Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 63 of 316
Found at i:18487997 original size:3 final size:3
Alignment explanation
Indices: 18487989--18488027 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
18487979 ATGTTACTAC
18487989 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18488028 TTGTATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:18488120 original size:18 final size:17
Alignment explanation
Indices: 18488097--18488138 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
18488087 TTGTATGTTC
*
18488097 GTATATTTTATATACTAT
1 GTATATTTAATATA-TAT
18488115 GTATATCTTAATATATAT
1 GTATAT-TTAATATATAT
18488133 GT-TATT
1 GTATATT
18488139 ATATTTGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 3 0.14
18 11 0.50
19 7 0.32
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (17 bp):
GTATATTTAATATATAT
Found at i:18510541 original size:45 final size:46
Alignment explanation
Indices: 18510474--18510597 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
18510464 CATATGACCT
*
18510474 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
18510517 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
18510563 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
18510598 ACTTATCACT
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:18510580 original size:46 final size:45
Alignment explanation
Indices: 18510474--18510707 Score: 198
Period size: 37 Copynumber: 5.8 Consensus size: 45
18510464 CATATGACCT
*
18510474 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
18510517 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
18510563 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG----CA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
18510599 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
18510636 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
18510673 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
18510708 CATTTATCAC
Statistics
Matches: 175, Mismatches: 7, Indels: 20
0.87 0.03 0.10
Matches are distributed among these distances:
36 34 0.19
37 65 0.37
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:18510647 original size:37 final size:37
Alignment explanation
Indices: 18510560--18510734 Score: 289
Period size: 37 Copynumber: 4.8 Consensus size: 37
18510550 GCTGAAGCTA
* **
18510560 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
*
18510597 -CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
*
18510633 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
18510670 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
*
18510707 CCATTTATCACTTTGTTTCTTGATCAGA
1 CCACTTATCACTTTGTTTCTTGATCAGA
18510735 AGTACTCAAA
Statistics
Matches: 131, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
36 34 0.26
37 97 0.74
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (37 bp):
CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
Found at i:18513497 original size:39 final size:40
Alignment explanation
Indices: 18513402--18513624 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
18513392 TTGAATGATG
*
18513402 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
18513440 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
18513481 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
18513520 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
18513559 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
18513598 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
18513625 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 93 0.57
40 59 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:18513588 original size:79 final size:81
Alignment explanation
Indices: 18513402--18513624 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
18513392 TTGAATGATG
* * *
18513402 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
18513464 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
18513481 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
18513542 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * *
18513559 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
18513623 TG
66 TG
18513625 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:18513646 original size:79 final size:79
Alignment explanation
Indices: 18513402--18513657 Score: 217
Period size: 79 Copynumber: 3.3 Consensus size: 79
18513392 TTGAATGATG
* * * *
18513402 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
18513463 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
18513481 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
18513545 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
*
18513559 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
18513622 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
18513639 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
18513658 TACGTGATTT
Statistics
Matches: 153, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.30
79 69 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:18521481 original size:39 final size:40
Alignment explanation
Indices: 18521386--18521608 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
18521376 TTGAATGATG
*
18521386 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
18521424 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
18521465 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
18521504 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
18521543 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
18521582 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
18521609 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 93 0.57
40 59 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:18521572 original size:79 final size:81
Alignment explanation
Indices: 18521386--18521608 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
18521376 TTGAATGATG
* * *
18521386 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
18521448 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
18521465 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
18521526 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * *
18521543 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
18521607 TG
66 TG
18521609 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:18521630 original size:79 final size:79
Alignment explanation
Indices: 18521386--18521641 Score: 217
Period size: 79 Copynumber: 3.3 Consensus size: 79
18521376 TTGAATGATG
* * * *
18521386 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
18521447 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
18521465 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
18521529 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
*
18521543 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
18521606 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
18521623 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
18521642 TACGTGATTT
Statistics
Matches: 153, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.30
79 69 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:18525046 original size:13 final size:12
Alignment explanation
Indices: 18525016--18525063 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
18525006 CCATTTCAAA
18525016 AAAAAAGAAAA-
1 AAAAAAGAAAAG
*
18525027 AGAAAAAGAAAAT
1 A-AAAAAGAAAAG
18525040 AAGAAAAGAAAAG
1 AA-AAAAGAAAAG
18525053 AAAAAAAGAAA
1 -AAAAAAGAAA
18525064 TTGGAAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 1 0.03
12 11 0.34
13 18 0.56
14 2 0.06
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:18525051 original size:18 final size:19
Alignment explanation
Indices: 18525015--18525063 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
18525005 TCCATTTCAA
18525015 AAAAAAAGAAAAAGAAAAAG
1 AAAAAAAG-AAAAGAAAAAG
*
18525035 AAAATAAGAAAAG-AAAAG
1 AAAAAAAGAAAAGAAAAAG
18525053 AAAAAAAGAAA
1 AAAAAAAGAAA
18525064 TTGGAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 15 0.56
19 5 0.19
20 7 0.26
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAAAAGAAAAGAAAAAG
Found at i:18525074 original size:26 final size:24
Alignment explanation
Indices: 18525016--18525063 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
18525006 CCATTTCAAA
*
18525016 AAAAAAGAAAAAGAAAAAGAAAAT
1 AAAAAAGAAAAAAAAAAAGAAAAT
18525040 AAGAAAAGAAAAGAAAAAAAGAAA
1 AA-AAAAGAAAA-AAAAAAAGAAA
18525064 TTGGAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.10
25 9 0.43
26 10 0.48
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (24 bp):
AAAAAAGAAAAAAAAAAAGAAAAT
Found at i:18526069 original size:45 final size:45
Alignment explanation
Indices: 18526020--18526413 Score: 443
Period size: 45 Copynumber: 8.9 Consensus size: 45
18526010 TTGAAGATAG
* * *
18526020 CAGATCTTATTTCTCTGTAATAGATGGGGAGCAGATCCAAGATGA
1 CAGATCTTATCTCTCTGTAATGGACGGGGAGCAGATCCAAGATGA
* * *
18526065 CAGATCTTATCTCTCTGTATTCGACGGGGAGCAGATCGAAGACAT-A
1 CAGATCTTATCTCTCTGTAATGGACGGGGAGCAGATCCAAG--ATGA
* * * *
18526111 GCAGATCTGA---C-CT-TCAT---C-GGG-GCAGATCTAAGATGG
1 -CAGATCTTATCTCTCTGTAATGGACGGGGAGCAGATCCAAGATGA
* *
18526147 CGGATCTTATCTCTCTGTAATAGACAGGGG-GCAGATCCAAGATGA
1 CAGATCTTATCTCTCTGTAATGGAC-GGGGAGCAGATCCAAGATGA
* *
18526192 CAGATCTTATCTCTCTGGAATGGACGGGGAGTAGATCCAAGATGA
1 CAGATCTTATCTCTCTGTAATGGACGGGGAGCAGATCCAAGATGA
* * *
18526237 CAGATCCTATCTCTCCGTAATGGACGGGGAGTAGATCCAAGATGA
1 CAGATCTTATCTCTCTGTAATGGACGGGGAGCAGATCCAAGATGA
* * *
18526282 CAGATCTTATCTCTCTATAATGGACGGGGAGTAGGTCCAAGATGA
1 CAGATCTTATCTCTCTGTAATGGACGGGGAGCAGATCCAAGATGA
**
18526327 CAGATCTTATCTCTCTGTAATGGACGGGGAATAGATCCAAGATGA
