3194 TTTGATATATTTACATATTTAAAT
1 TTTGATATATTCACA-ATTTAAAT
* *
3218 TTTGTTTTATTCACAATTTAA
1 TTTGATATATTCACAATTTAA
3239 TTTATTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTGATATATTCACAATTTAAAT
Found at i:3236 original size:23 final size:24
Alignment explanation
Indices: 3201--3251 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
3191 CAATTTGATA
*
3201 TATTTACATATTTAAATTT-TGTTT
1 TATTCACATATTT-AATTTATGTTT
*
3225 TATTCACA-ATTTAATTTATTTTT
1 TATTCACATATTTAATTTATGTTT
3248 TATT
1 TATT
3252 TATATCATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 12 0.50
24 7 0.29
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (24 bp):
TATTCACATATTTAATTTATGTTT
Found at i:23586 original size:2 final size:2
Alignment explanation
Indices: 23579--23622 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
23569 ACTTAAGCAA
23579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23620 AT A
1 AT A
23623 GGTTTAAACC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38048 original size:27 final size:28
Alignment explanation
Indices: 38018--38076 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
38008 AATATTTATA
* *
38018 TTAT-ATTATTTTTAAT-ATTTAATAATT
1 TTATAATT-TTTTTAATAATTAAAAAATT
*
38045 TTATAATTTTTTTATTAATTAAAAAATT
1 TTATAATTTTTTTAATAATTAAAAAATT
38073 TTAT
1 TTAT
38077 GTAATTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTATAATTTTTTTAATAATTAAAAAATT
Found at i:38442 original size:27 final size:27
Alignment explanation
Indices: 38412--38464 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
38402 TTTTTTAAAA
*
38412 TTTTATGTATTTTTGTTTGATAATTTT
1 TTTTATGGATTTTTGTTTGATAATTTT
*
38439 TTTTATGGATTTTTGTTTTATAATTT
1 TTTTATGGATTTTTGTTTGATAATTT
38465 CATATTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.11, T:0.70
Consensus pattern (27 bp):
TTTTATGGATTTTTGTTTGATAATTTT
Found at i:38556 original size:25 final size:24
Alignment explanation
Indices: 38517--38572 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
38507 AATGTTTGAG
* *
38517 TTGTTTTATTTTTATAATTTTAAT
1 TTGTTTAATTTTTATAATTATAAT
38541 TTGTTTAATATTTTATAATTATAAT
1 TTGTTTAAT-TTTTATAATTATAAT
*
38566 TTTTTTA
1 TTGTTTA
38573 TTATAATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (24 bp):
TTGTTTAATTTTTATAATTATAAT
Found at i:39052 original size:18 final size:18
Alignment explanation
Indices: 38997--39054 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
38987 CCTCTTTTGA
*
38997 ATTAAAATATTATTATTT
1 ATTAAAATATTATTTTTT
**
39015 ATTATCAT-TTATTTATTTTT
1 ATTAAAATATTA--T-TTTTT
39035 ATTAAAATATTATTTTTT
1 ATTAAAATATTATTTTTT
39053 AT
1 AT
39055 AGATGATGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
17 3 0.10
18 13 0.42
19 2 0.06
20 10 0.32
21 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTAAAATATTATTTTTT
Found at i:40937 original size:22 final size:21
Alignment explanation
Indices: 40909--41012 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 21
40899 AGGCGCAAGG
40909 AAAAAAAAGAAAAAGGGAAAA
1 AAAAAAAAGAAAAAGGGAAAA
40930 TGAAAAAAAA-AAAAAGGANGAAAA
1 --AAAAAAAAGAAAAAGG--GAAAA
*
40954 AAAAAAAAGGAAAAAGGGAAGA
1 AAAAAAAA-GAAAAAGGGAAAA
* * *
40976 AACAAGAAGAAATAAATGGAAAA
1 AAAAAAAAG-AA-AAAGGGAAAA
