Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005615.1 Hibiscus syriacus cultivar Beakdansim tig00013061_pilon, 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: 113915
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:204 original size:90 final size:90
Alignment explanation
Indices: 51--231 Score: 326
Period size: 90 Copynumber: 2.0 Consensus size: 90
41 CAGTTATTAT
*
51 TGACAAACTGTTCAAAATCACCATGAAGAGACCACCTAGAAAGATACTTGAAGATTTTAGCTTTT
1 TGACAAACTGTTCAAAATCACCATGAAGAGACCAACTAGAAAGATACTTGAAGATTTTAGCTTTT
116 CACTTGGTAGATGTTACGGAAAGGG
66 CACTTGGTAGATGTTACGGAAAGGG
* *
141 TGACAAACTGTTCAAAATCACCATGAAGAGACCAATTAGAAAGATTCTTGAAGATTTTAGCTTTT
1 TGACAAACTGTTCAAAATCACCATGAAGAGACCAACTAGAAAGATACTTGAAGATTTTAGCTTTT
*
206 CACTTGGTAGATGTTACGGAAGGGG
66 CACTTGGTAGATGTTACGGAAAGGG
231 T
1 T
232 AAAGAATCAA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (90 bp):
TGACAAACTGTTCAAAATCACCATGAAGAGACCAACTAGAAAGATACTTGAAGATTTTAGCTTTT
CACTTGGTAGATGTTACGGAAAGGG
Found at i:1878 original size:53 final size:54
Alignment explanation
Indices: 1835--2365 Score: 671
Period size: 53 Copynumber: 10.3 Consensus size: 54
1825 ATTATGTGGG
** * *
1835 TTGCACACAGAGTGCCG-AATGGTTATTCATCAACATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* *
1888 TTGTACACTTAGTGCCGAAACGGTTATTCATC-ACATATGATGAATTCTGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
1941 TTGCACACTTAGTGCCGAAACGGTTATTCAT---CA-AT-A-GAATTCCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
1989 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* * *
2043 TTGCACAC-TAGTGCCAAAATGGTTATTCATCAACATATGATGAATTCCGTTCT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* *
2096 TTGCACACTTA--GCCAAAACGGTTATTCATCAAC--ACGATGAATTCCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* ** *
2146 TTGCACACTTAGTTCCGAAACGGTTATTCATCAACATA-GACAAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
*
2199 TTGCACACTTAGTGCCG-AATGGTTATTCATCAACATATGATGAATTCCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* * * * *
2252 TTGCACACTTAATGTCGAAATGGTTATTCAT--A-ATATGAT-AATTCCATATT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* *
2302 TTG------TAGTGCCAAAACGGTTATTCATCACCATATGATGAATTCCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
*
2350 TTACACACTTAGTGCC
1 TTGCACACTTAGTGCC
2366 TATTTGGTAA
Statistics
Matches: 418, Mismatches: 36, Indels: 47
0.83 0.07 0.09
Matches are distributed among these distances:
44 18 0.04
47 7 0.02
48 53 0.13
49 1 0.00
50 40 0.10
51 11 0.03
52 63 0.15
53 169 0.40
54 56 0.13
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (54 bp):
TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
Found at i:2295 original size:156 final size:157
Alignment explanation
Indices: 1835--2365 Score: 705
Period size: 156 Copynumber: 3.4 Consensus size: 157
1825 ATTATGTGGG
** * * *
1835 TTGCACACAGAGTGCCG-AATGGTTATTCATCAACATATGATGAATTTCGTACTTTGTACACTTA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
* * *
1899 GTGCCGAAACGGTTATTCATC-ACATATGATGAATTCTGTACTTTGCACACTTAGTGCCGAAACG
66 GTGCCG-AATGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAATGCCGAAACG
1963 GTTATTCATCAATAG--AATTCCGTACT
130 GTTATTCATCAATAGATAATTCCGTACT
1989 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACAC-TA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
* * *
2053 GTGCCAAAATGGTTATTCATCAACATATGATGAATTCCGTTCTTTGCACACTT-A-GCCAAAACG
66 GTGCC-GAATGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAATGCCGAAACG
*
2116 GTTATTCATCAACACGATGAATTCCGTACT
130 GTTATTCATCAATA-GAT-AATTCCGTACT
* ** *
2146 TTGCACACTTAGTTCCGAAACGGTTATTCATCAACATA-GACAAATTTCGTACTTTGCACACTTA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
* *
2210 GTGCCGAATGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAATGTCGAAATGG
66 GTGCCGAATGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAATGCCGAAACGG
* *
2275 TTATTCAT-AATATGATAATTCCATATT
131 TTATTCATCAATA-GATAATTCCGTACT
* * *
2302 TTG------TAGTGCCAAAACGGTTATTCATCACCATATGATGAATTCCGTACTTTACACACTTA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
2361 GTGCC
66 GTGCC
2366 TATTTGGTAA
Statistics
Matches: 334, Mismatches: 32, Indels: 25
0.85 0.08 0.06
Matches are distributed among these distances:
150 26 0.08
151 27 0.08
153 21 0.06
154 36 0.11
155 70 0.21
156 77 0.23
157 62 0.19
158 15 0.04
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (157 bp):
TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
GTGCCGAATGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAATGCCGAAACGG
TTATTCATCAATAGATAATTCCGTACT
Found at i:6899 original size:7 final size:8
Alignment explanation
Indices: 6880--6907 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
6870 AACATATTTT
6880 TTTTTTAA
1 TTTTTTAA
6888 TTTTTTAA
1 TTTTTTAA
6896 TTTTTTAA
1 TTTTTTAA
6904 TTTT
1 TTTT
6908 ATTACAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTAA
Found at i:7302 original size:22 final size:22
Alignment explanation
Indices: 7272--7313 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
7262 TTTTTATTAC
7272 ATATATTTAA-TAAATTATATAT
1 ATATATTTAACTAAA-TATATAT
*
7294 ATATTTTTAACTAAATATAT
1 ATATATTTAACTAAATATAT
7314 TATTTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATATTTAACTAAATATATAT
Found at i:7311 original size:18 final size:17
Alignment explanation
Indices: 7288--7329 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 17
7278 TTAATAAATT
7288 ATATATATATTTTTAACTAA
1 ATATAT-TA-TTTTAA-TAA
7308 ATATATTATTTTAATAA
1 ATATATTATTTTAATAA
7325 ATATA
1 ATATA
7330 AATGTTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 6 0.27
19 2 0.09
20 6 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATTATTTTAATAA
Found at i:7378 original size:17 final size:17
Alignment explanation
Indices: 7337--7391 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
7327 ATAAATGTTC
7337 ATTTTTTA-TT-TTATGT
1 ATTTTTTATTTATTAT-T
*
7353 ATCTATTTATTTATTATT
1 AT-TTTTTATTTATTATT
7371 ATTTTTTATTTTATT-TT
1 ATTTTTTA-TTTATTATT
7388 ATTT
1 ATTT
7392 ACTTATCTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 2 0.06
17 16 0.48
18 11 0.33
19 4 0.12
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (17 bp):
ATTTTTTATTTATTATT
Found at i:9640 original size:48 final size:48
Alignment explanation
Indices: 9575--9670 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
9565 GTATGAAATG
* * *
9575 ATGAACGACTTTCTTTAAATATCCCTCATAAAAATAGGAAATATGTAT
1 ATGAACGACTTTATTTAAATATCCCTCATAAAAAGAGAAAATATGTAT
9623 ATGAACGACTTTATTTAAATATCCCTCATAAAAAGAGAAAATATGTAT
1 ATGAACGACTTTATTTAAATATCCCTCATAAAAAGAGAAAATATGTAT
9671 CCCTTGTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (48 bp):
ATGAACGACTTTATTTAAATATCCCTCATAAAAAGAGAAAATATGTAT
Found at i:9922 original size:18 final size:17
Alignment explanation
Indices: 9899--9978 Score: 85