1 CAGATCTTATCTCTCTGTAATGGACGGGGAGCAGATCCAAGATGA
* * *
18526372 CAGATCTTATCTCTCTGTATTCGACGGGGAGCAGATCAAAGA
1 CAGATCTTATCTCTCTGTAATGGACGGGGAGCAGATCCAAGA
18526414 CATAGCAGAT
Statistics
Matches: 300, Mismatches: 34, Indels: 30
0.82 0.09 0.08
Matches are distributed among these distances:
35 9 0.03
37 10 0.03
38 4 0.01
39 3 0.01
40 3 0.01
42 2 0.01
43 3 0.01
44 5 0.02
45 250 0.83
46 1 0.00
47 10 0.03
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (45 bp):
CAGATCTTATCTCTCTGTAATGGACGGGGAGCAGATCCAAGATGA
Found at i:18528426 original size:15 final size:15
Alignment explanation
Indices: 18528393--18528435 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
18528383 AAAATACTTA
18528393 TTATATTATTATTATT
1 TTATATTA-TATTATT
18528409 TTATATTATATT-TCT
1 TTATATTATATTAT-T
*
18528424 TTATATTTTATT
1 TTATATTATATT
18528436 CATATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 1 0.04
15 16 0.64
16 8 0.32
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATATTATATTATT
Found at i:18528642 original size:3 final size:3
Alignment explanation
Indices: 18528634--18528696 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
18528624 ATGTTACTAC
18528634 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18528682 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
18528697 TTGTATATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:18529703 original size:6 final size:7
Alignment explanation
Indices: 18529681--18529705 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18529671 TTAAAAAGAT
18529681 AAATTAA
1 AAATTAA
18529688 AAATTAA
1 AAATTAA
18529695 AAATTAA
1 AAATTAA
18529702 AAAT
1 AAAT
18529706 AATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATTAA
Found at i:18532370 original size:84 final size:83
Alignment explanation
Indices: 18532246--18532543 Score: 308
Period size: 84 Copynumber: 3.7 Consensus size: 83
18532236 TGAACGAGTG
* * * * * *
18532246 AGGCATAGTCTTGACAGAC-AAGTGGTAGGGGTGCTAAGAACCATAAATGATAACTTGTATTACA
1 AGGCATAGTCTTGACAGACAAAG-GGTAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACA
*
18532310 CGTATGAGCATGAGCAAGCA
65 CG-ATGAGCATAAGCAAGCA
* *
18532330 AGGCATAGTCTTGACAGACAAAGGGTAGAGGTGCCAAGAACCTTACATGGTAACTCGTATT--AC
1 AGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACAC
* *
18532393 -AT--GCATAAGGATG-A
66 GATGAGCATAAGCAAGCA
* * * *
18532407 A--AATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACAT
1 AGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACAC
* * *
18532470 GCATGAGCACAAGCCAGCG
66 G-ATGAGCATAAGCAAGCA
* * * *
18532489 AGGCATAGTGTTGACAGACAAATGGTAGAGATGCCAAGAGCCTTGAATGGTAACT
1 AGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTTAAATGGTAACT
18532544 TGTACAACAT
Statistics
Matches: 179, Mismatches: 25, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
75 53 0.30
77 3 0.02
78 8 0.04
79 2 0.01
80 2 0.01
81 7 0.04
82 3 0.02
84 98 0.55
85 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (83 bp):
AGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACAC
GATGAGCATAAGCAAGCA
Found at i:18532434 original size:75 final size:75
Alignment explanation
Indices: 18532334--18532473 Score: 244
Period size: 75 Copynumber: 1.9 Consensus size: 75
18532324 CAAGCAAGGC
* * *
18532334 ATAGTCTTGACAGACAAAGGGTAGAGGTGCCAAGAACCTTACATGGTAACTCGTATTACATGCAT
1 ATAGTCTTGACAGACAAAGGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
18532399 AAGGATGAAA
66 AAGGATGAAA
*
18532409 ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
1 ATAGTCTTGACAGACAAAGGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
18532474 GAGCACAAGC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.24
Consensus pattern (75 bp):
ATAGTCTTGACAGACAAAGGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
AAGGATGAAA
Found at i:18532539 original size:159 final size:159
Alignment explanation
Indices: 18532250--18532543 Score: 410
Period size: 159 Copynumber: 1.8 Consensus size: 159
18532240 CGAGTGAGGC
* * * * * * *
18532250 ATAGTCTTGACAGACAAGTGGTAGGGGTGCTAAGAACCATAAATGATAACTTGTATTACACGTAT
1 ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCATAAATGATAACTCGTATTACACGCAT
** *
18532315 GAGCATGAGCAAGCAAGGCATAGTCTTGACAGACAAAGGGTAGAGGTGCCAAGAACCTTACATGG
66 GAGCACAAGCAAGCAAGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTTACATGG
18532380 TAACTCGTATTACATGCATAAGGATGAAA
131 TAACTCGTATTACATGCATAAGGATGAAA
* * *
18532409 ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
1 ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCATAAATGATAACTCGTATTACACGCAT
* * * * *
18532474 GAGCACAAGCCAGCGAGGCATAGTGTTGACAGACAAATGGTAGAGATGCCAAGAGCCTTGA-ATG
66 GAGCACAAGCAAGCAAGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTT-ACATG
18532538 GTAACT
130 GTAACT
18532544 TGTACAACAT
Statistics
Matches: 116, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
159 115 0.99
160 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (159 bp):
ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCATAAATGATAACTCGTATTACACGCAT
GAGCACAAGCAAGCAAGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTTACATGG
TAACTCGTATTACATGCATAAGGATGAAA
Found at i:18532554 original size:84 final size:84
Alignment explanation
Indices: 18532409--18532562 Score: 236
Period size: 84 Copynumber: 1.8 Consensus size: 84
18532399 AAGGATGAAA
**
18532409 ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
1 ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTACAACATGCAT
18532474 GAGCACAAGCCAGCGAGGC
66 GAGCACAAGCCAGCGAGGC
* * * * * *
18532493 ATAGTGTTGACAGACAAATGGTAGAGATGCCAAGAGCCTTGAATGGTAACTTGTACAACATGGAT
1 ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTACAACATGCAT
18532558 GAGCA
66 GAGCA
18532563 TGAGCATGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 62 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (84 bp):
ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTACAACATGCAT
GAGCACAAGCCAGCGAGGC
Found at i:18533190 original size:22 final size:22
Alignment explanation
Indices: 18533160--18533204 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
18533150 ATTTTTATGG
*
18533160 TTTATTCATAAAAAATAATTTT
1 TTTACTCATAAAAAATAATTTT
18533182 TTTACTCATAAAAAATAATTTT
1 TTTACTCATAAAAAATAATTTT
18533204 T
1 T
18533205 CATCATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTACTCATAAAAAATAATTTT
Found at i:18533668 original size:78 final size:78
Alignment explanation
Indices: 18533534--18533694 Score: 286
Period size: 78 Copynumber: 2.1 Consensus size: 78
18533524 GTATCCATGT
* * *
18533534 AAGCATGCAACTTGTTTAGATGTAGTCAATAATCATATGAATTTAGAATTAGTTAGGCACTAAGC
1 AAGCATGCAACTTGTTTAGATGTAATCAATAATCATATGAATTTAGAATTAATTAGGCACTAAAC
*
18533599 ATCGAGTAAAGCA
66 ATCAAGTAAAGCA
18533612 AAGCATGCAACTTGTTTAGATGTAATCAATAATCATATGAATTTAGAATTAATTAGGCACTAAAC
1 AAGCATGCAACTTGTTTAGATGTAATCAATAATCATATGAATTTAGAATTAATTAGGCACTAAAC
18533677 ATCAAGTAAAGCA
66 ATCAAGTAAAGCA
18533690 AAGCA
1 AAGCA
18533695 ACCAAAGATA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.29
Consensus pattern (78 bp):
AAGCATGCAACTTGTTTAGATGTAATCAATAATCATATGAATTTAGAATTAATTAGGCACTAAAC
ATCAAGTAAAGCA
Found at i:18534207 original size:75 final size:75
Alignment explanation
Indices: 18534075--18534219 Score: 227
Period size: 75 Copynumber: 1.9 Consensus size: 75
18534065 CGCTGGCTTG
* * * * *
18534075 TGCTCATGCATGTAATACGAGTTACCATTTAAGGTTCTTGGCATCTCTATCATTTGTCTGTCAAG
1 TGCTCATGCATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCCCTACCACTTGTCTGTCAAG
18534140 ACTATTTTCA
66 ACTATTTTCA
* *
18534150 TGCTCATGCATGTAATACAAGTTATCATTTATGGTTCTTGGCACCCCTACCACTTGTCTGTCAAG
1 TGCTCATGCATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCCCTACCACTTGTCTGTCAAG
18534215 ACTAT
66 ACTAT
18534220 GCCTCACTGC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (75 bp):
TGCTCATGCATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCCCTACCACTTGTCTGTCAAG
ACTATTTTCA
Found at i:18534309 original size:93 final size:93
Alignment explanation
Indices: 18534150--18534318 Score: 257
Period size: 93 Copynumber: 1.8 Consensus size: 93
18534140 ACTATTTTCA
* * * * * *
18534150 TGCTCATGCATGTAATACAAGTTATCATTTATGGTTCTTGGCACCCCTACCACTTGTCTGTCAAG
1 TGCTCATGCATGTAAGACAAGTTACCATTCAAGGTTCTCGGCACCCCTACCAATTGTCTGTCAAG
*
18534215 ACTATGCCTCACTGCATGCTCATGCTTG
66 ACCATGCCTCACTGCATGCTCATGCTTG
* *
18534243 TGCTCATGCATGTAAGGCAAGTTACCATTCAAGGTTCTCGGCACCTCTACCAATTGTCTGTCAAG
1 TGCTCATGCATGTAAGACAAGTTACCATTCAAGGTTCTCGGCACCCCTACCAATTGTCTGTCAAG
18534308 ACCATGCCTCA
66 ACCATGCCTCA
18534319 AGCTTCCTAG
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 67 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (93 bp):
TGCTCATGCATGTAAGACAAGTTACCATTCAAGGTTCTCGGCACCCCTACCAATTGTCTGTCAAG
ACCATGCCTCACTGCATGCTCATGCTTG
Found at i:18536924 original size:41 final size:41
Alignment explanation
Indices: 18536867--18536947 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
18536857 TATTCGACGC
*
18536867 CGAAACAGGGTACAAGGTATTATCGGACTCGTCACACAAAT
1 CGAAACAGGGTACAAGGTATTACCGGACTCGTCACACAAAT
18536908 CGAAACAGGGTACAAGGTATTACCGGACTCGTCACACAAA
1 CGAAACAGGGTACAAGGTATTACCGGACTCGTCACACAAA
18536948 CTTTCACACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (41 bp):
CGAAACAGGGTACAAGGTATTACCGGACTCGTCACACAAAT
Found at i:18544407 original size:42 final size:42
Alignment explanation
Indices: 18544350--18544475 Score: 153
Period size: 42 Copynumber: 3.0 Consensus size: 42
18544340 TAGGGTTATG
** * *
18544350 TGTGATTTTGTGTAAGAGCATATCTGGGATATGGAATCGATA
1 TGTGATTTCATGTAAGACCATATCTGGGACATGGAATCGATA
* *
