Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012847.1 Kokia drynarioides strain JFW-HI SEQ_127861, 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: 299897
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:1852 original size:55 final size:55
Alignment explanation
Indices: 1786--1894 Score: 164
Period size: 55 Copynumber: 2.0 Consensus size: 55
1776 TGCTATGTAA
** *
1786 CAATCGATTCAAAAGAAGCAATATTTTAACATGACAATCGATTTAAACATATAAG
1 CAATCGATTCAAAAGAAGCAATATTCCAACATGACAATCAATTTAAACATATAAG
** *
1841 CAATCGATTCAAAAGAATTAGTATTCCAACATGACAATCAATTTAAACATATAA
1 CAATCGATTCAAAAGAAGCAATATTCCAACATGACAATCAATTTAAACATATAA
1895 AAAACCATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.28
Consensus pattern (55 bp):
CAATCGATTCAAAAGAAGCAATATTCCAACATGACAATCAATTTAAACATATAAG
Found at i:6331 original size:144 final size:144
Alignment explanation
Indices: 6103--6394 Score: 512
Period size: 144 Copynumber: 2.0 Consensus size: 144
6093 TTTAGTGAAA
6103 CTTTGGGATGAAGTTGAATTTTCTGTGAAAGTTGATCTAGTTTGGAAACCCTAATTATTTGGAGT
1 CTTTGGGATGAAGTTGAATTTTCTGTGAAAGTTGATCTAGTTTGGAAACCCTAATTATTTGGAGT
6168 CTCTTTGTGTAAATTACCCTTTTTGCTTGATTTAAAAACCCATTTTCTTTTTGTTTTGACTTTTG
66 CTCTTTGTGTAAATTACCCTTTTTGCTTGATTTAAAAACCCATTTTCTTTTTGTTTTGACTTTTG
6233 AACTCTCAATTCCC
131 AACTCTCAATTCCC
* * * *
6247 CTTTGGGATGAAGTTGAATTTTTTTTTAAAGTTGGTCTAGTTTGGAAACCCTAATTATTTGGAGT
1 CTTTGGGATGAAGTTGAATTTTCTGTGAAAGTTGATCTAGTTTGGAAACCCTAATTATTTGGAGT
* *
6312 CTTTTTGTGTAATTTACCCTTTTTGCTTGATTTAAAAACCCATTTTCTTTTTGTTTTGACTTTTG
66 CTCTTTGTGTAAATTACCCTTTTTGCTTGATTTAAAAACCCATTTTCTTTTTGTTTTGACTTTTG
* *
6377 AACTCTGATTTCCC
131 AACTCTCAATTCCC
6391 CTTT
1 CTTT
6395 TCTTTTTCCC
Statistics
Matches: 140, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
144 140 1.00
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.48
Consensus pattern (144 bp):
CTTTGGGATGAAGTTGAATTTTCTGTGAAAGTTGATCTAGTTTGGAAACCCTAATTATTTGGAGT
CTCTTTGTGTAAATTACCCTTTTTGCTTGATTTAAAAACCCATTTTCTTTTTGTTTTGACTTTTG
AACTCTCAATTCCC
Found at i:18833 original size:25 final size:28
Alignment explanation
Indices: 18784--18834 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
18774 AAAAGAGACT
*
18784 AAAAATTAGAGTAATTAATCTACCAAAA
1 AAAAATTAGAGTAATTAATCAACCAAAA
18812 AAAAATT-GAGTAATT-A-CAACCAA
1 AAAAATTAGAGTAATTAATCAACCAA
18835 TTACAATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 1 0.05
27 8 0.36
28 7 0.32
ACGTcount: A:0.57, C:0.12, G:0.08, T:0.24
Consensus pattern (28 bp):
AAAAATTAGAGTAATTAATCAACCAAAA
Found at i:19175 original size:2 final size:2
Alignment explanation
Indices: 19165--19203 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
19155 AATCAAAATT
*
19165 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19204 TTGTAGATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20997 original size:31 final size:31
Alignment explanation
Indices: 20954--21023 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
20944 TTGGTGATTG
*
20954 TTTTGTCACTTTTCGATAATGTTAGTAACTA
1 TTTTGTCACTTTTCGATAACGTTAGTAACTA
* * *
20985 TTTTGTCTCTTTTCGATAACGTTAGTGACTG
1 TTTTGTCACTTTTCGATAACGTTAGTAACTA
21016 TTTTGTCA
1 TTTTGTCA
21024 TATTTTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (31 bp):
TTTTGTCACTTTTCGATAACGTTAGTAACTA
Found at i:23735 original size:24 final size:23
Alignment explanation
Indices: 23698--23744 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
23688 AAAAATGATT
23698 AATTATTTAAATA-TATAATATTA
1 AATTATTTAAATATTATAA-ATTA
*
23721 AATTATTTTATATATTATAAATTA
1 AATTA-TTTAAATATTATAAATTA
23745 TGTGACATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTATTTAAATATTATAAATTA
Found at i:47539 original size:13 final size:13
Alignment explanation
Indices: 47521--47551 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
47511 GGTACTTAAC
*
47521 CTTAACATTTTTT
1 CTTAACACTTTTT
47534 CTTAACACTTTTT
1 CTTAACACTTTTT
47547 CTTAA
1 CTTAA
47552 TTTAACACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (13 bp):
CTTAACACTTTTT
Found at i:48148 original size:24 final size:24
Alignment explanation
Indices: 48066--48148 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 24
48056 CAGACAAAAA
** *
48066 AAAAAGATTAGGTACCAAATTAGG
1 AAAAAGATTAAATACCAAATTAAG
* *
48090 AAAAAGATTAAAGTATCAAATTGGACCACA
1 AAAAAGATTAAA-TACCAAATT--A--A-G
48120 AAAAAGATTAAATACCAAATTAAG
1 AAAAAGATTAAATACCAAATTAAG
48144 AAAAA
1 AAAAA
48149 AATGTTAAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
24 15 0.33
25 9 0.20
27 2 0.04
29 8 0.17
30 12 0.26
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (24 bp):
AAAAAGATTAAATACCAAATTAAG
Found at i:48148 original size:25 final size:25
Alignment explanation
Indices: 48065--48149 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 25
48055 TCAGACAAAA
**
48065 AAAAAAGATTAGGTACCAAATT-AG
1 AAAAAAGATTAAATACCAAATTAAG
* * *
48089 GAAAAAGATTAAAGTATCAAATTGGACCAC
1 AAAAAAGATTAAA-TACCAAATT--A--AG
48119 AAAAAAGATTAAATACCAAATTAAG
1 AAAAAAGATTAAATACCAAATTAAG
48144 AAAAAA
1 AAAAAA
48150 ATGTTAAGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
24 10 0.21
25 15 0.32
27 1 0.02
29 8 0.17
30 13 0.28
ACGTcount: A:0.59, C:0.09, G:0.13, T:0.19
Consensus pattern (25 bp):
AAAAAAGATTAAATACCAAATTAAG
Found at i:49610 original size:3 final size:3
Alignment explanation
Indices: 49602--49628 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
49592 TAAATTAAAA
49602 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
49629 ATTTGATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:49611 original size:23 final size:24
Alignment explanation
Indices: 49570--49616 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
49560 ATAATATTTG
49570 AAATTAATAATTTAATATT-TTAT
1 AAATTAATAATTTAATATTATTAT
*
49593 AAATTAA-AATATTATTATTATTAT
1 AAATTAATAAT-TTAATATTATTAT
49617 TATTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 14 0.67
24 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATTAATAATTTAATATTATTAT
Found at i:50121 original size:14 final size:14