*
40999 AAAAAGAA-AAAAAG
1 AAAAAAAAGAAAAAG
41013 AAGGATCCTA
Statistics
Matches: 68, Mismatches: 7, Indels: 15
0.76 0.08 0.17
Matches are distributed among these distances:
20 3 0.04
21 3 0.04
22 27 0.40
23 23 0.34
24 12 0.18
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.03
Consensus pattern (21 bp):
AAAAAAAAGAAAAAGGGAAAA
Found at i:40966 original size:14 final size:16
Alignment explanation
Indices: 40933--40968 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
40923 GGGAAAATGA
40933 AAAAAAAAAAAAGGANG
1 AAAAAAAAAAAAGGA-G
40950 AAAAAAAAAAAAGGA-
1 AAAAAAAAAAAAGGAG
40965 AAAA
1 AAAA
40969 GGGAAGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
17 15 0.79
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAGGAG
Found at i:40977 original size:25 final size:23
Alignment explanation
Indices: 40909--41009 Score: 73
Period size: 23 Copynumber: 4.3 Consensus size: 23
40899 AGGCGCAAGG
**
40909 AAAAAAAAGAAAAAGGGAAAATG
1 AAAAAAAAGAAAAAGGGAAAAAA
40932 AAAAAAAA-AAAAA-GGANGAAAAA
1 AAAAAAAAGAAAAAGGGA--AAAAA
* *
40955 AAAAAAAGGAAAAAGGGAAGAAAC
1 AAAAAAAAGAAAAAGGGAA-AAAA
* * * *
40979 AAGAAGAA-ATAAATGGAAAAAA
1 AAAAAAAAGAAAAAGGGAAAAAA
41001 AAAGAAAAA
1 AAA-AAAAA
41010 AAGAAGGATC
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
21 3 0.05
22 10 0.17
23 31 0.52
24 13 0.22
25 3 0.05
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.03
Consensus pattern (23 bp):
AAAAAAAAGAAAAAGGGAAAAAA
Found at i:43820 original size:20 final size:20
Alignment explanation
Indices: 43795--43874 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
43785 TAGTAATTTT
43795 AAGAAATTTAAAGAATTATA
1 AAGAAATTTAAAGAATTATA
* *
43815 AAGAAATTATAAAAAATAAT-
1 AAGAAATT-TAAAGAATTATA
*
43835 AA-TAATTTAGAA-AA--ATA
1 AAGAAATTTA-AAGAATTATA
*
43852 AA-AAATTTAAAGAATTTTA
1 AAGAAATTTAAAGAATTATA
43871 AAGA
1 AAGA
43875 GAAATTTGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
16 4 0.08
17 10 0.21
18 4 0.08
19 10 0.21
20 11 0.23
21 9 0.19
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (20 bp):
AAGAAATTTAAAGAATTATA
Found at i:43836 original size:21 final size:20
Alignment explanation
Indices: 43795--43836 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
43785 TAGTAATTTT
* *
43795 AAGAAATTTAAAGAATTATA
1 AAGAAATTTAAAAAATAATA
43815 AAGAAATTATAAAAAATAATA
1 AAGAAATT-TAAAAAATAATA
43836 A
1 A
43837 TAATTTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (20 bp):
AAGAAATTTAAAAAATAATA
Found at i:43848 original size:19 final size:17
Alignment explanation
Indices: 43812--43860 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
43802 TTAAAGAATT
43812 ATAAAGAAATTATA-AAAA
1 ATAAA-AAATT-TAGAAAA
43830 ATAATAATAATTTAGAAAA
1 ATAA-AA-AATTTAGAAAA
43849 ATAAAAAATTTA
1 ATAAAAAATTTA
43861 AAGAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.21
18 9 0.32
19 13 0.46
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (17 bp):
ATAAAAAATTTAGAAAA
Found at i:43872 original size:19 final size:19
Alignment explanation
Indices: 43798--43872 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 19
43788 TAATTTTAAG
43798 AAATTTAAAGAATTATAAA
1 AAATTTAAAGAATTATAAA
* *
43817 GAAATTATAAAAAATAAT-AA
