Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007961.1 Hibiscus syriacus cultivar Beakdansim tig00110388_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: 2700559
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 12
Found at i:4379 original size:99 final size:99
Alignment explanation
Indices: 4208--4407 Score: 382
Period size: 99 Copynumber: 2.0 Consensus size: 99
4198 TCTATTTAAA
4208 CTATTTAATCCGTTGATCAGCTCAATCGGTTAAAAAATATCAAGTACTTATAATAAAAATATTTG
1 CTATTTAATCCGTTGATCAGCTCAATCGGTTAAAAAATATCAAGTACTTATAATAAAAATATTTG
4273 ATTTTTCAAATCGAATACTTGGCCTACTATTTTT
66 ATTTTTCAAATCGAATACTTGGCCTACTATTTTT
*
4307 CTATTTAATCCGTTGATCAGCTGAATCGGTTAAAAAATATCAAGTACTTATAATAAAAATATTTG
1 CTATTTAATCCGTTGATCAGCTCAATCGGTTAAAAAATATCAAGTACTTATAATAAAAATATTTG
*
4372 ATTTTTCAAATCGAATACTTGGCCTATTATTTTT
66 ATTTTTCAAATCGAATACTTGGCCTACTATTTTT
4406 CT
1 CT
4408 CGAGTTTCTA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (99 bp):
CTATTTAATCCGTTGATCAGCTCAATCGGTTAAAAAATATCAAGTACTTATAATAAAAATATTTG
ATTTTTCAAATCGAATACTTGGCCTACTATTTTT
Found at i:4503 original size:13 final size:14
Alignment explanation
Indices: 4478--4512 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
4468 ACTCAATTTC
4478 TTATATATTTTTATT
1 TTATAT-TTTTTATT
4493 TT-TATTTTTTATT
1 TTATATTTTTTATT
4506 TTATATT
1 TTATATT
4513 AGATTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.53
14 7 0.37
15 2 0.11
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTATATTTTTTATT
Found at i:5424 original size:27 final size:29
Alignment explanation
Indices: 5382--5454 Score: 80
Period size: 32 Copynumber: 2.5 Consensus size: 29
5372 CCGAGCCGAG
**
5382 TCGAACTCGATTACT-AT-TAAGCTCGAC
1 TCGAACTCGAAAACTAATCTAAGCTCGAC
5409 TCGAACTCGAAAACTATAAATCTAAGCTCGAC
1 TCGAACTCGAAAAC--T-AATCTAAGCTCGAC
5441 TCG-ACTCGAAAACT
1 TCGAACTCGAAAACT
5455 CGCAAGCCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
27 12 0.31
29 2 0.05
31 12 0.31
32 13 0.33
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.25
Consensus pattern (29 bp):
TCGAACTCGAAAACTAATCTAAGCTCGAC
Found at i:5592 original size:23 final size:23
Alignment explanation
Indices: 5556--5611 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
5546 ACTCGATTGA
* *
5556 AGCTCGATTAAAGCTTGATTTTG
1 AGCTCGATTCAAGCTCGATTTTG
*
5579 AGCTCAATTCAAGCTCGATTTTG
1 AGCTCGATTCAAGCTCGATTTTG
5602 AGCTCGATTC
1 AGCTCGATTC
5612 TGTGCTCGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCGATTTTG
Found at i:5888 original size:13 final size:14
Alignment explanation
Indices: 5865--5897 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
5855 TCATCTTCTT
5865 TTTCTTCTCTCAAC-
1 TTTC-TCTCTCAACG
5879 TTTCTCTCTCAACG
1 TTTCTCTCTCAACG
5893 TTTCT
1 TTTCT
5898 TCAACAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.12, C:0.33, G:0.03, T:0.52
Consensus pattern (14 bp):
TTTCTCTCTCAACG
Found at i:7031 original size:17 final size:19
Alignment explanation
Indices: 6993--7031 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
6983 TTTGGGAAAC
*
6993 TGTGAAGCAGATATCAAGT
1 TGTGAAGCAGATATCAAAT
7012 TGTGAAGCAG-T-TCAAAT
1 TGTGAAGCAGATATCAAAT
7029 TGT
1 TGT
7032 ACATAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 10 0.53
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (19 bp):
TGTGAAGCAGATATCAAAT
Found at i:8181 original size:21 final size:20
Alignment explanation
Indices: 8157--8197 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
8147 TGGATTTAAT
8157 ATTTAGGGTTTAGGGTTTTAG
1 ATTTAGGGTTTA-GGTTTTAG
*
8178 ATTTATGGTTTAGGTTTTAG
1 ATTTAGGGTTTAGGTTTTAG
8198 GGCTTAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (20 bp):
ATTTAGGGTTTAGGTTTTAG
Found at i:8368 original size:14 final size:14
Alignment explanation
Indices: 8349--8378 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8339 TATAATTATC
*
8349 AATAATGTATTTTT
1 AATAATGTAATTTT
8363 AATAATGTAATTTT
1 AATAATGTAATTTT
8377 AA
1 AA
8379 AAATCTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:9220 original size:111 final size:111
Alignment explanation
Indices: 9079--9434 Score: 552
Period size: 111 Copynumber: 3.2 Consensus size: 111
9069 GTATTAATCC
* * **
9079 TTTTTATTAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGA
1 TTTTTA-T-AAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGA
* * * *
9144 ATCTGGTTTTGTCATATTTATACATGTTATATTGTAAAATATCGATCA
64 AACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATCA
*
9192 TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCTTTTTTGTCATAATGAAA
1 TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAAA
* *
9257 CTGATTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTATCC
66 CTGATTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATCA
*
9303 TTTTTATAAAAGGATCGATAATTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAAA
1 TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAAA
9368 CTGATTTTGTCATATTTTTTACCTGTTATATTGTAAAATATCGATACA
66 CTGATTTTGTCATA-TTTTTACCTGTTATATTGTAAAATATCGAT-CA
*
9416 TTTTTAT-AAAGTATCGATA
1 TTTTTATAAAAGGATCGATA
9435 TTTTATAGGC
Statistics
Matches: 226, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
111 171 0.76
112 41 0.18
113 14 0.06
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (111 bp):
TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAAA
CTGATTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATCA
Found at i:10079 original size:111 final size:111
Alignment explanation
Indices: 9882--10351 Score: 672
Period size: 111 Copynumber: 4.2 Consensus size: 111
9872 AAGATCGATT
* ** *
9882 CTTTTTATAAAAAGTATTTATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGA
1 CTTTTTAT-AAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGA
*
9947 AACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATATATA
65 AACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTATATATA
* * **
9994 TTTTTTATAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCATTTTTGTCATAATGAA
1 CTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAA
* * *
10059 ACTGATTTTGTCATAGTTTTACCTGTTATATTGTAAAGTATCTATC
66 ACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTATATATA
* *
10105 CTTTTTATAAAAGGATCGATACTTTCAACATATCAGATAAATTTTACCGTTTTTGTCATAATGAA
1 CTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAA
* * *
10170 ACTAATTTTTTCATATTTTTACCTGTTATATTGTAAAGTATATATC
66 ACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTATATATA
* * *
10216 CTTTTTATAAAAGGATAGATACTTTCAACATATCAAGTAAATTTTACCGGTTTTGTCATTATGAA
1 CTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAA
* * * * **
10281 ATTGGTTTTGTCATATTTTTACCTGTTACATTGTAAAATATCGATA
66 ACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTATATATA
*
10327 CATTTTTAT-AAAGTATCGATACTTT
1 C-TTTTTATAAAAGGATCGATACTTT
10352 ATAAGCACTA
Statistics
Matches: 323, Mismatches: 34, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
111 309 0.96
112 14 0.04
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (111 bp):
CTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAA
ACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTATATATA
Found at i:10804 original size:23 final size:23
Alignment explanation
Indices: 10743--10805 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
10733 ACATATTTAA
** *
10743 TATATAAAAGCTACCTATTACGT
1 TATATAAGTGCTACCTATTACAT
*
10766 TATATAAGTGCAACCTATTACAT
1 TATATAAGTGCTACCTATTACAT
*
10789 TATATAAGTGGTACCTA
1 TATATAAGTGCTACCTA
10806 ATATAATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (23 bp):
TATATAAGTGCTACCTATTACAT
Found at i:10877 original size:87 final size:87
Alignment explanation
Indices: 10765--10923 Score: 255
Period size: 87 Copynumber: 1.8 Consensus size: 87
10755 ACCTATTACG
* * *
10765 TTATATAAGTGCAACCTATTACATTATATAAGTGGTACCTAATATAATATTGTGCTTAATAATGT
1 TTATATAAGCGCAACCTATTACATTATATAAGCGGTACCTAATATAATATTGTACTTAATAATGT
10830 TTCCAGTAATTAACATATTTTA
66 TTCCAGTAATTAACATATTTTA
* ** *
10852 TTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTATTTAATAATGT
1 TTATATAAGCGCAACCTATTACATTATATAAGCGGTACCTAATATAATATTGTACTTAATAATGT
10917 TTCCAGT
66 TTCCAGT
10924 TAAATGATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 65 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (87 bp):
TTATATAAGCGCAACCTATTACATTATATAAGCGGTACCTAATATAATATTGTACTTAATAATGT
TTCCAGTAATTAACATATTTTA
Found at i:10901 original size:23 final size:23
Alignment explanation
Indices: 10851--10895 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
10841 AACATATTTT
*
10851 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
10874 ATTATATAAGCGGTACCTAATA
1 ATTATATAAGCGCTACCTAATA
10896 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:13777 original size:56 final size:56
Alignment explanation
Indices: 13706--13822 Score: 216
Period size: 56 Copynumber: 2.1 Consensus size: 56
13696 GACGCCTATT
* *
13706 GCTGCGAAAGTAAGCCTCCAGCTGCTGCCAAAGCTGAAGCCGGTATCGTTCCGCTC
1 GCTGTGAAAGTAAGCCTCCAGCTGCTACCAAAGCTGAAGCCGGTATCGTTCCGCTC
13762 GCTGTGAAAGTAAGCCTCCAGCTGCTACCAAAGCTGAAGCCGGTATCGTTCCGCTC
1 GCTGTGAAAGTAAGCCTCCAGCTGCTACCAAAGCTGAAGCCGGTATCGTTCCGCTC
13818 GCTGT
1 GCTGT
13823 TGCCGCAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.21, C:0.31, G:0.26, T:0.21
Consensus pattern (56 bp):
GCTGTGAAAGTAAGCCTCCAGCTGCTACCAAAGCTGAAGCCGGTATCGTTCCGCTC
Found at i:18195 original size:127 final size:126
Alignment explanation
Indices: 17969--18621 Score: 975
Period size: 127 Copynumber: 5.2 Consensus size: 126
17959 TACTATTCAT
* *
17969 GTGAAGGCGCATTCCCGGGGGCGCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
*
18034 ATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGAGGACC
66 ATTATGTCACTTATGTCCCCC-GGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
* * *
18096 GTGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTTTTTTGTCAGAGAATATGTTATCATTTCCCT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
** ** *
18161 ATTATGTCACTTATGTCCCATTGGAACTATTCATGTCAATATATATTATTCCTTAGGGGACT
66 ATTATGTCACTTATGTCCC-CCGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
* *
18223 GTGAAGGCGTGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
** *
18288 ATTATGTCACTTATGTCCCCAAGAACTATTTATGTCAATACCTATTATTCCTTAGGGGACC
66 ATTATGTCACTTATGTCCCCCGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
* * *
18349 GTGAAGGTGCGTTCCCGGGGGCACGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* * *