Alignment explanation
Indices: 50102--50130 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
50092 ATTACTTAAG
50102 AGTCCATTTACAAA
1 AGTCCATTTACAAA
50116 AGTCCATTTACAAA
1 AGTCCATTTACAAA
50130 A
1 A
50131 AGAACAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28
Consensus pattern (14 bp):
AGTCCATTTACAAA
Found at i:53434 original size:25 final size:26
Alignment explanation
Indices: 53392--53442 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
53382 TGAATCAGAC
*
53392 AAAAAAAAAAGATTAAGTACCAAATT
1 AAAAAAAAAAGATAAAGTACCAAATT
*
53418 AAAAAAAAAAG-TAAAGTATCAAATT
1 AAAAAAAAAAGATAAAGTACCAAATT
53443 GGACCCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.20
Consensus pattern (26 bp):
AAAAAAAAAAGATAAAGTACCAAATT
Found at i:56509 original size:17 final size:18
Alignment explanation
Indices: 56482--56515 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
56472 GCTTCGGAGA
56482 ATATGCCAAAATATTCAC
1 ATATGCCAAAATATTCAC
*
56500 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATATTCA
56516 TAATTGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.24, G:0.03, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATATTCAC
Found at i:59201 original size:18 final size:17
Alignment explanation
Indices: 59180--59214 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
59170 AAATCAAAAT
*
59180 TTTTTTAATAAGATAATA
1 TTTTGTAATAA-ATAATA
59198 TTTTGTAATAAATAATA
1 TTTTGTAATAAATAATA
59215 GATTATCGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
TTTTGTAATAAATAATA
Found at i:59765 original size:8 final size:7
Alignment explanation
Indices: 59739--59763 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
59729 GTTATATATT
59739 GGGGAAG
1 GGGGAAG
59746 GGGGAAG
1 GGGGAAG
59753 GGGGAAG
1 GGGGAAG
59760 GGGG
1 GGGG
59764 GAGAGAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (7 bp):
GGGGAAG
Found at i:60533 original size:19 final size:20
Alignment explanation
Indices: 60511--60548 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
60501 AAAATGAGCT
*
60511 TATTTTCTATAAAA-AAATA
1 TATTTTCCATAAAACAAATA
60530 TATTTTCCATAAAACAAAT
1 TATTTTCCATAAAACAAAT
60549 TCTTAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
TATTTTCCATAAAACAAATA
Found at i:60802 original size:2 final size:2
Alignment explanation
Indices: 60795--60828 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
60785 TTTAGCTGAA
60795 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
60829 TCAATATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74276 original size:2 final size:2
Alignment explanation
Indices: 74269--74298 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
74259 GTGGCTCAGC
74269 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
74299 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:80506 original size:26 final size:26
Alignment explanation
Indices: 80448--80538 Score: 101
Period size: 26 Copynumber: 3.5 Consensus size: 26
80438 GTGAGCAACA
* * *
80448 TCGTAAGAGTTAAACTCTGTTTGGGC
1 TCGTAAGAGCTAAACTCTGTCTGGAC
* *
80474 TCATAAGAGCTAAACTCTGTCTGAAC
1 TCGTAAGAGCTAAACTCTGTCTGGAC
* * *
80500 TTGTAAGAGCTAAACTTTATCTGGAC
1 TCGTAAGAGCTAAACTCTGTCTGGAC
*
80526 TCGTATGAGCTAA
1 TCGTAAGAGCTAA
80539 TTTCTGGAAG
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (26 bp):
TCGTAAGAGCTAAACTCTGTCTGGAC
Found at i:91724 original size:40 final size:40
Alignment explanation
Indices: 91649--91743 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
91639 TAATATTTTC
* ** **
91649 AAAATATTTTCAATTGAGGAAAATCCTCTGTCTGTTTTAG
1 AAAATATTTTCAATTAAGGAAAATCCTCTCACTGTTGCAG
91689 AAAATATTTTCAATTAAGGAAAATCCTCTCACTGTTGCAG
1 AAAATATTTTCAATTAAGGAAAATCCTCTCACTGTTGCAG
* *
91729 ACAATATTTCCAATT
1 AAAATATTTTCAATT
91744 GAAAAAAACC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (40 bp):
AAAATATTTTCAATTAAGGAAAATCCTCTCACTGTTGCAG
Found at i:96980 original size:2 final size:2
Alignment explanation
Indices: 96973--97042 Score: 97
Period size: 2 Copynumber: 35.0 Consensus size: 2
96963 TCAGATTTGG
96973 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
97014 TT TT TT ACT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
97043 TATTTTTTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.02
2 61 0.95
3 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:97026 original size:32 final size:33
Alignment explanation
Indices: 96990--97061 Score: 130
Period size: 32 Copynumber: 2.2 Consensus size: 33
96980 TATATATATA
96990 TATATATATATATATATATATTATTTTTTTA-C
1 TATATATATATATATATATATTATTTTTTTACC
97022 TATATATATATATATATATATTATTTTTTTACC
1 TATATATATATATATATATATTATTTTTTTACC
97055 TA-ATATA
1 TATATATA
97062 ATTTTTTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 36 0.92
33 3 0.08
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (33 bp):
TATATATATATATATATATATTATTTTTTTACC
Found at i:97078 original size:18 final size:18
Alignment explanation
Indices: 97032--97080 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
97022 TATATATATA
* *
97032 TATATATATATTATTTTT
1 TATATCTATATAATTTTT
*
97050 T-TACCTAATATAATTTTT
1 TATATCT-ATATAATTTTT
97068 TATATCTATATAA
1 TATATCTATATAA
97081 AATTTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.12
18 18 0.72
19 4 0.16
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATCTATATAATTTTT
Found at i:97286 original size:25 final size:25
Alignment explanation
Indices: 97240--97299 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
97230 ATATTTAATA
*
97240 TTTTCATTTTGTTGAATCTTTAAAG
1 TTTTCATTTTGTTCAATCTTTAAAG
* * * *
97265 TTTTCTTTTTGTTCATTTTTTAATG
1 TTTTCATTTTGTTCAATCTTTAAAG
*
97290 TTTTTATTTT
1 TTTTCATTTT
97300 TATATATATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.17, C:0.07, G:0.08, T:0.68
Consensus pattern (25 bp):
TTTTCATTTTGTTCAATCTTTAAAG
Found at i:103246 original size:18 final size:18
Alignment explanation
Indices: 103221--103265 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
103211 TTCTTAAAAA