1 -AAATT-TAAAGAATTATAAA
*
43837 TAATTTAGAA-AA--ATAAA
1 AAATTTA-AAGAATTATAAA
*
43854 AAATTTAAAGAATTTTAAA
1 AAATTTAAAGAATTATAAA
43873 GAGAAATTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
16 4 0.09
17 10 0.23
18 4 0.09
19 10 0.23
20 7 0.16
21 9 0.20
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAATTTAAAGAATTATAAA
Found at i:50667 original size:32 final size:33
Alignment explanation
Indices: 50631--50703 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
50621 CAATTTTTAT
50631 AAAATATTTT-CAGAAAATTCA-CCAAACAATAG
1 AAAATATTTTACA-AAAATTCATCCAAACAATAG
* ** *
50663 AAAATATTTTACATAGTTTCATCCAAACATTAG
1 AAAATATTTTACAAAAATTCATCCAAACAATAG
50696 AAAATATT
1 AAAATATT
50704 ACTTTTTCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 15 0.43
33 20 0.57
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (33 bp):
AAAATATTTTACAAAAATTCATCCAAACAATAG
Found at i:62332 original size:6 final size:6
Alignment explanation
Indices: 62321--62349 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
62311 CCACACCCGT
62321 AGGAAC AGGAAC AGGAAC AGGAAC AGGAA
1 AGGAAC AGGAAC AGGAAC AGGAAC AGGAA
62350 TCCTCTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.34, T:0.00
Consensus pattern (6 bp):
AGGAAC
Found at i:63789 original size:45 final size:45
Alignment explanation
Indices: 63725--63814 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
63715 AATTAAATAA
63725 ATAGAGAAAAGAGAAGGAATGGGAGATCTCCTTATATGGATTCTT
1 ATAGAGAAAAGAGAAGGAATGGGAGATCTCCTTATATGGATTCTT
63770 ATAGAGAAAAGAGAAGGAATGGGAGATCTCCTTATATGGATTCTT
1 ATAGAGAAAAGAGAAGGAATGGGAGATCTCCTTATATGGATTCTT
63815 TCTTTCTTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.27
Consensus pattern (45 bp):
ATAGAGAAAAGAGAAGGAATGGGAGATCTCCTTATATGGATTCTT
Found at i:90007 original size:2 final size:2
Alignment explanation
Indices: 90000--90048 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
89990 TCTATGTTTA
90000 AT AT AT AT AT AT 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 AT AT AT AT AT AT
90042 AT A- AT AT
1 AT AT AT AT
90049 TTTACATGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:94408 original size:24 final size:23
Alignment explanation
Indices: 94366--94410 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
94356 TTATAAAAAT
**
94366 TTAAATTTAATCTTTATTTTTAA
1 TTAAATTTAATCTAAATTTTTAA
94389 TTAAATTTAAATCTAAATTTTT
1 TTAAATTT-AATCTAAATTTTT
94411 TAAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTAAATTTAATCTAAATTTTTAA
Found at i:94409 original size:23 final size:23
Alignment explanation
Indices: 94366--94409 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
94356 TTATAAAAAT
* *
94366 TTAAATTTAATCTTTATTTTTAA
1 TTAAATTTAATCTTAAATTTTAA
94389 TTAAATTTAAATC-TAAATTTT
1 TTAAATTT-AATCTTAAATTTT
94410 TTAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (23 bp):
TTAAATTTAATCTTAAATTTTAA
Found at i:94669 original size:23 final size:23
Alignment explanation
Indices: 94621--94669 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
94611 TATAAAATAG
* *
94621 TTTTTTTTAAGTGACAATTTTTTT
1 TTTTTTTTAAGTGA-AATGTTGTT
94645 TTTTTTTTAGAGTG-AATGTTGTT
1 TTTTTTTTA-AGTGAAATGTTGTT
94668 TT
1 TT