Period size: 17 Copynumber: 4.6 Consensus size: 17
9889 AAGTCAACAC
9899 AAAAAAGAGAAAAGAAAG
1 AAAAAAGA-AAAAGAAAG
9917 AAAAAAAGAAAAAGAAAG
1 -AAAAAAGAAAAAGAAAG
9935 AAAAACA-AAAAAGCAAA-
1 AAAAA-AGAAAAAG-AAAG
9952 AAAAAAGAATAAAG-AAG
1 AAAAAAGAA-AAAGAAAG
*
9969 AAAGAAGAAA
1 AAAAAAGAAA
9979 GAAAACATAT
Statistics
Matches: 55, Mismatches: 1, Indels: 13
0.80 0.01 0.19
Matches are distributed among these distances:
16 4 0.07
17 26 0.47
18 17 0.31
19 8 0.15
ACGTcount: A:0.80, C:0.03, G:0.16, T:0.01
Consensus pattern (17 bp):
AAAAAAGAAAAAGAAAG
Found at i:9926 original size:17 final size:17
Alignment explanation
Indices: 9899--9960 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 17
9889 AAGTCAACAC
9899 AAAAAAGAGAAAAGAAAG
1 AAAAAA-AGAAAAGAAAG
9917 AAAAAAAGAAAAAGAAAG
1 AAAAAAAG-AAAAGAAAG
*
9935 AAAAACAA-AAAAGCAA-
1 AAAAA-AAGAAAAGAAAG
9951 AAAAAAAGAA
1 AAAAAAAGAA
9961 TAAAGAAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
15 2 0.05
16 7 0.17
17 9 0.22
18 20 0.50
19 2 0.05
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAGAAAG
Found at i:9952 original size:13 final size:12
Alignment explanation
Indices: 9908--9957 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
9898 CAAAAAAGAG
*
9908 AAAAGAAAGAAA
1 AAAAGAAAAAAA
9920 AAAAG--AAAAA
1 AAAAGAAAAAAA
*
9930 GAAAGAAAAACAA
1 AAAAGAAAAA-AA
9943 AAAAGCAAAAAAA
1 AAAAG-AAAAAAA
9956 AA
1 AA
9958 GAATAAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.26
12 8 0.26
13 10 0.32
14 5 0.16
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:9959 original size:42 final size:45
Alignment explanation
Indices: 9897--9983 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 45
9887 TCAAGTCAAC
*
9897 ACAAAAAAGAGAAAAGAAAGAA-AAA-AAGAAA-AAGAAAGAAAA
1 ACAAAAAAGAGAAAAAAAAGAATAAAGAAGAAAGAAGAAAGAAAA
9939 ACAAAAAAGCA-AAAAAAAAGAATAAAGAAGAAAGAAGAAAGAAAA
1 ACAAAAAAG-AGAAAAAAAAGAATAAAGAAGAAAGAAGAAAGAAAA
9984 CATATCAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
42 19 0.47
43 4 0.10
44 6 0.15
45 11 0.28
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.01
Consensus pattern (45 bp):
ACAAAAAAGAGAAAAAAAAGAATAAAGAAGAAAGAAGAAAGAAAA
Found at i:9972 original size:14 final size:14
Alignment explanation
Indices: 9910--9981 Score: 59
Period size: 12 Copynumber: 5.6 Consensus size: 14
9900 AAAAAGAGAA
9910 AAGAAAGAA-AAA-
1 AAGAAAGAAGAAAG
9922 AAGAAA-AAGAAAG
1 AAGAAAGAAGAAAG
* *
9935 AA-AAACAAAAAAG
1 AAGAAAGAAGAAAG
*
9948 CA-AAA-AA-AAAG
1 AAGAAAGAAGAAAG
*
9959 AATAAAGAAGAAAG
1 AAGAAAGAAGAAAG
9973 AAGAAAGAA
1 AAGAAAGAA
9982 AACATATCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
11 7 0.14
12 17 0.34
13 14 0.28
14 12 0.24
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (14 bp):
AAGAAAGAAGAAAG
Found at i:10971 original size:25 final size:25
Alignment explanation
Indices: 10897--10973 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
10887 AAAAAAAAAC
* * *
10897 TTCATCAAACATTTTTCAAGATTAT
1 TTCATAAAACATTTTTCAAAATTCT
* *
10922 TTCATTAAACATTTTTCAAATTTCT
1 TTCATAAAACATTTTTCAAAATTCT
10947 TTCATAAAACA-TTTTCAAAACTTCT
1 TTCATAAAACATTTTTCAAAA-TTCT
10972 TT
1 TT
10974 ATCGAACTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 8 0.18
25 37 0.82
ACGTcount: A:0.35, C:0.17, G:0.01, T:0.47
Consensus pattern (25 bp):
TTCATAAAACATTTTTCAAAATTCT
Found at i:13118 original size:18 final size:18
Alignment explanation
Indices: 13095--13130 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
13085 AAACTCGGTC
13095 CAGGCCC-AGACAACCCAG
1 CAGGCCCAAGA-AACCCAG
13113 CAGGCCCAAGAAACCCAG
1 CAGGCCCAAGAAACCCAG
13131 AATTCAGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.36, C:0.42, G:0.22, T:0.00
Consensus pattern (18 bp):
CAGGCCCAAGAAACCCAG
Found at i:14438 original size:22 final size:20
Alignment explanation
Indices: 14399--14458 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
14389 CTTTTATAAT
*
14399 TTTA-TTATTTAATCTTTTAA
1 TTTATTTATTTAATATTTT-A
*
14419 TTTATTATATTTATTATTTTA
1 TTTATT-TATTTAATATTTTA
*
14440 TTTCTTTATTTACATATTT
1 TTTATTTATTTA-ATATTT
14459 GTCAATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 10 0.30
21 12 0.36
22 11 0.33
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATTTATTTAATATTTTA
Found at i:20902 original size:40 final size:40
Alignment explanation
Indices: 20793--20902 Score: 102
Period size: 39 Copynumber: 2.8 Consensus size: 40
20783 TTACAACTTG
* * * *
20793 AAATGTTGGGGCATTTTGGAGG-CTTGTACCAGTATGAAAT
1 AAATGTTGGGGCATGTTGAAGGTC-TGTATCAGCATGAAAT
* * *
20833 -AATGTT-GGGCACTGTTGAA-ATATTATATCAGCATGAAAT
1 AAATGTTGGGGCA-TGTTGAAGGT-CTGTATCAGCATGAAAT
20872 AAATGTTGGGGCATGTTGAAGGTCTGTATCA
1 AAATGTTGGGGCATGTTGAAGGTCTGTATCA
20903 TGTTGGAGTG
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
38 5 0.09
39 24 0.44
40 19 0.35
41 6 0.11
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (40 bp):
AAATGTTGGGGCATGTTGAAGGTCTGTATCAGCATGAAAT
Found at i:22564 original size:168 final size:168
Alignment explanation
Indices: 22278--22583 Score: 454
Period size: 168 Copynumber: 1.8 Consensus size: 168
22268 TAAGTTATTT
* *
22278 TGAAAATGAGAAATCAATTCACAATGTTTCTCATTTAATCTATTTTCAGAAAAGGAAATTTTTAA
1 TGAAAATGAGAAAGCAATTCACAATGTTTCTCATTTAA-CTATTTTAAGAAAAGGAAATTTTTAA
* * * * *
22343 AAAGTAAGAAAGTGATTCTAAAGTTTCTTACCTAGTAAACTATTTCTCAAAGATGATAAGTCCTT
65 AAAGTAAAAAAGCGATTCGAAAGTTTCTTACCCAGTAAACTATTTCCCAAAGATGATAAGTCCTT
22408 CGGGTCATCCGTAAGACCTCCAGGTAGAATGTTTTCACA
130 CGGGTCATCCGTAAGACCTCCAGGTAGAATGTTTTCACA
* * * * *
22447 TGAAAATGAGAAAGCGATTACCCAA-GTTTCTCATTTAA-TGTTTTAAGAAAATGAAATTTTTGA
1 TGAAAATGAGAAAGCAATT-CACAATGTTTCTCATTTAACTATTTTAAGAAAAGGAAATTTTTAA
*
22510 AAAGTAAAAAAGCGATTTCGAAAGTTTCTTACCCAGTAAACTATTTCCCAAAGATGATAAGTTCT
65 AAAGTAAAAAAGCGA-TTCGAAAGTTTCTTACCCAGTAAACTATTTCCCAAAGATGATAAGTCCT
22575 TCGGGTCAT
129 TCGGGTCAT
22584 TAGTAAGTCT
Statistics
Matches: 122, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
167 34 0.28
168 54 0.44
169 30 0.25
170 4 0.03
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (168 bp):
TGAAAATGAGAAAGCAATTCACAATGTTTCTCATTTAACTATTTTAAGAAAAGGAAATTTTTAAA
AAGTAAAAAAGCGATTCGAAAGTTTCTTACCCAGTAAACTATTTCCCAAAGATGATAAGTCCTTC
GGGTCATCCGTAAGACCTCCAGGTAGAATGTTTTCACA
Found at i:22860 original size:3 final size:3
Alignment explanation
Indices: 22852--22897 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
22842 TCCCATTTCT
22852 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
22898 AAATAATAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:26051 original size:14 final size:12
Alignment explanation
Indices: 26020--26061 Score: 52
Period size: 11 Copynumber: 3.5 Consensus size: 12
26010 AAGGGAGTTC
26020 AAAGAAAAAAAG
1 AAAGAAAAAAAG
26032 -AAGAAAAAATCAG
1 AAAGAAAAAA--AG
26045 AAAGAAAAAAA-
1 AAAGAAAAAAAG
26056 AAAGAA
1 AAAGAA
26062 GAAAGAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 15 0.56