103221 TAAATTTTAT-AGCTTTT
1 TAAATTTTATGAGCTTTT
*
103238 ATCAATTTTATGAGCTTTT
1 -TAAATTTTATGAGCTTTT
103257 TAAATTTTA
1 TAAATTTTA
103266 AAAAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (18 bp):
TAAATTTTATGAGCTTTT
Found at i:104207 original size:32 final size:32
Alignment explanation
Indices: 104168--104235 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
104158 AAAATTATTT
*
104168 TTTTCATAAAGTAATAAATATTACTATCAATA
1 TTTTCATAAAGTAAAAAATATTACTATCAATA
104200 TTTTCATAAAGTAAAAAATATTACTATCAATA
1 TTTTCATAAAGTAAAAAATATTACTATCAATA
104232 TTTT
1 TTTT
104236 ATTTTTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (32 bp):
TTTTCATAAAGTAAAAAATATTACTATCAATA
Found at i:104455 original size:74 final size:74
Alignment explanation
Indices: 104334--104483 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 74
104324 TCAATTTCAA
*
104334 TTAAAACCTCATTTATATCCTAACTATTTATAAATACATTTATTACGTAAAATTGTTATAATTTA
1 TTAAAACCTCATTTATACCCTAACTATTTATAAATACATTTATTACGTAAAATTGTTATAATTTA
104399 GTACAAGTT
66 GTACAAGTT
104408 TTAAAACCTCATTTATACCCTAACTATTTATAAATACATTTATTACGTAAAATTGTTATAATTTA
1 TTAAAACCTCATTTATACCCTAACTATTTATAAATACATTTATTACGTAAAATTGTTATAATTTA
104473 GTACAAGTT
66 GTACAAGTT
104482 TT
1 TT
104484 TGAACAGAAT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.43
Consensus pattern (74 bp):
TTAAAACCTCATTTATACCCTAACTATTTATAAATACATTTATTACGTAAAATTGTTATAATTTA
GTACAAGTT
Found at i:105727 original size:31 final size:30
Alignment explanation
Indices: 105679--105739 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
105669 TAAAAATTTA
*
105679 ATTTTTAAAGGATTAAATCAAAATTTTATC
1 ATTTTTAAAGGACTAAATCAAAATTTTATC
* * *
105709 ATTTTTAAAAGGGCTAAATTATAATTTTATC
1 ATTTTT-AAAGGACTAAATCAAAATTTTATC
105740 TTTACTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (30 bp):
ATTTTTAAAGGACTAAATCAAAATTTTATC
Found at i:107369 original size:46 final size:46
Alignment explanation
Indices: 107256--107419 Score: 145
Period size: 46 Copynumber: 3.6 Consensus size: 46
107246 AATGTGTTTG
* *
107256 GTCACTCGTTAGGGTTGAACCTACACGAATAACATAATAGTGCCTA
1 GTCACCCGTTAAGGTTGAACCTACACGAATAACATAATAGTGCCTA
* * * *
107302 GTCACCCG-TCAGATTTGAACCTAGACGAATAACATAATAGTGTCT-
1 GTCACCCGTTAAG-GTTGAACCTACACGAATAACATAATAGTGCCTA
* * * ** *
107347 GATCAGCCGTTAAGGTTAAACCTACACGAATCAA-ATAATAATGTTTG
1 G-TCACCCGTTAAGGTTGAACCTACACGAAT-AACATAATAGTGCCTA
* * *
107394 GTCACACATTAGGGTTGAACCTACAC
1 GTCACCCGTTAAGGTTGAACCTACAC
107420 AACAGTTAGC
Statistics
Matches: 95, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
45 3 0.03
46 86 0.91
47 6 0.06
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (46 bp):
GTCACCCGTTAAGGTTGAACCTACACGAATAACATAATAGTGCCTA
Found at i:108414 original size:4 final size:4
Alignment explanation
Indices: 108405--108444 Score: 53
Period size: 4 Copynumber: 9.2 Consensus size: 4
108395 ACTTATATTG
108405 TTAA TTAA TTAA TTAA TTAA TCCTAA TTAA CTTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA T--TAA TTAA -TTAA TTAA T
108445 CATAATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 25 0.76
5 4 0.12
6 4 0.12
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (4 bp):
TTAA
Found at i:108441 original size:19 final size:18
Alignment explanation
Indices: 108410--108457 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
108400 TATTGTTAAT
*
108410 TAATTAATTAATTAATCC
1 TAATTAATTAATTAATCA
108428 TAATTAACTTAATTAATCA
1 TAATTAA-TTAATTAATCA
*
108447 TAATTTATTAA
1 TAATTAATTAA
108458 CATTAAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATTAATTAATTAATCA
Found at i:110949 original size:44 final size:43
Alignment explanation
Indices: 110883--111175 Score: 248
Period size: 42 Copynumber: 6.8 Consensus size: 43
110873 CTTAATTAAC
* **
110883 CTTATGCTCTATCCGACTCATAAGTTCTTCCATTTACAAATAAT
1 CTTATGCTCTAGCCGAGACATAAG-TCTTCCATTTACAAATAAT
*
110927 CTTATGCTCTAGCCGAGACATAAGTCTTCCATTTATAAATAAT
1 CTTATGCTCTAGCCGAGACATAAGTCTTCCATTTACAAATAAT
*
110970 CTTATGCTCTAACCGAGACATAAGTTCTTCCATTTACAAATAAAT
1 CTTATGCTCTAGCCGAGACATAAG-TCTTCCATTTACAAAT-AAT
*
111015 CTTATGCTCTAGCCGAGACGTAAGTCTTCC-TTTA-AACATAAT
1 CTTATGCTCTAGCCGAGACATAAGTCTTCCATTTACAA-ATAAT
* * ** *
111057 CTCT-TGCT-TATCCCGAGTCACGAGTATTCC-TTTA-AACATAAT
1 CT-TATGCTCTA-GCCGAGACATAAGTCTTCCATTTACAA-ATAAT
* * *
111099 CTCATGCTC-ATCCCAAGACA-AGAGTCTTCC-TTTA-AACATAAT
1 CTTATGCTCTA-GCCGAGACATA-AGTCTTCCATTTACAA-ATAAT
* * * *
111141 CTCATGCTC-ATCCCGACACATGAGTCTTCCATTTA
1 CTTATGCTCTA-GCCGAGACATAAGTCTTCCATTTA
111176 TACATCAAGT
Statistics
Matches: 217, Mismatches: 22, Indels: 21
0.83 0.08 0.08
Matches are distributed among these distances:
41 2 0.01
42 96 0.44
43 52 0.24
44 42 0.19
45 25 0.12
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.34
Consensus pattern (43 bp):
CTTATGCTCTAGCCGAGACATAAGTCTTCCATTTACAAATAAT
Found at i:111056 original size:87 final size:87
Alignment explanation
Indices: 110883--111058 Score: 284
Period size: 87 Copynumber: 2.0 Consensus size: 87
110873 CTTAATTAAC
* *
110883 CTTATGCTCTATCCGACTCATAAGTTCTTCCATTTACAAATAATCTTATGCTCTAGCCGAGACAT
1 CTTATGCTCTAACCGACACATAAGTTCTTCCATTTACAAATAATCTTATGCTCTAGCCGAGACAT
110948 AAGTCTTCCATTTATAAATAAT
66 AAGTCTTCCATTTATAAATAAT
* *
110970 CTTATGCTCTAACCGAGACATAAGTTCTTCCATTTACAAATAAATCTTATGCTCTAGCCGAGACG
1 CTTATGCTCTAACCGACACATAAGTTCTTCCATTTACAAAT-AATCTTATGCTCTAGCCGAGACA
111035 TAAGTCTTCC-TTTA-AACATAAT
65 TAAGTCTTCCATTTATAA-ATAAT
111057 CT
1 CT
111059 CTTGCTTATC
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
86 2 0.02
87 49 0.59
88 32 0.39
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.35
Consensus pattern (87 bp):
CTTATGCTCTAACCGACACATAAGTTCTTCCATTTACAAATAATCTTATGCTCTAGCCGAGACAT
AAGTCTTCCATTTATAAATAAT
Found at i:114249 original size:2 final size:2
Alignment explanation
Indices: 114244--114269 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
114234 TGAGTAGTAA
114244 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
114270 CGTTTTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115998 original size:42 final size:42
