Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 5 of 218
Found at i:1684522 original size:31 final size:31
Alignment explanation
Indices: 1684487--1684549 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1684477 ATTTAACAGC
*
1684487 TCAATAACTTAAATAAAAACTTTTAAATAGT
1 TCAATAACTTAAATAAAAACTTTCAAATAGT
* ** *
1684518 TCAATGACTTAAATGGAAACTTTCGAATAGT
1 TCAATAACTTAAATAAAAACTTTCAAATAGT
1684549 T
1 T
1684550 TAGTGACCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (31 bp):
TCAATAACTTAAATAAAAACTTTCAAATAGT
Found at i:1685672 original size:29 final size:30
Alignment explanation
Indices: 1685618--1685679 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
1685608 GCGGAAAATA
1685618 GCCCATTCCGGTAAATAATT-AAAAAACCG
1 GCCCATTCCGGTAAATAATTAAAAAAACCG
* *
1685647 GCCCATTTCGGTAAAT-TTTAAAAAAAACCG
1 GCCCATTCCGGTAAATAATT-AAAAAAACCG
1685677 GCC
1 GCC
1685680 TTTTTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 15 0.52
30 12 0.41
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.23
Consensus pattern (30 bp):
GCCCATTCCGGTAAATAATTAAAAAAACCG
Found at i:1696693 original size:8 final size:7
Alignment explanation
Indices: 1696666--1696691 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1696656 GAAATTTTCT
1696666 TTAAATC
1 TTAAATC
1696673 TTAAATC
1 TTAAATC
1696680 TTAAATC
1 TTAAATC
1696687 TTAAA
1 TTAAA
1696692 ATTATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAATC
Found at i:1698479 original size:16 final size:17
Alignment explanation
Indices: 1698460--1698502 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1698450 AAGATATATT
* *
1698460 ATTTTAAATTTGACTC-
1 ATTTTAAATTCGAATCA
1698476 ATTTTAAAATTCGAATCA
1 ATTTT-AAATTCGAATCA
1698494 ATTTTAAAT
1 ATTTTAAAT
1698503 ATCAATTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 13 0.57
18 5 0.22
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (17 bp):
ATTTTAAATTCGAATCA
Found at i:1719225 original size:23 final size:23
Alignment explanation
Indices: 1719194--1719263 Score: 113
Period size: 23 Copynumber: 3.0 Consensus size: 23
1719184 AGCTAGATTT
1719194 TTTTCAAATATTATCACTAAATAA
1 TTTT-AAATATTATCACTAAATAA
*
1719218 TTTTAAATATTATCACTAAATAG
1 TTTTAAATATTATCACTAAATAA
*
1719241 TTCTAAATATTATCACTAAATAA
1 TTTTAAATATTATCACTAAATAA
1719264 CTAAAATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
23 39 0.91
24 4 0.09
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.41
Consensus pattern (23 bp):
TTTTAAATATTATCACTAAATAA
Found at i:1719239 original size:13 final size:13
Alignment explanation
Indices: 1719199--1719262 Score: 61
Period size: 13 Copynumber: 5.4 Consensus size: 13
1719189 GATTTTTTTC
1719199 AAATATTATCACT
1 AAATATTATCACT
1719212 AAATAATT-T---T
1 AAAT-ATTATCACT
1719222 AAATATTATCACT
1 AAATATTATCACT
*
1719235 AAATAGT-T--CT
1 AAATATTATCACT
1719245 AAATATTATCACT
1 AAATATTATCACT
1719258 AAATA
1 AAATA
1719263 ACTAAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 16
0.69 0.03 0.27
Matches are distributed among these distances:
9 3 0.07
10 14 0.34
11 1 0.02
12 1 0.02
13 19 0.46
14 3 0.07
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (13 bp):
AAATATTATCACT
Found at i:1726393 original size:19 final size:19
Alignment explanation
Indices: 1726369--1726405 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1726359 TTTTGATATT
1726369 TGAACAAAAAAAAAAATTA
1 TGAACAAAAAAAAAAATTA
* *
1726388 TGAACAATAAATAAAATT
1 TGAACAAAAAAAAAAATT
1726406 TTACAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (19 bp):
TGAACAAAAAAAAAAATTA
Found at i:1729738 original size:31 final size:31
Alignment explanation
Indices: 1729698--1729756 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1729688 TAAATTACAT
1729698 TGAACTATTCGAAAGCTTTTATTTAAGTCAC
1 TGAACTATTCGAAAGCTTTTATTTAAGTCAC
*
1729729 TGAATTATTCGAAAGCTTTTATTTAAGT
1 TGAACTATTCGAAAGCTTTTATTTAAGT
1729757 AATTGAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (31 bp):
TGAACTATTCGAAAGCTTTTATTTAAGTCAC
Found at i:1733656 original size:15 final size:15
Alignment explanation
Indices: 1733636--1733668 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1733626 TTCACCTAAA
1733636 TTTTTA-ATAAATTAT
1 TTTTTACATAAATT-T
1733651 TTTTTACATAAATTT
1 TTTTTACATAAATTT
1733666 TTT
1 TTT
1733669 CATCTACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTTACATAAATTT
Found at i:1742966 original size:24 final size:24
Alignment explanation
Indices: 1742932--1742978 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1742922 TTTACAATTA
*
1742932 TTTTTATATTAAGATTTTAATTTT
1 TTTTTAAATTAAGATTTTAATTTT
*
1742956 TTTTTAAATTAAGTTTTTAATTT
1 TTTTTAAATTAAGATTTTAATTT
1742979 GATAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTTTAAATTAAGATTTTAATTTT
Found at i:1752516 original size:7 final size:6
Alignment explanation
Indices: 1752485--1752515 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
1752475 AACTATTTTC
1752485 TGAAAA TGAAAA TGAAAA TGAAAA CTGAAAA
1 TGAAAA TGAAAA TGAAAA TGAAAA -TGAAAA
1752516 CATATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.65, C:0.03, G:0.16, T:0.16
Consensus pattern (6 bp):
TGAAAA
Found at i:1752574 original size:13 final size:13
Alignment explanation
Indices: 1752556--1752580 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1752546 TTTTAAAAAT
1752556 ATTTTCTATTTTA
1 ATTTTCTATTTTA
1752569 ATTTTCTATTTT
1 ATTTTCTATTTT
1752581 TTAAAATTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTCTATTTTA
Found at i:1753428 original size:14 final size:14
Alignment explanation
Indices: 1753411--1753451 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
1753401 TTTAAATCAA
*
1753411 ACTTTTTGAAAAGC
1 ACTTTTTCAAAAGC
*
1753425 AC-TTCTCAAAAGC
1 ACTTTTTCAAAAGC
1753438 AC-TTTTCAAAAGC
1 ACTTTTTCAAAAGC
1753451 A
1 A
1753452 ATGAAGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 22 0.92
14 2 0.08
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (14 bp):
ACTTTTTCAAAAGC
Found at i:1753435 original size:13 final size:13
Alignment explanation
Indices: 1753419--1753451 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1753409 AAACTTTTTG
1753419 AAAAGCACTTCTC
1 AAAAGCACTTCTC
*
1753432 AAAAGCACTTTTC
1 AAAAGCACTTCTC
1753445 AAAAGCA
1 AAAAGCA
1753452 ATGAAGAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.21
Consensus pattern (13 bp):
AAAAGCACTTCTC
Found at i:1761668 original size:21 final size:20
Alignment explanation
Indices: 1761644--1761683 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1761634 CATTTCAAAC