12 1 0.04
13 2 0.07
14 9 0.33
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:26079 original size:30 final size:28
Alignment explanation
Indices: 26024--26089 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 28
26014 GAGTTCAAAG
*
26024 AAAAAAAGAAGAAAAAATCAGAAAGAAA
1 AAAAAAAGAAGAAAAAATCACAAAGAAA
**
26052 AAAAAAAGAAGAAAGAGAATTTCAAAGAAA
1 AAAAAAAGAAGAAA-A-AATCACAAAGAAA
*
26082 AACAAAAG
1 AAAAAAAG
26090 CCAAGGAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 14 0.44
29 1 0.03
30 17 0.53
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.06
Consensus pattern (28 bp):
AAAAAAAGAAGAAAAAATCACAAAGAAA
Found at i:26082 original size:28 final size:26
Alignment explanation
Indices: 26017--26083 Score: 64
Period size: 28 Copynumber: 2.5 Consensus size: 26
26007 ATCAAGGGAG
26017 TTCAAAG-AAAAAAAGAAGAAAAAAT
1 TTCAAAGAAAAAAAAGAAGAAAAAAT
***
26042 CAGAAAGAAAAAAAAAAGAAGAAAGAGAAT
1 TTCAAAG--AAAAAAAAGAAGAAA-A-AAT
26072 TTCAAAGAAAAA
1 TTCAAAGAAAAA
26084 CAAAAGCCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
25 4 0.13
28 19 0.61
29 1 0.03
30 7 0.23
ACGTcount: A:0.72, C:0.04, G:0.15, T:0.09
Consensus pattern (26 bp):
TTCAAAGAAAAAAAAGAAGAAAAAAT
Found at i:32298 original size:2 final size:2
Alignment explanation
Indices: 32291--32320 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
32281 TAAATGTGAA
32291 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
32321 GTATGATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32897 original size:13 final size:13
Alignment explanation
Indices: 32875--32933 Score: 50
Period size: 13 Copynumber: 4.4 Consensus size: 13
32865 ATATGTTATA
32875 TTTT-TATATATT
1 TTTTATATATATT
32887 TTTTATATATATT
1 TTTTATATATATT
* *
32900 TTAACTAGATATATT
1 TT--TTATATATATT
32915 ATTTT-TATATAATT
1 -TTTTATATAT-ATT
32929 TTTTA
1 TTTTA
32934 ATAAATATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
12 4 0.11
13 18 0.49
14 4 0.11
15 9 0.24
16 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (13 bp):
TTTTATATATATT
Found at i:45851 original size:32 final size:29
Alignment explanation
Indices: 45799--45875 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 29
45789 ATTTTTGAAA
*
45799 TTTACAAATTTAACATCTTAAAATATATATTTT
1 TTTA-AAATTTAACACCTT-AAA-ATAT-TTTT
*
45832 TTTAAAATTTGACACCTTAAAATATTTTT
1 TTTAAAATTTAACACCTTAAAATATTTTT
45861 TTT-AAATTTAACACC
1 TTTAAAATTTAACACC
45876 CCAAAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.27
29 7 0.17
30 4 0.10
31 3 0.07
32 12 0.29
33 4 0.10
ACGTcount: A:0.40, C:0.12, G:0.01, T:0.47
Consensus pattern (29 bp):
TTTAAAATTTAACACCTTAAAATATTTTT
Found at i:45881 original size:28 final size:28
Alignment explanation
Indices: 45825--45883 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
45815 CTTAAAATAT
* **
45825 ATATTTTTTTAAAATTTGACACCTTAAA
1 ATATTTTTTTAAAATTTAACACCCCAAA
*
45853 ATATTTTTTTTAAATTTAACACCCCAAA
1 ATATTTTTTTAAAATTTAACACCCCAAA
45881 ATA
1 ATA
45884 AATTTTCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.44
Consensus pattern (28 bp):
ATATTTTTTTAAAATTTAACACCCCAAA
Found at i:46047 original size:16 final size:17
Alignment explanation
Indices: 46026--46060 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
46016 ATATAAATAT
46026 GAAAATAAA-AATAAAA
1 GAAAATAAATAATAAAA
46042 GAAAATAAATAATAAAA
1 GAAAATAAATAATAAAA
46059 GA
1 GA
46061 TAATTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (17 bp):
GAAAATAAATAATAAAA
Found at i:46125 original size:3 final size:3
Alignment explanation
Indices: 46117--46145 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
46107 CGAAACTCCC
46117 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
46146 GCAGAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47669 original size:23 final size:23
Alignment explanation
Indices: 47643--47690 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
47633 ATAAAGTACA
*
47643 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
47666 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
47689 AT
1 AT
47691 TGACATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:48201 original size:23 final size:23
Alignment explanation
Indices: 48166--48238 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
48156 ATACTTTACA
* *
48166 ATATAAGCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
48189 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* * *
48212 ATATTAACGCTACATATTACATC
1 ATATAAACGCTACCTATTACATT
48235 ATAT
1 ATAT
48239 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:48239 original size:23 final size:23
Alignment explanation
Indices: 48175--48239 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
48165 AATATAAGCA
*
48175 CTACCTATTACATTATATAAACG
1 CTACCTATTACATTATATTAACG
48198 CTACCTATTACATTATATTAACG
1 CTACCTATTACATTATATTAACG
* *
48221 CTACATATTACATCATATT
1 CTACCTATTACATTATATT
48240 TTTACCTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (23 bp):
CTACCTATTACATTATATTAACG
Found at i:48682 original size:489 final size:491
Alignment explanation
Indices: 47764--49565 Score: 3454
Period size: 489 Copynumber: 3.7 Consensus size: 491
47754 TTATAATATG
*
47764 TTGAAAGTGTCTATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCTATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
47829 TTCAA--TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
66 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
*
47892 ACAAAAAATTATTTGAATGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
131 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
*
47957 TTAACCAAAGATAATAATAAATATGTAATATATATGGTTATTGTTTTTAATTTAATAATAATATA
196 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
*
48022 TACCGTAACGTAAAAAATAAATCATTAGACGTCTATAATTACTAAATTAATATCTTAAAACTCAC
261 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
48087 TCAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
326 TCAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
48152 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATT
391 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATA-T
48217 AA-CGCTACATATTACATCATATTTTTACCTATTATA
455 AAGCGCTACATATTACATCATATTTTTACCTATTATA
*
48253 TTGAAAGTGTTTATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCTATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
48317 TTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
66 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
48381 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
131 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
*
48446 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATAATAATATA
196 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
* *
48511 TACTGTAACGTAAAAAATAAATTATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