Alignment explanation
Indices: 115927--116095 Score: 216
Period size: 42 Copynumber: 4.0 Consensus size: 42
115917 TTACGAAATA
* * *
115927 AATCTTATGCTCTAGCC-GAGACATAAGTCTTCCTTTAAACAT
1 AATCTCATGCTC-ATCCTGAGACATGAGTCTTCCTTTAAACAT
* *
115969 AATCTCATGCTCATCCTGAGTCACGAGTCTTCCTTTAAACAT
1 AATCTCATGCTCATCCTGAGACATGAGTCTTCCTTTAAACAT
* * *
116011 AATCTCATGCTCATCCCGAGACATGAATCTTCCTTTAGACAT
1 AATCTCATGCTCATCCTGAGACATGAGTCTTCCTTTAAACAT
*
116053 AATCTCATGCTCAT-CTCGAGACATGAGTCTTCCATTTATACAT
1 AATCTCATGCTCATCCT-GAGACATGAGTCTTCC-TTTAAACAT
116096 CAGGTGATTT
Statistics
Matches: 111, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
41 4 0.04
42 99 0.89
43 8 0.07
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (42 bp):
AATCTCATGCTCATCCTGAGACATGAGTCTTCCTTTAAACAT
Found at i:118596 original size:25 final size:26
Alignment explanation
Indices: 118542--118616 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 26
118532 TTTCATTCCT
*
118542 ATTTTACCCAC-AGCAAAATTTTGACC
1 ATTTTACCC-CTAGTAAAATTTTGACC
**
118568 ATTTTACCCCTAGT-AAATTTTGATG
1 ATTTTACCCCTAGTAAAATTTTGACC
* * *
118593 ATTTTTCCCTTGGTAAAATTTTGA
1 ATTTTACCCCTAGTAAAATTTTGA
118617 GAAAATATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 21 0.51
26 20 0.49
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAATTTTGACC
Found at i:120379 original size:26 final size:26
Alignment explanation
Indices: 120350--120399 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
120340 AATTTTCACG
*
120350 ATTTTACCCTTGGTAAATTTTTGAAT
1 ATTTTACCCTTGGTAAAATTTTGAAT
**
120376 ATTTTGGCCTTGGTAAAATTTTGA
1 ATTTTACCCTTGGTAAAATTTTGA
120400 GAAAATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (26 bp):
ATTTTACCCTTGGTAAAATTTTGAAT
Found at i:122721 original size:10 final size:10
Alignment explanation
Indices: 122706--122741 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
122696 TACAACCAGA
122706 TTTATTTCAT
1 TTTATTTCAT
122716 TTTATTT-AT
1 TTTATTTCAT
*
122725 TTTATTTCGT
1 TTTATTTCAT
122735 TTTATTT
1 TTTATTT
122742 TTAGTTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (10 bp):
TTTATTTCAT
Found at i:127199 original size:37 final size:37
Alignment explanation
Indices: 127141--127311 Score: 254
Period size: 37 Copynumber: 4.6 Consensus size: 37
127131 CACCGGCAGA
* *
127141 AAGCCTACTAGGAAC-AAGCCTGAAAACACTAGCACG
1 AAGCCTACTAGGCACAAAGCCTGAAAACACCAGCACG
* * *
127177 AAGCCTAATAGGCACAAAGCCTGAAAACACAAGCACA
1 AAGCCTACTAGGCACAAAGCCTGAAAACACCAGCACG
* *
127214 AAGCCTACTAGGCATAAAACCTGAAAACACCAGCACG
1 AAGCCTACTAGGCACAAAGCCTGAAAACACCAGCACG
* *
127251 AAGCCTACTAGGTACAAAGCCTGAAAACACCAACACG
1 AAGCCTACTAGGCACAAAGCCTGAAAACACCAGCACG
127288 AAGCCTACTAGGCACAAAGCCTGA
1 AAGCCTACTAGGCACAAAGCCTGA
127312 TTAATTGAAT
Statistics
Matches: 120, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
36 13 0.11
37 107 0.89
ACGTcount: A:0.43, C:0.29, G:0.18, T:0.11
Consensus pattern (37 bp):
AAGCCTACTAGGCACAAAGCCTGAAAACACCAGCACG
Found at i:133102 original size:14 final size:14
Alignment explanation
Indices: 133083--133109 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
133073 TTACAATCAG
133083 ATTTATTTTATTTT
1 ATTTATTTTATTTT
133097 ATTTATTTTATTT
1 ATTTATTTTATTT
133110 CGTTTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
ATTTATTTTATTTT
Found at i:133739 original size:20 final size:19
Alignment explanation
Indices: 133716--133756 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
133706 TTTGAGTTCG
*
133716 AGGTTTAGGGTTCAAGTTTA
1 AGGTTTAAGG-TCAAGTTTA
*
133736 AGGTTTAAGGTCAGGTTTA
1 AGGTTTAAGGTCAAGTTTA
133755 AG
1 AG
133757 ATTCAGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.27, C:0.05, G:0.32, T:0.37
Consensus pattern (19 bp):
AGGTTTAAGGTCAAGTTTA
Found at i:133952 original size:17 final size:18
Alignment explanation
Indices: 133926--133968 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
133916 ATATTATTTT
133926 TTATTATATATATTTG-AA
1 TTATT-TATATATTTGTAA
*
133944 TTATTTATATGTTTGTAA
1 TTATTTATATATTTGTAA
133962 TT-TTTAT
1 TTATTTAT
133969 TTTTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (18 bp):
TTATTTATATATTTGTAA
Found at i:134017 original size:42 final size:42
Alignment explanation
Indices: 133926--134018 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 42
133916 ATATTATTTT
* *** * *
133926 TTATTATATATATTTGAATTATTTATATGTTTGTAATTTTTA
1 TTATTATATAAATTTGAATTATTTATAAAATTATAATTATTA
* *
133968 TTTTTATATAAATTTGAATTATTTATAAAATTATACTATATTA
1 TTATTATATAAATTTGAATTATTTATAAAATTATAAT-TATTA
134011 -TATTATAT
1 TTATTATAT
134019 TACTTATATA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
42 37 0.90
43 4 0.10
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (42 bp):
TTATTATATAAATTTGAATTATTTATAAAATTATAATTATTA
Found at i:134179 original size:20 final size:17
Alignment explanation
Indices: 134128--134190 Score: 67
Period size: 17 Copynumber: 3.5 Consensus size: 17
134118 TATATATTTG
134128 AATTATTTATATGTT-TAT
1 AATT-TTTATAT-TTATAT
134146 AATTTTTATATTTATAT
1 AATTTTTATATTTATAT
134163 AATTTTTGAATTATTTATA-
1 AATTTTT--A-TATTTATAT
134182 AATTTTTAT
1 AATTTTTAT
134191 TAATTTATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.07
17 18 0.44
18 4 0.10
19 8 0.20
20 8 0.20
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
AATTTTTATATTTATAT
Found at i:134205 original size:43 final size:41
Alignment explanation
Indices: 134108--134207 Score: 114
Period size: 43 Copynumber: 2.4 Consensus size: 41
134098 AATATTAATT
134108 TTTTATATTATAT-ATATTTGAATTATTTATATGTTTATAA
1 TTTTATATTATATAATATTTGAATTATTTATATGTTTATAA
* *
134148 TTTTTATATTTATATAATTTTTGAATTATTTATAAATTTTTATTAA
1 -TTTTATA-TTATATAATATTTGAATTATTTAT--ATGTTTA-TAA
*
134194 -TTTATAGTATATAA
1 TTTTATATTATATAA
134208 CTTATATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
41 7 0.14
42 6 0.12
43 23 0.45
44 6 0.12
45 6 0.12
46 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (41 bp):
TTTTATATTATATAATATTTGAATTATTTATATGTTTATAA
