Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001744.1 Kokia drynarioides strain JFW-HI SEQ_113455, 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: 57077
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:1193 original size:5 final size:5
Alignment explanation
Indices: 1185--1214 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1175 TGAGTTGAAT
1185 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
1215 ACACCATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:3452 original size:18 final size:19
Alignment explanation
Indices: 3415--3452 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3405 TCGTTTTAAG
* *
3415 TTTATAATATTATGTTATT
1 TTTATAATATTATATAATT
3434 TTTAT-ATATTATATAATT
1 TTTATAATATTATATAATT
3452 T
1 T
3453 AAAACACATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTATAATATTATATAATT
Found at i:19195 original size:19 final size:19
Alignment explanation
Indices: 19173--19215 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
19163 ATTTATTTAT
*
19173 TAAAAAATAATTTTATAAA
1 TAAAAAATAATCTTATAAA
* *
19192 TAAATAATAATCTTATACA
1 TAAAAAATAATCTTATAAA
19211 TAAAA
1 TAAAA
19216 CAATTTAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAAATAATCTTATAAA
Found at i:26810 original size:19 final size:19
Alignment explanation
Indices: 26772--26810 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
26762 AAGTACTTGA
* *
26772 TTTTTAAATTTTAAATAAT
1 TTTTTAAATTTAAAAAAAT
26791 TTTTTAAATTTAAAAAAAT
1 TTTTTAAATTTAAAAAAAT
26810 T
1 T
26811 AATTGGTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTTAAATTTAAAAAAAT
Found at i:28966 original size:24 final size:25
Alignment explanation
Indices: 28921--28973 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
28911 GCATTGGTCT
*
28921 AAAA-CATATTTAACTAGTAAAAAA
1 AAAATCATATTGAACTAGTAAAAAA
*
28945 AAAATCATATTGAATTAG-AAAAAA
1 AAAATCATATTGAACTAGTAAAAAA
*
28969 CAAAT
1 AAAAT
28974 GTGAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.25
Consensus pattern (25 bp):
AAAATCATATTGAACTAGTAAAAAA
Found at i:30257 original size:9 final size:9
Alignment explanation
Indices: 30245--30275 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
30235 TTGAATTGAA
30245 TTTTTTAAT
1 TTTTTTAAT
30254 TTTTTTAAT
1 TTTTTTAAT
30263 TTTTTTGAAT
1 TTTTTT-AAT
30273 TTT
1 TTT
30276 CAATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 15 0.71
10 6 0.29
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:30399 original size:42 final size:42
Alignment explanation
Indices: 30340--30435 Score: 192
Period size: 42 Copynumber: 2.3 Consensus size: 42
30330 CCGATGACCT
30340 AATTGAGGCGAAATTTAAAAAATATCAAGTAAACCCAAACAA
1 AATTGAGGCGAAATTTAAAAAATATCAAGTAAACCCAAACAA
30382 AATTGAGGCGAAATTTAAAAAATATCAAGTAAACCCAAACAA
1 AATTGAGGCGAAATTTAAAAAATATCAAGTAAACCCAAACAA
30424 AATTGAGGCGAA
1 AATTGAGGCGAA
30436 GCTCACAGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.53, C:0.14, G:0.15, T:0.19
Consensus pattern (42 bp):
AATTGAGGCGAAATTTAAAAAATATCAAGTAAACCCAAACAA
Found at i:32113 original size:11 final size:11