261 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
48576 TCAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
326 TCAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
*
48641 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACATATTACATTATATA
391 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
48706 AGCGCTACATATTACATCATATTTTTACCTATTATA
456 AGCGCTACATATTACATCATATTTTTACCTATTATA
48742 TTGAAAGTGTCTATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCTATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
48807 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
66 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
48872 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
131 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
48937 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
196 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
49002 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
261 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
*
49067 TCAAAAGATAACCTTAAATGAATATTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
326 TCAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
49132 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
391 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
*
49197 AGCGCTACCTATTACATCATATTTTTACCTATTATA
456 AGCGCTACATATTACATCATATTTTTACCTATTATA
49233 TTGAAAGTGTCTATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCTATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
49297 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
66 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
49362 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
131 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
49427 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
196 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
49492 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
261 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
49557 TCAAAAGAT
326 TCAAAAGAT
49566 GTACATACCT
Statistics
Matches: 1293, Mismatches: 16, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
488 55 0.04
489 438 0.34
490 370 0.29
491 430 0.33
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (491 bp):
TTGAAAGTGTCTATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
TCAAAAGATAACCTTAAATGAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
AGCGCTACATATTACATCATATTTTTACCTATTATA
Found at i:48690 original size:23 final size:23
Alignment explanation
Indices: 48655--48727 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
48645 ATACTTTACA
* *
48655 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACATATTACATT
*
48678 ATATAAACGCTACATATTACATT
1 ATATAAGCGCTACATATTACATT
*
48701 ATATAAGCGCTACATATTACATC
1 ATATAAGCGCTACATATTACATT
48724 ATAT
1 ATAT
48728 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACATATTACATT
Found at i:49181 original size:23 final size:23
Alignment explanation
Indices: 49146--49218 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
49136 ATACTTTACA
*
49146 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
49169 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
49192 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
49215 ATAT
1 ATAT
49219 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:52370 original size:183 final size:183
Alignment explanation
Indices: 52059--54280 Score: 3846
Period size: 183 Copynumber: 12.1 Consensus size: 183
52049 TACTTAAAAT
52059 TACCGACACAATATTA-AAACGTGTCGATATAGGTTGTAAGACCTATTCGCTCATAAAACCGGTA
1 TACCGACACAATATTAGAAA-GTGTCGATATAGGTTGT-AGACCTATTCGCTCATAAAACCGGTA
* *
52123 TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATTTGTAAAT
64 TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAAT
* *
52188 GTCGACACTTTTTGACAAT-GTATCGACACATTTTTCTTACAATCTGGACATAAAG
129 GTCGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
52243 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
52308 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
52373 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* *
52426 TACCGACACAATATTAGAAAGTGTCGATATAGGTTATAGACATATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* * * *
52491 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTTCGATTTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
*
52556 CGACACTTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
52609 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
52674 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
52739 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* * *
52792 TATCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACATATTCACTCATAAAACCGGTATA
1 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* * * *
52857 TTTATACCAGTTATATTACAAAATTATCTATTACATTATAATTTTGGGTTCCGATTTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
* * *
52922 CGACACTTTTTGACAAT-GTATCGACATATTTTTCTTCCAATATGGACATAAAG
131 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
52975 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
53040 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
53105 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* *
53158 TTCCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
53223 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCTGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
53288 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* * *
53341 TATCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACATATTCACTCATAAAACCGGTATA
1 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* * *
53406 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTTTGGGTTCCGATTTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
* * *
53471 CGACACTTTTTGACAAT-GTATCGACATATTTTTCTTCCAATATGGACATAAAG
131 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
53524 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
53589 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
53654 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* *
53707 TTCCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
53772 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCTGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
53837 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* *
53890 TTCCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* *
53955 TATATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
54020 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* *
54073 TTCCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* * * * * *
54138 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCTGAAGTTTTTTCAA
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCG-A--TGTGTAAA
* *
54203 --TCGACACTTTTTTAAATGGTATCGATACATTTTTCTTCCATTCTGGACATAAAG