Found at i:134236 original size:186 final size:185
Alignment explanation
Indices: 133922--134255 Score: 487
Period size: 186 Copynumber: 1.8 Consensus size: 185
133912 TTTTATATTA
* *
133922 TTTTTTATTATATATATTTGAATTATTTATATGTTTGTAATTTTTATTTTTATATAAATTTGAAT
1 TTTTTTATTATATATATTTGAATTATTTATATGTTTATAATTTTTATATTTATATAAATTTGAAT
* * *
133987 TATTTATAAAATTATACTATATTATATTATATTACTTATATAAAAATAAAAAAATTTATATATAT
66 TATTTATAAAATTATACTATATTATAGTATATAACTTATATAAAAATAAAAAAATTAATATATAT
*
134052 ATA-TTTAAAAATAAAAATATAGACGATGATTTGTTAGAATCAATAAAATATTAAT
131 A-ACTTCAAAAATAAAAATATAGACGATGATTTGTTAGAATCAATAAAATATTAAT
*
134107 TTTTTATATTATATATATTTGAATTATTTATATGTTTATAATTTTTATATTTATATAATTTTTGA
1 TTTTT-TATTATATATATTTGAATTATTTATATGTTTATAATTTTTATATTTATATAA-ATTTGA
* * * *
134172 ATTATTTATAAATTTTTATTA-ATTTATAGTATATAACTTATAT-AAAAT-TAAAAATTCAATAT
64 ATTATTTATAAAATTATACTATA-TTATAGTATATAACTTATATAAAAATAAAAAAATT-AATAT
*
134234 ATATAACTTCAAAAATACAAAT
127 ATATAACTTCAAAAATAAAAAT
134256 TTTCAAATTA
Statistics
Matches: 132, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
185 13 0.10
186 78 0.59
187 41 0.31
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (185 bp):
TTTTTTATTATATATATTTGAATTATTTATATGTTTATAATTTTTATATTTATATAAATTTGAAT
TATTTATAAAATTATACTATATTATAGTATATAACTTATATAAAAATAAAAAAATTAATATATAT
AACTTCAAAAATAAAAATATAGACGATGATTTGTTAGAATCAATAAAATATTAAT
Found at i:134514 original size:16 final size:17
Alignment explanation
Indices: 134495--134533 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
134485 ATTTTAGATA
* *
134495 TTTTTTGATTCTTTT-T
1 TTTTTTGAATATTTTAT
134511 TTTTTTGAATATTTTAT
1 TTTTTTGAATATTTTAT
134528 TTTTTT
1 TTTTTT
134534 ATAATTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTTTGAATATTTTAT
Found at i:142000 original size:161 final size:162
Alignment explanation
Indices: 141747--142114 Score: 422
Period size: 161 Copynumber: 2.3 Consensus size: 162
141737 ACAATTTACT
* * * ** *
141747 GAAAGAAAGGTTTTAATGCTTACTGTGGTTTGTTGGATTCATCCTTCTTTATAGAAAATAAAGAA
1 GAAAGAAAGATTTTGATGTTTACAATGATTTGTTGGATTCAT-CTTCTTTATAGAAAATAAAGAA
* * * ** * * *
141812 TATGAATAAAATGAATCATTTTAGGGTTTAATGTTTTCTTGGTTTGATTTTGAATTGAATGTAGA
65 TATGAATAAAAGGAATCATTCTAGGGTTTAATATTCGCTTGGTTTGATTTTGAACTGAACGCAGA
* *
141877 TAT-CTCTAGGTAAAGAATAAACATTGTTGAGAA
130 T-TCCTCAAGGTAAAGAATAAACATCGTTGAGAA
* * ** *
141910 GAAATAAAGATTTTGATGTTTACAATGATTTGTTGGATTTAT-TTCTTTATATCAAATAAAGAGT
1 GAAAGAAAGATTTTGATGTTTACAATGATTTGTTGGATTCATCTTCTTTATAGAAAATAAAGAAT
* **
141974 CTGTTTAAAAGGGAA-CATTCTAGGGTTTAATATTCGCTTGGTTTGATTTTGAACTGAACGCAGA
66 ATGAATAAAA-GGAATCATTCTAGGGTTTAATATTCGCTTGGTTTGATTTTGAACTGAACGCAGA
142038 TTCCTCAAGGTAAAGAATAAACATCGTTGAGAA
130 TTCCTCAAGGTAAAGAATAAACATCGTTGAGAA
* * *
142071 GAAAGAAAGATTTTGATG--TCCTAGTGATTTTTTGGATTCATCTT
1 GAAAGAAAGATTTTGATGTTTAC-AATGATTTGTTGGATTCATCTT
142115 TTTTCTATAT
Statistics
Matches: 172, Mismatches: 29, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
159 2 0.01
160 17 0.10
161 116 0.67
162 3 0.02
163 34 0.20
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (162 bp):
GAAAGAAAGATTTTGATGTTTACAATGATTTGTTGGATTCATCTTCTTTATAGAAAATAAAGAAT
ATGAATAAAAGGAATCATTCTAGGGTTTAATATTCGCTTGGTTTGATTTTGAACTGAACGCAGAT
TCCTCAAGGTAAAGAATAAACATCGTTGAGAA
Found at i:144121 original size:22 final size:22
Alignment explanation
Indices: 144093--144137 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
144083 TGGGGCAAAA
144093 CCTTAAAAACCAGAAGTCATAT
1 CCTTAAAAACCAGAAGTCATAT
**
144115 CCTTAAAAACCCTAAGTCATAT
1 CCTTAAAAACCAGAAGTCATAT
144137 C
1 C
144138 TCCCCGCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.24
Consensus pattern (22 bp):
CCTTAAAAACCAGAAGTCATAT
Found at i:152887 original size:12 final size:11
Alignment explanation
Indices: 152860--152893 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
152850 TTGTTATTGC
*
152860 ATTTTTCTGTT
1 ATTTTTCTTTT
152871 ATTTTTCTTTT
1 ATTTTTCTTTT
152882 ATTTTTTCTTTT
1 A-TTTTTCTTTT
152894 GATATGTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (11 bp):
ATTTTTCTTTT
Found at i:156266 original size:22 final size:22
Alignment explanation
Indices: 156215--156261 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
156205 TTAAAGGACC
* *
156215 AAATAATAAAATTAACCCAATTT
1 AAATAAT-TAATTAACCCAAATT
156238 AAATAATTAATTAAACCCAAATT
1 AAATAATTAATT-AACCCAAATT
156261 A
1 A
156262 TTAATGAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATAATTAATTAACCCAAATT
Found at i:172644 original size:21 final size:21
Alignment explanation
Indices: 172603--172650 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
172593 CTAGTTCTAT
**
172603 CGATACAAGTATGGTTTCTAC
1 CGATACAAGTATGGTAACTAC
172624 CGATACAAGTCAT-GTAACTAC
1 CGATACAAGT-ATGGTAACTAC
*
172645 GGATAC
1 CGATAC
172651 CAAAAACTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (21 bp):
CGATACAAGTATGGTAACTAC
Found at i:188817 original size:21 final size:21
Alignment explanation
Indices: 188787--188826 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
188777 GTACACAATT
*
188787 TTGATGTGGATGCATTTGATC
1 TTGATATGGATGCATTTGATC
188808 TTGATATGGATGCATTTGA
1 TTGATATGGATGCATTTGA
188827 GTATTCTGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (21 bp):
TTGATATGGATGCATTTGATC
Found at i:192710 original size:33 final size:32
Alignment explanation
Indices: 192663--192724 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
192653 ACCTTTATGT
* *
192663 CTTAAATTGGAAATGATTTTTATATAAGGGAAG
1 CTTAAATTGAAAATGACTTTTAT-TAAGGGAAG
192696 CTTAAATTGAAAATGACTTTTATTAAGGG
1 CTTAAATTGAAAATGACTTTTATTAAGGG
192725 GGAGAAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 6 0.22
33 21 0.78
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (32 bp):
CTTAAATTGAAAATGACTTTTATTAAGGGAAG
Found at i:192913 original size:20 final size:20
Alignment explanation
Indices: 192876--192929 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
192866 CTCCAGTGAG
* *
192876 ACTTCTACTGGTAGAACTTC
1 ACTTCTACTGATACAACTTC
* *