18544392 TGTGATTTCATGTAAGACCATGTCTGGGACATGGCATCGATA
1 TGTGATTTCATGTAAGACCATATCTGGGACATGGAATCGATA
* * ** *
18544434 TTTGATTTCATGTAAGACCATGTCTAAGACATGGAGTCGATA
1 TGTGATTTCATGTAAGACCATATCTGGGACATGGAATCGATA
18544476 CAAGATATCG
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (42 bp):
TGTGATTTCATGTAAGACCATATCTGGGACATGGAATCGATA
Found at i:18544490 original size:42 final size:42
Alignment explanation
Indices: 18544399--18544496 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
18544389 ATATGTGATT
** *** *
18544399 TCATGTAAGACCATGTCTGGGACATGGCATCGATATTTGATT
1 TCATGTAAGACCATGTCTAAGACATGGCATCGATACAAGATA
18544441 TCATGTAAGACCATGTCTAAGACATGG-AGTCGATACAAGATA
1 TCATGTAAGACCATGTCTAAGACATGGCA-TCGATACAAGATA
*
18544483 TCGTGTAAGACCAT
1 TCATGTAAGACCAT
18544497 AGTTGGGCTA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (42 bp):
TCATGTAAGACCATGTCTAAGACATGGCATCGATACAAGATA
Found at i:18551237 original size:42 final size:42
Alignment explanation
Indices: 18551189--18551335 Score: 170
Period size: 42 Copynumber: 3.3 Consensus size: 42
18551179 CATAGTTCAA
18551189 CTATGGTCTTACACATCTTCACATAATGATGCCATAGCCCAG
1 CTATGGTCTTACACATCTTCACATAATGATGCCATAGCCCAG
* * *
18551231 CTATGGTCTTACACATATTCATATATTGATGCCATAGCCCAG
1 CTATGGTCTTACACATCTTCACATAATGATGCCATAGCCCAG
* *
18551273 CCATGGTCTTACACGTAACCACATATCACAT-ATCGATGCCATAGCCCAG
1 CTATGGTCTTACAC---A--TC-T-TCACATAAT-GATGCCATAGCCCAG
18551322 CTATGGTCTTACAC
1 CTATGGTCTTACAC
18551336 GAATCACATA
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
42 52 0.59
45 1 0.01
48 2 0.02
49 33 0.38
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (42 bp):
CTATGGTCTTACACATCTTCACATAATGATGCCATAGCCCAG
Found at i:18551313 original size:49 final size:48
Alignment explanation
Indices: 18551242--18551347 Score: 158
Period size: 49 Copynumber: 2.2 Consensus size: 48
18551232 TATGGTCTTA
* *
18551242 CACATATTCATATATTGATGCCATAGCCCAGCCATGGTCTTACACGTAAC
1 CACATA-TCACATATCGATGCCATAGCCCAGCCATGGTCTTACACG-AAC
* *
18551292 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
1 CACATATCACATATCGATGCCATAGCCCAGCCATGGTCTTACACGAAC
18551340 CACATATC
1 CACATATC
18551348 TCACTGATGC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 10 0.19
49 36 0.69
50 6 0.12
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.26
Consensus pattern (48 bp):
CACATATCACATATCGATGCCATAGCCCAGCCATGGTCTTACACGAAC
Found at i:18551407 original size:47 final size:46
Alignment explanation
Indices: 18551258--18551427 Score: 169
Period size: 47 Copynumber: 3.6 Consensus size: 46
18551248 TTCATATATT
* ** * * *
18551258 GATGCCATAGCCCAGCCATGGTCTTACACGTAACCACATATCACATATC
1 GATGCCATATCCCAGATATGGTCTTATACG-AAGCACATATCAC--ACC
* * * * * *
18551307 GATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCACT
1 GATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACACC
* * *
18551353 GATGCCATATCCCAGATATGATCTTATACAGTAGCATATATCACACC
1 GATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACACC
18551400 GATGCCATATCCCAGATATGGTCTTATA
1 GATGCCATATCCCAGATATGGTCTTATA
18551428 TGGAAATCAC
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
46 26 0.25
47 39 0.37
48 11 0.10
49 29 0.28
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (46 bp):
GATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACACC
Found at i:18551482 original size:31 final size:31
Alignment explanation
Indices: 18551447--18551533 Score: 138
Period size: 31 Copynumber: 2.8 Consensus size: 31
18551437 CTTGTCACTT
*
18551447 GTAGCCGAAGCTACCACTGTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
** *
18551478 GTAGCAAAAGCTACAACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
18551509 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
18551534 TGTCATTTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:18551608 original size:50 final size:50
Alignment explanation
Indices: 18551509--18551685 Score: 282
Period size: 50 Copynumber: 3.5 Consensus size: 50
18551499 CACTGATCAG
* *
18551509 GTAGCCGAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
* *
18551560 GTAGTCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
18551610 GTAGCCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
18551660 GCAGCCGAAGCTATCATTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
18551686 GTTGCCATGG
Statistics
Matches: 116, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 93 0.80
51 23 0.20
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:18553897 original size:29 final size:29
Alignment explanation
Indices: 18553855--18553912 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
18553845 ACTATTAGAA
18553855 AAAGGGATAATCTATGTTTCATACAATCC
1 AAAGGGATAATCTATGTTTCATACAATCC
18553884 AAAGGGATAATCTATGTTTCATACAATCC
1 AAAGGGATAATCTATGTTTCATACAATCC
18553913 TTTCTCATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (29 bp):
AAAGGGATAATCTATGTTTCATACAATCC
Found at i:18559100 original size:14 final size:15
Alignment explanation
Indices: 18559077--18559106 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
18559067 ACATAAAATT
18559077 AAAATAATTTATAAA
1 AAAATAATTTATAAA
18559092 AAAAT-ATTTATAAA
1 AAAATAATTTATAAA
18559106 A
1 A
18559107 TTAAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATAATTTATAAA
Found at i:18570620 original size:23 final size:23
Alignment explanation
Indices: 18570561--18570624 Score: 103
Period size: 22 Copynumber: 2.8 Consensus size: 23
18570551 TAGGGTAGGA
*
18570561 AAAAGGAAAAGAAGAAAATGAGGG
1 AAAATGAAAA-AAGAAAATGAGGG
18570585 AAAAT-AAAAAAGAAAATGAGGG
1 AAAATGAAAAAAGAAAATGAGGG
18570607 AAAATGAAAAAAGAAAAT
1 AAAATGAAAAAAGAAAAT
18570625 AAAAAGATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
22 18 0.47
23 16 0.42
24 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (23 bp):
AAAATGAAAAAAGAAAATGAGGG
Found at i:18571157 original size:61 final size:61
Alignment explanation
Indices: 18571064--18571180 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
18571054 GTTTTAAAGC
* * * *
18571064 TAGAACTAAATTGTTAGATTTTGCAAATATTGAGGGCCAAATTTATTGAATTTTTTAGAAT
1 TAGAACTAAAATGATAAATTTTGCAAACATTGAGGGCCAAATTTATTGAATTTTTTAGAAT
* * ** *
18571125 TAGAACTAAAATGATAAATTTTGTAAACATTGAGTGTTAAATTTATTGATTTTTTT
1 TAGAACTAAAATGATAAATTTTGCAAACATTGAGGGCCAAATTTATTGAATTTTTT
18571181 TACATTTTGG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (61 bp):
TAGAACTAAAATGATAAATTTTGCAAACATTGAGGGCCAAATTTATTGAATTTTTTAGAAT
Found at i:18574223 original size:8 final size:8
Alignment explanation
Indices: 18574210--18574239 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
18574200 AGATCGGCAC
18574210 AAGCCGAA
1 AAGCCGAA
18574218 AAGCCGAA
1 AAGCCGAA
*
18574226 ATGCCGAA
1 AAGCCGAA
18574234 AAGCCG
1 AAGCCG
18574240 GTATTTTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.27, G:0.27, T:0.03
Consensus pattern (8 bp):
AAGCCGAA
Found at i:18574679 original size:27 final size:27
Alignment explanation
Indices: 18574638--18574749 Score: 118
Period size: 27 Copynumber: 4.1 Consensus size: 27
18574628 AGGAAGCGTC
*
18574638 CTGGTGGCTATGCCACAAATATCTGAT
1 CTGGTGGCTCTGCCACAAATATCTGAT
* * *
18574665 CTAGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAAATATCTGAT
* *
18574692 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAAATATCTG-AT
* * * *
18574720 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAAATATCTGAT
18574746 CTGG
1 CTGG
18574750 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.07
27 52 0.72
28 15 0.21
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAAATATCTGAT
Found at i:18574742 original size:54 final size:54
Alignment explanation
Indices: 18574638--18574749 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
18574628 AGGAAGCGTC
*
18574638 CTGGTGGCTATGCCACAAATATCTGATCTAGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAAATATCTGATCTAGTGACTCTGCCACATATATCTGTT
* * * * *
18574692 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAAATATCTG-ATCTAGTGACTCTGCCACATATATCTGTT
18574746 CTGG
1 CTGG
18574750 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 34 0.67
55 17 0.33
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATATCTGATCTAGTGACTCTGCCACATATATCTGTT
Found at i:18581668 original size:27 final size:27
Alignment explanation
Indices: 18581630--18581738 Score: 103
Period size: 27 Copynumber: 4.0 Consensus size: 27
18581620 AAGCGTCCTG
*
18581630 GTGGCTATGCCACAAATATCTGATCTA
1 GTGGCTCTGCCACAAATATCTGATCTA
* * *
18581657 GTGGCTCTGCCACATATATCTGTTCTG
1 GTGGCTCTGCCACAAATATCTGATCTA
* * *
18581684 GTGGCTCTGCCACGATTATCTGTATCTG
1 GTGGCTCTGCCACAAATATCTG-ATCTA
* * * *
18581712 GTGACTCTGTCAC-ATTATCTGTTCTA
1 GTGGCTCTGCCACAAATATCTGATCTA
18581738 G
1 G
18581739 CAGCCATGCT
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
26 4 0.06
27 50 0.72
28 15 0.22
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (27 bp):
GTGGCTCTGCCACAAATATCTGATCTA
Found at i:18581731 original size:54 final size:54
Alignment explanation
Indices: 18581627--18581736 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 54
18581617 AGGAAGCGTC
*
18581627 CTGGTGGCTATGCCACAAATATCTGATCTAGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAAATATCTGATCTAGTGACTCTGCCACATATATCTGTT
* * * * *
18581681 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAAATATCTG-ATCTAGTGACTCTGCCACATATATCTGTT
18581735 CT
1 CT
18581737 AGCAGCCATG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
54 32 0.65
55 17 0.35
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATATCTGATCTAGTGACTCTGCCACATATATCTGTT
Found at i:18584682 original size:22 final size:23
Alignment explanation