94670 GTGAAACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 9 0.41
24 9 0.41
25 4 0.18
ACGTcount: A:0.18, C:0.02, G:0.14, T:0.65
Consensus pattern (23 bp):
TTTTTTTTAAGTGAAATGTTGTT
Found at i:96823 original size:110 final size:110
Alignment explanation
Indices: 96612--96845 Score: 337
Period size: 110 Copynumber: 2.1 Consensus size: 110
96602 ATACATCTAT
* *
96612 AATTTTGAGCAATAACAGTATGCCACGTGCTCTTAAAACAATAGTAATACCACACCATTGCCTGC
1 AATTCTGAGCAATAACAGTATGCCACGTGCACTTAAAACAATAGTAATACCACACCATTGCCTGC
* * * *
96677 AATTATGGTAGCGGCAATCCCCTTTTGCGGCTGCAAAAATTTCCA
66 AATTATGGTAGCGGCAATACCCTTCTGCAGCGGCAAAAATTTCCA
* * *
96722 AATTCTGAGCAATAA-TGTTATGCCACGTGCACTTAAAACAATAGTAATACGACACCATTGCTTG
1 AATTCTGAGCAATAACAG-TATGCCACGTGCACTTAAAACAATAGTAATACCACACCATTGCCTG
* *
96786 CAATTATGGTAGCGGCAATTACTC-TCTGCAGCGGCAAAAGTTTCCA
65 CAATTATGGTAGCGGCAA-TACCCTTCTGCAGCGGCAAAAATTTCCA
96832 AATTCTGAGCAATA
1 AATTCTGAGCAATA
96846 GTGGCGTGCC
Statistics
Matches: 111, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
109 1 0.01
110 107 0.96
111 3 0.03
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (110 bp):
AATTCTGAGCAATAACAGTATGCCACGTGCACTTAAAACAATAGTAATACCACACCATTGCCTGC
AATTATGGTAGCGGCAATACCCTTCTGCAGCGGCAAAAATTTCCA
Found at i:100193 original size:31 final size:30
Alignment explanation
Indices: 100128--100199 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
100118 GTTACATTTA
* * *
100128 ACAAAACAGCCACTCAACTTTGAAAATGTG
1 ACAAAACAGTCACTAAAATTTGAAAATGTG
100158 ACAAAACAGTCACTAAAATTATCGAAAA-GTG
1 ACAAAACAGTCACTAAAATT-T-GAAAATGTG
100189 ACAAAACAGTC
1 ACAAAACAGTC
100200 CTATTGGCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 17 0.46
31 15 0.41
32 5 0.14
ACGTcount: A:0.49, C:0.21, G:0.12, T:0.18
Consensus pattern (30 bp):
ACAAAACAGTCACTAAAATTTGAAAATGTG
Found at i:102093 original size:17 final size:17
Alignment explanation
Indices: 102061--102094 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
102051 GAGTTTGAAG
*
102061 GAAAGAAATAAAGAAAA
1 GAAAGAAAGAAAGAAAA
*
102078 GAAAGAAAGAAGGAAAA
1 GAAAGAAAGAAAGAAAA
102095 AGGAGAATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (17 bp):
GAAAGAAAGAAAGAAAA
Found at i:102136 original size:12 final size:12
Alignment explanation
Indices: 102119--102150 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
102109 AAGATAATGT
102119 ATTTATTTTTAA
1 ATTTATTTTTAA
102131 ATTTATTTTTAA
1 ATTTATTTTTAA
102143 ATTTATTT
1 ATTTATTT
102151 AATTTGTTAG
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:0.00, T:0.69
Consensus pattern (12 bp):
ATTTATTTTTAA
Found at i:102823 original size:16 final size:16
Alignment explanation
Indices: 102778--102825 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
102768 AAATACTCTA
102778 AATTAATTACCAAAAT
1 AATTAATTACCAAAAT
102794 -A-TAATATA--AAAAT
1 AATTAAT-TACCAAAAT
102807 AATTAATTACCAAAAT
1 AATTAATTACCAAAAT
102823 AAT
1 AAT
102826 ATCACCATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
13 5 0.19
14 7 0.26
15 7 0.26
16 8 0.30
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
AATTAATTACCAAAAT
Found at i:104785 original size:45 final size:45
Alignment explanation