1761644 TTTAGTCACTTCAAC-TTTAAG
1 TTTAGTC-CTT-AACGTTTAAG
1761665 TTTAGTCCTTAACGTTTAA
1 TTTAGTCCTTAACGTTTAA
1761684 TGAATGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 8 0.44
21 7 0.39
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (20 bp):
TTTAGTCCTTAACGTTTAAG
Found at i:1767582 original size:20 final size:22
Alignment explanation
Indices: 1767553--1767597 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
1767543 AAGAAATTGT
*
1767553 AAAATTTTATAAAAT-CAT-AA
1 AAAATATTATAAAATGCATCAA
1767573 AAAATATTATAAAATGCATCAA
1 AAAATATTATAAAATGCATCAA
1767595 AAA
1 AAA
1767598 GGTGATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 3 0.14
22 5 0.23
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATATTATAAAATGCATCAA
Found at i:1767794 original size:19 final size:21
Alignment explanation
Indices: 1767748--1767803 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 21
1767738 GAAAAATTAT
1767748 AATTTTTATAATTTTCTTTAC
1 AATTTTTATAATTTTCTTTAC
*
1767769 AAATTTTAT-A-TTTCTTTAC
1 AATTTTTATAATTTTCTTTAC
*
1767788 -ATTTTTTTAATTTTCT
1 AATTTTTATAATTTTCT
1767804 CACAACTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 6 0.20
21 8 0.27
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (21 bp):
AATTTTTATAATTTTCTTTAC
Found at i:1769876 original size:15 final size:16
Alignment explanation
Indices: 1769851--1769883 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1769841 TCGATTCCCA
*
1769851 AAGATTTTATTGGTTT
1 AAGATTTTATTAGTTT
1769867 AAGA-TTTATTAGTTT
1 AAGATTTTATTAGTTT
1769882 AA
1 AA
1769884 CATACGAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (16 bp):
AAGATTTTATTAGTTT
Found at i:1772927 original size:23 final size:21
Alignment explanation
Indices: 1772889--1772930 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
1772879 TAAATTTTAA
1772889 TTATTATTAAATTAAATATAT
1 TTATTATTAAATTAAATATAT
*
1772910 TTATTAATTTAATGTAAATAT
1 TTATT-ATTAAAT-TAAATAT
1772931 TTTTTGTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTATTATTAAATTAAATATAT
Found at i:1778837 original size:25 final size:20
Alignment explanation
Indices: 1778791--1778830 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1778781 AATGAAAGAA
1778791 AGTAAAGTACAATCAAATTC
1 AGTAAAGTACAATCAAATTC
1778811 AGTAAAGTACAATCAAATTC
1 AGTAAAGTACAATCAAATTC
1778831 CAATCAGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (20 bp):
AGTAAAGTACAATCAAATTC
Found at i:1779396 original size:16 final size:17
Alignment explanation
Indices: 1779370--1779403 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1779360 CATTTCACGA
1779370 ATAATGGGATTCTTTTT
1 ATAATGGGATTCTTTTT
*
1779387 ATAA-GGGATTTTTTTT
1 ATAATGGGATTCTTTTT
1779403 A
1 A
1779404 ACGTTCTACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.53
Consensus pattern (17 bp):
ATAATGGGATTCTTTTT
Found at i:1779719 original size:21 final size:21
Alignment explanation
Indices: 1779676--1779750 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
1779666 TATACTTGAG
*
1779676 TTTTATTAGATTTTTATTATTATA
1 TTTTATTA-A-TTTAATT-TTATA
1779700 TTTTATTAATTTAATTTTATA
1 TTTTATTAATTTAATTTTATA
* * *
1779721 TTGTGATT-ATTCAATTATATA
1 TT-TTATTAATTTAATTTTATA
1779742 TTTTTATTA
1 -TTTTATTA
1779751 TCTCAAGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 22 0.51
22 12 0.28
23 1 0.02
24 8 0.19
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTATTAATTTAATTTTATA
Found at i:1804865 original size:6 final size:6
Alignment explanation
Indices: 1804854--1804882 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1804844 ATAACACATG
1804854 CATACA CATACA CATACA CATACA CATAC
1 CATACA CATACA CATACA CATACA CATAC
1804883 TCGTCGGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.17
Consensus pattern (6 bp):
CATACA
Found at i:1807051 original size:49 final size:49
Alignment explanation
Indices: 1806994--1807143 Score: 127
Period size: 49 Copynumber: 3.1 Consensus size: 49
1806984 ATCCGAATAT
1806994 GAAATAATCTTAACAAGTAACTCGAAATACTCAGAACATGGAGGAACTC
1 GAAATAATCTTAACAAGTAACTCGAAATACTCAGAACATGGAGGAACTC
** * * *
1807043 GAAATAATCCAAACATA-TAA-T-G-ATTCGACTCA-AA-AT-GATCCGAA-TAT
1 GAAATAATCTTAACA-AGTAACTCGAAAT--ACTCAGAACATGGA--GGAACT-C
*
1807090 GAAATAATCTTAACAAGTAACTCGAAATACCCAGAACATGGAGGAACTC
1 GAAATAATCTTAACAAGTAACTCGAAATACTCAGAACATGGAGGAACTC
*
1807139 AAAAT
1 GAAAT
1807144 GATCCAAACA
Statistics
Matches: 75, Mismatches: 12, Indels: 28
0.65 0.10 0.24
Matches are distributed among these distances:
45 2 0.03
46 6 0.08
47 22 0.29
48 11 0.15
49 26 0.35
50 6 0.08
51 2 0.03
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (49 bp):
GAAATAATCTTAACAAGTAACTCGAAATACTCAGAACATGGAGGAACTC
Found at i:1807149 original size:96 final size:96
Alignment explanation
Indices: 1806976--1807168 Score: 359
Period size: 96 Copynumber: 2.0 Consensus size: 96
1806966 TAACTTGAAT
*
1806976 TCAAAATGATCCGAATATGAAATAATCTTAACAAGTAACTCGAAATACTCAGAACATGGAGGAAC
1 TCAAAATGATCCGAATATGAAATAATCTTAACAAGTAACTCGAAATACCCAGAACATGGAGGAAC
*
1807041 TCGAAATAATCCAAACATATAATGATTCGAC
66 TCAAAATAATCCAAACATATAATGATTCGAC
1807072 TCAAAATGATCCGAATATGAAATAATCTTAACAAGTAACTCGAAATACCCAGAACATGGAGGAAC
1 TCAAAATGATCCGAATATGAAATAATCTTAACAAGTAACTCGAAATACCCAGAACATGGAGGAAC
*
1807137 TCAAAATGATCCAAACATATAATGATTCGAC
66 TCAAAATAATCCAAACATATAATGATTCGAC
1807168 T
1 T
1807169 TGAATAATAT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (96 bp):
TCAAAATGATCCGAATATGAAATAATCTTAACAAGTAACTCGAAATACCCAGAACATGGAGGAAC
TCAAAATAATCCAAACATATAATGATTCGAC
Found at i:1812280 original size:87 final size:88
Alignment explanation
Indices: 1812175--1812349 Score: 244
Period size: 87 Copynumber: 2.0 Consensus size: 88
1812165 ACTAAACAAG
* * * * *
1812175 TTGTTGTTGAACGTTAAAATATTAGCAACAACTTTAAAATGTTG-GTATGTAATTTACTTTCATG
1 TTGTTGTTAAACGTTAAAATATTAACAACAACCTTAAAATGTTGTGTATGTAATCTAATTTCATG
* *
1812239 CTTATTCGTTGCAATGGCACGAT
66 CTTATTCATTGCAATGACACGAT
* * *
1812262 TTGTTGTTAAATGTTAAAATATTAACAACAACCTTAAAATGTTGTTTATGTAATCTAATTTTATG
1 TTGTTGTTAAACGTTAAAATATTAACAACAACCTTAAAATGTTGTGTATGTAATCTAATTTCATG
*
1812327 CTTGTTCATTGCAATGACACGAT
66 CTTATTCATTGCAATGACACGAT
1812350 CTGCACGTTG
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
87 40 0.53
88 36 0.47
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (88 bp):
TTGTTGTTAAACGTTAAAATATTAACAACAACCTTAAAATGTTGTGTATGTAATCTAATTTCATG
CTTATTCATTGCAATGACACGAT
Found at i:1814231 original size:12 final size:12
Alignment explanation
Indices: 1814214--1814240 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1814204 AACAAATAAT