Indices: 18584629--18584689 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
18584619 TAAAGCTATC
*
18584629 ACCCACCAAACACAACCAATCAT
1 ACCCTCCAAACACAACCAATCAT
* * *
18584652 AGCCTCCAAGCACAACCAAT-TT
1 ACCCTCCAAACACAACCAATCAT
18584674 ACCCTCCAAACACAAC
1 ACCCTCCAAACACAAC
18584690 TATAAGTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.43, C:0.43, G:0.03, T:0.11
Consensus pattern (23 bp):
ACCCTCCAAACACAACCAATCAT
Found at i:18587390 original size:23 final size:23
Alignment explanation
Indices: 18587364--18587444 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
18587354 TGTACCTTCT
*
18587364 AAACACAACCAAATTTACCCTCC
1 AAACACAACCAAATATACCCTCC
* * *
18587387 AAACACAACCATATATGTAACATCC
1 AAACACAACCA-A-ATATACCCTCC
* *
18587412 GAACACAACCAAGTATACCCTCC
1 AAACACAACCAAATATACCCTCC
18587435 AAACACAACC
1 AAACACAACC
18587445 TTCAACATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 27 0.57
24 2 0.04
25 18 0.38
ACGTcount: A:0.46, C:0.36, G:0.04, T:0.15
Consensus pattern (23 bp):
AAACACAACCAAATATACCCTCC
Found at i:18594916 original size:22 final size:22
Alignment explanation
Indices: 18594890--18594944 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
18594880 CAATAGGCTA
*
18594890 GTCTCAAGACAATTTG-CCATAT
1 GTCTCGAGACAATTTGTCCAT-T
*
18594912 GTCTCGAGACAATTTGTCGATT
1 GTCTCGAGACAATTTGTCCATT
18594934 GTCTCGAGACA
1 GTCTCGAGACA
18594945 GGGCTCCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (22 bp):
GTCTCGAGACAATTTGTCCATT
Found at i:18597354 original size:22 final size:20
Alignment explanation
Indices: 18597304--18597355 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
18597294 AGGTCAACAT
*
18597304 ACCCATGTGGAAGGACACAC
1 ACCCATGTGAAAGGACACAC
** *
18597324 ACCTGTGTGAAAGGAGGCATAC
1 ACCCATGTGAAAGGA--CACAC
18597346 ACCCATGTGA
1 ACCCATGTGA
18597356 CTAAGTACAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 12 0.50
22 12 0.50
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (20 bp):
ACCCATGTGAAAGGACACAC
Found at i:18600336 original size:47 final size:46
Alignment explanation
Indices: 18600260--18600612 Score: 526
Period size: 47 Copynumber: 7.5 Consensus size: 46
18600250 CTTCGGGACT
* * * * * *
18600260 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCTC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC-C
*
18600307 TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
*
18600353 TCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCC
1 T-ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
18600400 TCATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 T-ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
**
18600447 TCATCACATATATACACTTTCACATTCATCACATCGGATATTAGGCC
1 T-ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
18600494 TGATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 T-ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
*
18600541 TTATCACATATATATACTTTCACATTCATCACATCGGCCATTAGGCC
1 -TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
* *
18600588 TTATCACATATATATACATTCACAT
1 -TATCACATATATACACTTTCACAT
18600613 CACAATTATC
Statistics
Matches: 287, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
46 2 0.01
47 284 0.99
48 1 0.00
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (46 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
Found at i:18610297 original size:25 final size:26
Alignment explanation
Indices: 18610269--18610320 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
18610259 TCAAGGATCA
* * *
18610269 TATATATCTTTATTTCCATT-CCATT
1 TATATACCCTTATTTCAATTCCCATT
18610294 TATATACCCTTATTTCAATTCCCATT
1 TATATACCCTTATTTCAATTCCCATT
18610320 T
1 T
18610321 TTATTTCCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (26 bp):
TATATACCCTTATTTCAATTCCCATT
Found at i:18613630 original size:12 final size:11
Alignment explanation
Indices: 18613599--18613631 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
18613589 ACCTAAACTC
18613599 ATTA-TATTTT
1 ATTATTATTTT
18613609 ATTATTATTTT
1 ATTATTATTTT
18613620 ATTACTTATTTT
1 ATTA-TTATTTT
18613632 TCTAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 10 0.48
12 7 0.33
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:18627855 original size:94 final size:95
Alignment explanation
Indices: 18627694--18627882 Score: 344
Period size: 94 Copynumber: 2.0 Consensus size: 95
18627684 ACTTTTATTA
18627694 TCTTTGCTAACTATCGGACAGTGATTGTAAATGTCTACATGGCTTTCTTTTTGTCATAATATACA
1 TCTTTGCTAACTATCGGACAGTGATTGTAAATGTCTACATGGCTTTCTTTTTGTCATAATATACA
*
18627759 TATTT-AAATTTTCTGTTCTATGTCTGTTT
66 TATTTAAAATTTACTGTTCTATGTCTGTTT
*
18627788 TCTTTGCTAACTATCGGACAGTGATTGTAAATGTCTACATGGCTTTCTTTTTTTCATAATATACA
1 TCTTTGCTAACTATCGGACAGTGATTGTAAATGTCTACATGGCTTTCTTTTTGTCATAATATACA
*
18627853 TATTTAAAATTTACTGTTTTATGTCTGTTT
66 TATTTAAAATTTACTGTTCTATGTCTGTTT
18627883 CAGGTTGGGA
Statistics
Matches: 91, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
94 69 0.76
95 22 0.24
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.48
Consensus pattern (95 bp):
TCTTTGCTAACTATCGGACAGTGATTGTAAATGTCTACATGGCTTTCTTTTTGTCATAATATACA
TATTTAAAATTTACTGTTCTATGTCTGTTT
Found at i:18639626 original size:21 final size:20
Alignment explanation
Indices: 18639602--18639645 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
18639592 AATATATATT
18639602 TTTAATAAAAAATCTTAAAAA
1 TTTAATAAAAAAT-TTAAAAA
* **
18639623 TTTATTTTAAAATTTAAAAA
1 TTTAATAAAAAATTTAAAAA
18639643 TTT
1 TTT
18639646 CAAAAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAATAAAAAATTTAAAAA
Found at i:18644993 original size:24 final size:24
Alignment explanation
Indices: 18644981--18645026 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
18644971 TATAACTTTT
18644981 TATAATTAATATTTTAACAATTAA
1 TATAATTAATATTTTAACAATTAA
18645005 TATAATTAATATTTTAACAATT
1 TATAATTAATATTTTAACAATT
18645027 TAATTGTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TATAATTAATATTTTAACAATTAA
Found at i:18651472 original size:15 final size:15
Alignment explanation
Indices: 18651454--18651544 Score: 50
Period size: 15 Copynumber: 6.0 Consensus size: 15
18651444 AGATATTTTT
18651454 TATTATAATATAATA
1 TATTATAATATAATA
*
18651469 TATTATATTATAAT-
1 TATTATAATATAATA
18651483 TACTTAATAA-ATAAGTA
1 TA-TT-ATAATATAA-TA
18651500 -A-TAT-ATATTAATTTA
1 TATTATAATA-TAA--TA
* *
18651515 TATTATTATATTATA
1 TATTATAATATAATA
18651530 TTATTAT-ATATAATA
1 -TATTATAATATAATA
18651545 AACAAAAGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
12 1 0.02
13 3 0.05
14 6 0.10
15 30 0.50
16 12 0.20
17 5 0.08
18 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (15 bp):
TATTATAATATAATA
Found at i:18651528 original size:13 final size:13
Alignment explanation
Indices: 18651512--18651538 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18651502 ATATATTAAT
18651512 TTATATTATTATA
1 TTATATTATTATA
18651525 TTATATTATTATA
1 TTATATTATTATA
18651538 T
1 T
18651539 ATAATAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATATTATTATA
Found at i:18652436 original size:16 final size:17
Alignment explanation
Indices: 18652405--18652437 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18652395 TTCATAAGTA
18652405 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
18652422 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
18652438 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:18653042 original size:46 final size:46
Alignment explanation
Indices: 18652718--18653040 Score: 454
Period size: 46 Copynumber: 7.0 Consensus size: 46
18652708 TTATCTTTGA
* * * * *
18652718 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATAT
* *
18652764 CATGTTGCC-TGGTATCTTTCTACCATGGTCTTATTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* ***
18652809 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
*
18652855 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
18652901 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
18652947 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
*
18652993 CA-GATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATG-TTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
18653039 CA
1 CA
18653041 GAGAGCACAC
Statistics
Matches: 256, Mismatches: 18, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
44 4 0.02
45 35 0.14
46 217 0.85
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
Found at i:18655201 original size:30 final size:30
Alignment explanation
Indices: 18655134--18655201 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
18655124 CACCCTTAAA
* * *
18655134 ATATTTGCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
18655164 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
18655193 AGTATTTAC
1 A-TATTTAC
18655202 TCTTAGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:18655601 original size:41 final size:41
Alignment explanation
Indices: 18655540--18655653 Score: 183
Period size: 41 Copynumber: 2.7 Consensus size: 41
18655530 CTCGAGTCAT
18655540 TGAGGCACTATATGTGTCGTAATATTGCTTCGAATAATTTCGA
1 TGAGGCAC--TATGTGTCGTAATATTGCTTCGAATAATTTCGA
18655583 TGAGGCACTATGTGTCGTAATATTGCTTCGAATAATTTCGA
1 TGAGGCACTATGTGTCGTAATATTGCTTCGAATAATTTCGA
* * *
18655624 CGAGGCACTATGTGTCGTATTATTGGTTCG
1 TGAGGCACTATGTGTCGTAATATTGCTTCG
18655654 GATTAAATCC
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
41 60 0.88
43 8 0.12
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.37
Consensus pattern (41 bp):
TGAGGCACTATGTGTCGTAATATTGCTTCGAATAATTTCGA
Found at i:18659359 original size:21 final size:20
Alignment explanation