Indices: 104721--104812 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
104711 GCCTAGCTCA
* * *
104721 TCAAGCCAAAGATATCAGCCTTAGTTTGATGAGCCACCGTAATAC
1 TCAAGCCAAAGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
*
104766 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAAGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
104811 TC
1 TC
104813 TACTCCTCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (45 bp):
TCAAGCCAAAGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:108471 original size:35 final size:36
Alignment explanation
Indices: 108401--108473 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
108391 TATTTTTATT
*
108401 AAATTAATAATTTTTTAATATTACTTTAGTCAAATA
1 AAATAAATAATTTTTTAATATTACTTTAGTCAAATA
108437 AAATAAATAATTTTTGT-ATATTA-TTTGAGT-AAATA
1 AAATAAATAATTTTT-TAATATTACTTT-AGTCAAATA
108472 AA
1 AA
108474 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
35 10 0.29
36 23 0.68
37 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (36 bp):
AAATAAATAATTTTTTAATATTACTTTAGTCAAATA
Found at i:112764 original size:24 final size:24
Alignment explanation
Indices: 112732--112778 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
112722 TAGATGTTCC
112732 ACTTTTCATTTTATTTGATTTTTA
1 ACTTTTCATTTTATTTGATTTTTA
*
112756 ACTTTTCATTTTTTTTGATTTTT
1 ACTTTTCATTTTATTTGATTTTT
112779 TTTATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (24 bp):
ACTTTTCATTTTATTTGATTTTTA
Found at i:118120 original size:17 final size:17
Alignment explanation
Indices: 118100--118132 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
118090 TCCCTTGATC
118100 TTTAACCTTTCATATTT
1 TTTAACCTTTCATATTT
118117 TTTAACCTTTCATATT
1 TTTAACCTTTCATATT
118133 CTTGTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAACCTTTCATATTT
Found at i:125990 original size:13 final size:13
Alignment explanation
Indices: 125972--125997 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
125962 AGTTGTAGAC
125972 TTTTTTTTTTTGT
1 TTTTTTTTTTTGT
125985 TTTTTTTTTTTGT
1 TTTTTTTTTTTGT
125998 GAAAATCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTTGT
Found at i:127594 original size:6 final size:6
Alignment explanation
Indices: 127583--127610 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
127573 CTCCTCTCCG
127583 CACCCC CACCCC CACCCC CACCCC CACC
1 CACCCC CACCCC CACCCC CACCCC CACC
127611 GTCCCTCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.82, G:0.00, T:0.00
Consensus pattern (6 bp):
CACCCC
Found at i:128152 original size:123 final size:127
Alignment explanation
Indices: 127924--128152 Score: 324
Period size: 123 Copynumber: 1.8 Consensus size: 127
127914 AATTTATTGA
* *
127924 CCCCATAACTTTATAATTTAATGTATTAAAGAGAGAATTTCTTCGAAGATAATTGTAACTTTTTG
1 CCCCATAACTTTATAATTTAATATATTAAAGAGAGAA-TTCTTCGAAGATAATTGTAAC-TCTTG
* *
127989 TTGTTTCTTATGTTATTGTTAATCAAGAAAAATAACGACCCCAATAAGCATCGATTCTATTGCC
64 CTGTTTCTTATGTTATTATTAATCAAGAAAAATAACGACCCCAATAAGCATCGATTCTATTGCC
* * *
128053 CCCCATAACTTTATATTTTGATATATTAAAGAGA-AA-TCTTTGAAGATAATTGTCAAC-CTT-C
1 CCCCATAACTTTATAATTTAATATATTAAAGAGAGAATTCTTCGAAGATAATTGT-AACTCTTGC
*
128114 TGTTT-TTATGTTATTATTAATCAAGAAAAATAATGACCC
65 TGTTTCTTATGTTATTATTAATCAAGAAAAATAACGACCC
128153 ATCCCCCAAT