1814214 ATATATACATAC
1 ATATATACATAC
1814226 ATATATACATAC
1 ATATATACATAC
1814238 ATA
1 ATA
1814241 CATATACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATATACATAC
Found at i:1814237 original size:16 final size:16
Alignment explanation
Indices: 1814212--1814246 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1814202 ATAACAAATA
*
1814212 ATATATATACATACAT
1 ATATACATACATACAT
1814228 ATATACATACATACAT
1 ATATACATACATACAT
1814244 ATA
1 ATA
1814247 CATGTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATACATACATACAT
Found at i:1825237 original size:3 final size:3
Alignment explanation
Indices: 1825229--1825259 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1825219 TCGCTTGCTT
1825229 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1825260 TCTTTGAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1826128 original size:17 final size:16
Alignment explanation
Indices: 1826100--1826152 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
1826090 TTTGGTTCGC
1826100 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1826116 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
1826133 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1826149 TGTA
1 TGTA
1826153 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:1826217 original size:44 final size:45
Alignment explanation
Indices: 1826133--1826223 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
1826123 GGATTAGAGG
* * *
1826133 TGTATTGGATTAGAGGTGTAATAGCTAATCCGCTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCGCTGTTTGGTTGAA
*
1826178 TGTAATGGAATAGAGGCGTAATAG-TAATCTTG-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATC-CGCTGTTTGGTTGAA
1826222 TG
1 TG
1826224 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
44 19 0.46
45 22 0.54
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCGCTGTTTGGTTGAA
Found at i:1826407 original size:18 final size:17
Alignment explanation
Indices: 1826386--1826420 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1826376 TTATTATTAA
*
1826386 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1826404 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1826421 TCTCATAATT
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:1826496 original size:66 final size:64
Alignment explanation
Indices: 1826425--1826622 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 64
1826415 TAAAATTCTC
1826425 ATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA-TTA
1 ATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT-TAAAATA-AAATTTA
1826489 A
64 A
* ** * * * *
1826490 CATAATTATTATT-AAATAT--A-TTA-T--AAT--TAAAATAT-ATAATT-TAATAAAATTCTT
1 -ATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTTAAAATAAAATT-TA
1826544 A
64 A
*
1826545 ATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTGA
1 ATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT-TAAAATAAAATTT-A
1826610 A
64 A
1826611 ATAATTAATATT
1 ATAATTAATATT
1826623 AAATATATTT
Statistics
Matches: 102, Mismatches: 15, Indels: 30
0.69 0.10 0.20
Matches are distributed among these distances:
53 3 0.03
54 16 0.16
55 7 0.07
56 4 0.04
57 8 0.08
58 3 0.03
59 4 0.04
61 4 0.04
62 3 0.03
63 8 0.08
64 4 0.04
65 6 0.06
66 32 0.31
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (64 bp):
ATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTTAAAATAAAATTTAA
Found at i:1826504 original size:119 final size:121
Alignment explanation
Indices: 1826364--1826660 Score: 494
Period size: 120 Copynumber: 2.5 Consensus size: 121
1826354 ATTTAATCAT
* *
1826364 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TCATA
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
1826428 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
*
1826485 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1826548 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* *
1826604 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
1826661 TAAAATAATT
Statistics
Matches: 166, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
119 56 0.34
120 107 0.64
121 3 0.02
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:1826533 original size:14 final size:15
Alignment explanation
Indices: 1826484--1826535 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1826474 GTAAAATATA
1826484 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
1826499 TATTAAATATATTAT
1 AATTAAATATATTAT
1826514 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
1826527 AATTTAATA
1 AATTAAATA
1826536 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:1832628 original size:19 final size:19
Alignment explanation
Indices: 1832604--1832660 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1832594 ATTTTTTTCC
1832604 TTAAATTTATATTATTGAA
1 TTAAATTTATATTATTGAA
* *
1832623 TTAAATTTCACATT-TTGTA
1 TTAAATTT-ATATTATTGAA
*
1832642 CT--ATTTATATTATTGAA
1 TTAAATTTATATTATTGAA
1832659 TT
1 TT
1832661 GTTTAATCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 4 0.13
17 9 0.30
19 13 0.43
20 4 0.13
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (19 bp):
TTAAATTTATATTATTGAA
Found at i:1839776 original size:13 final size:13
Alignment explanation
Indices: 1839758--1839782 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1839748 TTAATGTTTA
1839758 ATATTTTAAATAT
1 ATATTTTAAATAT
1839771 ATATTTTAAATA
1 ATATTTTAAATA
1839783 AGTTGGTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTTTAAATAT
Found at i:1840543 original size:20 final size:19
Alignment explanation
Indices: 1840508--1840547 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1840498 GGTCCTAGGT
*
1840508 TTTTATTTAGATAAAATAAA
1 TTTTATTTAGA-AAAAAAAA
*
1840528 TTTTATTTTGAAAAAAAAA
1 TTTTATTTAGAAAAAAAAA
1840547 T
1 T
1840548 CACGAACATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
TTTTATTTAGAAAAAAAAA
Found at i:1852788 original size:37 final size:35
Alignment explanation
Indices: 1852745--1852816 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 35
1852735 ATTTTATTTT
1852745 TTAATAGTTCAAAAATATATAATA-TATAATATAAAAA
1 TTAATAGTTCAAAAA-ATA-AATAGT-TAATATAAAAA
*
1852782 TTAATAGTTCAAAAAATACATAGTTAATATAAAAA
1 TTAATAGTTCAAAAAATAAATAGTTAATATAAAAA
1852817 ATATATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
35 14 0.42
36 4 0.12
37 15 0.45
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (35 bp):
TTAATAGTTCAAAAAATAAATAGTTAATATAAAAA
Found at i:1862615 original size:18 final size:18
Alignment explanation