Indices: 18659335--18659373 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18659325 CCGTGTTGAT
18659335 TTCGTACTTTGGCCCATTTTC
1 TTCGT-CTTTGGCCCATTTTC
* *
18659356 TTCGTTTTTGGCCTATTT
1 TTCGTCTTTGGCCCATTT
18659374 CTTGTTCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.08, C:0.23, G:0.15, T:0.54
Consensus pattern (20 bp):
TTCGTCTTTGGCCCATTTTC
Found at i:18681444 original size:94 final size:94
Alignment explanation
Indices: 18681197--18681552 Score: 399
Period size: 94 Copynumber: 3.8 Consensus size: 94
18681187 ATATATTACC
* * * *
18681197 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATATACGTGCTGATGCATGTCCTAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATATG-GCTGATGCATGTCCCAAA
*
18681262 CATGTCTTACACTAGCA--CAACTCT-TAGCT
64 CATGTCTTACACTAGCACTCATCTCTGT-GCT
* * *
18681291 GATG-CGTGTCCTAGACAT-GTCTTACACTGGCTATCTC-T-GTCGA-GGCTGATGCATGTCCCA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC--TCTCATAAT--ATGGCTGATGCATGTCCCA
* *
18681351 GACATGTCTTACTCTAGCACTCATCTCTGTGCT
62 AACATGTCTTACACTAGCACTCATCTCTGTGCT
* * *
18681384 GATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCATAATATGGCTGATGCATATCCCAAACA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATGGCTGATGCATGTCCCAAACA
* * *
18681449 TGTCTTACACTAGCCCTCATCT-GGATGCA
66 TGTCTTACACTAGCACTCATCTCTG-TGCT
* * *
18681478 GATGCCATGTCCCAGACATGATCTTAC-CTGGCTCTCATAATGTGGCTGAAGCATGTCCCAAACA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATGGCTGATGCATGTCCCAAACA
18681542 TGTCTTACACT
66 TGTCTTACACT
18681553 GGCGCACAAA
Statistics
Matches: 225, Mismatches: 24, Indels: 27
0.82 0.09 0.10
Matches are distributed among these distances:
91 34 0.15
92 14 0.06
93 77 0.34
94 87 0.39
95 13 0.06
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (94 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATGGCTGATGCATGTCCCAAACA
TGTCTTACACTAGCACTCATCTCTGTGCT
Found at i:18681468 original size:46 final size:45
Alignment explanation
Indices: 18681197--18681552 Score: 274
Period size: 47 Copynumber: 7.6 Consensus size: 45
18681187 ATATATTACC
* *
18681197 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATATACGTGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATATAT--G-GCT
* * * * *
18681247 GATGCATGTCCTAGACATGTCTTACACTAGCAC-AACTCT-TAGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCA-TATATGGCT
* * * *
18681291 GATGCGTGTCCTAGACATGTCTTACACTGGCTATCTC-TGTCGA-GGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGC--TCTCATAT--ATGGCT
* * * *
18681338 GATGCATGTCCCAGACATGTCTTACTCTAGCACTCATCTCTGTGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATATATG-GCT
*
18681384 GATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCATAATATGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCAT-ATATGGCT
* * * * *
18681432 GATGCATATCCCAAACATGTCTTACACTAGCCCTCATCTGGAT-GCA
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAT--ATGGCT
* *
18681478 GATGCCATGTCCCAGACATGATCTTAC-CTGGCTCTCATAATGTGGCT
1 GATG-CATGTCCCAGACATG-TCTTACACTAGCTCTCAT-ATATGGCT
* *
18681525 GAAGCATGTCCCAAACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
18681553 GGCGCACAAA
Statistics
Matches: 247, Mismatches: 39, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
44 32 0.13
45 13 0.05
46 51 0.21
47 85 0.34
48 46 0.19
49 16 0.06
50 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATATATGGCT
Found at i:18681534 original size:187 final size:186
Alignment explanation
Indices: 18681197--18681549 Score: 439
Period size: 187 Copynumber: 1.9 Consensus size: 186
18681187 ATATATTACC
* * * *
18681197 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATATACGTGCTGATGCATGTCCTAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATATACGTGCTGATGCATATCCCAAA
* * * *
18681262 CATGTCTTACACTAGCACAACTCTTAGCTGATGCGTGTCCTAGACATGTCTTACACTGGCTATCT
66 CATGTCTTACACTAGCACAACTCTGAGCAGATGCATGTCCCAGACATGTCTTACACTGGC-ATCT
* * *
18681327 CTGTCGAGGCTGATGCATGTCCCAGACATGTCTTACTCTAGCACTCATCTCTGTGCT
130 CTATCGAGGCTGAAGCATGTCCCAAACATGTCTTACTCTAGCACTCATCTCTGTGCT
* * *
18681384 GATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCATA-ATATG-GCTGATGCATATCCCAAA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATATACGTGCTGATGCATATCCCAAA
**
18681447 CATGTCTTACACTAGC-CCTCATCTGGATGCAGATGCCATGTCCCAGACATGATCTTAC-CTGGC
66 CATGTCTTACACTAGCACAAC-TCT-GA-GCAGATG-CATGTCCCAGACATG-TCTTACACTGGC
*
18681510 -TCTCATAAT-GTGGCTGAAGCATGTCCCAAACATGTCTTAC
126 ATCTC-T-ATCGAGGCTGAAGCATGTCCCAAACATGTCTTAC
18681550 ACTGGCGCAC
Statistics
Matches: 142, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
184 2 0.01
185 34 0.24
186 9 0.06
187 72 0.51
188 19 0.13
189 6 0.04
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (186 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATATACGTGCTGATGCATATCCCAAA
CATGTCTTACACTAGCACAACTCTGAGCAGATGCATGTCCCAGACATGTCTTACACTGGCATCTC
TATCGAGGCTGAAGCATGTCCCAAACATGTCTTACTCTAGCACTCATCTCTGTGCT
Found at i:18682289 original size:12 final size:12
Alignment explanation
Indices: 18682272--18682296 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18682262 TAAAAATGTA
18682272 AAAATCATCAAG
1 AAAATCATCAAG
18682284 AAAATCATCAAG
1 AAAATCATCAAG
18682296 A
1 A
18682297 TCACTTACAT
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:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:18688957 original size:48 final size:46
Alignment explanation
Indices: 18688790--18689094 Score: 224
Period size: 47 Copynumber: 6.5 Consensus size: 46
18688780 CTGATGCCAA
* * *
18688790 GTCCCAGACATGGTCTTACACTGTCTCTCATATATGCGTGCTGATGCAT
1 GTCCCAGACAT-GTCTTACACTGGCTCTCATA-AT-TGTGCCGATGCAT
* * * * * *
18688839 GTTCCAAACACGTCTTACACTGGCTATCTC-T-GTCGAGGCCGATGCAT
1 GTCCCAGACATGTCTTACACTGGC--TCTCATAATTG-TGCCGATGCAT
* * * *
18688886 ATCCCAGACATGTCTTACTCTGGCACTCATAATTGTGCCGACGCCAT
1 GTCCCAGACATGTCTTACACTGGCTCTCATAATTGTGCCGATG-CAT
* *
18688933 GCCCCAGACATGGTCTTACACTGGCTCTCATAATATG-GCTGATGCAT
1 GTCCCAGACAT-GTCTTACACTGGCTCTCATAAT-TGTGCCGATGCAT
* * * ** * * *
18688980 GTCCTAGACATGTCTTACACTAGCCCTTGT-CTGGATGCTGATGCCAT
1 GTCCCAGACATGTCTTACACTGGCTCTCATAATTG-TGCCGATG-CAT
*
18689027 GTCCCAGACATGGTCTTACACTGGCTCTCATAA-TGTGGCCGAAGCAT
1 GTCCCAGACAT-GTCTTACACTGGCTCTCATAATTGT-GCCGATGCAT
* *
18689074 GTCCTAAACATGTCTTACACT
1 GTCCCAGACATGTCTTACACT
18689095 AGCGTACAAA
Statistics
Matches: 200, Mismatches: 42, Indels: 31
0.73 0.15 0.11
Matches are distributed among these distances:
44 1 0.00
45 4 0.02
46 41 0.20
47 81 0.41
48 58 0.29
49 11 0.05
50 4 0.02
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (46 bp):
GTCCCAGACATGTCTTACACTGGCTCTCATAATTGTGCCGATGCAT
Found at i:18689085 original size:141 final size:141
Alignment explanation
Indices: 18688792--18689094 Score: 334
Period size: 141 Copynumber: 2.1 Consensus size: 141
18688782 GATGCCAAGT
* *
18688792 CCCAGACATGGTCTTACACTGTCTCTCATATATGCGTGCTGATGCATGTTCCAAACACGTCTTAC
1 CCCAAACATGGTCTTACACTGGCTCTCATATAT-CGTGCTGATGCATGTTCCAAACACGTCTTAC
* *
18688857 ACTGGCTATCTCTGTCGAGGCCGATGCATATCCCAGACATGTCTTACTCTGGCACTCATAATTGT
65 ACTGCCTATCTCTG-CGAGGCCGATGCATATCCCAGACATGTCTTACACTGGCACTCATAATTGT
*
18688922 GCCGACGCCATGC
129 GCCGAAGCCATGC
* * *
18688935 CCCAGACATGGTCTTACACTGGCTCTCATAATAT-G-GCTGATGCATG-TCCTAGACATGTCTTA
1 CCCAAACATGGTCTTACACTGGCTCTCAT-ATATCGTGCTGATGCATGTTCC-AAACACGTCTTA
* * * * *
18688997 CACTAGCCCT-TGTCTG-GATGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAA
64 CACT-G-CCTATCTCTGCGAGGCCGATG-CATATCCCAGACAT-GTCTTACACTGGCACTCATAA
*
18689060 -TGTGGCCGAAG-CATGT
125 TTGT-GCCGAAGCCATGC
*
18689076 CCTAAACAT-GTCTTACACT
1 CCCAAACATGGTCTTACACT
18689095 AGCGTACAAA
Statistics
Matches: 139, Mismatches: 14, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
140 21 0.15
141 52 0.37
142 32 0.23
143 30 0.22
144 4 0.03
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (141 bp):
CCCAAACATGGTCTTACACTGGCTCTCATATATCGTGCTGATGCATGTTCCAAACACGTCTTACA
CTGCCTATCTCTGCGAGGCCGATGCATATCCCAGACATGTCTTACACTGGCACTCATAATTGTGC
CGAAGCCATGC
Found at i:18691806 original size:13 final size:13
Alignment explanation
Indices: 18691790--18691819 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18691780 ATATATTAAT
*
18691790 TTATATTATTATA
1 TTATACTATTATA
18691803 TTATACTATTATA
1 TTATACTATTATA
18691816 TTAT
1 TTAT
18691820 TATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATACTATTATA
Found at i:18695428 original size:44 final size:44
Alignment explanation
Indices: 18695378--18695468 Score: 119
Period size: 44 Copynumber: 2.1 Consensus size: 44
18695368 TACCATGCTC
* * * *
18695378 GTAAGTGTGACATGTTCACCTGCTGTGAATCGCTTTGACCTTTA
1 GTAAGTGTGACATGTCCACCTGCTATGAACCGCTTTGACCTTCA
** *
18695422 GTAAGTGTGACATGTCCATTTGTTATGAACCGCTTTGACCTTCA
1 GTAAGTGTGACATGTCCACCTGCTATGAACCGCTTTGACCTTCA
18695466 GTA
1 GTA
18695469 CCCAGCAGAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (44 bp):
GTAAGTGTGACATGTCCACCTGCTATGAACCGCTTTGACCTTCA
Found at i:18697185 original size:25 final size:25
Alignment explanation
Indices: 18697154--18697212 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
18697144 GAAAAAGATG
18697154 TAGAAGATGAGAAAATGAAACAGAA
1 TAGAAGATGAGAAAATGAAACAGAA
*
18697179 TAGAAGAGGAGAAAATGAAACAGAA
1 TAGAAGATGAGAAAATGAAACAGAA
*
18697204 T-TAAGATGA
1 TAGAAGATGA
18697213 ATCCTATCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
24 6 0.19
25 25 0.81
ACGTcount: A:0.58, C:0.03, G:0.25, T:0.14
Consensus pattern (25 bp):
TAGAAGATGAGAAAATGAAACAGAA
Found at i:18714005 original size:15 final size:14
Alignment explanation
Indices: 18713980--18714021 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
18713970 ATGTTCAGCA
18713980 TTCTA-ATCTGTTAT