128 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* *
54257 TACAGACACAATATTAAAAAGTGT
1 TACCGACACAATATTAGAAAGTGT
54281 GAAAACTTTG
Statistics
Matches: 1949, Mismatches: 78, Indels: 22
0.95 0.04 0.01
Matches are distributed among these distances:
182 12 0.01
183 1812 0.93
184 117 0.06
185 3 0.00
186 5 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (183 bp):
TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
Found at i:55496 original size:9 final size:9
Alignment explanation
Indices: 55482--55559 Score: 84
Period size: 9 Copynumber: 8.7 Consensus size: 9
55472 CCTTTTTTGG
55482 ATCATCATC
1 ATCATCATC
55491 ATCATCATC
1 ATCATCATC
55500 ATCATCATC
1 ATCATCATC
*
55509 GTCATCATC
1 ATCATCATC
* *
55518 GTCATCGTC
1 ATCATCATC
* *
55527 AGCTTCATC
1 ATCATCATC
*
55536 GTCATCATC
1 ATCATCATC
*
55545 ATCGTCATC
1 ATCATCATC
*
55554 TTCATC
1 ATCATC
55560 GTCAGCTTCA
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 56 1.00
ACGTcount: A:0.24, C:0.33, G:0.08, T:0.35
Consensus pattern (9 bp):
ATCATCATC
Found at i:55560 original size:12 final size:12
Alignment explanation
Indices: 55486--55576 Score: 92
Period size: 12 Copynumber: 7.3 Consensus size: 12
55476 TTTTGGATCA
* *
55486 TCATCATCATCA
1 TCATCTTCATCG
*
55498 TCATCATCATCG
1 TCATCTTCATCG
55510 TCATCATCGTCATCG
1 TCATC-T--TCATCG
*
55525 TCAGCTTCATCG
1 TCATCTTCATCG
*
55537 TCATCATCATCG
1 TCATCTTCATCG
55549 TCATCTTCATCG
1 TCATCTTCATCG
* *
55561 TCAGCTTCATCT
1 TCATCTTCATCG
55573 TCAT
1 TCAT
55577 TGACCGCTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
12 56 0.84
14 1 0.01
15 10 0.15
ACGTcount: A:0.22, C:0.33, G:0.09, T:0.36
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:55570 original size:18 final size:18
Alignment explanation
Indices: 55513--55576 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
55503 ATCATCGTCA
55513 TCATCGTCATCGTCAGCT
1 TCATCGTCATCGTCAGCT
* * *
55531 TCATCGTCATCATCATCG
1 TCATCGTCATCGTCAGCT
*
55549 TCATCTTCATCGTCAGCT
1 TCATCGTCATCGTCAGCT
*
55567 TCATCTTCAT
1 TCATCGTCAT
55577 TGACCGCTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.19, C:0.33, G:0.11, T:0.38
Consensus pattern (18 bp):
TCATCGTCATCGTCAGCT
Found at i:55576 original size:6 final size:6
Alignment explanation
Indices: 55482--55559 Score: 84
Period size: 6 Copynumber: 13.0 Consensus size: 6
55472 CCTTTTTTGG
* * * *
55482 ATCATC ATCATC ATCATC ATCATC ATCGTC ATCATC GTCATC GTCAGC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* * * *
55530 TTCATC GTCATC ATCATC GTCATC TTCATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC
55560 GTCAGCTTCA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.24, C:0.33, G:0.08, T:0.35
Consensus pattern (6 bp):
ATCATC
Found at i:57402 original size:200 final size:200
Alignment explanation
Indices: 57083--57815 Score: 1335
Period size: 200 Copynumber: 3.7 Consensus size: 200
57073 TTATATACCA
*
57083 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* *
57148 TTGGTTTTCGATGTTTTTGGGATCGACACTTTCTATATATGGATCGACACTTTATGGTTGCACCA
66 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
*
57213 TGTTTTCCATTCATTCTGGACCAAAAATATCAACACAAACTAAAAAAGTGTCGAC-CAATTATTT
131 TGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACAC-ATTATTT
57277 AGACAT
195 AGACAT
57283 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
57348 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
66 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
* *
57413 TGTTTTCCATTCATTCTGGGCCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTT
131 TGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTA
57478 GACAT
196 GACAT
*
57483 ATTCTCTCATAAAACCAGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* *
57548 TTGGTTTTCAATGTTTTTGGGATCGACACTTTTTATATATGGATCGTCACTTTATGGTTGCA-CC
66 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
57612 TGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTA
131 TGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTA
57677 GACAT
196 GACAT
57682 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* * *
57747 TTGCTTTTCGAAGTTTTTGGGATCGACACTTTTTATATATGGTTCGACACTTTATGGTTGCACCC
66 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
57812 TGTT
131 TGTT
57816 GGCCATATTG
Statistics
Matches: 514, Mismatches: 17, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
199 191 0.37
200 322 0.63
201 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (200 bp):
ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
TGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTA
GACAT
Found at i:57798 original size:399 final size:400
Alignment explanation
Indices: 57083--57815 Score: 1362
Period size: 399 Copynumber: 1.8 Consensus size: 400
57073 TTATATACCA
* *
57083 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTT
1 ATTCTCTCATAAAACCAGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
*
57148 TTGGTTTTCGATGTTTTTGGGATCGACACTTTCTATATATGGATCGACACTTTATGGTTGCACCA
66 TTGGTTTTCAATGTTTTTGGGATCGACACTTTCTATATATGGATCGACACTTTATGGTTGCACCA
57213 TGTTTTCCATTCATTCTGGACCAAAAATATCAACACAAACTAAAAAAGTGTCGACCAATTATTTA
131 TGTTTTCCATTCATTCTGGACCAAAAATATCAACACAAACTAAAAAAGTGTCGACCAATTATTTA
57278 GACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTA
196 GACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTA
* *
57343 TACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTG
261 TACTTTTGCTTTTCGAAGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTG
57408 CACCCTGTTTTCCATTCATTCTGGGCCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATT
326 CACCCTGTTTTCCATTCATTCTGGGCCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATT
57473 ATTTTGACAT
391 ATTTTGACAT
57483 ATTCTCTCATAAAACCAGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCAGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* *
57548 TTGGTTTTCAATGTTTTTGGGATCGACACTTTTTATATATGGATCGTCACTTTATGGTTGCACC-
66 TTGGTTTTCAATGTTTTTGGGATCGACACTTTCTATATATGGATCGACACTTTATGGTTGCACCA
*
57612 TGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGA-CACATTATTT
131 TGTTTTCCATTCATTCTGGACCAAAAATATCAACACAAACTAAAAAAGTGTCGACCA-ATTATTT
57676 AGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATT
195 AGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATT
*
57741 ATACTTTTGCTTTTCGAAGTTTTTGGGATCGACACTTTTTATATATGGTTCGACACTTTATGGTT
260 ATACTTTTGCTTTTCGAAGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
57806 GCACCCTGTT
325 GCACCCTGTT
57816 GGCCATATTG
Statistics
Matches: 323, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
398 2 0.01
399 197 0.61
400 124 0.38
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (400 bp):
ATTCTCTCATAAAACCAGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
TTGGTTTTCAATGTTTTTGGGATCGACACTTTCTATATATGGATCGACACTTTATGGTTGCACCA
TGTTTTCCATTCATTCTGGACCAAAAATATCAACACAAACTAAAAAAGTGTCGACCAATTATTTA
GACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTA
TACTTTTGCTTTTCGAAGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTG
CACCCTGTTTTCCATTCATTCTGGGCCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATT
ATTTTGACAT
Found at i:57945 original size:18 final size:18
Alignment explanation
Indices: 57922--57982 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
57912 TCTCATTCAT
*
57922 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
57940 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
57959 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
57978 AATTA
1 AATTA
57983 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:57958 original size:19 final size:19
Alignment explanation
Indices: 57934--57982 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
57924 TTATATTCAC
57934 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
57953 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
57972 ATACAAAATTA
1 ATACAAAATTA
57983 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:59767 original size:33 final size:33
Alignment explanation
Indices: 59730--59795 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
59720 CATCTTAATA
*
59730 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
59763 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
59796 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:59854 original size:21 final size:21
Alignment explanation
Indices: 59829--59893 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
59819 CCCCTTATGC
* *
59829 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
59850 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
59871 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
59892 CT
1 CT
59894 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:61945 original size:24 final size:24
Alignment explanation
Indices: 61917--61969 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
61907 CCGTTCTATC
61917 TATTTTCATAGGATAT-TTAGCTTA
1 TATTTTCATAGGATATGTTA-CTTA
* *
61941 TATTTTCATCGGATATGTTATTTA
1 TATTTTCATAGGATATGTTACTTA
61965 TATTT
1 TATTT
61970 AATCGATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (24 bp):
TATTTTCATAGGATATGTTACTTA
Found at i:62160 original size:20 final size:18
Alignment explanation
Indices: 62109--62169 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 18
62099 ATATATCTGG
*
62109 TATCA-TTTTACCGGTTT
1 TATCATTTTTACCTGTTT
62126 TATCATTTTGATACCTGTTT
1 TATCATTTT--TACCTGTTT
*
62146 TATCTTATTTTTACCTGTTA
1 TATC--ATTTTTACCTGTTT
62166 TATC
1 TATC
62170 GTTGTGGATC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
17 5 0.14
18 3 0.08
20 24 0.65
22 5 0.14
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (18 bp):
TATCATTTTTACCTGTTT
Found at i:62322 original size:20 final size:20
Alignment explanation
Indices: 62295--62341 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
62285 TCCGGTAATG
62295 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
62314 TTCTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
62335 TTTTACC
1 TTTTACC
62342 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.19, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:62385 original size:181 final size:181
Alignment explanation
Indices: 62081--62552 Score: 657
Period size: 181 Copynumber: 2.6 Consensus size: 181
62071 GGTACTTACG
* * * *
62081 AAAGTATCGACACTTTCAATATATCTGGT-ATCATTTTACCGGTTTTATCATTTTGATACCTGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAAT-GTTTTACCGGTTTTATCATTTTCATACCGGTT
* *
62145 TTATCTTATTTTTACCTGTTATATCGTTGTGGATCGATATATATTTTTAAAGTATCGACACATTA
65 TTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACAT-TTTTTAAAGTATCGACACATTA
*
62210 TAGG-CGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
129 TAGGAC-CTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
*
62262 AAAGTATCGACACTTTCAATATATCCGGTAATGTTTTACCGGTTTTATCATTTTCTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAATGTTTTACCGGTTTTATCATTTTCATACCGGTTT
* *
62327 TATCATATTTTTACCTGGTATATCGTTGTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTT-AAAGTATCGACACATTAT
* *
62392 AGGACTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AGGACCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * ** *
62444 AAAGTACCGACACTTTAAATGTAT-CGGTAGCGCTTTACCGGTTTTATCA-TTTCAATACCGGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAATGTTTTACCGGTTTTATCATTTTC-ATACCGGTT
* * * * *
62507 TTGTCATAGTTTTACCTGTTATATCATTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
62553 AATTTGGATC
Statistics
Matches: 261, Mismatches: 25, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
180 9 0.03
181 227 0.87
182 25 0.10
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAATGTTTTACCGGTTTTATCATTTTCATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTAAAGTATCGACACATTATA
GGACCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:64395 original size:19 final size:20
Alignment explanation
Indices: 64371--64413 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
64361 AGCATTTATC
*
64371 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
64390 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
64410 TTCA
1 TTCA
64414 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:64765 original size:14 final size:14
Alignment explanation
Indices: 64746--64785 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
64736 TAAGATACTA
64746 TTTCCATCACCATC
1 TTTCCATCACCATC
*
64760 TTTCCATTACCATC
1 TTTCCATCACCATC
*
64774 -CTCCATCACCAT
1 TTTCCATCACCAT
64786 TCACGCCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:65468 original size:18 final size:16
Alignment explanation
Indices: 65436--65470 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
65426 ACTTTCCTAC
65436 TATTTCATTTTCTTAT
1 TATTTCATTTTCTTAT
65452 TATTTCATATATTCTTAT
1 TATTTCAT-T-TTCTTAT
65470 T
1 T
65471 CCATTACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTCATTTTCTTAT
Found at i:68547 original size:20 final size:19
Alignment explanation
Indices: 68512--68552 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
68502 AGCATTTATC
*
68512 TTCATTAAAATTATGTATT
1 TTCATTAAAATCATGTATT
*
68531 TTCATTAAAAATCATGTGTT
1 TTCATT-AAAATCATGTATT
68551 TT
1 TT
68553 TAAAGGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (19 bp):
TTCATTAAAATCATGTATT
Found at i:68909 original size:14 final size:14
Alignment explanation
Indices: 68887--68926 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
68877 TAAGATACTA
68887 TTTCCATCACCATC
1 TTTCCATCACCATC
*
68901 TTTCTATCACCATC
1 TTTCCATCACCATC
*
68915 -CTCCATCACCAT
1 TTTCCATCACCAT
68927 TCACGCCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:69179 original size:36 final size:36
Alignment explanation
Indices: 69134--69212 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