18414 ATTATGTCACGTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGAGATC
66 ATTATGTCACTTATGTCCCCCG-GAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
* * * *
18476 GTGAAGACGCGTTCCCGGTGGCGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTTCCCT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* * *
18541 ATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATATCTACTATTTCTTAGGGGA-C
66 ATTATGTCACTTATGTCCCCCG-GAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
* * *
18602 TTTAAAGCGCGTTCCCGGGG
1 GTGAAGGCGCGTTCCCGGGG
18622 AACTATAGAT
Statistics
Matches: 473, Mismatches: 51, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
126 130 0.27
127 343 0.73
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (126 bp):
GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
ATTATGTCACTTATGTCCCCCGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
Found at i:18417 original size:253 final size:252
Alignment explanation
Indices: 17967--18621 Score: 983
Period size: 253 Copynumber: 2.6 Consensus size: 252
17957 GGTACTATTC
* *
17967 ATGTGAAGGCGCATTCCCGGGGGCGCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCC
1 ATGTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCC
* *
18032 CTATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGAGGACCG
65 CTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCG
** * * *
18097 TGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTTTTTTGTCAGAGAATATGTTATCATTTCCCTA
130 TGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTA
* ** * *
18162 TTATGTCACTTATGTCCCATTG-GAACTATTCATGTCAATATATATTATTCCTTAGGGG
195 TTATGTCACGTATGTCCC-CCGAGAACTATTCATGTCAATACATATTATTCCTTAGGAG
*
18220 ACTGTGAAGGCGTGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGC
1 A-TGTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGC
* *
18285 CCTATTATGTCACTTATGT-CCCCAAGAACTATTTATGTCAATACCTATTATTCCTTAGGGGACC
64 CCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
*
18349 GTGAAGGTGCGTTCCCGGGGGCACGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCT
129 GTGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCT
*
18414 ATTATGTCACGTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGAG
194 ATTATGTCACGTATGTCCCCCGAGAACTATTCATGTCAATACATATTATTCCTTAGGAG
* * *
18473 ATCGTGAAGACGCGTTCCCGGTGGCGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTTC
1 AT-GTGAAGGCGCGTTCCCGG-GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGC
* * *
18538 CCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATATCTACTATTTCTTAGGGGA-C
64 CCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
* * *
18602 TTTAAAGCGCGTTCCCGGGG
129 GTGAAGGCGCGTTCCCGGGG
18622 AACTATAGAT
Statistics
Matches: 364, Mismatches: 33, Indels: 10
0.89 0.08 0.02
Matches are distributed among these distances:
252 4 0.01
253 244 0.67
254 116 0.32
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (252 bp):
ATGTGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
TATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGT
GAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTAT
TATGTCACGTATGTCCCCCGAGAACTATTCATGTCAATACATATTATTCCTTAGGAG
Found at i:19069 original size:34 final size:34
Alignment explanation
Indices: 19031--19129 Score: 144
Period size: 34 Copynumber: 2.9 Consensus size: 34
19021 GAATTTAATG
*
19031 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
* * *
19065 TTAAATTTCGAATAATATTATTTGTATTTTAATT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
* *
19099 TTGAATTTGGAATACTATAATTTGTATTTTA
1 TTAAATTTCGAATACTATAATTTGTATTTTA
19130 TAAACATTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (34 bp):
TTAAATTTCGAATACTATAATTTGTATTTTAAAT
Found at i:19710 original size:21 final size:21
Alignment explanation
Indices: 19643--19711 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
19633 TATAGTATAA
*
19643 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
19664 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
19685 AACCCTGCGGGCTAGGAAAGT
1 AACCCTGCGGGCTAGGAATGT
19706 AACCCT
1 AACCCT
19712 TCGGAGATGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.25, C:0.26, G:0.32, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:21368 original size:19 final size:20
Alignment explanation
Indices: 21344--21394 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
21334 CGGCCAAGAG
* *
21344 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
21363 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
21383 CATGTATTTTCA
1 CATGTATTTTCA
21395 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:22149 original size:19 final size:19
Alignment explanation
Indices: 22096--22145 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
22086 TTGGAGTGCA
**
22096 AAAAGAAG-AGAAAA-ATC
1 AAAAGAAGAAGAAAAGAAG
22113 AAAAGAAGAAGAAAAGAAG
1 AAAAGAAGAAGAAAAGAAG
22132 AAAAGAA-AAGAAAA
1 AAAAGAAGAAGAAAA
22146 AGAATTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.28
18 13 0.45
19 8 0.28
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (19 bp):
AAAAGAAGAAGAAAAGAAG
Found at i:25539 original size:19 final size:20
Alignment explanation
Indices: 25515--25565 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
25505 CGGCCAAGAG
* *
25515 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
25534 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
25554 CATGTATTTTCA
1 CATGTATTTTCA
25566 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:27472 original size:14 final size:14
Alignment explanation
Indices: 27391--27474 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 14
27381 GCACAAAAAT
27391 TAATTA-ATTAATA
1 TAATTATATTAATA
* *
27404 -AATTTAAATAAATAA
1 TAA-TTATATTAAT-A
27419 TAATTATA-TAA-A
1 TAATTATATTAATA
*
27431 T-ATTATTTTAATA
1 TAATTATATTAATA
* ** *
27444 AAAAAATATTTATA
1 TAATTATATTAATA
27458 TAATTATATTAATA
1 TAATTATATTAATA
27472 TAA
1 TAA
27475 AATATAATAA
Statistics
Matches: 51, Mismatches: 13, Indels: 13
0.66 0.17 0.17
Matches are distributed among these distances:
11 5 0.10
12 7 0.14
13 4 0.08
14 28 0.55
15 5 0.10
16 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATTATATTAATA
Found at i:29715 original size:29 final size:29
Alignment explanation
Indices: 29672--29730 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
29662 AAAATTCTTA
*
29672 ACAAATATTACTTTATAATCACCTCAAAC
1 ACAAATATTACTTTATAATCACATCAAAC
*
29701 ACAAATATTATTTTATAATCACATCAAAC
1 ACAAATATTACTTTATAATCACATCAAAC
29730 A
1 A
29731 ATTCAAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.32
Consensus pattern (29 bp):
ACAAATATTACTTTATAATCACATCAAAC
Found at i:33601 original size:57 final size:57
Alignment explanation
Indices: 33515--33624 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
33505 GTCAAATCAT
* *
33515 TCAAATGTCGAGTGCTACAACTTCAGCAAGCATGGGCATTATGCAAAAGAGTGCAAA
1 TCAAATATCGAGTGCTACAACTTCAGCAAGCATGGGCACTATGCAAAAGAGTGCAAA
* * *
33572 TCAAATATCGAGTGCTATAA-TTGCGGCAAGCATGGGCACTATGCAAAGGAGTG
1 TCAAATATCGAGTGCTACAACTT-CAGCAAGCATGGGCACTATGCAAAAGAGTG
33625 TTATTCCGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
56 2 0.04
57 45 0.96
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (57 bp):
TCAAATATCGAGTGCTACAACTTCAGCAAGCATGGGCACTATGCAAAAGAGTGCAAA
Found at i:44796 original size:11 final size:11
Alignment explanation
Indices: 44780--44805 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44770 CGGCACGATA
44780 ATTTGTTAAGC
1 ATTTGTTAAGC
44791 ATTTGTTAAGC
1 ATTTGTTAAGC
44802 ATTT
1 ATTT
44806 CCCAGCCCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (11 bp):
ATTTGTTAAGC
Found at i:50526 original size:17 final size:17
Alignment explanation
Indices: 50504--50543 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
50494 AATTCCGGTG
* *
50504 TCCACAGTCTTGAGTGT
1 TCCACAGCCTTGAGCGT
50521 TCCACAGCCTTGAGCGT
1 TCCACAGCCTTGAGCGT
50538 TCCACA
1 TCCACA
50544 TAAATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.28
Consensus pattern (17 bp):
TCCACAGCCTTGAGCGT
Found at i:60145 original size:13 final size:14
Alignment explanation
Indices: 60117--60143 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
60107 CTTTGAGATG
60117 GAAAAGGAAAAAAA
1 GAAAAGGAAAAAAA
60131 GAAAAGGAAAAAA
1 GAAAAGGAAAAAA
60144 GATGGCTATA
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:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
GAAAAGGAAAAAAA
Found at i:70400 original size:2 final size:2
Alignment explanation
Indices: 70393--70441 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
70383 TTTATAAAAC
70393 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
70434 TA TA TA TA
1 TA TA TA TA
70442 CTTAGGTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:70637 original size:2 final size:2
Alignment explanation
Indices: 70630--70668 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
70620 AATCATAATA
*
70630 AT AT AT AT AT AT AG AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70669 TTCATGTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:71944 original size:139 final size:127
Alignment explanation
Indices: 71851--72074 Score: 359
Period size: 123 Copynumber: 1.8 Consensus size: 127
71841 CGTAGATGTT
* * * *
71851 GAATCAATC-TAAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCCTCTTTAGATGAGTT
1 GAATCAAGCGTAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTT
*
71915 CTTCTCATTATGAACTCTTCCTGGCAATGTTG----AAGTTGATCTATCTCCTTTTGTGATA
66 CTTCTCATTATGAACTCTTCCTGGCAATGTTGATCCAAGTTGATCTATCTCATTTTGTGATA
*
71973 GAATCAAGCGAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTT
1 GAATCAAGCGTAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTT
72038 CTTCTCATTATGAACTCTTCCTGGCAATGTTGATCCA
66 CTTCTCATTATGAACTCTTCCTGGCAATGTTGATCCA
72075 TCGAGTGATG
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
122 8 0.09
123 83 0.90
127 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (127 bp):
GAATCAAGCGTAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTT
CTTCTCATTATGAACTCTTCCTGGCAATGTTGATCCAAGTTGATCTATCTCATTTTGTGATA
Found at i:72599 original size:18 final size:18
Alignment explanation
Indices: 72576--72630 Score: 110
Period size: 18 Copynumber: 3.1 Consensus size: 18
72566 ATAAAAGAAT
72576 AAATTGAATTTCGAAAAG
1 AAATTGAATTTCGAAAAG
72594 AAATTGAATTTCGAAAAG
1 AAATTGAATTTCGAAAAG
72612 AAATTGAATTTCGAAAAG
1 AAATTGAATTTCGAAAAG
72630 A
1 A