1 TTCTATATCTGTT-T
18713994 TTCTATATCTG-TT
1 TTCTATATCTGTTT
*
18714007 TTCTGTATCTGTTT
1 TTCTATATCTGTTT
18714021 T
1 T
18714022 GGGGTGGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 11 0.44
14 9 0.36
15 5 0.20
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.62
Consensus pattern (14 bp):
TTCTATATCTGTTT
Found at i:18716141 original size:15 final size:15
Alignment explanation
Indices: 18716123--18716160 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
18716113 TCATTATAAA
*
18716123 ATTAATTTATATATT
1 ATTAATTTACATATT
*
18716138 ATTATTTTACATATT
1 ATTAATTTACATATT
18716153 ATTAATTT
1 ATTAATTT
18716161 TTGTCCTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTAATTTACATATT
Found at i:18717387 original size:24 final size:24
Alignment explanation
Indices: 18717360--18717408 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
18717350 CGTAAAATTG
18717360 ATTGGTTTCTATCCTTTTGTTGAA
1 ATTGGTTTCTATCCTTTTGTTGAA
* *
18717384 ATTGTTTTCTGTCCTTTTGTTGAA
1 ATTGGTTTCTATCCTTTTGTTGAA
18717408 A
1 A
18717409 ATTTAAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.55
Consensus pattern (24 bp):
ATTGGTTTCTATCCTTTTGTTGAA
Found at i:18718315 original size:10 final size:10
Alignment explanation
Indices: 18718300--18718331 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
18718290 TGCACATAAA
18718300 GAAAATTTGG
1 GAAAATTTGG
18718310 GAAAATTTGG
1 GAAAATTTGG
18718320 GAAAATTTGG
1 GAAAATTTGG
18718330 GA
1 GA
18718332 TTGATTAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (10 bp):
GAAAATTTGG
Found at i:18722746 original size:29 final size:29
Alignment explanation
Indices: 18722704--18722765 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
18722694 TTCACTTAAG
*
18722704 ATAGTCAAATGGATCAGAGAAATCATGAA
1 ATAGTCAAATGGATCAGAGAAATCATAAA
18722733 ATAGTCAAATGGATCAGAGAAATCATAAA
1 ATAGTCAAATGGATCAGAGAAATCATAAA
18722762 ATAG
1 ATAG
18722766 GAAAAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.50, C:0.10, G:0.19, T:0.21
Consensus pattern (29 bp):
ATAGTCAAATGGATCAGAGAAATCATAAA
Found at i:18726991 original size:27 final size:26
Alignment explanation
Indices: 18726954--18727068 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
18726944 AGCATGGCTG
* *
18726954 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
18726980 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
18727008 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * * *
18727035 CCAGATCAGATATTTCTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
18727062 CCAGAAC
1 CCAGAAC
18727069 GCTTCCTCCA
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
26 5 0.06
27 57 0.72
28 17 0.22
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:18727013 original size:54 final size:54
Alignment explanation
Indices: 18726954--18727068 Score: 162
Period size: 54 Copynumber: 2.1 Consensus size: 54
18726944 AGCATGGCTG
*
18726954 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATA-ATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATATATC-TGGCAGAGCCA
* * *
18727008 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTCTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATATATCTGGCAGAGCCA
18727062 CCAGAAC
1 CCAGAAC
18727069 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
54 35 0.64
55 20 0.36
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATATATCTGGCAGAGCCA
Found at i:18728722 original size:26 final size:26
Alignment explanation
Indices: 18728686--18728795 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
18728676 CATGAAATTC
*
18728686 TTATCATGAAACATTTACCTAGCCCA
1 TTATCATGAAACATTTACCTAACCCA
18728712 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
18728738 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
18728764 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
18728790 TTATCA
1 TTATCA
18728796 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:18729368 original size:25 final size:24
Alignment explanation
Indices: 18729334--18729380 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
18729324 CAGAAATGAA
18729334 TAAAATTAAAATTAGAAAAGAAAAT
1 TAAAATTAAAATT-GAAAAGAAAAT
*
18729359 TAAAATTAAAATTGCAAAGAAA
1 TAAAATTAAAATTGAAAAGAAA
18729381 GTTGACTGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (24 bp):
TAAAATTAAAATTGAAAAGAAAAT
Found at i:18734755 original size:23 final size:22
Alignment explanation
Indices: 18734717--18734792 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
18734707 TATAAAACCT
*
18734717 AATAAAAATAAGCTTAGAGA-AA
1 AATAAAAATAAGCTTA-AAATAA
*
18734739 AATAAAAAGTAATCTTAAAATAA
1 AATAAAAA-TAAGCTTAAAATAA
*
18734762 AATAAAAATAA-C--AACATAA
1 AATAAAAATAAGCTTAAAATAA
18734781 AATAATAAATAA
1 AATAA-AAATAA
18734793 AAGTTTTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
19 11 0.23
20 6 0.12
21 1 0.02
22 13 0.27
23 17 0.35
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (22 bp):
AATAAAAATAAGCTTAAAATAA
Found at i:18740722 original size:19 final size:18
Alignment explanation
Indices: 18740698--18740743 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
18740688 TCTTTTTAGT
*
18740698 TTTGCATTCATCTCATGCA
1 TTTGCATTCATCACAT-CA
18740717 TTTGCATTTCATCACATCA
1 TTTGCA-TTCATCACATCA
*
18740736 TGTGCATT
1 TTTGCATT
18740744 GAATTTCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 13 0.54
20 9 0.38
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (18 bp):
TTTGCATTCATCACATCA
Found at i:18749464 original size:177 final size:177
Alignment explanation
Indices: 18749003--18749639 Score: 947
Period size: 177 Copynumber: 3.6 Consensus size: 177
18748993 GGCATCAGTG
* * *
18749003 AAATTGCAGATCTTATCTCCCTAAGCAGTAATGAAGCAGATCGAAGATGGCGAATCTTATCTCCA
1 AAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGAATCTTATCTCCA
* * * * * *
18749068 TGTATTGATAATGGAGTAGATTTTAGCTACCAGCCTTATCTCTATGAGGTAGCAAGAGAGCAGGT
66 TGTATCGACAATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGGT
*
18749133 TGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGGAAG-AAGACTAA
131 TGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAA-ACTGA
* **
18749180 AAATTGCAGATCTTATCTCCCTAAG-AGTAGTGGAGCAGGTCAAAGATGGAAAATCTTATCTCCA
1 AAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGAATCTTATCTCCA
* * * *
18749244 TGTGTCGGCAATGGAGTAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAAGT
66 TGTATCGACAATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGGT
* *
18749309 TAAAGATACAAGTCTTATCTTCTTGAGGTAGCAAGGAAGCAAACTGA
131 TGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAAACTGA
* *
18749356 AAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCCA
1 AAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGAATCTTATCTCCA
*
18749421 TGTATC-AGCAATGGAGCAGATTTTAGCCACCAGTCTTATCTCTCTAAGGTAGCAAGAGAGCAGG
66 TGTATCGA-CAATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGG
* * *
18749485 TTGAAGATACAAGTCTTATCTTCCTGAGGTAACAAGGAGGCAGACTGA
130 TTGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAAACTGA
* * *
18749533 AAATTGCAGATCTTATCTCCCTATGCAGTAGTGGAGCAGATCAAAGACGGCGAATCTTATCTCTA
1 AAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGAATCTTATCTCCA
* * **
18749598 TGTATCGATAATGGAGCAGATTTAAGCCATTAGCCTTATCTC
66 TGTATCGACAATGGAGCAGATTTTAGCCACCAGCCTTATCTC
18749640 CCTGAAGTTG
Statistics
Matches: 414, Mismatches: 42, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
176 155 0.37
177 258 0.62
178 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (177 bp):
AAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGAATCTTATCTCCA
TGTATCGACAATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGGT
TGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAAACTGA
Found at i:18751287 original size:10 final size:11
Alignment explanation
Indices: 18751251--18751299 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
18751241 CTTTTTTTTG
18751251 TATATATTATT
1 TATATATTATT
*
18751262 TATACTAAAGTATT
1 TATA-T--ATTATT
18751276 TATAT-TTATT
1 TATATATTATT
18751286 TATATATTATT
1 TATATATTATT
18751297 TAT
1 TAT
18751300 TTTTGATGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 9 0.28
11 12 0.38
12 1 0.03
13 1 0.03
14 9 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
TATATATTATT
Found at i:18751390 original size:15 final size:15
Alignment explanation
Indices: 18751372--18751409 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
18751362 TCATTATAAA
*
18751372 ATTAATTTATATATT
1 ATTAATTTACATATT
*
18751387 ATTATTTTACATATT
1 ATTAATTTACATATT
18751402 ATTAATTT
1 ATTAATTT
18751410 CTGTTCTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTAATTTACATATT
Found at i:18753165 original size:18 final size:18
Alignment explanation
Indices: 18753142--18753179 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
18753132 AAACATAATA
18753142 AAATATGAAGGTTTTGCT
1 AAATATGAAGGTTTTGCT
18753160 AAATATGAAGGTTTTGCT
1 AAATATGAAGGTTTTGCT
18753178 AA
1 AA
18753180 GTCCTAGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (18 bp):
AAATATGAAGGTTTTGCT
Found at i:18754427 original size:21 final size:20
Alignment explanation
Indices: 18754388--18754427 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
18754378 TGAAATAATG
*
18754388 TTATTTATTAAAGATTATTT
1 TTATTTATAAAAGATTATTT
*
18754408 TTATTTAATAAAATATTATT
1 TTATTT-ATAAAAGATTATT
18754428 AATATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTATTTATAAAAGATTATTT
Found at i:18754459 original size:20 final size:19
Alignment explanation
Indices: 18754434--18754478 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
18754424 TATTAATATT
18754434 TTTTATAAAAAAATTAAACA