192896 ACTTCTATTGATACAACTTT
1 ACTTCTACTGATACAACTTC
* *
192916 AGTTCTACCGATAC
1 ACTTCTACTGATAC
192930 CTTGAAGACT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (20 bp):
ACTTCTACTGATACAACTTC
Found at i:199503 original size:17 final size:17
Alignment explanation
Indices: 199481--199513 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
199471 ACTAATATTA
199481 AAATGCAATGACAATAG
1 AAATGCAATGACAATAG
*
199498 AAATGCATTGACAATA
1 AAATGCAATGACAATA
199514 TGCACAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATAG
Found at i:199920 original size:15 final size:16
Alignment explanation
Indices: 199894--199923 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
199884 TGGGTACAGT
199894 ATTATGTTCTCAGCAG
1 ATTATGTTCTCAGCAG
199910 ATTAT-TTCTCAGCA
1 ATTATGTTCTCAGCA
199924 TCTTCTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (16 bp):
ATTATGTTCTCAGCAG
Found at i:202664 original size:26 final size:26
Alignment explanation
Indices: 202611--202664 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
202601 CACCCAGGAA
**
202611 TGTCACTGCATGAACATGTCCAGTAT
1 TGTCACTGCATGAACATGTCCAAAAT
*
202637 TGTCGCTGCATGAACATGTCCAAAAT
1 TGTCACTGCATGAACATGTCCAAAAT
202663 TG
1 TG
202665 CTCCCAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (26 bp):
TGTCACTGCATGAACATGTCCAAAAT
Found at i:205691 original size:17 final size:17
Alignment explanation
Indices: 205669--205711 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
205659 CTGTAGTATA
*
205669 ATTGTCCCTACATTTTT
1 ATTGTCACTACATTTTT
205686 ATTGTCACTACATTTTT
1 ATTGTCACTACATTTTT
205703 ATTGTCACT
1 ATTGTCACT
205712 GCATCTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.51
Consensus pattern (17 bp):
ATTGTCACTACATTTTT
Found at i:206866 original size:37 final size:38
Alignment explanation
Indices: 206796--206872 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 38
206786 TGAGCAGTTC
* *
206796 CAGATTGCACCAAAAACTGTCACCGCAGGAATATT-TT
1 CAGAATGCACCAAAAACTGTCACCGCAGAAATATTCTT
* * * *
206833 CAGAATGCACCGAAGACTGTCACTGCATAAATATTCTT
1 CAGAATGCACCAAAAACTGTCACCGCAGAAATATTCTT
206871 CA
1 CA
206873 AATTGCATCT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
37 29 0.88
38 4 0.12
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (38 bp):
CAGAATGCACCAAAAACTGTCACCGCAGAAATATTCTT
Found at i:206965 original size:26 final size:26
Alignment explanation
Indices: 206929--206978 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
206919 TAAGAATGTA
*
206929 GCTGTATGAACATGTCCAAAATTGTC
1 GCTGCATGAACATGTCCAAAATTGTC
*
206955 GCTGCATGAACGTGTCCAAAATTG
1 GCTGCATGAACATGTCCAAAATTG
206979 CACCCAGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (26 bp):
GCTGCATGAACATGTCCAAAATTGTC
Found at i:207785 original size:16 final size:16
Alignment explanation
Indices: 207764--207794 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
207754 TTGTGGATCC
207764 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
207780 CATTTTATCTTTATT
1 CATTTTACCTTTATT
207795 TTCACATTAT
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:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:218425 original size:52 final size:53
Alignment explanation
Indices: 218333--218438 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
218323 GGTATAGTTA
218333 TGCAAAAAAGATTGAAACATGAAAATTTTAAAAATTTGTGCAAATGTTTGCCT
1 TGCAAAAAAGATTGAAACATGAAAATTTTAAAAATTTGTGCAAATGTTTGCCT
218386 TGCAAAAAAGATTGAAACATGAAAATTTT-AAAATTTGTGCAAATGTTTGCCT
1 TGCAAAAAAGATTGAAACATGAAAATTTTAAAAATTTGTGCAAATGTTTGCCT
218438 T
1 T
218439 ACCCCTTTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 24 0.45
53 29 0.55
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (53 bp):
TGCAAAAAAGATTGAAACATGAAAATTTTAAAAATTTGTGCAAATGTTTGCCT
Found at i:218479 original size:20 final size:20
Alignment explanation
Indices: 218454--218499 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
218444 TTTTAAAAAG
218454 AAACAATGTCCTCATTGTGA
1 AAACAATGTCCTCATTGTGA
218474 AAACAATGTCCTCATTGTGA
1 AAACAATGTCCTCATTGTGA
218494 AAACAA
1 AAACAA
218500 AGTAATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (20 bp):
AAACAATGTCCTCATTGTGA
Found at i:227422 original size:28 final size:28
Alignment explanation
Indices: 227390--227479 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 28
227380 ACCACATTAT
227390 TTAACTTAATTCATTATTAACATGCTTA
1 TTAACTTAATTCATTATTAACATGCTTA
* **
227418 TTAACATTCGAA--AAACATT--CTATGCTTA
1 TTAAC-TT--AATTCATTATTAAC-ATGCTTA
*
227446 TTTAACTTAATTCATTATTAACATGTTTA
1 -TTAACTTAATTCATTATTAACATGCTTA
227475 TTAAC
1 TTAAC
227480 ATTTGGAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 18
0.65 0.10 0.25
Matches are distributed among these distances:
26 2 0.04
27 1 0.02
28 23 0.50
29 17 0.37
30 1 0.02
31 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.44
Consensus pattern (28 bp):
TTAACTTAATTCATTATTAACATGCTTA
Found at i:227454 original size:57 final size:57
Alignment explanation
Indices: 227386--227494 Score: 191
Period size: 57 Copynumber: 1.9 Consensus size: 57
227376 GACAACCACA
227386 TTATTTAACTTAATTCATTATTAACATGCTTATTAACATTCGAAAAACATTCTATGC
1 TTATTTAACTTAATTCATTATTAACATGCTTATTAACATTCGAAAAACATTCTATGC
* * *
227443 TTATTTAACTTAATTCATTATTAACATGTTTATTAACATTTGGAAAACATTC
1 TTATTTAACTTAATTCATTATTAACATGCTTATTAACATTCGAAAAACATTC
227495 CATGACAAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.44
Consensus pattern (57 bp):
TTATTTAACTTAATTCATTATTAACATGCTTATTAACATTCGAAAAACATTCTATGC
Found at i:233055 original size:15 final size:15
Alignment explanation
Indices: 233035--233063 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
233025 GTATTGTTGC
233035 TTGATAACACGGTGA
1 TTGATAACACGGTGA
233050 TTGATAACACGGTG
1 TTGATAACACGGTG
233064 TGTGAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGATAACACGGTGA
Found at i:241666 original size:20 final size:20
Alignment explanation
Indices: 241630--241667 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
241620 CACATATAAT
*