Indices: 1862592--1862633 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1862582 CATTAATACA
*
1862592 AGAACCTGAAACAGAACC
1 AGAACCGGAAACAGAACC
* *
1862610 AGAACCGGAAGCCGAACC
1 AGAACCGGAAACAGAACC
1862628 AGAACC
1 AGAACC
1862634 AGAGCATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.31, G:0.21, T:0.02
Consensus pattern (18 bp):
AGAACCGGAAACAGAACC
Found at i:1862730 original size:3 final size:3
Alignment explanation
Indices: 1862722--1862754 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1862712 GTCACCCTTT
1862722 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1862755 AAATCACTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1866587 original size:21 final size:21
Alignment explanation
Indices: 1866562--1866601 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1866552 TACTACTTTA
1866562 ATATAAATT-TTTAACTTTTTC
1 ATATAAATTCTTTAA-TTTTTC
*
1866583 ATATATATTCTTTAATTTT
1 ATATAAATTCTTTAATTTT
1866602 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATAAATTCTTTAATTTTTC
Found at i:1868633 original size:26 final size:28
Alignment explanation
Indices: 1868597--1868649 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
1868587 TCACAAGTTC
1868597 AGTTCTAATGTATATTTT-TC-TCGAAG
1 AGTTCTAATGTATATTTTCTCTTCGAAG
*
1868623 AGTTTTAATGTATATTTTCTCTTCGAA
1 AGTTCTAATGTATATTTTCTCTTCGAA
1868650 TTTGATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 17 0.71
27 2 0.08
28 5 0.21
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (28 bp):
AGTTCTAATGTATATTTTCTCTTCGAAG
Found at i:1869865 original size:213 final size:215
Alignment explanation
Indices: 1869484--1869950 Score: 688
Period size: 213 Copynumber: 2.2 Consensus size: 215
1869474 TTGTGCTCTC
* * *
1869484 TTTTTTGTAAATTGGGGTTCTTGAGATGAA-GCTGCTTTCTGATTTGTTTTTGTTGGTTTCTTAT
1 TTTTTTGTGAATTGGGGTTCTTGAGAT-AATGCTGCTTTCTCATTTGTTTTTATTGGTTTCTTAT
* * * ** *
1869548 TGTATATATATTGGGGATGTTTAGTTCTTCTAGGACCTAGGTTAATGCTTATTTCATGTTTATCC
65 TATATATATATTGGGGATATTTAGTTCCTCTAGGACCTAGCCTAACGCTTATTTCATGTTTATCC
*
1869613 TGCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAGCTATGACCAGTCCAA
130 TGCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAGCTATGACCAATCCAA
* *
1869678 TTTGTGCTGGTTTTTACTCCA
195 TTTGTGCTGGCTTTTAATCCA
* * *
1869699 -TTTTTGTGAATT-GGGTTCTTGAGATAATGGTGTTTTTTCATTTGTTTTTATTGGTTTCTTATT
1 TTTTTTGTGAATTGGGGTTCTTGAGATAATGCTGCTTTCTCATTTGTTTTTATTGGTTTCTTATT
* * * * *
1869762 ATATATTTGTTGGGTATATTTAGTTCCTCTAGGACCTAGCCTAACGCTTCTTTCATGTTTATTCT
66 ATATATATATTGGGGATATTTAGTTCCTCTAGGACCTAGCCTAACGCTTATTTCATGTTTATCCT
* *
1869827 GCATATTTGGTGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGGAGCTATGACCAATCCAAT
131 GCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAGCTATGACCAATCCAAT
1869892 TTGTGCTGGCTTTTAATCCA
196 TTGTGCTGGCTTTTAATCCA
*
1869912 TTTTTTTGTGAATTGGGGTTCTTGAGATAATTCTGCTTT
1 -TTTTTTGTGAATTGGGGTTCTTGAGATAATGCTGCTTT
1869951 TCCGGTAAAA
Statistics
Matches: 223, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
212 2 0.01
213 177 0.79
214 11 0.05
215 12 0.05
216 21 0.09
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.48
Consensus pattern (215 bp):
TTTTTTGTGAATTGGGGTTCTTGAGATAATGCTGCTTTCTCATTTGTTTTTATTGGTTTCTTATT
ATATATATATTGGGGATATTTAGTTCCTCTAGGACCTAGCCTAACGCTTATTTCATGTTTATCCT
GCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAGCTATGACCAATCCAAT
TTGTGCTGGCTTTTAATCCA
Found at i:1875203 original size:28 final size:28
Alignment explanation
Indices: 1875169--1875253 Score: 170
Period size: 28 Copynumber: 3.0 Consensus size: 28
1875159 TATAGCACAG
1875169 AAAGGAACTAAAAACCAAATTGGCACGT
1 AAAGGAACTAAAAACCAAATTGGCACGT
1875197 AAAGGAACTAAAAACCAAATTGGCACGT
1 AAAGGAACTAAAAACCAAATTGGCACGT
1875225 AAAGGAACTAAAAACCAAATTGGCACGT
1 AAAGGAACTAAAAACCAAATTGGCACGT
1875253 A
1 A
1875254 TATGCTAGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.14
Consensus pattern (28 bp):
AAAGGAACTAAAAACCAAATTGGCACGT
Found at i:1878341 original size:26 final size:27
Alignment explanation
Indices: 1878293--1878344 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1878283 TCATATAAAT
*
1878293 AAAATAAATTATTATTTTAATATATTA
1 AAAATAAATTATTAGTTTAATATATTA
*
1878320 AAAATAAATTATT-GTTTCATATATT
1 AAAATAAATTATTAGTTTAATATATT
1878345 TACGGTGGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
AAAATAAATTATTAGTTTAATATATTA
Found at i:1878526 original size:25 final size:25
Alignment explanation
Indices: 1878463--1878526 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 25
1878453 AAATATTTTA
*
1878463 ATATATAATTTATACACATACAAGT
1 ATATATAATATATACACATACAAGT
* * *
1878488 ATATCTTAATTATATACATATA-AATT
1 ATAT-ATAA-TATATACACATACAAGT
1878514 ATATATGAATATA
1 ATATAT-AATATA
1878527 ATTTTTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 9 0.29
26 12 0.39
27 10 0.32
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATATATAATATATACACATACAAGT
Found at i:1880065 original size:24 final size:22
Alignment explanation
Indices: 1880025--1880068 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
1880015 TTGTTTTATT
1880025 TAAAAATTTTATATAAAAAAAA
1 TAAAAATTTTATATAAAAAAAA
*
1880047 TAAAAACTTATTATTTAAAAAA
1 TAAAAA-TT-TTATATAAAAAA
1880069 TTAATTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 2 0.11
24 11 0.58
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAAAATTTTATATAAAAAAAA
Found at i:1887380 original size:186 final size:183
Alignment explanation
Indices: 1887004--1887399 Score: 447
Period size: 184 Copynumber: 2.1 Consensus size: 183
1886994 CACGGCGATG
* ** * * * * ** * * *
1887004 TCAAGAATTGTCAGAATACCGATAAAGACTGTATGTGAATATCACATGAACCAACCAACATTATG
1 TCAAGAATTGTCGGAATACTAATAAAGACCGTACGTAAACATTGCACGAGCCAACCAACATTACG
* * *
1887069 TAACTAGTTCAAATGGCAAACCCTTTGCGGGTACGAACATTGGATCATTCTTATCAAACATTAGG
66 TAACTAGTGCAAAAGGCAAACCCTTTGCGGGTACGAACATTGGATCATTCTTATCAAACACTAGG
* * * **
1887134 ACAAGTTTATGCTCTAACAACGATTGAAGTTGCAAAACATCATTCACAGTGACA
131 ACAAGCTTATACTCTAACAACGATTGAAATTG-AAAACATCATTCACAGCAACA
*
1887188 TCAAGAATTGTC-GAGATACTAATAAAGACCGTACGTAAACATTGCACGAGCCAACCTACATTAC
1 TCAAGAATTGTCGGA-ATACTAATAAAGACCGTACGTAAACATTGCACGAGCCAACCAACATTAC
** * * * ** *
1887252 GTGGCTAGTGCAAAAGGCAAACCCTTTGGGGGATTCGAACTTTGGATTGTTCTTATCAAACGCTA
65 GTAACTAGTGCAAAAGGCAAACCCTTTGCGGG-TACGAACATTGGATCATTCTTATCAAACACTA
1887317 GGACAAGCTTATACATCTAACAATC-ATTGAAATCATG-AAACATCATTCACAGCAACA
129 GGACAAGCTTATAC-TCTAACAA-CGATTGAAAT--TGAAAACATCATTCACAGCAACA
1887374 TCAAGAATTGTCGGAATACTAATAAA
1 TCAAGAATTGTCGGAATACTAATAAA
1887400 CACTGTATGG