1 TTTTATAAAAAAATTAAA-A
* *
18754454 TTTTAT-TAAAATTTAAAA
1 TTTTATAAAAAAATTAAAA
18754472 TTTTATA
1 TTTTATA
18754479 GTTGAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 7 0.32
19 9 0.41
20 6 0.27
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTTATAAAAAAATTAAAA
Found at i:18754869 original size:28 final size:28
Alignment explanation
Indices: 18754825--18754881 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
18754815 AGATTGATTG
* *
18754825 TTATAGAGAAGATTGACCCTATAAAAAT
1 TTATAGAGAAGACTGACCCGATAAAAAT
*
18754853 TTATAGAGGAGACTGACCCGATAAAAAT
1 TTATAGAGAAGACTGACCCGATAAAAAT
18754881 T
1 T
18754882 AACTAAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (28 bp):
TTATAGAGAAGACTGACCCGATAAAAAT
Found at i:18757065 original size:18 final size:18
Alignment explanation
Indices: 18757042--18757079 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
18757032 AAGCTCACTC
18757042 AGGATTAGAACACAGAGA
1 AGGATTAGAACACAGAGA
18757060 AGGATTAGAACACAGAGA
1 AGGATTAGAACACAGAGA
18757078 AG
1 AG
18757080 CATGGACCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.29, T:0.11
Consensus pattern (18 bp):
AGGATTAGAACACAGAGA
Found at i:18770722 original size:15 final size:18
Alignment explanation
Indices: 18770690--18770725 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 18
18770680 AATAAAAATA
18770690 TTATTATATTAATATTTG
1 TTATTATATTAATATTTG
18770708 TTATT-TATT-AT-TTTG
1 TTATTATATTAATATTTG
18770723 TTA
1 TTA
18770726 AAATTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.39
16 2 0.11
17 4 0.22
18 5 0.28
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (18 bp):
TTATTATATTAATATTTG
Found at i:18771034 original size:14 final size:14
Alignment explanation
Indices: 18771017--18771047 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
18771007 TGTTATCATT
18771017 TTACTATTATATTG
1 TTACTATTATATTG
*
18771031 TTACTATTTTATTG
1 TTACTATTATATTG
18771045 TTA
1 TTA
18771048 GATATAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (14 bp):
TTACTATTATATTG
Found at i:18772518 original size:13 final size:13
Alignment explanation
Indices: 18772500--18772535 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
18772490 AAAAATCAGA
18772500 ATATAATTTGTTT
1 ATATAATTTGTTT
18772513 ATATAATTTGTTT
1 ATATAATTTGTTT
* *
18772526 GTACAATTTG
1 ATATAATTTG
18772536 CATCTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.56
Consensus pattern (13 bp):
ATATAATTTGTTT
Found at i:18782490 original size:75 final size:75
Alignment explanation
Indices: 18782367--18782516 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
18782357 CAAACTAGTA
*
18782367 TCAAAATGGCACTATTTGAGGCACTTTAAGGGAAAAAATGCAAGACTCCATTGTATTGGTCTGAA
1 TCAAAATGGCACCATTTGAGGCACTTTAAGGGAAAAAATGCAAGACTCCATTGTATTGGTCTGAA
18782432 TTTAGTGAAT
66 TTTAGTGAAT
18782442 TCAAAATGGCACCATTTGAGGCACTTTAAGGGAAAAAATGCAAGACTCCATTGTATTGGTCTGAA
1 TCAAAATGGCACCATTTGAGGCACTTTAAGGGAAAAAATGCAAGACTCCATTGTATTGGTCTGAA
18782507 TTTAGTGAAT
66 TTTAGTGAAT
18782517 CTAAGTTAGT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (75 bp):
TCAAAATGGCACCATTTGAGGCACTTTAAGGGAAAAAATGCAAGACTCCATTGTATTGGTCTGAA
TTTAGTGAAT
Found at i:18783354 original size:52 final size:52
Alignment explanation
Indices: 18783276--18783380 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
18783266 CAAATATTTT
18783276 TATAAATATTTACAGAGTGTCATTGAGCTAGTATTAAAGTTTCGTTAGAAAA
1 TATAAATATTTACAGAGTGTCATTGAGCTAGTATTAAAGTTTCGTTAGAAAA
* *
18783328 TATAAATATTTACGGAGTGTCATTGAGTTAGTATTAAAGTTTCGTTAGAAAA
1 TATAAATATTTACAGAGTGTCATTGAGCTAGTATTAAAGTTTCGTTAGAAAA
18783380 T
1 T
18783381 TTAATCTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (52 bp):
TATAAATATTTACAGAGTGTCATTGAGCTAGTATTAAAGTTTCGTTAGAAAA
Found at i:18784580 original size:103 final size:101
Alignment explanation
Indices: 18784371--18784584 Score: 229
Period size: 103 Copynumber: 2.1 Consensus size: 101
18784361 GAATTAATGG
* **
18784371 ATAAGACCATGGTTGGACCATGGAAATATGTAAATGTAAGACCATAGCTAGGCTATGGCATTTTA
1 ATAAGACCATGGTTGGACCATGGAAATATATAAATGTAAGACCATAGCTAGGCTATGGCATCCTA
* *
18784436 ATGAAAAGACCATAACAGGGTTATGGCATCTTGAAC
66 ATGAAAAGACCATAACAGGGTTATGACATCTCGAAC
* ** *
18784472 GTAAGACCATGGTTGGACCAT-GACAGTATATATATGTGTAAGACCATAGCTGGGCTATGGCATC
1 ATAAGACCATGGTTGGACCATGGA-A--ATATATAAATGTAAGACCATAGCTAGGCTATGGCATC
* * * *
18784536 CTGATGGTAAA-ACCATAACTA-GTTTATGACA-CTACGAAT
63 CTAAT-GAAAAGACCATAAC-AGGGTTATGACATCT-CGAAC
18784575 ATAAGACCAT
1 ATAAGACCAT
18784585 AGCAGGGCCA
Statistics
Matches: 93, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
100 2 0.02
101 21 0.23
102 2 0.02
103 63 0.68
104 5 0.05
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (101 bp):
ATAAGACCATGGTTGGACCATGGAAATATATAAATGTAAGACCATAGCTAGGCTATGGCATCCTA
ATGAAAAGACCATAACAGGGTTATGACATCTCGAAC
Found at i:18788940 original size:20 final size:20
Alignment explanation
Indices: 18788912--18788954 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
18788902 TTTTGTTTAT
18788912 CTCACATGAGCTTCAGTTAA
1 CTCACATGAGCTTCAGTTAA
* *
18788932 CTCATATGAGTTTCAGTTAA
1 CTCACATGAGCTTCAGTTAA
18788952 CTC
1 CTC
18788955 TAATGGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (20 bp):
CTCACATGAGCTTCAGTTAA
Found at i:18788964 original size:20 final size:21
Alignment explanation
Indices: 18788917--18788990 Score: 82
Period size: 20 Copynumber: 3.6 Consensus size: 21
18788907 TTTATCTCAC
*
18788917 ATGAGCTTCAGTTAACTC-AT
1 ATGAGTTTCAGTTAACTCTAT
18788937 ATGAGTTTCAGTTAACTCTA-
1 ATGAGTTTCAGTTAACTCTAT
*
18788957 ATGGGTTTCAGTTCAACTCT-T
1 ATGAGTTTCAGTT-AACTCTAT
* *
18788978 ACGAGTTTTAGTT
1 ATGAGTTTCAGTT
18788991 TAACCCTACT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 29 0.63
21 17 0.37
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.41
Consensus pattern (21 bp):
ATGAGTTTCAGTTAACTCTAT
Found at i:18788985 original size:21 final size:21
Alignment explanation
Indices: 18788923--18789049 Score: 73
Period size: 21 Copynumber: 6.1 Consensus size: 21
18788913 TCACATGAGC
* *
18788923 TTCAGTT-AACTCATATGAGT
1 TTCAGTTCAACTCTTACGAGT
* * *
18788943 TTCAGTT-AACTCTAATGGGT
1 TTCAGTTCAACTCTTACGAGT
18788963 TTCAGTTCAACTCTTACGAGT
1 TTCAGTTCAACTCTTACGAGT
* * * *
18788984 TTTAGTTTAAC-CCTACTGGGTT
1 TTCAGTTCAACTCTTAC-GAG-T
* * * *
18789006 TTC-GTTCAGCTTTTATGAGC
1 TTCAGTTCAACTCTTACGAGT
* *
18789026 TTCTGTTCAACCCTTACGAGT
1 TTCAGTTCAACTCTTACGAGT
18789047 TTC
1 TTC
18789050 CGTTAGCACT
Statistics
Matches: 79, Mismatches: 23, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
20 31 0.39
21 43 0.54
22 5 0.06
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (21 bp):
TTCAGTTCAACTCTTACGAGT
Found at i:18789013 original size:42 final size:41
Alignment explanation
Indices: 18788923--18789006 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 41
18788913 TCACATGAGC
* *
18788923 TTCAGTT-AACTCATATGAGTTTCAGTTAACTCTAATGGGT
1 TTCAGTTCAACTCATACGAGTTTCAGTTAACCCTAATGGGT
* * *
18788963 TTCAGTTCAACTCTTACGAGTTTTAGTTTAACCCTACTGGGT
1 TTCAGTTCAACTCATACGAGTTTCAG-TTAACCCTAATGGGT
18789005 TT
1 TT
18789007 TCGTTCAGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 7 0.19
41 15 0.41
42 15 0.41
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.42
Consensus pattern (41 bp):
TTCAGTTCAACTCATACGAGTTTCAGTTAACCCTAATGGGT
Found at i:18795590 original size:67 final size:67
Alignment explanation
Indices: 18795480--18795614 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
18795470 ATAGTATAGT
18795480 TTAACCAAAAAACAATTAACCTCTAACCTTCTAATCGAATAAAATTCATTCATTAGAAAATTTTG
1 TTAACCAAAAAACAATTAACCTCTAACCTTCTAATCGAATAAAATTCATTCATTAGAAAATTTTG
18795545 AG
66 AG
* * *
18795547 TTAACCAAAAAACAATTAACCTCTAACGTTCTAATCGAGTAAAATTCATTCATTAGAACATTTTG
1 TTAACCAAAAAACAATTAACCTCTAACCTTCTAATCGAATAAAATTCATTCATTAGAAAATTTTG
18795612 AG
66 AG
18795614 T
1 T
18795615 AAAATTCATC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (67 bp):
TTAACCAAAAAACAATTAACCTCTAACCTTCTAATCGAATAAAATTCATTCATTAGAAAATTTTG
AG
Found at i:18798100 original size:18 final size:20
Alignment explanation
Indices: 18798085--18798121 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18798075 TAATAATAAA
*
18798085 ATATCTCATTAAAATAATAT
1 ATATCTAATTAAAATAATAT
18798105 ATATCTAATT-AAATAAT
1 ATATCTAATTAAAATAAT
18798122 CATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATCTAATTAAAATAATAT
Found at i:18801619 original size:12 final size:12
Alignment explanation
Indices: 18801602--18801631 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18801592 TCAGTGAGTT
18801602 ACACGGCCTAGC
1 ACACGGCCTAGC
*
18801614 ACACGGCCTGGC
1 ACACGGCCTAGC
18801626 ACACGG
1 ACACGG
18801632 GTGTATGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:18805207 original size:21 final size:21
Alignment explanation
Indices: 18805181--18805223 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
18805171 GGTTCGCTGT
*
18805181 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
18805202 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
18805223 A
1 A
18805224 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:18805223 original size:16 final size:16
Alignment explanation
Indices: 18805204--18805236 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18805194 TGTATTGGAT
*
18805204 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
18805220 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
18805236 T
1 T
18805237 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:18805281 original size:45 final size:44
Alignment explanation
Indices: 18805215--18805309 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