69124 TTAATTATCA
* *
69134 AATTACTTAATCAATTCTACTTCTTTTATGTAGATT
1 AATTTCTTAATCAATTATACTTCTTTTATGTAGATT
69170 AATTTCTTAATCAATTATACTTCTTTTATGTAGATT
1 AATTTCTTAATCAATTATACTTCTTTTATGTAGATT
69206 AATTTCT
1 AATTTCT
69213 ATTCAACATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.30, C:0.13, G:0.05, T:0.52
Consensus pattern (36 bp):
AATTTCTTAATCAATTATACTTCTTTTATGTAGATT
Found at i:79153 original size:17 final size:17
Alignment explanation
Indices: 79131--79165 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
79121 CCATGCTGAG
79131 TAAGTGTGAGTTATGGC
1 TAAGTGTGAGTTATGGC
79148 TAAGTGTGAGTTATGGC
1 TAAGTGTGAGTTATGGC
79165 T
1 T
79166 CAACAAGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.34, T:0.37
Consensus pattern (17 bp):
TAAGTGTGAGTTATGGC
Found at i:85777 original size:4 final size:4
Alignment explanation
Indices: 85770--86451 Score: 1341
Period size: 4 Copynumber: 171.0 Consensus size: 4
85760 TACATACATA
85770 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
85818 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
85866 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
85914 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
85962 GTAT GTAT GTAT GTAT GTAT G--T GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
86008 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
86056 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
86104 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
86152 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
86200 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
86248 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
86296 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
86344 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
86392 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
86440 GTAT TTAT GTAT
1 GTAT GTAT GTAT
86452 ACTTTTATAT
Statistics
Matches: 674, Mismatches: 2, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.00
4 672 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:86464 original size:2 final size:2
Alignment explanation
Indices: 86457--86675 Score: 125
Period size: 2 Copynumber: 109.5 Consensus size: 2
86447 TGTATACTTT
86457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
86499 TA TA TA TA TA TA TA CT- TA TG TA CA TA AA TCA TA AA TA TA TA GA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
* * * *
86542 CTT TA TA CT- TA TA TG TA CA TG TA TA TA TA TA TA TA TA TA TA -A
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
86584 GA -A TA TA TA TA CT- TA TG TA CA TA CA TCA TA CA TGA T- TCA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA T-A TA TA T-A TA T-A TA
* *
86625 TA TA CT- TA TG TA TA TA CT- TA TA TA TA TA TA TA TA -A T- TA TT
1 TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
*
86665 TA TA TT TA TA T
1 TA TA TA TA TA T
86676 TTTTTTATAA
Statistics
Matches: 165, Mismatches: 32, Indels: 40
0.70 0.14 0.17
Matches are distributed among these distances:
1 10 0.06
2 143 0.87
3 12 0.07
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:89539 original size:30 final size:30
Alignment explanation
Indices: 89503--89591 Score: 117
Period size: 30 Copynumber: 2.9 Consensus size: 30
89493 TTAACTCCAT
*
89503 TCTTAAATTTTAAATAAAATATTAATTTTA
1 TCTTAAATTTTAAATAAAATATTAATTTAA
*
89533 TCTTAAA-TTTAAGATAAAATATCAATTTAA
1 TCTTAAATTTTAA-ATAAAATATTAATTTAA
* *
89563 CCTTTAAATTTTAAATATAATATTAATTT
1 TC-TTAAATTTTAAATAAAATATTAATTT
89592 GACGGCGATT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.10
30 23 0.45
31 18 0.35
32 5 0.10
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (30 bp):
TCTTAAATTTTAAATAAAATATTAATTTAA
Found at i:94327 original size:181 final size:175
Alignment explanation
Indices: 93829--94315 Score: 514
Period size: 179 Copynumber: 2.7 Consensus size: 175
93819 AAATTGAATG
* * * *
93829 CATATAGTGACAACTTTTGTAACTAAAAGTTTTAGTAATTATGACAAAAAAATTGTCACAACAAA
1 CATATAGTGACAAATTTTGTAACTATAAG-TTTAATAATTATTACAAAAAAATTGTCACAACAAA
* * * * *
93894 TAATGAGATTTAGATTTGTTGTGACAAATTTTGTTTGTAATTATATATTTTAATTATAGTGACAA
65 TAATGAGATTCAG-TTTTTTGTGACAAATTATATTTGTAGTTATATATTTTAATTATAGTGACAA
93959 A-ATATATAGTCACAAATGATTATCTCCAATTTTTGGTAAAAAAAAAT
129 ATATAT-TAGTCACAAATGATTATCTCCAATTTTTGGTAAAAAAAAAT
* * ** * * *
94006 TATATAATGACATGTTTTGTAACTATAAGCTATAATTATTGTTACAAAAACAAATTGTCACAACA
1 CATATAGTGACAAATTTTGTAACTATAAG-TTTAATAATTATTAC-AAAA-AAATTGTCACAACA
* * * * * * *
94071 AATAATGAGATTCAAGTTTTTAGTAAAAAATAATATTTTTCGTTATATGTTTTAATTATAGTGAC
63 AATAATGAGATTC-AGTTTTTTGTGACAAATTATATTTGTAGTTATATATTTTAATTATAGTGAC
* * *
94136 AAAGTATATTA-TCACAAA-GATTTTCTTCCATATTTTTTTTGCG-CAAAAAAAGT
127 AAA-TATATTAGTCACAAATGATTATC-TCCA-A---TTTTTG-GTAAAAAAAAAT
*
94189 CATATAGTGACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAAATTGTCACAAAAAA
1 CATATAGTGACAAATTTTGTAACTATAAGT-TTAATAATTATTACAAAAAAATTGTCACAACAAA
* * * * *
94254 TAATTATATTCACGTTTTTTGTGACAAATTATATTTGTAGTTGTAAATTTTAACTATAGTGA
65 TAATGAGATTCA-GTTTTTTGTGACAAATTATATTTGTAGTTATATATTTTAATTATAGTGA
94316 TAGTATATAT
Statistics
Matches: 251, Mismatches: 46, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
177 34 0.14
178 10 0.04
179 78 0.31
180 6 0.02
181 67 0.27
182 5 0.02
183 50 0.20
184 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (175 bp):
CATATAGTGACAAATTTTGTAACTATAAGTTTAATAATTATTACAAAAAAATTGTCACAACAAAT
AATGAGATTCAGTTTTTTGTGACAAATTATATTTGTAGTTATATATTTTAATTATAGTGACAAAT
ATATTAGTCACAAATGATTATCTCCAATTTTTGGTAAAAAAAAAT
Found at i:94486 original size:360 final size:359
Alignment explanation
Indices: 93829--94486 Score: 747
Period size: 360 Copynumber: 1.8 Consensus size: 359
93819 AAATTGAATG
* * * *
93829 CATATAGTGACAACTTTTGTAACTAAAAGTTTTAGTAATTATGACAAAAAAATTGTCACAACAAA
1 CATATAGTGACAAATTTTGTAACTAAAAGTGTTAATAATTATGACAAAAAAATTGTCACAAAAAA
* * * * *
93894 TAATGAGATTTAGATTTGTTGTGACAAATTTTGTTTGTAATTATATATTTTAATTATAGTGACAA
66 TAATGAGATTCAGATTTGTTGTGACAAATTATATTTGTAATTATAAATTTTAACTATAGTGACAA
93959 AATATATAGTCACAAATGATTATCTCCAATTTTTGGTAAAAAAAAATTATATAATGACATGTTTT
131 AATATATAGTCACAAATGATTATCTCCAATTTTTGGT-AAAAAAAATTATATAATGACATGTTTT
* * * *
94024 GTAACTATAAGCTATAATTATTGTTACAAAAACAAATTGTCACAACAAATAATGAGATTCAAGTT
195 ATAACTATAAGCTATAATTATTGTTACAAAAACAAATTATCACAACAAATAATAAAATTCAAGTT
** *
94089 TTTAGTAAAAAATAATATTTTTCGTTATATGTTTTAATTATAGTGACAAAGTATATTATCACAAA
260 TTTAGTAAAAAATAATATTTTTAATTATATATTTTAATTATAGTGACAAAGTATATTATCACAAA
94154 GATTTTCTTCCATATTTTTTTTGCGCAAAAAAAGT
325 GATTTTCTTCCATATTTTTTTTGCGCAAAAAAAGT
* *
94189 CATATAGTGACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAAATTGTCACAAAAAA
1 CATATAGTGACAAATTTTGTAACTAAAAGTGTTAATAATTATGACAAAAAAATTGTCACAAAAAA
* * * * * *
94254 TAATTATATTCACG-TTTTTTGTGACAAATTATATTTGTAGTTGTAAATTTTAACTATAGTGATA
66 TAATGAGATTCA-GATTTGTTGTGACAAATTATATTTGTAATTATAAATTTTAACTATAGTGACA