Alignment explanation
Indices: 32097--32121 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
32087 AGGTTGCCCA
32097 CTTTCATCCTC
1 CTTTCATCCTC
32108 CTTTCATCCTC
1 CTTTCATCCTC
32119 CTT
1 CTT
32122 CAAAATCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (11 bp):
CTTTCATCCTC
Found at i:37751 original size:19 final size:19
Alignment explanation
Indices: 37727--37766 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
37717 ATTAGTGATT
*
37727 AATTAAGTAAGATTAAGTA
1 AATTAAATAAGATTAAGTA
* *
37746 AATTAAATAAGCTTAATTA
1 AATTAAATAAGATTAAGTA
37765 AA
1 AA
37767 CTAATTTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (19 bp):
AATTAAATAAGATTAAGTA
Found at i:41819 original size:47 final size:47
Alignment explanation
Indices: 41745--41846 Score: 177
Period size: 47 Copynumber: 2.1 Consensus size: 47
41735 GTGTTTTAGG
* *
41745 ACTCACTCGCACATACTTGCTTTCAGATGAAAGAAACAAAAATAATTT
1 ACTC-CTCGCACATACTTGATTTCAGATGAAAGAAACAAAAACAATTT
41793 ACTCCTCGCACATACTTGATTTCAGATGAAAGAAACAAAAACAATTT
1 ACTCCTCGCACATACTTGATTTCAGATGAAAGAAACAAAAACAATTT
41840 ACTCCTC
1 ACTCCTC
41847 TTACTATTCA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
47 48 0.92
48 4 0.08
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (47 bp):
ACTCCTCGCACATACTTGATTTCAGATGAAAGAAACAAAAACAATTT
Found at i:43879 original size:62 final size:64
Alignment explanation
Indices: 43769--43913 Score: 204
Period size: 62 Copynumber: 2.3 Consensus size: 64
43759 ACTCTTTTTT
* * * *
43769 TTTTTTCAAATAAAAAAATTTCAAAATTTTTTTTTGTGTTGGCCATGCAATGGTCGACACCCCC
1 TTTTTTCAGATAAAAAATTTTCAAAATTTTTTTTAGTGTCGGCCATGCAATGGTCGACACCCCC
* *
43833 TTTTTGCAGATAAAAAATTTTC-GAA-TTTTTTTAGTGTCGGCCATGCAATGGTCGACACCCCC
1 TTTTTTCAGATAAAAAATTTTCAAAATTTTTTTTAGTGTCGGCCATGCAATGGTCGACACCCCC
*
43895 TTTTTATCTGATAAAAAAT
1 TTTTT-TCAGATAAAAAAT
43914 CAAATTTTTG
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
62 40 0.56
63 13 0.18
64 19 0.26
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (64 bp):
TTTTTTCAGATAAAAAATTTTCAAAATTTTTTTTAGTGTCGGCCATGCAATGGTCGACACCCCC
Found at i:47676 original size:11 final size:12
Alignment explanation
Indices: 47636--47684 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
47626 TATTTGTGTA
47636 AAAATTAATTTG
1 AAAATTAATTTG
47648 AAAATTAATTTAAG
1 AAAATTAATTT--G
*
47662 TTGAAATTAATTTG
1 --AAAATTAATTTG
47676 AAAATTAAT
1 AAAATTAAT
47685 GAACATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:48021 original size:84 final size:86
Alignment explanation
Indices: 47798--48097 Score: 493
Period size: 84 Copynumber: 3.5 Consensus size: 86
47788 AATTTAACAT
* *
47798 TATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTGATAAT
1 TATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
* *
47863 ACATTATTTATCAAATTTT-CA
66 ACATTATTTA-CTAATTTTAAA
47884 TATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
1 TATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
47949 ACATTATTTACTAATTTTAAA
66 ACATTATTTACTAATTTTAAA
*
47970 TATTTAAAT-AAAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAA
1 TATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
*
48033 ATATTATTTACTAATTTTAAA
66 ACATTATTTACTAATTTTAAA
*
48054 TATTTAAAT--CAAAGATTATTATTATATTACAATTTTTATCAAAT
1 TATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAAT
48098 TCTAAATTTA
Statistics
Matches: 205, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
83 3 0.01
84 107 0.52
85 12 0.06
86 83 0.40
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (86 bp):
TATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
ACATTATTTACTAATTTTAAA
Found at i:48049 original size:45 final size:45
Alignment explanation
Indices: 47905--48050 Score: 114
Period size: 45 Copynumber: 3.4 Consensus size: 45
47895 AAAAGATTAT
*
47905 TATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATA
1 TATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAAA
* * * ** * *
47950 CATTAT-TTACTAA--TTT-T-AAAT-A--T-TTAAATAAAAAATTAT
1 TATTATATTAC-AATTTTTATCAAATAATGTGTTGATTTGACAA--AA
47989 TATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAAA
1 TATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAAA
48034 TATTAT-TTACTAATTTT
1 TATTATATTAC-AATTTT
48051 AAATATTTAA
Statistics
Matches: 73, Mismatches: 15, Indels: 26
0.64 0.13 0.23
Matches are distributed among these distances:
37 7 0.10
38 1 0.01
39 7 0.10
40 5 0.07
41 7 0.10
42 2 0.03
43 7 0.10
44 9 0.12
45 20 0.27
46 1 0.01
47 7 0.10
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.48
Consensus pattern (45 bp):
TATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAAA
Found at i:48211 original size:22 final size:22
Alignment explanation
Indices: 48186--48250 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
48176 GCATTAGCCC
*
48186 ACCGAAATTCCAGCTCACCTAA
1 ACCGAAATTCCAGCTCACCAAA
* *
48208 ACCGAAATTCCAACTCAGCAAA
1 ACCGAAATTCCAGCTCACCAAA
* *
48230 ACTGAAATTACAGCTCACCAA
1 ACCGAAATTCCAGCTCACCAA
48251 CACTCAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.42, C:0.32, G:0.09, T:0.17
Consensus pattern (22 bp):
ACCGAAATTCCAGCTCACCAAA
Found at i:49340 original size:29 final size:29
Alignment explanation
Indices: 49285--49341 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
49275 ATGTAAGATA
49285 TATTTTCGAATTTTTTATAATATTTTTTC
1 TATTTTCGAATTTTTTATAATATTTTTTC
*
49314 TATTTTCGAAATGTTTTT-TTATATTTTT
1 TATTTTCG-AAT-TTTTTATAATATTTTT
49342 GAATTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 8 0.32
30 12 0.48
31 5 0.20
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (29 bp):
TATTTTCGAATTTTTTATAATATTTTTTC
Found at i:50561 original size:30 final size:30
Alignment explanation
Indices: 50527--50618 Score: 123
Period size: 30 Copynumber: 3.1 Consensus size: 30
50517 TCAGTTTACT
* * *
50527 TTTTAAATTTAATTTTTAATTTCGTTTTTA
1 TTTTAAATTTAATTTTTAATTTCCTGTATA
*
50557 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTTTAATTTCCTGTATA
*
50587 TTTT-AATTTTATTTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTT-TAATTTCCTGTATA
50617 TT
1 TT
50619 CTAATTATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 9 0.16
30 46 0.84
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (30 bp):