241630 GTGAATCATTTGTTAAACTC
1 GTGAATCAATTGTTAAACTC
241650 GTGAATCTAATTG-TAAAC
1 GTGAATC-AATTGTTAAAC
241668 ACGTATGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (20 bp):
GTGAATCAATTGTTAAACTC
Found at i:242533 original size:4 final size:4
Alignment explanation
Indices: 242519--242559 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
242509 AGTTAATCTA
* * *
242519 ACAT TCAT ACAT ACAA ACAT ACAT ACAT ACAT ACAT GCAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
242560 TATAAATAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:245438 original size:13 final size:13
Alignment explanation
Indices: 245408--245432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
245398 ATAAAACTAT
245408 TCAAATTTAAATA
1 TCAAATTTAAATA
245421 TCAAATTTAAAT
1 TCAAATTTAAAT
245433 GACAAAATCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TCAAATTTAAATA
Found at i:249373 original size:13 final size:13
Alignment explanation
Indices: 249357--249390 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
249347 AAAAAAAACT
*
249357 TCAACAAAATCAA
1 TCAACAAAACCAA
249370 TCAACAAAACCAA
1 TCAACAAAACCAA
*
249383 CCAACAAA
1 TCAACAAA
249391 CCGTGCACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.62, C:0.29, G:0.00, T:0.09
Consensus pattern (13 bp):
TCAACAAAACCAA
Found at i:258901 original size:102 final size:102
Alignment explanation
Indices: 258771--258974 Score: 399
Period size: 102 Copynumber: 2.0 Consensus size: 102
258761 ATCCTGAGGG
*
258771 TTCTAGAAACTTATTACCCAACTCTTTTATCTTTTTCGGTAAGGAACTTGAATAGGGTTTTGGTA
1 TTCTAGAAACTTATTACCCAACTCTTTTATCTTCTTCGGTAAGGAACTTGAATAGGGTTTTGGTA
258836 ACCCTCGTTTACCAAACTCATGATGTCTCACCTCACT
66 ACCCTCGTTTACCAAACTCATGATGTCTCACCTCACT
258873 TTCTAGAAACTTATTACCCAACTCTTTTATCTTCTTCGGTAAGGAACTTGAATAGGGTTTTGGTA
1 TTCTAGAAACTTATTACCCAACTCTTTTATCTTCTTCGGTAAGGAACTTGAATAGGGTTTTGGTA
258938 ACCCTCGTTTACCAAACTCATGATGTCTCACCTCACT
66 ACCCTCGTTTACCAAACTCATGATGTCTCACCTCACT
258975 CTGTCTTCTA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (102 bp):
TTCTAGAAACTTATTACCCAACTCTTTTATCTTCTTCGGTAAGGAACTTGAATAGGGTTTTGGTA
ACCCTCGTTTACCAAACTCATGATGTCTCACCTCACT
Found at i:261246 original size:40 final size:41
Alignment explanation
Indices: 261192--261307 Score: 135
Period size: 43 Copynumber: 2.8 Consensus size: 41
261182 GCAAACCATC
* * *
261192 CACCGACTCATAGCCTACCAAGCCGTAGCTTGA-CTTGTAA
1 CACCGGCTCGTAGCCTACTAAGCCGTAGCTTGATCTTGTAA
* * * *
261232 CACCGGCTCGTAGCCTGCTAAGCTGTAGCTTGAATTTTTTTAA
1 CACCGGCTCGTAGCCTACTAAGCCGTAGCTTG-A-TCTTGTAA
*
261275 CACCGGCTCGTAGCCTACTAAGCCGTAACTTGA
1 CACCGGCTCGTAGCCTACTAAGCCGTAGCTTGA
261308 ATTTGTTCAA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
40 27 0.43
41 1 0.02
42 1 0.02
43 34 0.54
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (41 bp):
CACCGGCTCGTAGCCTACTAAGCCGTAGCTTGATCTTGTAA
Found at i:261286 original size:43 final size:43
Alignment explanation
Indices: 261229--261311 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
261219 GCTTGACTTG
* * *
261229 TAACACCGGCTCGTAGCCTGCTAAGCTGTAGCTTGAATTTTTT
1 TAACACCGGCTCGTAGCCTACTAAGCCGTAACTTGAATTTTTT
261272 TAACACCGGCTCGTAGCCTACTAAGCCGTAACTTGAATTT
1 TAACACCGGCTCGTAGCCTACTAAGCCGTAACTTGAATTT
261312 GTTCAATCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.31
Consensus pattern (43 bp):
TAACACCGGCTCGTAGCCTACTAAGCCGTAACTTGAATTTTTT
Found at i:262640 original size:23 final size:23
Alignment explanation
Indices: 262614--262661 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
262604 TCAAACAAAT
*
262614 TAGAATTGCTCCAGGACAAGAAG
1 TAGAATTGCTCCAGGACAAAAAG
262637 TAGAATTGCTCCAGGACAAAAAG
1 TAGAATTGCTCCAGGACAAAAAG
262660 TA
1 TA
262662 TTGATACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.19
Consensus pattern (23 bp):
TAGAATTGCTCCAGGACAAAAAG
Found at i:262811 original size:21 final size:22
Alignment explanation
Indices: 262764--262829 Score: 116
Period size: 21 Copynumber: 3.0 Consensus size: 22
262754 TCAAACAATG
*
262764 ACAAAAAGTATCTATACCTTTT
1 ACAAAAAGTATCGATACCTTTT
262786 ACAAAAAGTATCGATACCTTTT
1 ACAAAAAGTATCGATACCTTTT
262808 -CAAAAAGTATCGATACCTTTT
1 ACAAAAAGTATCGATACCTTTT
262829 A
1 A
262830 TAAGGTATCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
21 21 0.50
22 21 0.50
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (22 bp):
ACAAAAAGTATCGATACCTTTT
Found at i:265971 original size:22 final size:21
Alignment explanation
Indices: 265947--266030 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
265937 AGACAATGAA
265947 AAAAAGTATAGATACCTTTTC
1 AAAAAGTATAGATACCTTTTC
** *
265968 AAAAAGTATCTATACATTTTAC
1 AAAAAGTATAGATACCTTTT-C
*
265990 AAAATGTATCA-ATACCTTTTC
1 AAAAAGTAT-AGATACCTTTTC
*
266011 AAAAAGTATCGATACCTTTT
1 AAAAAGTATAGATACCTTTT
266031 ATCAGGTATC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
21 35 0.67
22 17 0.33
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (21 bp):
AAAAAGTATAGATACCTTTTC
Found at i:268168 original size:23 final size:21
Alignment explanation
Indices: 268116--268168 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
268106 CATTTATCAT
*
268116 TAAATAATTATAAATTATAATA
1 TAAAT-ATTATAAAATATAATA
**
268138 TATTTATTATTAAAATATTAATA
1 TAAATATTA-TAAAATA-TAATA
268161 TAAATATT
1 TAAATATT
268169 TTTCAATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 4 0.17
22 9 0.38
23 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAATATTATAAAATATAATA
Found at i:271704 original size:19 final size:20
Alignment explanation
Indices: 271680--271717 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
271670 AAGGAAGTGT
271680 CTGATATAGAC-TTATGTGC
1 CTGATATAGACTTTATGTGC
271699 CTGATATAGACTTTATGTG
1 CTGATATAGACTTTATGTG
271718 GGAAGGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.39
Consensus pattern (20 bp):
CTGATATAGACTTTATGTGC
Found at i:272385 original size:30 final size:30
Alignment explanation
Indices: 272311--272386 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
272301 CCATCCTATT
* *