Statistics
Matches: 177, Mismatches: 28, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
183 2 0.01
184 76 0.43
185 38 0.21
186 56 0.32
187 3 0.02
188 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (183 bp):
TCAAGAATTGTCGGAATACTAATAAAGACCGTACGTAAACATTGCACGAGCCAACCAACATTACG
TAACTAGTGCAAAAGGCAAACCCTTTGCGGGTACGAACATTGGATCATTCTTATCAAACACTAGG
ACAAGCTTATACTCTAACAACGATTGAAATTGAAAACATCATTCACAGCAACA
Found at i:1887549 original size:155 final size:155
Alignment explanation
Indices: 1887267--1887554 Score: 400
Period size: 155 Copynumber: 1.9 Consensus size: 155
1887257 TAGTGCAAAA
** * * *
1887267 GGCAAACCCTTTGGGGGATTCGAACTTTGGATTGTTCTTATCAAACGCTAGGACAAGCTTATACA
1 GGCAAACCCTTTGCAGGATTCGAACTTTGCATTGATCTTATCAAACACTAGGACAAGCTTATACA
* *
1887332 TCTAACAATCATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTAAT
66 TCCAACAATAATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTAAT
1887397 AAACACTGTATGGAAACGCCGCAAC
131 AAACACTGTATGGAAACGCCGCAAC
*
1887422 GGCAAACCCTTTGCAGGATTCGAAC-TT-CATCTCGATCTTATCAAACATTAGGACAAGCTTATA
1 GGCAAACCCTTTGCAGGATTCGAACTTTGCAT-T-GATCTTATCAAACACTAGGACAAGCTTATA
* * ** ** **
1887485 CGTCCAACAATAATTGAAGTTGTGAAACATCATTCACAGTGATGTCAAGAATTGTCGGAATACTA
64 CATCCAACAATAATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTA
1887550 ATAAA
129 ATAAA
1887555 GACCGTACGT
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
153 2 0.02
154 3 0.03
155 110 0.96
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (155 bp):
GGCAAACCCTTTGCAGGATTCGAACTTTGCATTGATCTTATCAAACACTAGGACAAGCTTATACA
TCCAACAATAATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTAAT
AAACACTGTATGGAAACGCCGCAAC
Found at i:1890137 original size:25 final size:27
Alignment explanation
Indices: 1890109--1890159 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1890099 GGTACTACTA
*
1890109 CTTGTT-ATA-AATATTTTTATAAAGG
1 CTTGTTAATAGAATATATTTATAAAGG
1890134 CTTGTTAATAGAATATATTTATAAAG
1 CTTGTTAATAGAATATATTTATAAAG
1890160 TTTATGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.26
26 3 0.13
27 14 0.61
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (27 bp):
CTTGTTAATAGAATATATTTATAAAGG
Found at i:1892875 original size:51 final size:53
Alignment explanation
Indices: 1892792--1892932 Score: 155
Period size: 54 Copynumber: 2.7 Consensus size: 53
1892782 TGCAGTGGAA
* * * *
1892792 GTTGATTCCCTTCTCA-TAATTTGGTTTACAGTAATGCTG-TC-AGAAGCAGAG
1 GTTGATTCTCTTCT-AGAAATTTGGTTTCCAGTAATGCTGCACTAGAAGCAGAG
* *
1892843 GTTGATT-TCATTCTAGAAATTTGATTTCCAGTAATGGTGCCACTAGAAGCAGAG
1 GTTGATTCTC-TTCTAGAAATTTGGTTTCCAGTAATGCTG-CACTAGAAGCAGAG
* *
1892897 TTTGATTCTCTTCTAGAAATTCGGTTTCCAGTAATG
1 GTTGATTCTCTTCTAGAAATTTGGTTTCCAGTAATG
1892933 ATCCTCTCAG
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
50 2 0.03
51 30 0.40
53 1 0.01
54 40 0.53
55 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (53 bp):
GTTGATTCTCTTCTAGAAATTTGGTTTCCAGTAATGCTGCACTAGAAGCAGAG
Found at i:1893020 original size:108 final size:107
Alignment explanation
Indices: 1892951--1893184 Score: 308
Period size: 108 Copynumber: 2.2 Consensus size: 107
1892941 AGGGGTTATG
* * * *
1892951 GTTGATTCCTTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGACATTAATTCCGC
1 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTAGCAGGAGTGGACATTAATTCCGC
* * *
1893016 TCTAGGAAGTTGATCCCCAGTAACGATCCCACCGGAAGTGGGA
66 TCTA-GAAATTGATCCCCAGTAACGATCCCACAGGAAGTAGGA
**
1893059 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTAGCAGGAGTGGATGTTAATTCCGC
1 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTAGCAGGAGTGGACATTAATTCCGC
* * * * *
1893124 TCTAGGAAGTTGATCGCCAGTAATGAGCCCACCA-GAAGTGGGA
66 TCTA-GAAATTGATCCCCAGTAACGATCCCA-CAGGAAGTAGGA
1893167 GTTGATTCCCTTCTAGAA
1 GTTGATTCCCTTCTAGAA
1893185 ATCTGAATTC
Statistics
Matches: 115, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
108 114 0.99
109 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (107 bp):
GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTAGCAGGAGTGGACATTAATTCCGC
TCTAGAAATTGATCCCCAGTAACGATCCCACAGGAAGTAGGA
Found at i:1893148 original size:54 final size:52
Alignment explanation
Indices: 1892978--1893149 Score: 143
Period size: 54 Copynumber: 3.2 Consensus size: 52
1892968 AGTTTGGTTT
* *
1892978 CCAGTAATGACCTTATCAGGATTGGACATTAATTCCGCTCTAGGAAGTTGATCC
1 CCAGTAATGACCTTA-CAGGAGTGGA-GTTAATTCCGCTCTAGGAAGTTGATCC
* * * * * **
1893032 CCAGTAACGATCC-CACCGGAAGTGGGAGTTGATTCC-CTTCTA-GAAGTTTGGTTT
1 CCAGTAATGA-CCTTACAGG-AGT-GGAGTTAATTCCGC-TCTAGGAAG-TTGATCC
* *
1893086 CCAATAATGACCTTAGCAGGAGTGGATGTTAATTCCGCTCTAGGAAGTTGATCG
1 CCAGTAATGACCTTA-CAGGAGTGGA-GTTAATTCCGCTCTAGGAAGTTGATCC
1893140 CCAGTAATGA
1 CCAGTAATGA
1893150 GCCCACCAGA
Statistics
Matches: 90, Mismatches: 18, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
53 13 0.14
54 64 0.71
55 13 0.14
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (52 bp):
CCAGTAATGACCTTACAGGAGTGGAGTTAATTCCGCTCTAGGAAGTTGATCC
Found at i:1893182 original size:54 final size:53
Alignment explanation
Indices: 1893016--1893182 Score: 160
Period size: 54 Copynumber: 3.1 Consensus size: 53
1893006 TTAATTCCGC
* *
1893016 TCTAGGAAGTTGATCCCCAGTAACGATCCCACCGGAAGTGGGAGTTGATTCCCT
1 TCTAGGAAGTTGATCCCCAGTAATGA-CCCACCAGAAGTGGGAGTTGATTCCCT
* ** * * * * *
1893070 TCTA-GAAGTTTGGTTTCCAATAATGACCTTAGCAGGAGT-GGATGTTAATTCCGC-
1 TCTAGGAAG-TTGATCCCCAGTAATGACC-CACCAGAAGTGGGA-GTTGATTCC-CT
*
1893124 TCTAGGAAGTTGATCGCCAGTAATGAGCCCACCAGAAGTGGGAGTTGATTCCCT
1 TCTAGGAAGTTGATCCCCAGTAATGA-CCCACCAGAAGTGGGAGTTGATTCCCT
1893178 TCTAG
1 TCTAG
1893183 AAATCTGAAT
Statistics
Matches: 87, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
53 10 0.11
54 67 0.77
55 10 0.11
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.28
Consensus pattern (53 bp):
TCTAGGAAGTTGATCCCCAGTAATGACCCACCAGAAGTGGGAGTTGATTCCCT
Found at i:1900564 original size:24 final size:24
Alignment explanation
Indices: 1900519--1900564 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1900509 ATATAGGTAG
*
1900519 AAAAAATATAAAAGTAATTTTTAA
1 AAAAAATATAAAAGAAATTTTTAA
1900543 AAAAAATATAAAA-AAATATTTT
1 AAAAAATATAAAAGAAAT-TTTT
1900565 CATAATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
AAAAAATATAAAAGAAATTTTTAA
Found at i:1906091 original size:21 final size:21
Alignment explanation
Indices: 1906067--1906110 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1906057 AGATAGGATA
1906067 GTGTCTTCGA-TCCGCTCCGCT
1 GTGTCTTCGACT-CGCTCCGCT
*
1906088 GTGTCTTCGACTTGCTCCGCT
1 GTGTCTTCGACTCGCTCCGCT