18805205 GGATTAGAGG
* *
18805215 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
18805260 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
18805304 TGTAAT
1 TGTAAT
18805310 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:18805492 original size:18 final size:17
Alignment explanation
Indices: 18805471--18805505 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18805461 TTATTATTTA
*
18805471 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
18805489 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
18805506 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:18805499 original size:28 final size:27
Alignment explanation
Indices: 18805429--18805501 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
18805419 TTTATTATCA
*
18805429 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
18805457 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
18805484 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
18805502 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:18805633 original size:16 final size:17
Alignment explanation
Indices: 18805607--18805648 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
18805597 AAACATAATT
18805607 ATTATAAATATAT-TTTA
1 ATTA-AAATATATATTTA
18805624 ATTAAAATATATAATTTA
1 ATTAAAATATAT-ATTTA
18805642 A-TAAAAT
1 ATTAAAAT
18805649 TCTTAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 10 0.43
18 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTAAAATATATATTTA
Found at i:18805641 original size:18 final size:17
Alignment explanation
Indices: 18805614--18805648 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18805604 ATTATTATAA
*
18805614 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
18805632 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
18805649 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:18805654 original size:143 final size:147
Alignment explanation
Indices: 18805390--18805660 Score: 478
Period size: 143 Copynumber: 1.9 Consensus size: 147
18805380 ATGATTATTG
18805390 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
18805455 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
18805520 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
18805539 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
18805601 ATAATTATTA-TAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
18805661 ATATTCTTAT
Statistics
Matches: 120, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
143 49 0.41
144 42 0.35
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:18805723 original size:143 final size:142
Alignment explanation
Indices: 18805402--18805790 Score: 384
Period size: 129 Copynumber: 2.8 Consensus size: 142
18805392 ATTGTTATTT
18805402 AAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAAACATAATTATTA
1 AAATTTTAATAAGATTA---A-TATCAAAAATAAATAATTTAATCATATTTAAACATAATTATTA
* *
18805467 TTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAATTTGTTT
62 TTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA--AGAAATTTGTTA
* ** ***
18805532 TGGTAAATTATTTTATTT
125 TGGTAAATTACTCAAACC
*
18805550 AAATTTTAATAAGATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTA-TAA
1 AAATTTTAATAAGATTAATATCAAAAATAAATAATTTAATCATATTTAAACATAATTATTATTAA
*
18805614 ATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT-A-ATATTCT-TATAT-G-
66 ATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAGAAATT-TGT-TATGGT
*
18805674 AATTTACTCAAACC
129 AAATTACTCAAACC
* *** *
18805688 ATAATTATTATTAA-A-T-ATGAT--ACTGT-AA-AATATAA--A-A--T-AACATAATTATTAT
1 A-AATT-TTAATAAGATTAAT-ATCAAAAATAAATAATTTAATCATATTTAAACATAATTATTAT
* *
18805740 TAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
63 TAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
18805791 TATTCTTATA
Statistics
Matches: 216, Mismatches: 18, Indels: 32
0.81 0.07 0.12
Matches are distributed among these distances:
128 13 0.06
129 48 0.22
130 1 0.00
131 1 0.00
132 1 0.00
134 6 0.03
135 2 0.01
136 2 0.01
137 2 0.01
138 11 0.05
139 11 0.05
140 10 0.05
143 48 0.22
144 42 0.19
145 1 0.00
148 17 0.08
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (142 bp):
AAATTTTAATAAGATTAATATCAAAAATAAATAATTTAATCATATTTAAACATAATTATTATTAA
ATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAGAAATTTGTTATGGTAA
ATTACTCAAACC
Found at i:18805755 original size:129 final size:129
Alignment explanation
Indices: 18805598--18805830 Score: 414
Period size: 129 Copynumber: 1.8 Consensus size: 129
18805588 ATCATATTTA
* *
18805598 AACATAATTATTATAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
1 AACATAATTATTATAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
*
18805663 ATTCTTATATGAATTTACTCAAACCATAAT-TATTATTAAATATGATACTGTAAAATATAAAAT
66 ATTCTTATATGAATTTACTCAAACCATAATATATGATTAAATATGATACTGTAAAATATAAAAT
18805726 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTA-TAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
18805791 TATTCTTATATGAATTTACTCAAATCATAATATATGATTA
65 TATTCTTATATGAATTTACTCAAACCATAATATATGATTA
18805831 TAACTAATAT
Statistics
Matches: 99, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
128 13 0.13
129 79 0.80
130 7 0.07
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (129 bp):
AACATAATTATTATAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
ATTCTTATATGAATTTACTCAAACCATAATATATGATTAAATATGATACTGTAAAATATAAAAT
Found at i:18805764 original size:18 final size:17
Alignment explanation
Indices: 18805743--18805777 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18805733 TTATTATTAA
18805743 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
18805761 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
18805778 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:18805840 original size:17 final size:16
Alignment explanation
Indices: 18805818--18805864 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
18805808 ACTCAAATCA
18805818 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
18805835 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
18805849 TAAATATATGATTTAA
1 T-AATATATGATTTAA
18805865 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:18805865 original size:17 final size:17
Alignment explanation
Indices: 18805837--18805870 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18805827 ATTATAACTA
*
18805837 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
18805854 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
18805871 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:18806013 original size:93 final size:91
Alignment explanation
Indices: 18805903--18806096 Score: 284
Period size: 92 Copynumber: 2.1 Consensus size: 91
18805893 GATTATAGTT
* *
18805903 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTA-ATATAATTAT-ATAATAATATATAATTTC
* *
18805966 ATAAAATTCTTGATAATAAAAATTTTCTTA
63 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
18805996 TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAGTGATATATAATTTCATA
1 TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAATAATATATAATTTCATA
18806061 AAATTCTTAATAATAAAATGTTCTTA
66 AAATTCTTAATAATAAAATGTTCTTA
18806087 TATGAATTTA
1 TATGAATTTA
18806097 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
91 21 0.23
92 40 0.43
93 29 0.31
94 3 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (91 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAATAATATATAATTTCATA
AAATTCTTAATAATAAAATGTTCTTA
Found at i:18807510 original size:11 final size:11
Alignment explanation
Indices: 18807496--18807522 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
18807486 AAAAATCAAT
18807496 ACAAAAGTTTC
1 ACAAAAGTTTC
18807507 ACAAAAGTTTC
1 ACAAAAGTTTC
18807518 ACAAA
1 ACAAA
18807523 CTAATTTCTA
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:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:18829381 original size:15 final size:15
Alignment explanation
Indices: 18829342--18829386 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
18829332 AATGCATAAC
*
18829342 TTCTACTCTGTTCTA
1 TTCTACTTTGTTCTA
18829357 TTCTACTTTGTTCTA
1 TTCTACTTTGTTCTA
* *
18829372 TTCTATTTTGCTCTA
1 TTCTACTTTGTTCTA
18829387 CTTTGCTCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.13, C:0.22, G:0.07, T:0.58
Consensus pattern (15 bp):
TTCTACTTTGTTCTA
Found at i:18829405 original size:25 final size:25
Alignment explanation
Indices: 18829358--18829405 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
18829348 TCTGTTCTAT
* *
18829358 TCTACTTTGTTCTATTCTATTTTGC
1 TCTACTTTGCTCTATTCGATTTTGC
* *
18829383 TCTACTTTGCTCTGTTCGGTTTT
1 TCTACTTTGCTCTATTCGATTTT
18829406 ATTTGATTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.08, C:0.21, G:0.12, T:0.58
Consensus pattern (25 bp):
TCTACTTTGCTCTATTCGATTTTGC
Found at i:18830342 original size:14 final size:15
Alignment explanation
Indices: 18830322--18830362 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
18830312 AAAAGCAATT
*
18830322 TATTTTCAATAAATC
1 TATTTTCTATAAATC
18830337 -ATTTTCTA-AAATC
1 TATTTTCTATAAATC
18830350 TATTTTCTATAAA
1 TATTTTCTATAAA
18830363 ACAAACATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 5 0.22
14 15 0.65
15 3 0.13
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTTTCTATAAATC
Found at i:18834423 original size:3 final size:3
Alignment explanation
Indices: 18834415--18834441 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
18834405 ACCAAATAGG
18834415 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
18834442 AATATAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.