TTTTAAATTTAATTTTTAATTTCCTGTATA
Found at i:50595 original size:17 final size:18
Alignment explanation
Indices: 50568--50624 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 18
50558 TTTAAATTTA
50568 ATTTCTAATTTCCTGTAT
1 ATTTCTAATTTCCTGTAT
50586 ATTT-TAA-TT--T-TAT
1 ATTTCTAATTTCCTGTAT
50599 -TTTCTAATTTCCTGTAT
1 ATTTCTAATTTCCTGTAT
50616 A-TTCTAATT
1 ATTTCTAATT
50625 ATTATTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
12 3 0.09
13 6 0.18
14 3 0.09
16 3 0.09
17 14 0.42
18 4 0.12
ACGTcount: A:0.25, C:0.12, G:0.04, T:0.60
Consensus pattern (18 bp):
ATTTCTAATTTCCTGTAT
Found at i:50624 original size:30 final size:30
Alignment explanation
Indices: 50527--50630 Score: 120
Period size: 30 Copynumber: 3.4 Consensus size: 30
50517 TCAGTTTACT
* * * *
50527 TTTTAAATTTAATTTT-TAATTTCGTTTTTA
1 TTTT-AATTTTATTTTCTAATTTCCTGTATA
* *
50557 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTTAATTTTATTTTCTAATTTCCTGTATA
50587 TTTTAATTTTATTTTCTAATTTCCTGTATA
1 TTTTAATTTTATTTTCTAATTTCCTGTATA
*
50617 TTCTAATTATTATT
1 TTTTAATT-TTATT
50631 ATTATTTTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 8 0.13
30 50 0.79
31 5 0.08
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTTAATTTTATTTTCTAATTTCCTGTATA
Found at i:51559 original size:63 final size:61
Alignment explanation
Indices: 51492--51611 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 61
51482 TTTACTAAAT
* *
51492 AAAAAGGGGGTGTCGACCATAGCATGGCCAACACCAAAAAAAAATTGAAATTTTTTTATTTGC
1 AAAAAGGGGGTGTCGACCATAGCATGACCAACACC--AAAAAAATTGAAAATTTTTTATTTGC
* * *
51555 AAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAATTTGAAAATTTTTTAT
1 AAAAAGGGGGTGTCGACCATAGCATGACCAACACCAAAAAAATTGAAAATTTTTTAT
51612 CTGAGAAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
61 20 0.38
63 32 0.62
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (61 bp):
AAAAAGGGGGTGTCGACCATAGCATGACCAACACCAAAAAAATTGAAAATTTTTTATTTGC
Found at i:51649 original size:164 final size:163
Alignment explanation
Indices: 51468--51775 Score: 442
Period size: 164 Copynumber: 1.9 Consensus size: 163
51458 GACCAACACA
*
51468 AAAAATTTTAATTTTTTA-CTAAATAAAAAGGGGGTGTCGACCATAGCATGGCCAACAC-CAAAA
1 AAAAATTTGAATTTTTTATC-AAATAAAAAGGGGGTGTCGACCATAGCATGGCCAACACAC-AAA
*
51531 AAAAATTGAAATTTTTTTATTTGCA-AAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAA
64 AAAAATTGAAATTTTTTTATATG-AGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAA
51595 ATTTGAAAATTTTTTATCTGAGAAATGGCCGACACCC
128 ATTT-AAAATTTTTTATCTGAGAAATGGCCGACACCC
* * * * *
51632 AAAAATTTGATTTTTTTATCAGATAAAAAGGGGGTGTCGACTATTGCATGGCTAACACACAAAAA
1 AAAAATTTGAATTTTTTATCAAATAAAAAGGGGGTGTCGACCATAGCATGGCCAACACACAAAAA
* * * *
51697 AATTTGAAATTTTTTTATATGAGAAAAGGGGGTGTCGGCTATTGCATGGCCAACACCCAAAAATT
66 AAATTGAAATTTTTTTATATGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAATT
**
51762 TAATTTTTTTTATC
131 TAAAATTTTTTATC
51776 AGATAAATAG
Statistics
Matches: 128, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
163 12 0.09
164 114 0.89
165 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (163 bp):