272311 AACCACTTGAAAATATGAGGTGTGTCGTAC
1 AACCACTTGAAAATGTGAGGTGTGTCCTAC
272341 AACCACTTGAAAATGTGAGGTGTGTCCTAC
1 AACCACTTGAAAATGTGAGGTGTGTCCTAC
*
272371 AACCACTGGAAAATGT
1 AACCACTTGAAAATGT
272387 AAGGGGTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (30 bp):
AACCACTTGAAAATGTGAGGTGTGTCCTAC
Found at i:274737 original size:21 final size:21
Alignment explanation
Indices: 274694--274740 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
274684 CTATAAATAG
* *
274694 TTCTATCGAAACAAGTGAAGC
1 TTCTATCGAAACAAATCAAGC
*
274715 TTCTATCGAAACAAATCATGC
1 TTCTATCGAAACAAATCAAGC
274736 TTCTA
1 TTCTA
274741 CCAGTACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (21 bp):
TTCTATCGAAACAAATCAAGC
Found at i:275839 original size:195 final size:195
Alignment explanation
Indices: 275583--275946 Score: 482
Period size: 195 Copynumber: 1.9 Consensus size: 195
275573 GTAAACTGTC
** * *
275583 CCCTAACGATGCTGCTCACACGTGCTGTCGAGAATATGCATTCAAGCATAAATCCCAACCATTGT
1 CCCTAACGATGCTGCTCACACAAGCTGTCGAGAATATGCATTCAAGCAAAAATCCCAACCATCGT
* * * * * *
275648 AGGGCCTATCATCCATT-TAGGATT-TCATATCTCTTTTTTCGACTCATAATGCTGCTCACACGA
66 AAGGCCTATAATCCATTCTAGGATTCT-ATA-CTCATTTCTCGACTCACAATGCTACTCACACGA
* *
275711 GCTGTCGAGAACTCGTAACACATGCGGTACCTCAGCCATCGATACGATATTTGTGCATATAACTA
129 GCTGTCGAGAACTCATAACACATGCGATACCTCAGCCATCGATACGATATTTGTGCATATAACTA
275776 TT
194 TT
* * *
275778 CCCTAACGATGCTGCTCACACAAGTTGTCGAGAATATGCACTT-ATGCAAAAATCTCAACCATCG
1 CCCTAACGATGCTGCTCACACAAGCTGTCGAGAATATGCA-TTCAAGCAAAAATCCCAACCATCG
* * * * *
275842 TAAGGCCTGTAATCCGTTCTTGGATTCTTTACTCATTTCTCGACTCACGATGCTACTCACACGAG
65 TAAGGCCTATAATCCATTCTAGGATTCTATACTCATTTCTCGACTCACAATGCTACTCACACGAG
* *
275907 TTGTCGAGGACTCATAACACATGCGATACCTCAGCCATCG
130 CTGTCGAGAACTCATAACACATGCGATACCTCAGCCATCG
275947 TGTCGGTTTT
Statistics
Matches: 144, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
195 133 0.92
196 10 0.07
197 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (195 bp):
CCCTAACGATGCTGCTCACACAAGCTGTCGAGAATATGCATTCAAGCAAAAATCCCAACCATCGT
AAGGCCTATAATCCATTCTAGGATTCTATACTCATTTCTCGACTCACAATGCTACTCACACGAGC
TGTCGAGAACTCATAACACATGCGATACCTCAGCCATCGATACGATATTTGTGCATATAACTATT
Found at i:281144 original size:90 final size:90
Alignment explanation
Indices: 280968--281160 Score: 217
Period size: 90 Copynumber: 2.1 Consensus size: 90
280958 TTAATATAAC
* * * ** *
280968 ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGAAACTTAAATTTTTTTTGGTCTAATTTGG
1 ATTTGGTACCTAAACCTGACACTTTTTCCTAAGTTGAAACTTAAACTTTTTGGGGTCCAATTTGG
*
281033 TACTCAAGCTTGACACATTTTCCTA
66 TACTCAAGCTTCACACATTTTCCTA
* ** **
281058 ATTTAGTACCTAAACCTGACACTTTTTTTTAAGTTGGTACTTAAACTTTTTGGGGTCCAATTTGG
1 ATTTGGTACCTAAACCTGACACTTTTTCCTAAGTTGAAACTTAAACTTTTTGGGGTCCAATTTGG
* * * *
281123 TCCCTGAA-CTTCACTCTTTTTCCTA
66 T-ACTCAAGCTTCACACATTTTCCTA
*
281148 ATTTGGAACCTAA
1 ATTTGGTACCTAA
281161 TTAATATTAT
Statistics
Matches: 84, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
90 80 0.95
91 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.43
Consensus pattern (90 bp):
ATTTGGTACCTAAACCTGACACTTTTTCCTAAGTTGAAACTTAAACTTTTTGGGGTCCAATTTGG
TACTCAAGCTTCACACATTTTCCTA
Found at i:281365 original size:30 final size:28
Alignment explanation
Indices: 281324--281468 Score: 107
Period size: 28 Copynumber: 5.0 Consensus size: 28
281314 GAATCTAGAA
*
281324 AAAGCTTAGGTACCAAATTAGAAAAAAT
1 AAAGTTTAGGTACCAAATTAGAAAAAAT
*
281352 GCCAAGTTTAGGTACCAAATT-GAATCAAAA-
1 --AAAGTTTAGGTACCAAATTAGAA--AAAAT
*
281382 AAAGTTTAGATACCAAATTAGAAAAAATT
1 AAAGTTTAGGTACCAAATTAGAAAAAA-T
* * * **
281411 ATCAAGTTCAGGTATCAAATTGGGTCAAAA-
1 A--AAGTTTAGGTACCAAATT-AGAAAAAAT
*
281441 AAAGTTTTAGGTACCAAATTAAAAAAAA
1 AAAG-TTTAGGTACCAAATTAGAAAAAA
281469 GTATCAAGTT
Statistics
Matches: 90, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
27 4 0.04
28 24 0.27
29 20 0.22
30 18 0.20
31 19 0.21
32 5 0.06
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (28 bp):
AAAGTTTAGGTACCAAATTAGAAAAAAT
Found at i:281474 original size:60 final size:58
Alignment explanation
Indices: 281302--281490 Score: 234
Period size: 59 Copynumber: 3.2 Consensus size: 58
281292 TGATACATTT
* * * ** *
281302 AGGTACCAAGTTGAATCTAGAAAAAGCTTAGGTACCAAATTAGAAAAAATGCCAAGTTT
1 AGGTACCAAATTGAATC-AAAAAAAGTTTAGGTACCAAATTAGAAAAAATATCAAGTTC
*
281361 AGGTACCAAATTGAATCAAAAAAAGTTTAGATACCAAATTAGAAAAAATTATCAAGTTC
1 AGGTACCAAATTGAATCAAAAAAAGTTTAGGTACCAAATTAGAAAAAA-TATCAAGTTC
* ** *
281420 AGGTATCAAATTGGGTCAAAAAAAGTTTTAGGTACCAAATTAAAAAAAAGTATCAAGTTC
1 AGGTACCAAATTGAATCAAAAAAAG-TTTAGGTACCAAATTAGAAAAAA-TATCAAGTTC
*
281480 AAGTACCAAAT
1 AGGTACCAAAT
281491 GTTATATTAA
Statistics
Matches: 113, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
58 28 0.25
59 45 0.40
60 40 0.35
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (58 bp):
AGGTACCAAATTGAATCAAAAAAAGTTTAGGTACCAAATTAGAAAAAATATCAAGTTC
Found at i:286205 original size:19 final size:19
Alignment explanation
Indices: 286181--286257 Score: 79
Period size: 18 Copynumber: 4.2 Consensus size: 19
286171 TGTTATCCAA
286181 TATTGCTCTTACGAGCCAG
1 TATTGCTCTTACGAGCCAG
*
286200 TATTGCTCTATA--AGCTAG
1 TATTGCTCT-TACGAGCCAG
* * *
286218 AATTGCTC-AACGAACCAG
1 TATTGCTCTTACGAGCCAG
*
286236 TATTACTCTTACGAGCCAG
1 TATTGCTCTTACGAGCCAG
286255 TAT
1 TAT
286258 ACTATTCCCT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
16 1 0.02
18 22 0.49
19 20 0.44
20 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (19 bp):
TATTGCTCTTACGAGCCAG
Found at i:291568 original size:12 final size:12
Alignment explanation
Indices: 291551--291603 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
291541 CAAGTTCAGT
291551 TTCTTCCTTCTC
1 TTCTTCCTTCTC
291563 TTCTTCCTTTCCTTC
1 TTCTTCC-TT-C-TC
* *
291578 TTCTTCTTTTTC
1 TTCTTCCTTCTC
*
291590 TTCATCCTTCTC
1 TTCTTCCTTCTC
291602 TT
1 TT
291604 GATCACCTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
12 20 0.61
13 2 0.06
14 3 0.09
15 8 0.24
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTTCCTTCTC
Done.