1906109 GT
1 GT
1906111 AATCTTAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.05, C:0.34, G:0.25, T:0.36
Consensus pattern (21 bp):
GTGTCTTCGACTCGCTCCGCT
Found at i:1906170 original size:44 final size:45
Alignment explanation
Indices: 1906100--1906259 Score: 125
Period size: 46 Copynumber: 3.6 Consensus size: 45
1906090 GTCTTCGACT
* * *
1906100 TGCTCCGCTGTAATCTTAGGGAGATAAGACCT-C-TGGCTTCAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGACCTGCAT-GCTTCAATC
* * * **
1906144 TGCTCCACTGTAACCTCAGGGGGATAAGATCTGCAATTCTTCGGTC
1 TGCTCCACTGTAACCTCAGGGAGATAAGACCTGC-ATGCTTCAATC
* * *
1906190 TACTCCACTGTAACCTCAGAGAGATAAGACCTG-ATG--T-GATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGACCTGCATGCTTCAATC
* * * *
1906231 TTCTCTACTGTAACTTCAGAGAGATAAGA
1 TGCTCCACTGTAACCTCAGGGAGATAAGA
1906260 TCATTTAATC
Statistics
Matches: 96, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
41 29 0.30
42 1 0.01
44 29 0.30
45 1 0.01
46 35 0.36
47 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (45 bp):
TGCTCCACTGTAACCTCAGGGAGATAAGACCTGCATGCTTCAATC
Found at i:1906690 original size:88 final size:88
Alignment explanation
Indices: 1906400--1907354 Score: 1428
Period size: 88 Copynumber: 10.9 Consensus size: 88
1906390 TGTAACCTTT
* ** * * *
1906400 AACCAGCTCCAAT-GCAACCGATGGAGGCAAGGCTTTGT-T-TTTGATCTGCTTTGCTGTTAATG
1 AACCAGCTCC-ATCACAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATG
* ** *
1906462 CAGGAAGGCAAGATCTGCT-TCTTT
64 CAGAAAGGCAAGATCTTTTGTCTTC
* * * ** * *
1906486 AACTAGCTCCA-CTGCAATCGATGGATGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATG
1 AACCAGCTCCATC-ACAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATG
* * * ** *
1906548 TAGGAAGGTAAGATCTGCT-TCTTT
64 CAGAAAGGCAAGATCTTTTGTCTTC
* * *
1906572 AACCAGCTCCA-CTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGC
1 AACCAGCTCCATC-ACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGC
*
1906636 AGGAAGGCAAGATCTTTTGTCTTC
65 AGAAAGGCAAGATCTTTTGTCTTC
*
1906660 AACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
*
1906725 GCAAGGCAAGATCTTTTGTCTTC
66 GAAAGGCAAGATCTTTTGTCTTC
*
1906748 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCAATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1906813 GAAAGGCAAGATCTTTTGTCTTC
66 GAAAGGCAAGATCTTTTGTCTTC
1906836 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1906901 GAAAGGCAAGATCTTTTGTCTTC
66 GAAAGGCAAGATCTTTTGTCTTC
1906924 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1906989 GAAAGGCAAGATCTTTTGTCTTC
66 GAAAGGCAAGATCTTTTGTCTTC
1907012 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1907077 GAAAGGCAAGATCTTTTGTCTTC
66 GAAAGGCAAGATCTTTTGTCTTC
1907100 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1907165 GAAAGGCAAGATCTTTTGTCTTC
66 GAAAGGCAAGATCTTTTGTCTTC
*
1907188 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
**
1907253 GGCAGGCAAG--CTTTTGTCTTC
66 GAAAGGCAAGATCTTTTGTCTTC
* * * * * *
1907274 AACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTATGTCTTCAACCTGTTTCACTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
*
1907339 GGAAGGCAAGATCTTT
66 GAAAGGCAAGATCTTT
1907355 AACTTCATTG
Statistics
Matches: 820, Mismatches: 41, Indels: 14
0.94 0.05 0.02
Matches are distributed among these distances:
85 6 0.01
86 181 0.22
87 35 0.04
88 597 0.73
89 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (88 bp):
AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
GAAAGGCAAGATCTTTTGTCTTC
Found at i:1909564 original size:7 final size:8
Alignment explanation
Indices: 1909539--1909568 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
1909529 CTATTTTGAC
1909539 TTTGATTTT
1 TTTGA-TTT
1909548 TTTGATTT
1 TTTGATTT
1909556 TTTGATTT
1 TTTGATTT
1909564 TTTGA
1 TTTGA
1909569 ATTCATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (8 bp):
TTTGATTT
Found at i:1916747 original size:12 final size:12
Alignment explanation
Indices: 1916730--1916754 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1916720 AACCCTCAAA
1916730 CTAATCCAAGAT
1 CTAATCCAAGAT
1916742 CTAATCCAAGAT
1 CTAATCCAAGAT
1916754 C
1 C
1916755 ACCATTGAGC
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:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (12 bp):
CTAATCCAAGAT
Found at i:1917289 original size:28 final size:28
Alignment explanation
Indices: 1917258--1917314 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1917248 ATAGAGAGAC
1917258 TAAAAATAATCAAAAAACATAGACTAAA
1 TAAAAATAATCAAAAAACATAGACTAAA
1917286 TAAAAATAATCAAAAAACATAGACTAAA
1 TAAAAATAATCAAAAAACATAGACTAAA
1917314 T
1 T
1917315 CTACAACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.67, C:0.11, G:0.04, T:0.19
Consensus pattern (28 bp):
TAAAAATAATCAAAAAACATAGACTAAA
Found at i:1922437 original size:275 final size:276
Alignment explanation
Indices: 1921944--1922464 Score: 857
Period size: 275 Copynumber: 1.9 Consensus size: 276
1921934 AAAAAAACCA
* *
1921944 AAGAAACAATCACTAAAAGTTTCATATGACTTTGCTTAAATTAAATTTCTTCAAAAAAAATTTAA
1 AAGAAACAATCACTAAAAGTTTAATACGACTTTGCTTAAATTAAATTTCTTC-AAAAAAATTTAA
* * * *
1922009 AATTGAAATAAAACTTATGCTTCTCATTACATTTGGTTGAATACAATGAGTGTTACAAGCTCAAC
65 AATTGAAATAAAACTTATGCTTCCCATGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAAC
*
1922074 CTTGCAAATCATGTAAGCTAAAAAAGTTAATAAAATCCATTTTTCTTGTATTTTCTATAACTTTC
130 CTTGCAAATCATGTAAGCTAAAAAAGTTAACAAAATCCATTTTTCTTGTATTTTCTATAACTTTC
* *
1922139 CTCGAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAATAACTAAATTTCCAAAAAAAG
195 CTCAAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAAGAACTAAATTTCCAAAAAAAG
1922204 TGACGCAAACATGAGCT
260 TGACGCAAACATGAGCT
* * * *
1922221 AAGAAACAATTACTACAGGTTTAATACGACTTTGCTTAAATTAAATTTCTTC-AAAAATTTTAAA
1 AAGAAACAATCACTAAAAGTTTAATACGACTTTGCTTAAATTAAATTTCTTCAAAAAAATTTAAA
1922285 A-TGAAATAAAACTTATGCTTCCCACTGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAAC
66 ATTGAAATAAAACTTATGCTTCCCA-TGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAAC
* * *
1922349 CTTGCAAATCATGTAAGCTAAAAAAGTTAACGAACTCCATTTTTCTTGTATTTTCTATCACTTTC
130 CTTGCAAATCATGTAAGCTAAAAAAGTTAACAAAATCCATTTTTCTTGTATTTTCTATAACTTTC
*
1922414 CTCAAACTTTCTCGACACCCAAACAGAGCTTCATCATTCAACAAGAACTAA
195 CTCAAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAAGAACTAA
1922465 GTCCCCCCCC
Statistics
Matches: 226, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
274 22 0.10
275 157 0.69
277 47 0.21
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (276 bp):