72631 TAAACTTGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.27
Consensus pattern (18 bp):
AAATTGAATTTCGAAAAG
Found at i:73026 original size:13 final size:14
Alignment explanation
Indices: 72997--73062 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 14
72987 TTATTATTTC
*
72997 TTTCTTTCTTTCTT
1 TTTCTTTCTTCCTT
73011 TTTCTTT-TTCCTT
1 TTTCTTTCTTCCTT
73024 TTT-TTTCTTCCTCT
1 TTTCTTTCTTCCT-T
73038 TCTT-TATTCTT-CTT
1 T-TTCT-TTCTTCCTT
*
73052 TTTTTTTCTTC
1 TTTCTTTCTTC
73063 TTCAAGCATA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
12 3 0.07
13 20 0.44
14 12 0.27
15 5 0.11
16 5 0.11
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCTTTCTTCCTT
Found at i:73028 original size:16 final size:18
Alignment explanation
Indices: 72993--73032 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
72983 ATTATTATTA
*
72993 TTTCTTTCTTTCTTTCTT
1 TTTCTTTCTTCCTTTCTT
73011 TTTCTTT-TTCCTTT-TT
1 TTTCTTTCTTCCTTTCTT
73027 TTTCTT
1 TTTCTT
73033 CCTCTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 6 0.29
18 7 0.33
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTCTTTCTTCCTTTCTT
Found at i:73063 original size:16 final size:16
Alignment explanation
Indices: 73002--73065 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
72992 ATTTCTTTCT
* *
73002 TTCTTTCTTTTTCTTT
1 TTCTTTTTTTTTCTTC
*
73018 TTCCTTTTTTTTCTTC
1 TTCTTTTTTTTTCTTC
* * *
73034 CTCTTCTTTATTCTTC
1 TTCTTTTTTTTTCTTC
73050 TT-TTTTTTTCTTCTTC
1 TTCTTTTTTT-TTCTTC
73066 AAGCATAATA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
15 5 0.14
16 32 0.86
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (16 bp):
TTCTTTTTTTTTCTTC
Found at i:80014 original size:15 final size:15
Alignment explanation
Indices: 79976--80015 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
79966 ACTTATGATT
*
79976 AATGTATGAAAAATG
1 AATGTATGTAAAATG
79991 AATGTATGTAAAATG
1 AATGTATGTAAAATG
80006 AATGTATGTA
1 AATGTATGTA
80016 GAAAGGTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (15 bp):
AATGTATGTAAAATG
Found at i:83601 original size:2 final size:2
Alignment explanation
Indices: 83594--83626 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
83584 CATAATGAAT
83594 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 T
83627 TCATGTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:98258 original size:13 final size:13
Alignment explanation
Indices: 98240--98271 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
98230 GAAAAGTCGG
98240 GGAGGAGGGGGGA
1 GGAGGAGGGGGGA
98253 GGAGGAGGGGGGA
1 GGAGGAGGGGGGA
98266 GG-GGAG
1 GGAGGAG
98272 AGTTGAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.22, C:0.00, G:0.78, T:0.00
Consensus pattern (13 bp):
GGAGGAGGGGGGA
Found at i:98496 original size:12 final size:13
Alignment explanation
Indices: 98479--98511 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
98469 TTTCTTTTAT
98479 TTTTTAAAATA-A
1 TTTTTAAAATATA
98491 TTTTTAAAATATA
1 TTTTTAAAATATA
*
98504 ATTTTAAA
1 TTTTTAAA
98512 GAATATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTTAAAATATA
Found at i:98504 original size:14 final size:14
Alignment explanation
Indices: 98477--98518 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
98467 TATTTCTTTT
*
98477 ATTTTTTAAA-ATA
1 ATTTTTAAAATATA
98490 ATTTTTAAAATATA
1 ATTTTTAAAATATA
*
98504 ATTTTAAAGAATATA
1 ATTTTTAA-AATATA
98519 TTAAGTTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 9 0.36
14 10 0.40
15 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATTTTTAAAATATA
Found at i:98655 original size:13 final size:14
Alignment explanation
Indices: 98621--98654 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
98611 CAGTAATCTA
98621 AATTTTTACAATTT
1 AATTTTTACAATTT
*
98635 AATTTTTATAATTT
1 AATTTTTACAATTT
*
98649 TATTTT
1 AATTTT
98655 AATTATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
AATTTTTACAATTT
Found at i:115145 original size:186 final size:190
Alignment explanation
Indices: 114902--115254 Score: 552
Period size: 191 Copynumber: 1.8 Consensus size: 190
114892 AACCCGAACC
114902 CGACCCGAATATCACACTTAAAAAATCCGACCTGACCCGAACAAAATAAAGTTTCATCCGACCCG
1 CGACCCGAATATCACACTTAAAAAA-CC-ACCTGACCCGAACAAAATAAAGTTTCATCCGACCCG
* * *
114967 ACCCAAATATATTAATTAGAAAT-CCGACCCGACCTGAAATAATAAAAAATTATTTTTATTTAAT
64 ACCCAAATATATGAATTAGAAATCCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAAT
115031 AAAAACAGTGACTTAATCCGACCCGACCCGAATATCACACTTAAAAAAAACCCGACCAAACT
129 AAAAACAGTGACTTAATCCGACCCGACCCGAATATCACACTTAAAAAAAACCCGACCAAACT
* *
115093 CGACCCGAATATCACACTTAAAAAA-C-CC-GACCCGAACAAAATAAAGTTTCATCTGACCTGAC
1 CGACCCGAATATCACACTTAAAAAACCACCTGACCCGAACAAAATAAAGTTTCATCCGACCCGAC
*
115155 CCGAATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTA
66 CCAAATATATGAATTAGAAAT----CCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTA
* *
115220 ATAAAAACAGTGACTTAATCCGGCCCGACCTGAAT
127 ATAAAAACAGTGACTTAATCCGACCCGACCCGAAT
115255 TATATATATT
Statistics
Matches: 149, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
186 51 0.34
187 2 0.01
189 1 0.01
191 95 0.64
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (190 bp):
CGACCCGAATATCACACTTAAAAAACCACCTGACCCGAACAAAATAAAGTTTCATCCGACCCGAC
CCAAATATATGAATTAGAAATCCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAA
AAACAGTGACTTAATCCGACCCGACCCGAATATCACACTTAAAAAAAACCCGACCAAACT
Found at i:127597 original size:20 final size:20
Alignment explanation
Indices: 127572--127644 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
127562 TTTTCTTAAT
*
127572 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGATTACGTAAA
127592 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGATTACGTAAA
127612 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGATTACGTAAA
* *
127632 TCACAACGAGATT
1 TCGCAACGCGATT
127645 CTGACTATAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGATTACGTAAA
Found at i:128495 original size:24 final size:23
Alignment explanation
Indices: 128460--128512 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 23
128450 GTATTCGAAA
128460 TTTGATTTGGTCAATACCCGGAC
1 TTTGATTTGGTCAATACCCGGAC
* *
128483 TTTGATCTTGGTCAATACTCGGAT
1 TTTGAT-TTGGTCAATACCCGGAC
128507 TTTGAT
1 TTTGAT
128513 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.42
Consensus pattern (23 bp):
TTTGATTTGGTCAATACCCGGAC
Found at i:130528 original size:20 final size:20
Alignment explanation
Indices: 130498--130606 Score: 97
Period size: 20 Copynumber: 5.8 Consensus size: 20
130488 CAATCATCTT
*
130498 AATGTCTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
130518 AATTACTATCGCAACGCG--
1 AATGACTATCGCAACGCGAA
130536 -A-GA--ATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
* * *
130552 TATGAATATCGCAACGCGGA
1 AATGACTATCGCAACGCGAA
*
130572 AATGACTATCGCAATGCG-A
1 AATGACTATCGCAACGCGAA
**
130591 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
130607 AGAGAATCGC
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
14 11 0.15
16 1 0.01
17 2 0.03
18 2 0.03
19 14 0.19
20 43 0.59
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:130548 original size:34 final size:34
Alignment explanation
Indices: 130505--130671 Score: 162
Period size: 33 Copynumber: 4.9 Consensus size: 34
130495 CTTAATGTCT
* ** *
130505 ATCGCAACGCGAAAATTACTATCGCAACGCGAGA
1 ATCGCAACGCGAAAATGAAAATCGCAACGAGAGA
* * *
130539 ATCGCAACGCGAATATGAATATCGCAACGCGGAAATGA
1 ATCGCAACGCGAAAATGAAAATCGCAA--C-GAGA-GA
*
130577 CTATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
1 --ATCGCAACGCGAAAATGAAAATCGCAACGAGAGA
*
130612 ATCGCAATGCG-AAATGAAAATCGCAACGAG-GA
1 ATCGCAACGCGAAAATGAAAATCGCAACGAGAGA
*
130644 ATCGCAAAGCG-AAATGAAAATCGCAACG
1 ATCGCAACGCGAAAATGAAAATCGCAACG
130672 GGAATTTAGT
Statistics
Matches: 117, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
32 29 0.25
33 30 0.26
34 24 0.21
35 2 0.02
36 4 0.03
37 3 0.03
38 2 0.02
39 13 0.11
40 10 0.09
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGAAAATCGCAACGAGAGA
Found at i:130621 original size:33 final size:33
Alignment explanation
Indices: 130525--130671 Score: 179
Period size: 33 Copynumber: 4.3 Consensus size: 33
130515 GAAAATTACT
* * *
130525 ATCGCAACGCGAGAATCGCAACGCGAATATGAAT
1 ATCGCAACGAGAGAATCGCAATGCGAA-ATGAAA
*
130559 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAA
1 ATCGCAA--C-GAGA-GA--ATCGCAATGCGAAATGAAA
130598 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
*
130631 ATCGCAACGAG-GAATCGCAAAGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
130663 ATCGCAACG
1 ATCGCAACG
130672 GGAATTTAGT
Statistics
Matches: 101, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
32 29 0.29
33 30 0.30
34 7 0.07
35 2 0.02
36 4 0.04
37 3 0.03
38 2 0.02
39 12 0.12
40 12 0.12
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:130698 original size:19 final size:19
Alignment explanation
Indices: 130676--130733 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
130666 GCAACGGGAA
*
130676 TTTAGTTTCGCGTTGTGAT
1 TTTAGTTTCGCGTTGCGAT
130695 TTTAGTTTCGCGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
*
130714 TTTCA-TTTCGCATTGCGAT
1 TTT-AGTTTCGCGTTGCGAT
130733 T
1 T
130734 CATTTTTGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 35 0.97
20 1 0.03
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (19 bp):
TTTAGTTTCGCGTTGCGAT
Found at i:136155 original size:21 final size:21
Alignment explanation
Indices: 136131--136200 Score: 50
Period size: 21 Copynumber: 3.3 Consensus size: 21
136121 TCATTCCTCG
136131 AGAGCCCCCTCCCACCGTTCA
1 AGAGCCCCCTCCCACCGTTCA
* * ** ** *
136152 AGAGGCCACTGTCGTCGTTGA
1 AGAGCCCCCTCCCACCGTTCA
** *
136173 AGAGGTCCCTCCCACCATTCA
1 AGAGCCCCCTCCCACCGTTCA
136194 AGAGCCC
1 AGAGCCC
136201 GATTCACATT
Statistics
Matches: 32, Mismatches: 17, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.17
Consensus pattern (21 bp):
AGAGCCCCCTCCCACCGTTCA
Found at i:137825 original size:14 final size:14
Alignment explanation
Indices: 137806--137841 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
137796 ATTGTTTAAT
137806 TGATTTGTAAAAAA
1 TGATTTGTAAAAAA
**
137820 TGATTTGTAAAAGT
1 TGATTTGTAAAAAA
137834 TGATTTGT
1 TGATTTGT
137842 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAAA
Found at i:138121 original size:24 final size:24
Alignment explanation
Indices: 138087--138140 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
138077 CTGAAAAATC
138087 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