AAAAATTTGAATTTTTTATCAAATAAAAAGGGGGTGTCGACCATAGCATGGCCAACACACAAAAA
AAATTGAAATTTTTTTATATGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAATT
TAAAATTTTTTATCTGAGAAATGGCCGACACCC
Found at i:51768 original size:123 final size:119
Alignment explanation
Indices: 51619--51892 Score: 334
Period size: 123 Copynumber: 2.2 Consensus size: 119
51609 TATCTGAGAA
* *
51619 ATGGCCGACACCCAAAAATTTGATTTTTTTATCAGATAAAAAGGGGGTGTCGACTATTGCATGGC
1 ATGGCCAACACCCAAAAATTTGATTTTTTTATCAGATAAAAA-GGGGTGTCGACCATTGCATGGC
* * * * *
51684 TAACACACAAAAAAATTTGAAATTTTTTTATATG-AGAAAAGGGGGTGTCGGCTATTGC
65 CAACAC-C-AAAAAA-TTG-AATTCTTTTATATGAAAAAAAGGGAGTGTCGGCCATTGC
* * *
51742 ATGGCCAACACCCAAAAATTTAATTTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGCATGGC
1 ATGGCCAACACCCAAAAATTTGA-TTTTTTTATCAGATAAAAAGGGGTGTCGACCATTGCATGGC
* *
51807 CAACACCAAAAAATTGAATTCTTTTATCTGACAAAAAAGGGAGTGTCGGCCATTGT
65 CAACACCAAAAAATTGAATTCTTTTATATGA-AAAAAAGGGAGTGTCGGCCATTGC
* * *
51863 ATGACCCACACCAAAAAAATTTGATTTTTT
1 ATGGCCAACACC-CAAAAATTTGATTTTTT
51893 CAAATTCTCG
Statistics
Matches: 131, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
119 12 0.09
120 3 0.02
121 42 0.32
122 10 0.08
123 46 0.35
124 18 0.14
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (119 bp):
ATGGCCAACACCCAAAAATTTGATTTTTTTATCAGATAAAAAGGGGTGTCGACCATTGCATGGCC
AACACCAAAAAATTGAATTCTTTTATATGAAAAAAAGGGAGTGTCGGCCATTGC
Found at i:51801 original size:60 final size:60
Alignment explanation
Indices: 51619--51892 Score: 275
Period size: 60 Copynumber: 4.5 Consensus size: 60
51609 TATCTGAGAA
* * * * *
51619 ATGGCCGACACCCAAAAATTTGA-TTTTTTTATCAGATAAAAAGGGGGTGTCGACTATTGC
1 ATGGCCAACACCAAAAAATTTAATTTTTTTTATCAGATAAAAA-GGGGTGTCGGCCATTGC
* * * * *
51679 ATGGCTAACACACAAAAAAATTTGAAATTTTTTTAT-ATGAGAAAAGGGGGTGTCGGCTATTGC
1 ATGGCCAACAC-C-AAAAAATTT-AATTTTTTTTATCA-GATAAAAAGGGGTGTCGGCCATTGC
* *
51742 ATGGCCAACACCCAAAAATTTAATTTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGC
1 ATGGCCAACACCAAAAAATTTAATTTTTTTTATCAGATAAAAAGGGGTGTCGGCCATTGC
* * * * *
51802 ATGGCCAACACCAAAAAATTGAA-TTCTTTTATCTGACAAAAAAGGGAGTGTCGGCCATTGT
1 ATGGCCAACACCAAAAAATTTAATTTTTTTTATCAGA-TAAAAAGGG-GTGTCGGCCATTGC
* * *
51863 ATGACCCACACCAAAAAAATTTGATTTTTT
1 ATGGCCAACACC-AAAAAATTTAATTTTTT
51893 CAAATTCTCG
Statistics
Matches: 178, Mismatches: 26, Indels: 17
0.81 0.12 0.08
Matches are distributed among these distances:
59 11 0.06
60 69 0.39
61 33 0.19
62 18 0.10
63 32 0.18
64 15 0.08
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (60 bp):
ATGGCCAACACCAAAAAATTTAATTTTTTTTATCAGATAAAAAGGGGTGTCGGCCATTGC
Found at i:52763 original size:17 final size:18
Alignment explanation
Indices: 52728--52769 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
52718 TAATGTTTAC
52728 ATTATAATATTATATATT
1 ATTATAATATTATATATT
52746 ATTATAGAT-TTA-ATATT
1 ATTATA-ATATTATATATT
*
52763 AATATAA
1 ATTATAA
52770 ACTTAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 10 0.45
18 9 0.41
19 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTATAATATTATATATT
Done.