AAGAAACAATCACTAAAAGTTTAATACGACTTTGCTTAAATTAAATTTCTTCAAAAAAATTTAAA
ATTGAAATAAAACTTATGCTTCCCATGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAACC
TTGCAAATCATGTAAGCTAAAAAAGTTAACAAAATCCATTTTTCTTGTATTTTCTATAACTTTCC
TCAAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAAGAACTAAATTTCCAAAAAAAGT
GACGCAAACATGAGCT
Found at i:1925325 original size:60 final size:60
Alignment explanation
Indices: 1925255--1925368 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
1925245 CTCACATTGG
* *
1925255 GGCTTAAACTTTCTTT-TAGTCCAAGTTAGCTCCTAAAGTTGA-TAATTGTTCCCATATTAA
1 GGCTTAAACTTT-TTTGTAGTCCAAATTAG-TCCTAAAATTGATTAATTGTTCCCATATTAA
* * *
1925315 GGCTTGAACTTTTTTGTTGTCCAAATTAGTCTTAAAATTGATTAATTGTTCCCA
1 GGCTTAAACTTTTTTGTAGTCCAAATTAGTCCTAAAATTGATTAATTGTTCCCA
1925369 CACTGGAGCT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 13 0.28
60 34 0.72
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (60 bp):
GGCTTAAACTTTTTTGTAGTCCAAATTAGTCCTAAAATTGATTAATTGTTCCCATATTAA
Found at i:1936806 original size:27 final size:27
Alignment explanation
Indices: 1936792--1936847 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
1936782 ATTAATCAAA
*
1936792 AAATATCTAAAAAATAAATAAATAAAT
1 AAATATATAAAAAATAAATAAATAAAT
*
1936819 AAATATATAAAAAATCAA-AAATAAA-
1 AAATATATAAAAAATAAATAAATAAAT
1936844 AAAT
1 AAAT
1936848 CGAACCCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 4 0.15
26 7 0.26
27 16 0.59
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (27 bp):
AAATATATAAAAAATAAATAAATAAAT
Found at i:1936812 original size:4 final size:4
Alignment explanation
Indices: 1936799--1936847 Score: 52
Period size: 4 Copynumber: 13.2 Consensus size: 4
1936789 AAAAAATATC
* *
1936799 TAAA -AAA TAAA TAAA TAAA TAAA TATA TAAA -AAA TCAA -AAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1936844 -AAA T
1 TAAA T
1936848 CGAACCCAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 11 0.30
4 26 0.70
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (4 bp):
TAAA
Found at i:1936816 original size:8 final size:8
Alignment explanation
Indices: 1936799--1936847 Score: 52
Period size: 7 Copynumber: 6.6 Consensus size: 8
1936789 AAAAAATATC
1936799 TAAA-AAA
1 TAAATAAA
1936806 TAAATAAA
1 TAAATAAA
1936814 TAAATAAA
1 TAAATAAA
*
1936822 TATATAAA
1 TAAATAAA
*
1936830 -AAATCAA
1 TAAATAAA
1936837 -AAATAAA
1 TAAATAAA
1936844 -AAAT
1 TAAAT
1936848 CGAACCCAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
7 19 0.51
8 18 0.49
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (8 bp):
TAAATAAA
Found at i:1938315 original size:14 final size:13
Alignment explanation
Indices: 1938276--1938317 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
1938266 ATCACTGATA
1938276 ATTTAATTTAATT
1 ATTTAATTTAATT
1938289 -TTTGAACTTTAATT
1 ATTT-AA-TTTAATT
1938303 ATTTAATTATAATT
1 ATTTAATT-TAATT
1938317 A
1 A
1938318 ATCAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.12
13 4 0.16
14 15 0.60
15 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (13 bp):
ATTTAATTTAATT
Found at i:1945363 original size:48 final size:48
Alignment explanation
Indices: 1945292--1945391 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
1945282 TAAGTGCTGA
1945292 AATAGCAACCAGTCGGTAACACTTGACATATCACGTGTACCTTATGTT
1 AATAGCAACCAGTCGGTAACACTTGACATATCACGTGTACCTTATGTT
1945340 AATAGCAACCAGTCGGTAACACTTGACATATCACGTGTACCTTATGTT
1 AATAGCAACCAGTCGGTAACACTTGACATATCACGTGTACCTTATGTT
1945388 AATA
1 AATA
1945392 TGGAGGGACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (48 bp):
AATAGCAACCAGTCGGTAACACTTGACATATCACGTGTACCTTATGTT
Found at i:1948071 original size:30 final size:29
Alignment explanation
Indices: 1948035--1948102 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
1948025 ATAGTTGGAC
* *
1948035 CTAAATT-TTGAAAATTGAAAAGTAGAGGGA
1 CTAAATTCCTGAAAA-T-AAAAGTACAGGGA
*
1948065 CTAAATTCCTGGAAATAAAAGTACAGGGA
1 CTAAATTCCTGAAAATAAAAGTACAGGGA
1948094 CTAAATTCC
1 CTAAATTCC
1948103 AAATTTTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 21 0.62
30 8 0.24
31 5 0.15
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (29 bp):
CTAAATTCCTGAAAATAAAAGTACAGGGA
Found at i:1950773 original size:31 final size:30
Alignment explanation
Indices: 1950730--1950794 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
1950720 AAATCAATTT
1950730 AAAAGATGGAAC-TTCTGTACAATTAACCAA
1 AAAAGATGGAACTTTCTGTA-AATTAACCAA
* * *
1950760 AAAAGTTGAGAACTTTTTGTAAATTAACCCA
1 AAAAGATG-GAACTTTCTGTAAATTAACCAA
1950791 AAAA
1 AAAA
1950795 TAACATTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 7 0.23
31 17 0.57
32 6 0.20
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (30 bp):
AAAAGATGGAACTTTCTGTAAATTAACCAA
Found at i:1957216 original size:21 final size:21
Alignment explanation
Indices: 1957192--1957239 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1957182 GCTATCCCAG
1957192 TCAAAGATTTATGTTCAAACT
1 TCAAAGATTTATGTTCAAACT
1957213 TCAAAGATTTATGTTCAAACT
1 TCAAAGATTTATGTTCAAACT
1957234 TCAAAG
1 TCAAAG
1957240 TTAAAAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (21 bp):
TCAAAGATTTATGTTCAAACT
Found at i:1967904 original size:18 final size:18
Alignment explanation
Indices: 1967883--1967926 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1967873 GAAACAGAAT
*
1967883 AAAAAATAATAAGCCCAA
1 AAAAAATAACAAGCCCAA
* *
1967901 AAAAATTTACAAGCCCAA
1 AAAAAATAACAAGCCCAA
1967919 AAGAAAAT
1 AA-AAAAT
1967927 TTATTACAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.64, C:0.16, G:0.07, T:0.14
Consensus pattern (18 bp):
AAAAAATAACAAGCCCAA
Found at i:1969337 original size:28 final size:29
Alignment explanation
Indices: 1969297--1969353 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
1969287 GCAACCCATT
*
1969297 TTTATTATCATATC-GAACGCTATTCCTA
1 TTTATTATCATATCAAAACGCTATTCCTA
1969325 TTTATTATCATATCAAAACGCTATTCCTA
1 TTTATTATCATATCAAAACGCTATTCCTA
1969354 ATAGAAGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (29 bp):
TTTATTATCATATCAAAACGCTATTCCTA
Found at i:1970952 original size:15 final size:16
Alignment explanation
Indices: 1970932--1970963 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1970922 ATTATTTAAA
1970932 TTTTAAAA-TTATTAT
1 TTTTAAAATTTATTAT
1970947 TTTTAAAATTTATTAT
1 TTTTAAAATTTATTAT
1970963 T
1 T
1970964 AAAATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAAAATTTATTAT
Found at i:1970979 original size:21 final size:21
Alignment explanation
Indices: 1970953--1971016 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1970943 TTATTTTTAA