138111 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
138135 ATCAAA
1 ATCAAA
138141 TTTCGAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:138154 original size:24 final size:24
Alignment explanation
Indices: 138087--138154 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
138077 CTGAAAAATC
* * *
138087 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
138111 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
138135 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
138155 TAGTACTCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:138497 original size:12 final size:12
Alignment explanation
Indices: 138480--138504 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
138470 GTTTAATTTC
138480 ATTTGTAACACG
1 ATTTGTAACACG
138492 ATTTGTAACACG
1 ATTTGTAACACG
138504 A
1 A
138505 ACAATTAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ATTTGTAACACG
Found at i:142827 original size:21 final size:21
Alignment explanation
Indices: 142786--142832 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
142776 TAACCGTCGA
*
142786 TATT-TATTATTTTTTTATTT
1 TATTATATTATTATTTTATTT
142806 TATTATATTATATATTTT-TTT
1 TATTATATTAT-TATTTTATTT
*
142827 TCTTAT
1 TATTAT
142833 TTTGTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 14 0.61
22 5 0.22
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (21 bp):
TATTATATTATTATTTTATTT
Found at i:147935 original size:15 final size:16
Alignment explanation
Indices: 147905--147939 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
147895 GCGATGCATG
*
147905 AAATAAATTTTTTTAA
1 AAATAAATTATTTTAA
147921 AAATAAA-TATTTTAA
1 AAATAAATTATTTTAA
147936 AAAT
1 AAAT
147940 CAAGATAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATAAATTATTTTAA
Found at i:153156 original size:18 final size:19
Alignment explanation
Indices: 153120--153156 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
153110 CACGGAATGT
153120 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
153140 AAGATTACCAG-GGAATA
1 AAGATTACCAGAGGAATA
153157 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:155899 original size:30 final size:30
Alignment explanation
Indices: 155863--155964 Score: 149
Period size: 30 Copynumber: 3.5 Consensus size: 30
155853 ATTCTTTAAA
*
155863 AAAACTAGTGATATTCCGTCGCTATTCTTT
1 AAAACTAGTGATATTCCGTCTCTATTCTTT
155893 AAAACTAGTG--ATT--GTCTCTATTCTTT
1 AAAACTAGTGATATTCCGTCTCTATTCTTT
*
155919 AAAACTAGTGATGTTCCGTCTCTATTCTTT
1 AAAACTAGTGATATTCCGTCTCTATTCTTT
*
155949 AAAACTAGGGATATTC
1 AAAACTAGTGATATTC
155965 TGGCGTTGTA
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
26 22 0.34
28 5 0.08
30 37 0.58
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (30 bp):
AAAACTAGTGATATTCCGTCTCTATTCTTT
Found at i:166912 original size:39 final size:40
Alignment explanation
Indices: 166862--166971 Score: 129
Period size: 39 Copynumber: 2.8 Consensus size: 40
166852 TGCGATTTTC
* *
166862 CAAATTCGCAACACTGA-ATTTTAAATTCGCAACA-AAAA-T
1 CAAATTCGCAACAC-GATA-GTCAAATTCGCAACACAAAAGT
*
166901 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACACGATAGTCAAATTCGCAACACAAAAGT
* *
166941 -AAATTCGCAACGCGATAGTCAAATTCACAAC
1 CAAATTCGCAACACGATAGTCAAATTCGCAAC
166972 GCGAAACACA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
38 15 0.23
39 48 0.75
40 1 0.02
ACGTcount: A:0.44, C:0.24, G:0.12, T:0.21
Consensus pattern (40 bp):
CAAATTCGCAACACGATAGTCAAATTCGCAACACAAAAGT
Found at i:166925 original size:20 final size:20
Alignment explanation
Indices: 166900--166975 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
166890 GCAACAAAAA
166900 TCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACGCGATAG
* * *
166920 TCAAATTCGCAACACAAAAG
1 TCAAATTCGCAACGCGATAG
166940 T-AAATTCGCAACGCGATAG
1 TCAAATTCGCAACGCGATAG
*
166959 TCAAATTCACAACGCGA
1 TCAAATTCGCAACGCGA
166976 AACACAATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.33
20 32 0.67
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (20 bp):
TCAAATTCGCAACGCGATAG
Found at i:166933 original size:38 final size:39
Alignment explanation
Indices: 166884--166971 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 39
166874 ACTGAATTTT
166884 AAATTCGCAACA-AAAA-TCAAATTCGCAACGCGATAGTC
1 AAATTCGCAACACAAAAGT-AAATTCGCAACGCGATAGTC
166922 AAATTCGCAACACAAAAGTAAATTCGCAACGCGATAGTC
1 AAATTCGCAACACAAAAGTAAATTCGCAACGCGATAGTC
*
166961 AAATTCACAAC
1 AAATTCGCAAC
166972 GCGAAACACA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
38 12 0.26
39 34 0.72
40 1 0.02
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.18
Consensus pattern (39 bp):
AAATTCGCAACACAAAAGTAAATTCGCAACGCGATAGTC
Found at i:167112 original size:22 final size:22
Alignment explanation
Indices: 167087--167137 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
167077 CTACGGCGGC
*
167087 ATCCGTCCCCATCTCCGATGAA
1 ATCCGTCCCCATCTCCGACGAA
*
167109 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
167131 ATCCGTC
1 ATCCGTC
167138 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:171214 original size:59 final size:59
Alignment explanation
Indices: 171119--171231 Score: 201
Period size: 59 Copynumber: 1.9 Consensus size: 59
171109 TTTTACATTG
171119 AAAGTTGATTTGTTTAATTGATGAGTAAATAAGAATTA-TTTTTTGCTTGTTTATTGTA
1 AAAGTTGATTTGTTTAATTGATGAGTAAATAAGAATTATTTTTTTGCTTGTTTATTGTA
*
171177 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTA
1 AAAGTTGATTTGTTTAA-TTGATGAGTAAATAAGAATTATTTTTTTGCTTGTTTA
171232 ATTGATTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
58 17 0.33
59 20 0.38
60 15 0.29
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.51
Consensus pattern (59 bp):
AAAGTTGATTTGTTTAATTGATGAGTAAATAAGAATTATTTTTTTGCTTGTTTATTGTA
Found at i:171335 original size:20 final size:20
Alignment explanation
Indices: 171310--171359 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
171300 GTTGAAGGTA
171310 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
171330 CAAATTCGCAACGCTAAAGT
1 CAAATTCGCAACGCGAAAGT
171350 CAAATTCGCA
1 CAAATTCGCA
171360 TTGCGATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:183302 original size:12 final size:12
Alignment explanation
Indices: 183281--183314 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
183271 GGTTGTGGGT
*
183281 TTTGAGATTGTG
1 TTTGATATTGTG
183293 TTTGATATTGTG
1 TTTGATATTGTG
*
183305 TTTGGTATTG
1 TTTGATATTG
183315 GAAATGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:183938 original size:14 final size:15
Alignment explanation
Indices: 183902--183939 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
183892 AGAAATCATT
183902 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
183917 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
183932 AAAAATTA
1 AAAAATTA
183940 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:184116 original size:19 final size:19
Alignment explanation
Indices: 184091--184197 Score: 83
Period size: 19 Copynumber: 6.0 Consensus size: 19
184081 AAACTAAAAC
184091 CTGTTGCGAATTT-AAATT
1 CTGTTGCGAATTTGAAATT
*
184109 CGTGTTGCGAATTTGAAAAT
1 C-TGTTGCGAATTTGAAATT
*
184129 CTAGTTGCGGATTTGAAA--
1 CT-GTTGCGAATTTGAAATT
184147 ---TT-C-AATTT-AAATT
1 CTGTTGCGAATTTGAAATT
184160 CGTGTTGCGAATTTGAAA-T
1 C-TGTTGCGAATTTGAAATT
184179 CTAGTTGCG-ATTTGAAATT
1 CT-GTTGCGAATTTGAAATT
184198 TTGAATTTGA
Statistics
Matches: 72, Mismatches: 3, Indels: 27
0.71 0.03 0.26
Matches are distributed among these distances:
11 3 0.04
12 4 0.06
13 1 0.01
14 2 0.03
17 2 0.03
18 11 0.15
19 27 0.38
20 22 0.31
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (19 bp):
CTGTTGCGAATTTGAAATT
Found at i:184137 original size:20 final size:20
Alignment explanation
Indices: 184092--184146 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
184082 AACTAAAACC
*
184092 TGTTGCGAATTT-AAATTCG
1 TGTTGCGAATTTGAAAATCG
184111 TGTTGCGAATTTGAAAATC-
1 TGTTGCGAATTTGAAAATCG
*
184130 TAGTTGCGGATTTGAAA
1 T-GTTGCGAATTTGAAA
184147 TTCAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (20 bp):
TGTTGCGAATTTGAAAATCG
Found at i:184205 original size:51 final size:50
Alignment explanation
Indices: 184098--184228 Score: 183
Period size: 51 Copynumber: 2.5 Consensus size: 50
184088 AACCTGTTGC
184098 GAATTTAAATTCGTGTTGCGAATTTGAAAATCTAGTTGCGGATTTGAAATT
1 GAATTTAAATTCGTGTTGCGAATTTG-AAATCTAGTTGCGGATTTGAAATT
*
184149 CAATTTAAATTCGTGTTGCGAATTTGAAATCTAGTTGC-GATTTGAAATTTT
1 GAATTTAAATTCGTGTTGCGAATTTGAAATCTAGTTGCGGATTTGAAA--TT
* *
184200 GAATTTGAAATTCCGCGTTACGAATTTGA
1 GAATTT-AAATT-CGTGTTGCGAATTTGA
184229 TTTTTTGTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
49 9 0.12
50 12 0.17
51 32 0.44
52 5 0.07
53 14 0.19
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.40
Consensus pattern (50 bp):
GAATTTAAATTCGTGTTGCGAATTTGAAATCTAGTTGCGGATTTGAAATT
Found at i:184297 original size:40 final size:37
Alignment explanation
Indices: 184235--184384 Score: 122
Period size: 40 Copynumber: 3.8 Consensus size: 37
184225 TTGATTTTTT
*
184235 GTGTTGCGAATTTGAC-TATCGCGTTGTGAATTTGACTTC
1 GTGTTGCG-ATTT-ACAT-TCGCGTTGCGAATTTGACTTC
184274 TGTGTTGCGATTTACAGATTCGCGTTGCGAATTTGACTATC
1 -GTGTTGCGATTTAC--ATTCGCGTTGCGAATTTGACT-TC
* * * * *
184315 GCGTTGTGAATTTGACTTTTGTGTTGCGAATTTGACTTCC
1 GTGTTGCG-ATTT-ACATTCGCGTTGCGAATTTGACTT-C
*
184355 GTGTTGCGATTTACGTATTAGCGTTGCGAA
1 GTGTTGCGATTTAC--ATTCGCGTTGCGAA
184385 ATTAGAAACT
Statistics
Matches: 90, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
38 4 0.04
39 9 0.10
40 68 0.76
41 7 0.08
42 2 0.02
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41
Consensus pattern (37 bp):
GTGTTGCGATTTACATTCGCGTTGCGAATTTGACTTC
Found at i:184352 original size:20 final size:20
Alignment explanation
Indices: 184220--184363 Score: 123
Period size: 20 Copynumber: 7.2 Consensus size: 20
184210 TTCCGCGTTA
* *
184220 CGAATTTGATTTTTTGTGTTG
1 CGAATTTGA-CTTTCGTGTTG
* *
184241 CGAATTTGACTATCGCGTTG
1 CGAATTTGACTTTCGTGTTG
*
184261 TGAATTTGAC-TTCTGTGTTG
1 CGAATTTGACTTTC-GTGTTG
* *
184281 CG-ATTT-ACAGATTCGCGTTG
1 CGAATTTGAC--TTTCGTGTTG
* *
184301 CGAATTTGACTATCGCGTTG
1 CGAATTTGACTTTCGTGTTG
* *
184321 TGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTCGTGTTG
*
184341 CGAATTTGACTTCCGTGTTG
1 CGAATTTGACTTTCGTGTTG
184361 CGA
1 CGA
184364 TTTACGTATT
Statistics
Matches: 99, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
18 2 0.02
19 6 0.06
20 73 0.74