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
123 32 0.35
124 5 0.05
125 2 0.02
126 16 0.18
127 3 0.03
128 2 0.02
129 31 0.34
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (127 bp):
CCCCATAACTTTATAATTTAATATATTAAAGAGAGAATTCTTCGAAGATAATTGTAACTCTTGCT
GTTTCTTATGTTATTATTAATCAAGAAAAATAACGACCCCAATAAGCATCGATTCTATTGCC
Found at i:128548 original size:51 final size:51
Alignment explanation
Indices: 128446--128549 Score: 122
Period size: 51 Copynumber: 2.0 Consensus size: 51
128436 TGTTTCTTTA
* * * * * *
128446 AATTTTTTGAATTTATGATTAAATTGAGAATATTTGTAAATTTTGAGAGTT
1 AATTTTTTAAATTTATGATTAAATTCAGAATATATGTAAATATTAAAAGTT
128497 AATTTTTTAAATTTATGATTAAA-TCA-ATATAATATGTAAATATTAAAAGTT
1 AATTTTTTAAATTTATGATTAAATTCAGA-AT-ATATGTAAATATTAAAAGTT
128548 AA
1 AA
128550 ATTTGTTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 1 0.02
50 4 0.09
51 40 0.89
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.46
Consensus pattern (51 bp):
AATTTTTTAAATTTATGATTAAATTCAGAATATATGTAAATATTAAAAGTT
Found at i:130661 original size:109 final size:109
Alignment explanation
Indices: 130469--130686 Score: 321
Period size: 109 Copynumber: 2.0 Consensus size: 109
130459 GATGGGCAAA
* * *
130469 TTGCAAAATGGTCCTTCCCTGATTTGCCAGTTGAAGTGTCCTTTCAGCCCGCACTTGCCACATAT
1 TTGCAAAATGGTCCTTCCCTGATCTGCCAGTTGAAATGTCCTTTCAGCCCGCACTTACCACATAT
* **
130534 GAATACGTAATTGATCCACGTGGCAAAATCTATCAGAAATAAAT
66 CAATACGTAATTGATCCACGTAACAAAATCTATCAGAAATAAAT
* * * *
130578 TTGCAAAATGGTCCTTCCTTGATCTGTCC-GTTGAAATGTCCTTTCAGCCCGTACTTACCACGTG
1 TTGCAAAATGGTCCTTCCCTGATCTG-CCAGTTGAAATGTCCTTTCAGCCCGCACTTACCACATA
*
130642 TCAATACGTAATTGGTCCACGTAACAAAATCTATCAGAAATAAAT
65 TCAATACGTAATTGATCCACGTAACAAAATCTATCAGAAATAAAT
130687 AGCGTTAGTG
Statistics
Matches: 97, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
109 95 0.98
110 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (109 bp):
TTGCAAAATGGTCCTTCCCTGATCTGCCAGTTGAAATGTCCTTTCAGCCCGCACTTACCACATAT
CAATACGTAATTGATCCACGTAACAAAATCTATCAGAAATAAAT
Found at i:140155 original size:31 final size:30
Alignment explanation
Indices: 140078--140155 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 30
140068 ATTAATAAAA
*
140078 ATAAAATTATAATTTAATATTTTTTAAAAATTG
1 ATAAAATTA-AATTT--GATTTTTTAAAAATTG
* *
140111 ATAAAATTTAATTTGATTTTTTAAAAGTT-
1 ATAAAATTAAATTTGATTTTTTAAAAATTG
140140 ATAGAAATATAAATTT
1 ATA-AAAT-TAAATTT
140156 TTAAAAGAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 3 0.08
30 17 0.44
31 6 0.15
32 5 0.13
33 8 0.21
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (30 bp):
ATAAAATTAAATTTGATTTTTTAAAAATTG
Found at i:165003 original size:59 final size:59
Alignment explanation
Indices: 164935--165046 Score: 206
Period size: 59 Copynumber: 1.9 Consensus size: 59
164925 TAAGTTGCAC
* *
164935 ATATCTTAGTGTTATTTAATTATAAAGATTTTTTTTTAATTTTTTAATTTGTTCGGCTA
1 ATATCTTAGTGTTATTTAATTATAAAGATTTTTTTTAAATTTTTCAATTTGTTCGGCTA
164994 ATATCTTAGTGTTATTTAATTATAAAGATTTTTTTTAAATTTTTCAATTTGTT
1 ATATCTTAGTGTTATTTAATTATAAAGATTTTTTTTAAATTTTTCAATTTGTT
165047 ATTTAATTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (59 bp):
ATATCTTAGTGTTATTTAATTATAAAGATTTTTTTTAAATTTTTCAATTTGTTCGGCTA
Done.