* * * * * * * *** *
94318 GTATATATTAATTGTCATAACT-ATTTTTCTCCACTTTTTTGT-TTCAAAATT-TATATTGACAA
130 --AAATA-T-ATAGTCACAAATGA-TTATCTCCAATTTTTGGTAAAAAAAATTATATAATGAC-A
* ** * * *
94380 T-TTTTATAATTATAATTTATAGTTATTGTTATAGAAA-AAATTATCA-AATCAAATAATAAAAT
189 TGTTTTATAACTATAAGCTATAATTATTGTTACAAAAACAAATTATCACAA-CAAATAATAAAAT
* * ** **
94442 TCAGGTTTTTTGTAATCAATTCT-TTTTTAAATTATATATTTTAAT
253 TCAAGTTTTTAGTAAAAAATAATATTTTT-AATTATATATTTTAAT
94487 CATTATAAAA
Statistics
Matches: 242, Mismatches: 47, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
359 7 0.03
360 159 0.66
361 38 0.16
362 12 0.05
363 2 0.01
364 24 0.10
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.42
Consensus pattern (359 bp):
CATATAGTGACAAATTTTGTAACTAAAAGTGTTAATAATTATGACAAAAAAATTGTCACAAAAAA
TAATGAGATTCAGATTTGTTGTGACAAATTATATTTGTAATTATAAATTTTAACTATAGTGACAA
AATATATAGTCACAAATGATTATCTCCAATTTTTGGTAAAAAAAATTATATAATGACATGTTTTA
TAACTATAAGCTATAATTATTGTTACAAAAACAAATTATCACAACAAATAATAAAATTCAAGTTT
TTAGTAAAAAATAATATTTTTAATTATATATTTTAATTATAGTGACAAAGTATATTATCACAAAG
ATTTTCTTCCATATTTTTTTTGCGCAAAAAAAGT
Found at i:94562 original size:62 final size:63
Alignment explanation
Indices: 94484--94622 Score: 153
Period size: 62 Copynumber: 2.3 Consensus size: 63
94474 TATATATTTT
* * * *
94484 AATCAT-TA-TAAAAAAATATACTATCATAACCATTTATCC-CTAT-TTTT-TTAGTGTCAAAAA
1 AATCATATAGTAACAAAATATACTATCATAAACATTT-TCCTCTATGTTTTATT-GCGCCAAAAA
* * * *
94544 TATTATATAGTAACAAAATATATTATCATAAAGATTTTCCTCTATGTTTTATTGCGCCAAAAA
1 AATCATATAGTAACAAAATATACTATCATAAACATTTTCCTCTATGTTTTATTGCGCCAAAAA
94607 AATCATATAGTAACAA
1 AATCATATAGTAACAA
94623 TTTTTGTAAC
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
60 4 0.06
61 5 0.08
62 27 0.42
63 26 0.41
64 2 0.03
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (63 bp):
AATCATATAGTAACAAAATATACTATCATAAACATTTTCCTCTATGTTTTATTGCGCCAAAAA
Found at i:99502 original size:61 final size:62
Alignment explanation
Indices: 99427--99554 Score: 213
Period size: 62 Copynumber: 2.1 Consensus size: 62
99417 TTTAAAGGAG
*
99427 GAAAATGCACTT-AAAGTGACTCTGAATATGGTACTGGAGACCCAAATACTGAACGTAAAGT
1 GAAAATGCACTTAAAAGTGACTCAGAATATGGTACTGGAGACCCAAATACTGAACGTAAAGT
* * *
99488 GAAAATGCAGTTAAAAGTGACTCAGATTATGGTACTGGAGACCCAAATTCTGAACGTAAAGT
1 GAAAATGCACTTAAAAGTGACTCAGAATATGGTACTGGAGACCCAAATACTGAACGTAAAGT
99550 GAAAA
1 GAAAA
99555 ATTACCTCCA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
61 11 0.18
62 51 0.82
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.23
Consensus pattern (62 bp):
GAAAATGCACTTAAAAGTGACTCAGAATATGGTACTGGAGACCCAAATACTGAACGTAAAGT
Found at i:100162 original size:22 final size:22
Alignment explanation
Indices: 100137--100181 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
100127 TATAGGTTTA
* *
100137 AAATTTAAAATATACAAAAAAT
1 AAATATAAAAAATACAAAAAAT
*
100159 AAATATAAAAAATACTAAAAAT
1 AAATATAAAAAATACAAAAAAT
100181 A
1 A
100182 GAAACTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATATAAAAAATACAAAAAAT
Found at i:101216 original size:3 final size:3
Alignment explanation
Indices: 101208--101249 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
101198 CTATGCTTTA
* *
101208 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
101250 TTCTTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:101354 original size:24 final size:23
Alignment explanation
Indices: 101327--101371 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
101317 TATGATTTTG
*
101327 TTTAATATTTAATTTATTGTTATA
1 TTTAATATTTAAATT-TTGTTATA
*
101351 TTTAATTTTTAAATTTTGTTA
1 TTTAATATTTAAATTTTGTTA
101372 CAAGTTGGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (23 bp):
TTTAATATTTAAATTTTGTTATA
Found at i:105122 original size:22 final size:23
Alignment explanation
Indices: 105071--105122 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
105061 ATAAGATATT
*
105071 AAAATATATTTTTAGTTATCATAA
1 AAAAT-TATTTTTAGTTATAATAA
**
105095 CCAATTA-TTTTAGTTATAATAA
1 AAAATTATTTTTAGTTATAATAA
105117 AAAATT
1 AAAATT
105123 TAAATAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
22 18 0.78
23 2 0.09
24 3 0.13
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (23 bp):
AAAATTATTTTTAGTTATAATAA
Found at i:105691 original size:65 final size:64
Alignment explanation
Indices: 105622--105754 Score: 162
Period size: 65 Copynumber: 2.1 Consensus size: 64
105612 TCGTCCCAAT
* *
105622 TTTATCAAAATGAAAAATTGTGACAAAT-TTATT-TAATCAAAATAACAAATTATAACAAATATT
1 TTTATCAAAATAAAAAATTGTGACAAATAATATTCT-ATCAAAATAACAAATTATAACAAA-ATT
105685 AA
64 -A
** * * *
105687 TTTATCATTATAAAAAATTGTGACAAATAATATTCTTTCATAATAACAAATTGTAACAAAATTA
1 TTTATCAAAATAAAAAATTGTGACAAATAATATTCTATCAAAATAACAAATTATAACAAAATTA
105751 TTTA
1 TTTA
105755 GTCACAGTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
64 5 0.08
65 28 0.47
66 25 0.42
67 1 0.02
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (64 bp):
TTTATCAAAATAAAAAATTGTGACAAATAATATTCTATCAAAATAACAAATTATAACAAAATTA
Found at i:105713 original size:33 final size:32
Alignment explanation
Indices: 105622--105754 Score: 126
Period size: 33 Copynumber: 4.1 Consensus size: 32
105612 TCGTCCCAAT
* * *
105622 TTTATCAAAATGAAAAATTGTGACAAAT-TTA
1 TTTATCATAATAAAAAATTGTAACAAATATTA
* * *
105653 TTTAATCAAAATAACAAATTATAACAAATATTAA
1 TTT-ATCATAATAAAAAATTGTAACAAATATT-A
* * *
105687 TTTATCATTATAAAAAATTGTGACAAATAATA
1 TTTATCATAATAAAAAATTGTAACAAATATTA
* *
105719 TTCTTTCATAATAACAAATTGTAACAAA-ATTA
1 TT-TATCATAATAAAAAATTGTAACAAATATTA
105751 TTTA
1 TTTA
105755 GTCACAGTAA
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
31 4 0.05
32 29 0.35
33 45 0.55
34 4 0.05
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (32 bp):
TTTATCATAATAAAAAATTGTAACAAATATTA
Found at i:105745 original size:66 final size:63
Alignment explanation
Indices: 105634--105754 Score: 163
Period size: 66 Copynumber: 1.9 Consensus size: 63
105624 TATCAAAATG
*
105634 AAAAATTGTGACAAATTTATTTAATCAAAATAACAAATTATAACAAATATTAATTTATCATTATA
1 AAAAATTGTGACAAATATATTTAATCAAAATAACAAATTATAACAAA-ATT-ATTTATCATTATA
* * *
105699 AAAAATTGTGACAAATAATATTCT-TTCATAATAACAAATTGTAACAAAATTATTTA
1 AAAAATTGTGACAAAT-ATATT-TAATCAAAATAACAAATTATAACAAAATTATTTA
105755 GTCACAGTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
64 5 0.10
65 19 0.38
66 25 0.50
67 1 0.02
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.36
Consensus pattern (63 bp):
AAAAATTGTGACAAATATATTTAATCAAAATAACAAATTATAACAAAATTATTTATCATTATA
Found at i:109123 original size:17 final size:18
Alignment explanation
Indices: 109103--109141 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
109093 ATAATAGAAT
109103 ATAAAAATATA-ATTATA
1 ATAAAAATATATATTATA
*
109120 ATAAAAATATATTTTATA
1 ATAAAAATATATATTATA
109138 ATAA
1 ATAA
109142 CCCACTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAAATATATATTATA
Done.