21 16 0.16
22 2 0.02
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.43
Consensus pattern (20 bp):
CGAATTTGACTTTCGTGTTG
Found at i:184361 original size:60 final size:58
Alignment explanation
Indices: 184235--184363 Score: 188
Period size: 60 Copynumber: 2.2 Consensus size: 58
184225 TTGATTTTTT
184235 GTGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTTCTGTGTTGCGATTTACAGATTC
1 GTGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTTCTGTGTTGCGATTTAC--ATTC
* *
184295 GCGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTTTTGTGTTGCGAATTTGAC-TTCC
1 GTGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTTCTGTGTTGCG-ATTT-ACATT-C
184355 GTGTTGCGA
1 GTGTTGCGA
184364 TTTACGTATT
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
59 2 0.03
60 55 0.87
61 4 0.06
62 2 0.03
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.41
Consensus pattern (58 bp):
GTGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTTCTGTGTTGCGATTTACATTC
Found at i:191502 original size:23 final size:22
Alignment explanation
Indices: 191468--191511 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
191458 CAAAATTACA
* **
191468 AAAATATAATAATTTTATTTAT
1 AAAATACAATAAAATTATTTAT
191490 AAAATACAGATAAAATTATTTA
1 AAAATACA-ATAAAATTATTTA
191512 GGAATATATG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
AAAATACAATAAAATTATTTAT
Found at i:193857 original size:17 final size:18
Alignment explanation
Indices: 193818--193864 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
193808 TGTTTATGAG
*
193818 GGAATTGAAATATGTGAA
1 GGAATTGAAATCTGTGAA
*
193836 GGAATTGAAATCTGT-CA
1 GGAATTGAAATCTGTGAA
*
193853 GGAATTGGAATC
1 GGAATTGAAATC
193865 CAATTTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.38, C:0.06, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAATTGAAATCTGTGAA
Found at i:196391 original size:18 final size:18
Alignment explanation
Indices: 196368--196415 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
196358 TATATGGTTT
196368 TAAAATATAAAATTCTAC
1 TAAAATATAAAATTCTAC
*
196386 TAAAAT-TATAAGTTCTAC
1 TAAAATATA-AAATTCTAC
* *
196404 CAAAACATAAAA
1 TAAAATATAAAA
196416 ATATCATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAATATAAAATTCTAC
Found at i:199279 original size:29 final size:30
Alignment explanation
Indices: 199229--199291 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
199219 AAACATAATG
*
199229 AATAGCCAAATAAATATTTTTGTAATTTTT
1 AATAGCCAAATAAATATTTTTGTAACTTTT
*
199259 AATAGCC-AATAGATCA-TTTTGTAACTTTT
1 AATAGCCAAATAAAT-ATTTTTGTAACTTTT
199288 AATA
1 AATA
199292 TTCAAATGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.43
Consensus pattern (30 bp):
AATAGCCAAATAAATATTTTTGTAACTTTT
Found at i:199565 original size:23 final size:23
Alignment explanation
Indices: 199520--199562 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
199510 ATCATTTTTA
*
199520 CTAAAAAATTTAATTAAATAATT
1 CTAAAAAATCTAATTAAATAATT
*
199543 CTAAAAAA-CTAATTCAATAA
1 CTAAAAAATCTAATTAAATAA
199563 ATTGATTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (23 bp):
CTAAAAAATCTAATTAAATAATT
Found at i:203078 original size:19 final size:19
Alignment explanation
Indices: 203027--203079 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
203017 TTGTTTTTTG
*
203027 ATTAATTATTAT-TATTAA
1 ATTAATTATTATAAATTAA
203045 ATTAATTAATT-TAAATTAA
1 ATTAATT-ATTATAAATTAA
*
203064 ATTAAATATTATAAAT
1 ATTAATTATTATAAAT
203080 ATTAATTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTAATTATTATAAATTAA
Found at i:207897 original size:19 final size:18
Alignment explanation
Indices: 207869--207907 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
207859 TATAAATTTA
*
207869 ATTTATTAATGGTTAATC
1 ATTTATTAATCGTTAATC
207887 ATTTCATTAATCGTTAATC
1 ATTT-ATTAATCGTTAATC
207906 AT
1 AT
207908 CATTTTTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (18 bp):
ATTTATTAATCGTTAATC
Found at i:210299 original size:35 final size:35
Alignment explanation
Indices: 210225--210292 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
210215 TTCATGTTTA
210225 AAATTCCAAAACACTTCAATTATATTCTAAACCCC
1 AAATTCCAAAACACTTCAATTATATTCTAAACCCC
* * * *
210260 AAATTCCAAAATATTTTAATTATTTTCTAAACC
1 AAATTCCAAAACACTTCAATTATATTCTAAACC
210293 TTAAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTATATTCTAAACCCC
Found at i:217608 original size:63 final size:63
Alignment explanation
Indices: 217523--217643 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 63
217513 TTTAAAATAA
* *
217523 AAACATCGAATGCCATCAGTGTATCGATGCACAAGTAGTGCATCGATGCACCCCTTAATATTC
1 AAACATCGAATGCCATCAGTGTACCGATGCACAAGTAGTGCATCAATGCACCCCTTAATATTC
** ** * *
217586 AAACATCGAATGGGATTTGTGTACCGATGCACAGGTAGTGCATCAATGCACCCGTTAA
1 AAACATCGAATGCCATCAGTGTACCGATGCACAAGTAGTGCATCAATGCACCCCTTAA
217644 GGGATGCATC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 50 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (63 bp):
AAACATCGAATGCCATCAGTGTACCGATGCACAAGTAGTGCATCAATGCACCCCTTAATATTC
Found at i:218000 original size:32 final size:32
Alignment explanation
Indices: 217938--218001 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
217928 TACTCATGTA
*
217938 CATGCATACATATATTATTTTTATAGTGATAT
1 CATGCATACATATATTATTTTAATAGTGATAT
*
217970 CATGCATA-ATTTATTATGCTTTAATA-TGATAT
1 CATGCATACATATATTAT--TTTAATAGTGATAT
218002 TATGTGAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 8 0.29
32 14 0.50
33 6 0.21
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (32 bp):
CATGCATACATATATTATTTTAATAGTGATAT
Found at i:218211 original size:22 final size:22
Alignment explanation
Indices: 218186--218369 Score: 231
Period size: 22 Copynumber: 8.7 Consensus size: 22
218176 GAGGGTTTAT
* *
218186 AGTGGTCATTCGGGACATATCC
1 AGTGGTCCTTCGGGACGTATCC
218208 AGTGGTCCTTCGGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
*
218230 AGTGGTCCTTCAGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
*
218252 AGTGGTCATTCGGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
*
218274 AGTGGTCCTTCGGGATGTATCC
1 AGTGGTCCTTCGGGACGTATCC
218296 AGTGGTCCTTCGGGACG--T--
1 AGTGGTCCTTCGGGACGTATCC
*
218314 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACGTATCC
* * *
218336 AATGGTTCTTAGGGACGTA---
1 AGTGGTCCTTCGGGACGTATCC
218355 A-TGGTCCTTCGGGAC
1 AGTGGTCCTTCGGGAC
218370 AAATATTTAC
Statistics
Matches: 143, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
18 28 0.20
19 1 0.01
20 2 0.01
22 112 0.78
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.28
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACGTATCC
Found at i:224433 original size:22 final size:22
Alignment explanation
Indices: 224405--224546 Score: 122
Period size: 22 Copynumber: 6.8 Consensus size: 22
224395 CGAGGGTTTA
*
224405 TAGTGGTCCTTCGGGATATATC
1 TAGTGGTCCTTCGGGACATATC
*
224427 TAGTGGTCCTTCGGGACGTATC
1 TAGTGGTCCTTCGGGACATATC
* * *
224449 CAGTGGTCATTCGGGACGTATC
1 TAGTGGTCCTTCGGGACATATC
* * *
224471 CAGTGGTCTTTCGGGAC----G
1 TAGTGGTCCTTCGGGACATATC
224489 TAGTGGTCCTTCGGGACATAT-
1 TAGTGGTCCTTCGGGACATATC
* *
224510 TCAGTGGTCCTTAGGGACGTA--
1 T-AGTGGTCCTTCGGGACATATC
224531 -A-TGGTCCTTCGGGACA
1 TAGTGGTCCTTCGGGACA
224547 AATATTCACT
Statistics
Matches: 103, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
18 28 0.27
19 1 0.01
21 1 0.01
22 73 0.71
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (22 bp):
TAGTGGTCCTTCGGGACATATC
Found at i:224505 original size:40 final size:40
Alignment explanation
Indices: 224405--224546 Score: 176
Period size: 40 Copynumber: 3.5 Consensus size: 40
224395 CGAGGGTTTA
* *
224405 TAGTGGTCCTTCGGGATATATCTAGTGGTCCTTCGGGACG
1 TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGACG
* * *
224445 TATCCAGTGGTCATTCGGGACGTATCCAGTGGTCTTTCGGGACG
1 --T--AGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGACG
* *
224489 TAGTGGTCCTTCGGGACATATTCAGTGGTCCTTAGGGACG
1 TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGACG
*
224529 TAATGGTCCTTCGGGACA
1 TAGTGGTCCTTCGGGACA
224547 AATATTCACT
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
40 51 0.59
42 2 0.02
44 34 0.39
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (40 bp):
TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGACG
Found at i:232356 original size:23 final size:23
Alignment explanation
Indices: 232326--232398 Score: 137
Period size: 23 Copynumber: 3.2 Consensus size: 23
232316 ATACTTTACA
232326 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
232349 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
232372 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
232395 ATAT
1 ATAT
232399 TTTTACCTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:232442 original size:22 final size:22
Alignment explanation
Indices: 232417--232461 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
232407 AATATATTGT
*
232417 AAAGCATCGATCCTTTTTATAA
1 AAAGCATCGATACTTTTTATAA
* *
232439 AAAGGATCGATACTTTTTTTAA
1 AAAGCATCGATACTTTTTATAA
232461 A
1 A
232462 GTTATGTAAT
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:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (22 bp):
AAAGCATCGATACTTTTTATAA
Found at i:232852 original size:23 final size:23
Alignment explanation
Indices: 232817--232889 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
232807 ATACTTTACA
* *
232817 ATATAAGCACTACATATTACATT
1 ATATAAGCGCTACCTATTACATT
*
232840 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
232863 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
232886 ATAT
1 ATAT
232890 TTTTACCTGT
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:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:233128 original size:490 final size:490
Alignment explanation
Indices: 231928--233803 Score: 3158
Period size: 491 Copynumber: 3.8 Consensus size: 490
231918 TTATAATATG
231928 TTGAAAGTGTCCATACTTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
* * *
231993 TTCAA---TTTTTAATAGTGTTTTATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTGC
65 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
*
232055 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA
232120 TTAACCAAAGATAATAATAAATATGT-A-ATATATG-TTATTGTTTTTAATTTAATGATAATATA
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATA
* * *
232182 TACCGTAACATAAAAAATAAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCAC
260 TACCGTAACGTAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCAC
* * * *
232247 TCAAAAGATAACCTTAAATTAATGTTTTCTACAATGAAATAAGTATGGACACTTCTATAAAAAGG
325 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
* * *
232312 ATAGATACTTTACAATATAAGCGCTACCTATTACATTATATAAGCGCTACCTATTACATTATATA
390 ATAGATACTTTACAATATAAGCACTACATATTACATTATATAAACGCTACCTATTACATTATATA
*
232377 AGCGCTACCTATTACATCATATTTTTACCTAATATA
455 AGCGCTACCTATTACATCATATTTTTACCTATTATA
** * * *
232413 TTGTAAAGCATCGATCCTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTG-AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
* *
232478 TTCAATTTTTTTTAATAGTGTTTCATGTTTTTCACCTCCAATATTAATTTAATAATTTCATTTAC
65 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
* *
232543 ACAAAAAATTATTTAATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAATAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA
* *
232608 TTAACCAAATATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATA
*
232673 TACCGTAACGTAAAAAATAAATCATTAGACACATATAATTACTAAATTGATATCTTAAAACTCAC
260 TACCGTAACGTAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCAC
* *
232738 TCAAAAGATAACCTTAAATTAATGTTTTCTACAGTGAAAAAAGTATGAACACTTTTATAAAAAGG
325 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
232803 ATAGATACTTTACAATATAAGCACTACATATTACATTATATAAACGCTACCTATTACATTATATA
390 ATAGATACTTTACAATATAAGCACTACATATTACATTATATAAACGCTACCTATTACATTATATA
*
232868 AGCGCTACCTATTACATCATATTTTTACCTGTTATA
455 AGCGCTACCTATTACATCATATTTTTACCTATTATA
* * * *
232904 TTGAAATTGTCCATATTTTTTATAAAAAAAGATCGATATTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTAT-AAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
232969 TTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
65 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
233033 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA
233098 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTTAATTTAATGATAATAT
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTG-TTTTTAATTTAATGATAATAT
* * *
233163 ATACCGTAACGT-AAAAA-AAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAACCTCA
259 ATACCGTAACGTAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCA
* *
233226 CTCAAAAGATAACCTTAAATTAATATTTTCCACAGTTAAAAAAGTATGGACACTTTTATAAAAAG
324 CTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAG
*
233291 GATAGATACTTTACAATATAAGCACTACTTATTACATTATATAAACGCTACCTATTACATTATAT
389 GATAGATACTTTACAATATAAGCACTACATATTACATTATATAAACGCTACCTATTACATTATAT
*
233356 AAGCGTTACCTATTACATCATATTTTTACCTATTATA
454 AAGCGCTACCTATTACATCATATTTTTACCTATTATA
* *
233393 TTTAAAGTGTCCATACTTTTTATAAAAATGATCGATATTTTTTTTAAAGTTATATGTAATTTATG
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAG-T-TATGTAATTTATG
* * *
233458 TTTCAATTTTTTTTAACAGTGTTTCATATTTTTCACCTACAATATTAATTTAATAATTTCATTTA
64 TTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTA
*
233523 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAAT
129 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAAT
233588 ATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATAT
194 ATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATAT
* * *
233653 ATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTTA
259 ATACCGTAACGTAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCA
* *
233718 CTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTTAAAAAAGTATGGACACTTTTATAAAAAT
324 CTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAG
*
233783 GATAAATACTTTACAATATAA
389 GATAGATACTTTACAATATAA
233804 CAGGTAAAAA
Statistics
Matches: 1313, Mismatches: 64, Indels: 21
0.94 0.05 0.02
Matches are distributed among these distances:
485 55 0.04
486 9 0.01
488 164 0.12
489 224 0.17
490 240 0.18
491 494 0.38
492 127 0.10
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (490 bp):
TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAT
TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATAT
ACCGTAACGTAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCACT
CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
TAGATACTTTACAATATAAGCACTACATATTACATTATATAAACGCTACCTATTACATTATATAA
GCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:233341 original size:23 final size:23
Alignment explanation
Indices: 233306--233378 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
233296 ATACTTTACA
* *
233306 ATATAAGCACTACTTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
233329 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
233352 ATATAAGCGTTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
233375 ATAT
1 ATAT
233379 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:233773 original size:981 final size:976
Alignment explanation
Indices: 231928--233803 Score: 3220
Period size: 981 Copynumber: 1.9 Consensus size: 976
231918 TTATAATATG
*
231928 TTGAAAGTGTCCATACTTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
* * *
231993 TTCAATTTTTAATAGTGTTTTATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTGCACA
66 TTCAATTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACA
232058 AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTA
131 AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTA
232123 ACCAAAGATAATAATAAATATGTAATATATGTTATTGTTTTTAATTTAATGATAATATATACCGT
196 ACCAAAGATAATAATAAATATGTAATATATGTTATTGTTTTTAATTTAATGATAATATATACCGT
* *
232188 AACATAAAAAATAAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCACTCAAAA
261 AACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCACTCAAAA
* * *
232253 GATAACCTTAAATTAATGTTTTCTACAATGAAATAAGTATGGACACTTCTATAAAAAGGATAGAT
326 GATAACCTTAAATTAATATTTTCCACAATGAAAAAAGTATGGACACTTCTATAAAAAGGATAGAT
* *
232318 ACTTTACAATATAAGCGCTACCTATTACATTATATAAGCGCTACCTATTACATTATATAAGCGCT
391 ACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCT
* *
232383 ACCTATTACATCATATTTTTACCTAATATATTGTAAAGCATCGATCCTTTTTATAAAAAGGATCG
456 ACCTATTACATCATATTTTTACCTAATATATTGTAAAGCATCCATACTTTTTATAAAAAGGATCG
* *
232448 ATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTTCAC
521 ATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAACAGTGTTTCATATTTTTCAC
*
232513 CTCCAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTAATTGTTTTGATATTTTATAA
586 CTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTAATTGTTTTGATATTTTATAA
* *
232578 AATATTATTTAGAATTTAAATTTAATAATATTAACCAAATATAATAATAAATATGTAATATATAT
651 AATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATAT
232643 GTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACACATA
716 GTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACACATA
* *
232708 TAATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCTACAGT
781 TAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGT
*
232773 GAAAAAAGTATGAACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACATATTACA
846 GAAAAAAGTATGAACACTTTTATAAAAAGGATAAATACTTTACAATATAAGCACTACATATTACA
232838 TTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTGTTAT
911 TTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTGTTAT
232903 A
976 A
* *
232904 TTGAAATTGTCCATA-TTTTTTATAAAAAAAGATCGATATTTTTTTTAAAGTTATGTAATTTATG
1 TTGAAAGTGTCCATACTTTTTTAT-AAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATG
232968 TTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
65 TTTCAA--TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
*
233033 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA
128 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
233098 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTTAATTTAATGATAATAT
193 TTAACCAAAGATAATAATAAATATGT-A-ATATATG-TTATTG-TTTTTAATTTAATGATAATAT
* * * *
233163 ATACCGTAACGT-AAAAA-AAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAACCTCA
254 ATACCGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCA
* * *
233226 CTCAAAAGATAACCTTAAATTAATATTTTCCACAGTTAAAAAAGTATGGACACTTTTATAAAAAG
319 CTCAAAAGATAACCTTAAATTAATATTTTCCACAATGAAAAAAGTATGGACACTTCTATAAAAAG
*
233291 GATAGATACTTTACAATATAAGCACTACTTATTACATTATATAAACGCTACCTATTACATTATAT
384 GATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATAT
* * **
233356 AAGCGTTACCTATTACATCATATTTTTACCTATTATATT-TAAAGTGTCCATACTTTTTATAAAA
449 AAGCGCTACCTATTACATCATATTTTTACCTAATATATTGTAAAGCATCCATACTTTTTATAAAA
* *
233420 ATGATCGATATTTTTTTTAAAGTTATATGTAATTTATGTTTCAATTTTTTTTAACAGTGTTTCAT
514 AGGATCGATACTTTTTTTAAAG-T-TATGTAATTTATGTTTCAATTTTTTTTAACAGTGTTTCAT
*
233485 ATTTTTCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGAT
577 ATTTTTCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTAATTGTTTTGAT
*
233550 ATTTTATAAAATATTATTTAGTATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGT
642 ATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGT
*
233615 AATATATATGTTTATTGTTTTTAATTTAATGATAATATATACCGTAACGTAAAAAATAAATCATT
707 AATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATT
* * *
233680 AGACGCCTATAATTACTAAATTAATATCTTAAAACTTACTCAAAAGATAACCTTAAATTAATGTT
772 AGACACATATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
* * *
233745 TTCCACAGTTAAAAAAGTATGGACACTTTTATAAAAATGATAAATACTTTACAATATAA
837 TTCCACAGTGAAAAAAGTATGAACACTTTTATAAAAAGGATAAATACTTTACAATATAA
233804 CAGGTAAAAA
Statistics
Matches: 844, Mismatches: 47, Indels: 13
0.93 0.05 0.01
Matches are distributed among these distances:
975 8 0.01
976 58 0.07
978 144 0.17
979 42 0.05
980 207 0.25
981 353 0.42
982 32 0.04
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (976 bp):
TTGAAAGTGTCCATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
TTCAATTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACA
AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTA
ACCAAAGATAATAATAAATATGTAATATATGTTATTGTTTTTAATTTAATGATAATATATACCGT
AACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCACTCAAAA
GATAACCTTAAATTAATATTTTCCACAATGAAAAAAGTATGGACACTTCTATAAAAAGGATAGAT
ACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCT
ACCTATTACATCATATTTTTACCTAATATATTGTAAAGCATCCATACTTTTTATAAAAAGGATCG
ATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAACAGTGTTTCATATTTTTCAC
CTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTAATTGTTTTGATATTTTATAA
AATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATAT
GTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACACATA
TAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGT
GAAAAAAGTATGAACACTTTTATAAAAAGGATAAATACTTTACAATATAAGCACTACATATTACA
TTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTGTTAT
A
Found at i:237632 original size:10 final size:11
Alignment explanation
Indices: 237606--237632 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
237596 AATTATTTTG
237606 ATTTTTATTTA
1 ATTTTTATTTA
237617 ATTTTTATTTA
1 ATTTTTATTTA
237628 ATTTT
1 ATTTT
237633 CTCGTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTTATTTA
Found at i:237968 original size:6 final size:7
Alignment explanation
Indices: 237954--237986 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
237944 AATATAAAGA
*
237954 TTAAATT
1 TTAATTT
237961 TTAATTT
1 TTAATTT
237968 TTAATTT
1 TTAATTT
237975 TTAATTT
1 TTAATTT
237982 TTAAT
1 TTAAT
237987 AGTATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TTAATTT
Found at i:238533 original size:43 final size:43
Alignment explanation
Indices: 238472--238555 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
238462 CCATCATATT
**
238472 ACTAATAATTATTAAATTTGGGGTAAGGTATATAAATGATCCA
1 ACTAATAATTATTAAATTTAAGGTAAGGTATATAAATGATCCA
238515 ACTAATAATTATTAAATTTAAGGTAAGGTATATAAATGATC
1 ACTAATAATTATTAAATTTAAGGTAAGGTATATAAATGATC
238556 TTTCAACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (43 bp):
ACTAATAATTATTAAATTTAAGGTAAGGTATATAAATGATCCA
Found at i:239561 original size:2 final size:2
Alignment explanation
Indices: 239554--239617 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
239544 ATAATTTATT
239554 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
239596 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
239618 ACAAATGAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:242091 original size:152 final size:152
Alignment explanation
Indices: 241860--242164 Score: 610
Period size: 152 Copynumber: 2.0 Consensus size: 152
241850 TCATTTAATT
241860 ATTTTTTGTTTCAAAATCATAACTAGAGCCACATTTTGGTCACCCATCACTAAAAAATAAATAAA
1 ATTTTTTGTTTCAAAATCATAACTAGAGCCACATTTTGGTCACCCATCACTAAAAAATAAATAAA
241925 ACTGTTAATTTGATCATCTTTTTATTTTTTTAATGATGTGGCATTATCATAGTAATACGTCAATT
66 ACTGTTAATTTGATCATCTTTTTATTTTTTTAATGATGTGGCATTATCATAGTAATACGTCAATT
241990 TAAGTGTCAACATAAGTAATCA
131 TAAGTGTCAACATAAGTAATCA
242012 ATTTTTTGTTTCAAAATCATAACTAGAGCCACATTTTGGTCACCCATCACTAAAAAATAAATAAA
1 ATTTTTTGTTTCAAAATCATAACTAGAGCCACATTTTGGTCACCCATCACTAAAAAATAAATAAA
242077 ACTGTTAATTTGATCATCTTTTTATTTTTTTAATGATGTGGCATTATCATAGTAATACGTCAATT
66 ACTGTTAATTTGATCATCTTTTTATTTTTTTAATGATGTGGCATTATCATAGTAATACGTCAATT
242142 TAAGTGTCAACATAAGTAATCA
131 TAAGTGTCAACATAAGTAATCA
242164 A
1 A
242165 AACATAACAT
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 153 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (152 bp):
ATTTTTTGTTTCAAAATCATAACTAGAGCCACATTTTGGTCACCCATCACTAAAAAATAAATAAA
ACTGTTAATTTGATCATCTTTTTATTTTTTTAATGATGTGGCATTATCATAGTAATACGTCAATT
TAAGTGTCAACATAAGTAATCA
Found at i:246566 original size:12 final size:11
Alignment explanation
Indices: 246549--246588 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
246539 ATTGTACCTA
246549 AAAAATTAAAAT
1 AAAAA-TAAAAT
246561 AAAAATAAGAAT
1 AAAAATAA-AAT
246573 AAAAAT-AAAT
1 AAAAATAAAAT
246583 AAAAAT
1 AAAAAT
246589 GTATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.33
11 4 0.15
12 14 0.52
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:246684 original size:37 final size:37
Alignment explanation
Indices: 246642--246985 Score: 304
Period size: 37 Copynumber: 9.4 Consensus size: 37
246632 GTTTTCTAAA
* *
246642 ATATATTATATATATTTTCCAAAAACATCTT-AAAATT
1 ATATATTATATATATTTT-CAAAAATATTTTCAAAATT
* *
246679 ATATATTATACATATTTTCGAAAAATGA-TTTCAAAACT
1 ATATATTATATATATTTTC-AAAAAT-ATTTTCAAAATT
* * *
246717 ATATATTATATATATTTTTTCAAAAATGTTTTTTTAAAATC
1 ATATATTATATATA--TTTTCAAAAA--TATTTTCAAAATT
*
246758 ATATATTATAT-T-TTTT-AAAAATGTTTTCAAAATT
1 ATATATTATATATATTTTCAAAAATATTTTCAAAATT
* *
246792 ATATATTATATAT-TTTTCTAAAATGTTTTCAAAATT
1 ATATATTATATATATTTTCAAAAATATTTTCAAAATT
* *
246828 ATATATTATATAGATTTTTAAAAATATTTTCAAAATT
1 ATATATTATATATATTTTCAAAAATATTTTCAAAATT
*
246865 ATATATTATATATATTTT-AAAAATGTTTTC---A--
1 ATATATTATATATATTTTCAAAAATATTTTCAAAATT
* * *
246896 A-A-ACTGTATATATTTTCGAACAATATTTTCAAAATT
1 ATATATTATATATATTTTC-AAAAATATTTTCAAAATT
* * **
246932 GTATACTATATATATATTTTCAAAAACGATTTT-AAAACC
1 ATATA-T-TATATATATTTTCAAAAA-TATTTTCAAAATT
246971 ATATATTATATATAT
1 ATATATTATATATAT
246986 ATGTATATAT
Statistics
Matches: 253, Mismatches: 31, Indels: 46
0.77 0.09 0.14
Matches are distributed among these distances:
29 12 0.05
30 1 0.00
31 11 0.04
33 1 0.00
34 22 0.09
35 5 0.02
36 46 0.18
37 75 0.30
38 21 0.08
39 17 0.07
40 23 0.09
41 19 0.08
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (37 bp):
ATATATTATATATATTTTCAAAAATATTTTCAAAATT
Found at i:246726 original size:75 final size:72
Alignment explanation
Indices: 246642--246985 Score: 278
Period size: 73 Copynumber: 4.7 Consensus size: 72
246632 GTTTTCTAAA
* * *
246642 ATATATTATATATATTTTCCAAAAACATCTTAAAATTATATATTATACATATTTTCGAAAAATGA
1 ATATATTATATATATTTT-CAAAAATATTTTAAAATTATATATTATA-ATATTTT-TAAAAATGA
*
246707 TTTCAAAACT
63 TTTCAAAATT
* *
246717 ATATATTATATATATTTTTTCAAAAATGTTTTTTTAAAATCATATATTAT-AT-TTTTTAAAAAT
1 ATATATTATATATA--TTTTCAAAAA---TATTTTAAAATTATATATTATAATATTTTTAAAAAT
*
246780 GTTTTCAAAATT
61 GATTTCAAAATT
* * *
246792 ATATATTATATAT-TTTTCTAAAATGTTTTCAAAATTATATATTATATAGATTTTTAAAAAT-AT
1 ATATATTATATATATTTTCAAAAATATTTT-AAAATTATATATTATA-ATATTTTTAAAAATGA-
246855 TTTCAAAATT
63 TTTCAAAATT
* * * ** *
246865 ATATATTATATATATTTT-AAAAATGTTTTCAAAA--CTGTA-TAT-AT-TTTCGAACAAT-ATT
1 ATATATTATATATATTTTCAAAAATATTTT-AAAATTATATATTATAATATTTTTAAAAATGA-T
246923 TTCAAAATT
64 TTCAAAATT
* * **
246932 GTATACTATATATATATTTTCAAAAACGATTTTAAAACCATATATTATATATAT
1 ATATA-T-TATATATATTTTCAAAAA-TATTTTAAAATTATATATTATA-ATAT
246986 ATGTATATAT
Statistics
Matches: 224, Mismatches: 24, Indels: 41
0.78 0.08 0.14
Matches are distributed among these distances:
67 24 0.11
68 2 0.01
69 17 0.08
70 26 0.12
71 7 0.03
72 13 0.06
73 52 0.23
74 4 0.02
75 45 0.20
76 11 0.05
77 6 0.03
79 17 0.08
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (72 bp):
ATATATTATATATATTTTCAAAAATATTTTAAAATTATATATTATAATATTTTTAAAAATGATTT
CAAAATT
Found at i:246772 original size:36 final size:35
Alignment explanation
Indices: 246673--246909 Score: 214
Period size: 36 Copynumber: 6.4 Consensus size: 35
246663 AAAACATCTT
* *
246673 AAAATTATATATTATACATATTTTCGAAAAATG-ATTTC
1 AAAATTATATATTAT--AT-TTTT-TAAAAATGTTTTTC
*
246711 AAAACTATATATTATATATATTTTTTCAAAAATGTTTTTTT
1 AAAA-T-TATA-TAT-TATATTTTTT-AAAAATG-TTTTTC
*
246752 AAAATCATATATTATATTTTTTAAAAATG-TTTTC
1 AAAATTATATATTATATTTTTTAAAAATGTTTTTC
*
246786 AAAATTATATATTATATATTTTTCTAAAATG-TTTTC
1 AAAATTATATATTATAT-TTTTT-AAAAATGTTTTTC
*
246822 AAAATTATATATTATATAGATTTTTAAAAAT-ATTTTC
1 AAAATTATATATTATAT---TTTTTAAAAATGTTTTTC
246859 AAAATTATATATTATATATATTTTAAAAATG-TTTTC
1 AAAATTATATATTATAT-T-TTTTAAAAATGTTTTTC
246895 AAAACTGTATATATT
1 AAAA-T-TATATATT
246910 TTCGAACAAT
Statistics
Matches: 175, Mismatches: 8, Indels: 32
0.81 0.04 0.15
Matches are distributed among these distances:
34 20 0.11
35 7 0.04
36 54 0.31
37 38 0.22
38 21 0.12
39 15 0.09
40 7 0.04
41 10 0.06
42 3 0.02
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (35 bp):
AAAATTATATATTATATTTTTTAAAAATGTTTTTC
Found at i:246925 original size:31 final size:29
Alignment explanation
Indices: 246873--246936 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
246863 TTATATATTA
*
246873 TATATATTTTAAAAATGTTTTCAAAACTG
1 TATATATTTTAAAAATATTTTCAAAACTG
* *
246902 TATATATTTTCGAACAATATTTTCAAAATTG
1 TATATATTTT--AAAAATATTTTCAAAACTG
246933 TATA
1 TATA
246937 CTATATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 10 0.33
31 20 0.67
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (29 bp):
TATATATTTTAAAAATATTTTCAAAACTG
Found at i:248304 original size:2 final size:2
Alignment explanation
Indices: 248297--248324 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
248287 TAGCAACACA
248297 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
248325 GAGAGATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:249947 original size:2 final size:2
Alignment explanation
Indices: 249936--249970 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
249926 GATTTAGTAT
249936 TA TA -A 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
249971 AAAGAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:250695 original size:55 final size:55
Alignment explanation
Indices: 250611--250731 Score: 233
Period size: 55 Copynumber: 2.2 Consensus size: 55
250601 AATTAGGTAA
*
250611 TATTTGTTTTTATCATATCTCTTAAATTATTGATTCAAACGTATTTTCCAAGCTT
1 TATTTGTTTTTATCATATCTCTTAAATTATTGATTCAAACATATTTTCCAAGCTT
250666 TATTTGTTTTTATCATATCTCTTAAATTATTGATTCAAACATATTTTCCAAGCTT
1 TATTTGTTTTTATCATATCTCTTAAATTATTGATTCAAACATATTTTCCAAGCTT
250721 TATTTGTTTTT
1 TATTTGTTTTT
250732 TTAGTTGACT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 65 1.00
ACGTcount: A:0.26, C:0.13, G:0.07, T:0.54
Consensus pattern (55 bp):
TATTTGTTTTTATCATATCTCTTAAATTATTGATTCAAACATATTTTCCAAGCTT
Found at i:251644 original size:23 final size:23
Alignment explanation
Indices: 251616--251673 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
251606 AAATTAATAA
251616 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
251639 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
251662 TATA--ATGTAAAA
1 TATATTATGTAAAA
251674 ATTATAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (23 bp):
TATATTATGTAAAATGTTTCGAT
Found at i:255042 original size:125 final size:126
Alignment explanation
Indices: 254819--255295 Score: 877
Period size: 125 Copynumber: 3.8 Consensus size: 126
254809 CTATAATCGG
*
254819 TTCACTATTCATGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
254884 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
254945 TTCACTATTCACGTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
255009 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
255070 TTCACTATTCACGTGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
255135 TCATTGCCCTATTATGTCATTCATGTCCCTC-GGGTCACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
* *
255195 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCAGTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
255260 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
255296 ATAACTTAAA
Statistics
Matches: 339, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
125 242 0.71
126 97 0.29
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:255262 original size:251 final size:251
Alignment explanation
Indices: 254819--255295 Score: 893
Period size: 251 Copynumber: 1.9 Consensus size: 251
254809 CTATAATCGG
* *
254819 TTCACTATTCATGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
254884 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
*
254949 CTATTCACGTGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCATT
131 CTATTCACGTGAAGGCGCGTTCCCGGGGCGCGCCTTCCAGTATTTCGTCAGAGAATATTATCATT
*
255014 GCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
196 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
255070 TTCACTATTCACGTGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
255135 TCATTGCCCTATTATGTCATTCATGTCCCTC-GGGTCACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
255199 CTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCAGTATTTCGTCAGAGAATATTATCAT
131 CTATTCACGTGAAGGCGCGTTCCCGGGG-CGCGCCTTCCAGTATTTCGTCAGAGAATATTATCAT
255264 TGCCCTATTATGTCACTCATGTCCCTCGGGGA
195 TGCCCTATTATGTCACTCATGTCCCTCGGGGA
255296 ATAACTTAAA
Statistics
Matches: 220, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
250 60 0.27
251 160 0.73
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (251 bp):
TTCACTATTCACGTGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
CTATTCACGTGAAGGCGCGTTCCCGGGGCGCGCCTTCCAGTATTTCGTCAGAGAATATTATCATT
GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
Found at i:255741 original size:33 final size:34
Alignment explanation
Indices: 255680--255779 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
255670 AAAATTAATG
*
255680 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
255714 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
255747 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
255780 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:256384 original size:21 final size:21
Alignment explanation
Indices: 256296--256389 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
256286 ATATGGTATA
*
256296 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
256317 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
256338 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
256359 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
256380 AACCCTGCGG
1 AACCCTGCGG
256390 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:263452 original size:10 final size:10
Alignment explanation
Indices: 263423--263510 Score: 94
Period size: 10 Copynumber: 9.1 Consensus size: 10
263413 GCTGCTGGAA
263423 AACCGGTTTG
1 AACCGGTTTG
*
263433 -ACCAGTTTTG
1 AACC-GGTTTG
263443 AACCGGTTTG
1 AACCGGTTTG
*
263453 -ACCGGTTCG
1 AACCGGTTTG
263462 AACCGGTTTG
1 AACCGGTTTG
*
263472 -ACCGGTCTG
1 AACCGGTTTG
263481 AACCGGTTTG
1 AACCGGTTTG
*
263491 -ACCGGTCTG
1 AACCGGTTTG
*
263500 AACCGGGTTG
1 AACCGGTTTG
263510 A
1 A
263511 CCCGACCCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
9 27 0.42
10 34 0.53
11 3 0.05
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:263466 original size:19 final size:19
Alignment explanation
Indices: 263423--263512 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
263413 GCTGCTGGAA
* *
263423 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
263443 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
263462 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
263481 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
263500 AACCGGGTTGACC
1 AACCGGTTTGACC
263513 CGACCCGACC
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
18 1 0.02
19 51 0.77
20 14 0.21
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:263528 original size:17 final size:17
Alignment explanation
Indices: 263506--263563 Score: 116
Period size: 17 Copynumber: 3.4 Consensus size: 17
263496 TCTGAACCGG
263506 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
263523 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
263540 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
263557 GTTGACC
1 GTTGACC
263564 GTGACCGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.17, C:0.45, G:0.24, T:0.14
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:263570 original size:6 final size:7
Alignment explanation
Indices: 263553--263582 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
263543 GACCCGACCC
263553 GACCGTT
1 GACCGTT
263560 GACCG-T
1 GACCGTT
263566 GACCGTT
1 GACCGTT
263573 GACCGTT
1 GACCGTT
263580 GAC
1 GAC
263583 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:263571 original size:13 final size:13
Alignment explanation
Indices: 263553--263578 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
263543 GACCCGACCC
263553 GACCGTTGACCGT
1 GACCGTTGACCGT
263566 GACCGTTGACCGT
1 GACCGTTGACCGT
263579 TGACTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:271327 original size:21 final size:21
Alignment explanation
Indices: 271289--271329 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
271279 CATGTGTCAA
271289 AAACAAGCCAAAAACATCAGGG
1 AAACAAG-CAAAAACATCAGGG
271311 AAACAAG-AAAAAGCATCAG
1 AAACAAGCAAAAA-CATCAG
271330 AATTCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.59, C:0.20, G:0.17, T:0.05
Consensus pattern (21 bp):
AAACAAGCAAAAACATCAGGG
Found at i:286508 original size:37 final size:39
Alignment explanation
Indices: 286459--286554 Score: 133
Period size: 37 Copynumber: 2.5 Consensus size: 39
286449 TTGAAAATAT
* *
286459 TTTTTGAAAACATATAATATATAGTTTTTAGAAAA-C-G
1 TTTTTGAAAACATATAATATATAGTTTTTAAAAAATCAA
* *
286496 TTTTAGAAAACATATTATATATAGTTTTTAAAAAATCAA
1 TTTTTGAAAACATATAATATATAGTTTTTAAAAAATCAA
*
286535 TTTTTGAAAATATATAATAT
1 TTTTTGAAAACATATAATAT
286555 GATTTTGAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 32 0.64
38 1 0.02
39 17 0.34
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (39 bp):
TTTTTGAAAACATATAATATATAGTTTTTAAAAAATCAA
Found at i:286561 original size:21 final size:21
Alignment explanation
Indices: 286536--286590 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
286526 AAAAATCAAT
*
286536 TTTTGAAAATATATAATATGA
1 TTTTGAAAACATATAATATGA
*
286557 TTTTGAAAACATATAATATATA
1 TTTTGAAAACATATAATAT-GA
286579 GTTTTGAAAACA
1 -TTTTGAAAACA
286591 CATTTTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 18 0.60
22 1 0.03
23 11 0.37
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (21 bp):
TTTTGAAAACATATAATATGA
Found at i:286577 original size:23 final size:21
Alignment explanation
Indices: 286495--286590 Score: 69
Period size: 23 Copynumber: 4.6 Consensus size: 21
286485 TTTAGAAAAC
286495 GTTTTAGAAAACATATTATATATA
1 GTTTT-GAAAACATA-TA-ATATA
* *
286519 GTTTTTAAAA-A-ATCA-AT-
1 GTTTTGAAAACATATAATATA
*
286536 -TTTTGAAAATATATAATAT-
1 GTTTTGAAAACATATAATATA
286555 GATTTTGAAAACATATAATATATA
1 G-TTTTGAAAACATAT-A-ATATA
286579 GTTTTGAAAACA
1 GTTTTGAAAACA
286591 CATTTTTGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
16 8 0.14
17 1 0.02
18 5 0.08
19 3 0.05
20 1 0.02
21 14 0.24
22 2 0.03
23 19 0.32
24 6 0.10
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (21 bp):
GTTTTGAAAACATATAATATA
Found at i:286579 original size:97 final size:97
Alignment explanation
Indices: 286460--286669 Score: 257
Period size: 97 Copynumber: 2.1 Consensus size: 97
286450 TGAAAATATT
* * * *
286460 TTTTGAAAACATATAATATATAGTTTTTAGAAA-ACGTTTTAG-AAAAC-ATATTATATATAGTT
1 TTTTGAAAACATATAATATATAGTTTTGA-AAACACATTTTAGAAAAACGATAATATACATAG-T
* *
286522 TTTAAAAAATCAATTTTTGAAAA-TATATAATATGA
64 TTT-AAAAAT-AATTTTTAAAAACTATATAATATAA
*
286557 TTTTGAAAACATATAATATATAGTTTTGAAAACACATTTTTGAAAAACGTATAATATACATAGTT
1 TTTTGAAAACATATAATATATAGTTTTGAAAACACATTTTAGAAAAACG-ATAATATACATAGTT
*
286622 TTAAAAATGATTTTTAAAAACGTATATAATATAA
65 TTAAAAATAATTTTTAAAAAC-TATATAATATAA
*
286656 TTTTAAAAACATAT
1 TTTTGAAAACATAT
286670 TTTGAAAATA
Statistics
Matches: 98, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
96 3 0.03
97 45 0.46
98 11 0.11
99 28 0.29
100 11 0.11
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (97 bp):
TTTTGAAAACATATAATATATAGTTTTGAAAACACATTTTAGAAAAACGATAATATACATAGTTT
TAAAAATAATTTTTAAAAACTATATAATATAA
Found at i:286610 original size:38 final size:36
Alignment explanation
Indices: 286557--286677 Score: 131
Period size: 38 Copynumber: 3.2 Consensus size: 36
286547 TATAATATGA
*
286557 TTTTG-AAAACATATAATATATAGTTTTGAAAACACAT
1 TTTTGAAAAACGTATAATATATAGTTTT-AAAA-ACAT
*
286594 TTTTGAAAAACGTATAATATACATAGTTTTAAAAATGAT
1 TTTTGAAAAACGTATAATAT--ATAGTTTTAAAAA-CAT
*
286633 TTTT-AAAAACGTAT-ATAATATAATTTTAAAAACAT
1 TTTTGAAAAACGTATAAT-ATATAGTTTTAAAAACAT
286668 ATTTTGAAAA
1 -TTTTGAAAA
286678 TATATATAGT
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
35 2 0.03
36 16 0.22
37 11 0.15
38 26 0.36
39 10 0.14
40 8 0.11
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (36 bp):
TTTTGAAAAACGTATAATATATAGTTTTAAAAACAT
Found at i:286684 original size:36 final size:36
Alignment explanation
Indices: 286556--286724 Score: 93
Period size: 37 Copynumber: 4.6 Consensus size: 36
286546 ATATAATATG
*
286556 ATTTTGAAAACATATA-ATATATAGTTTTGAAAACACAT
1 ATTTTGAAAA-ATATATA-ATATAATTTT-AAAACACAT
** *
286594 -TTTTGAAAAACGTATAATATACATAGTTTTAAA-A-AT
1 ATTTTGAAAAATATATAATATA-AT--TTTAAAACACAT
*
286630 GATTTTTAAAAACGTATATAATATAATTTTAAAA-ACAT
1 -ATTTTGAAAAA--TATATAATATAATTTTAAAACACAT
* * *
286668 ATTTTG-AAAATATAT-ATAGT-TTTTTAAAAGAGAT
1 ATTTTGAAAAATATATAATA-TAATTTTAAAACACAT
* *
286702 TTTTTAGAAACATATATAATATA
1 ATTTT-GAAAAATATATAATATA
286725 TAATTTTTGA
Statistics
Matches: 103, Mismatches: 13, Indels: 31
0.70 0.09 0.21
Matches are distributed among these distances:
33 11 0.11
34 13 0.13
35 1 0.01
36 23 0.22
37 27 0.26
38 14 0.14
39 5 0.05
40 9 0.09
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (36 bp):
ATTTTGAAAAATATATAATATAATTTTAAAACACAT
Found at i:286736 original size:25 final size:25
Alignment explanation
Indices: 286702--286757 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
286692 TAAAAGAGAT
286702 TTTTTAGAAACATAT-ATAATATATAA
1 TTTTTAGAAA-ATATAATAATATAT-A
*
286728 TTTTT-GAAAATATAATATTATATA
1 TTTTTAGAAAATATAATAATATATA
286752 TTTTTA
1 TTTTTA
286758 ATATTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 10 0.37
25 12 0.44
26 5 0.19
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (25 bp):
TTTTTAGAAAATATAATAATATATA
Done.