1970953 AATTTATTATTAAAATAAAAT
1 AATTTATTATTAAAATAAAAT
* *
1970974 AATTTATTA-CAATAATAAATT
1 AATTTATTATTAA-AATAAAAT
*
1970995 ATTTATATTATTAAATATAAAA
1 AATT-TATTATTAAA-ATAAAA
1971017 AAATATGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 2 0.06
21 19 0.56
22 6 0.18
23 7 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTTATTATTAAAATAAAAT
Found at i:1979545 original size:197 final size:196
Alignment explanation
Indices: 1979134--1979716 Score: 737
Period size: 197 Copynumber: 2.9 Consensus size: 196
1979124 ATGTTGTTCG
*
1979134 GACTCTTCATTTTTCTTGAAGCAC-CAGTGTTTGACAGATGGATATTACATGGAAAACCTTTGAA
1 GACTCTTCATTTTTCTTGAAGCACTC-GTGTTTGACACATGGATATTACATGGAAAACCTTTG-A
* * * *
1979198 AAATGAAAATTCTTACGATA-T-TCGTGTCAAATGCACACCCGTATTTGACACTCACACCCAAGT
64 AAA-G-----TCTAACGATACTCTCGT-T-AAATACAAACCCATATTTGACACTCACACCCAAGT
* * *
1979261 CCGAATAACATAGGGCAAAATTCACTATGCCAACTAACAATTGACAGCTAGGGATCACACAATGA
121 CCGAGTAACATAGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAGGGATCACACAATGA
1979326 TAAGTTGCTCA
186 TAAGTTGCTCA
** *
1979337 GACTCTTCATTTTTCTTGAAGCACTCGTGTCGGACACATGGATATTACATAGAAAACCTTTGAAA
1 GACTCTTCATTTTTCTTGAAGCACTCGTGTTTGACACATGGATATTACATGGAAAACCTTTGAAA
* * * *
1979402 AGCCTAATGATACTCTCGTTAAATACAAACCCATATTTGACACTTACA-CCAGAGTCAGAGTAAC
66 AGTCTAACGATACTCTCGTTAAATACAAACCCATATTTGACACTCACACCCA-AGTCCGAGTAAC
* * * * *
1979466 GTAAGGGCAAAATTAACTATGTCAACTGACAATTGACAGCAAGCGG-TCACACAATGCTATGTTG
130 AT-AGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAG-GGATCACACAATGATAAGTTG
1979530 CTCA
193 CTCA
* * * *
1979534 TACTCTTCATTTTTCTTGAAGCACTCGTGTTTGATATATGTATATTACATGGAAAACCTTTGAAA
1 GACTCTTCATTTTTCTTGAAGCACTCGTGTTTGACACATGGATATTACATGGAAAACCTTTGAAA
* *
1979599 AGTCTAACGATACTCGT-GTTAAATACATACCCATTTTTGACACTCACACCCAAGTCCGAGTAAC
66 AGTCTAACGATACTC-TCGTTAAATACAAACCCATATTTGACACTCACACCCAAGTCCGAGTAAC
*
1979663 ATAGGGCAAAATTCACTATGTCAACTAACAAATCGACAGCAAGGGATCATCACA
130 ATAGGGCAAAATTCACTATGTCAACTAAC-AATTGACAGCAAGGGATCA-CACA
1979717 CAAGATTTTT
Statistics
Matches: 332, Mismatches: 37, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
195 3 0.01
196 69 0.21
197 184 0.55
198 14 0.04
201 1 0.00
202 4 0.01
203 56 0.17
204 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.28
Consensus pattern (196 bp):
GACTCTTCATTTTTCTTGAAGCACTCGTGTTTGACACATGGATATTACATGGAAAACCTTTGAAA
AGTCTAACGATACTCTCGTTAAATACAAACCCATATTTGACACTCACACCCAAGTCCGAGTAACA
TAGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAGGGATCACACAATGATAAGTTGCTC
A
Found at i:1992194 original size:24 final size:24
Alignment explanation
Indices: 1992166--1992217 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
1992156 TTTCTAGAAA
*
1992166 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
*
1992190 ATTTAGCATTTATTAGTATAATTT
1 ATTTAGCATTTATTAGTATAATAT
1992214 ATTT
1 ATTT
1992218 GACTTACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTATAATAT
Found at i:1996590 original size:16 final size:16
Alignment explanation
Indices: 1996569--1996604 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1996559 TAACTCAGGA
1996569 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
1996585 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
1996601 GCTG
1 GCTG
1996605 TGATTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.19, G:0.39, T:0.19
Consensus pattern (16 bp):
GCTGCAGGAGTACATG
Found at i:1997447 original size:120 final size:120
Alignment explanation
Indices: 1997321--1997610 Score: 485
Period size: 120 Copynumber: 2.4 Consensus size: 120
1997311 AATTATTTTA
* *
1997321 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTT-TCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTTATATTT
* *
1997385 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGACTATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
1997441 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATT-ATTATTTTAATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTAAATTTATATTT
1997505 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
1997561 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTAT
1997611 GTTTAAATAT
Statistics
Matches: 159, Mismatches: 8, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
119 7 0.04
120 149 0.94
121 3 0.02
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:1997503 original size:15 final size:14
Alignment explanation
Indices: 1997451--1997506 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 14
1997441 AATTTTATTA
1997451 AATTATA-TATTTT
1 AATTATATTATTTT
*
1997464 AATTATAATATATTT
1 AATTATATTAT-TTT
*
1997479 AATAATTATTATTTT
1 AATTA-TATTATTTT
1997494 AATT-TA-TATTTT
1 AATTATATTATTTT
1997506 A
1 A
1997507 CAGTATCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 7 0.19
13 9 0.24
14 3 0.08
15 13 0.35
16 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTATATTATTTT
Found at i:1997567 original size:61 final size:61
Alignment explanation
Indices: 1997382--1997568 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
1997372 TCAAATTTTC
*
1997382 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGACTATTAATTATTAAGAA
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
* * * * * * *
1997443 TTTTATTA-AATTATATATT-TTAATT-A-T-AATAT-ATTTAATAATTATT-ATT-TTAATTTA
1 TTTTA-TAGTATCATATATTATGATTTGAGTAAAT-TCATATAAGAA-TATTAATTATTAA--GA
1997500 TA
61 -A
*
1997502 TTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
1997563 TTTTAT
1 TTTTAT
1997569 TAAATTATAT
Statistics
Matches: 95, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
56 4 0.04
57 12 0.13
58 8 0.08
59 16 0.17
60 8 0.08
61 21 0.22
62 9 0.09
63 13 0.14
64 4 0.04
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (61 bp):
TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
Found at i:1997590 original size:18 final size:17
Alignment explanation
Indices: 1997562--1997596 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1997552 ATTATTAAGA
*
1997562 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1997579 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1997597 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1997626 original size:67 final size:67
Alignment explanation
Indices: 1997555--1997772 Score: 176
Period size: 67 Copynumber: 3.1 Consensus size: 67
1997545 AATATTAATT
1997555 ATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATA
1 ATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATA
1997620 TG
66 TG
* * * *
1997622 ATTAA-ATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAAATAATTTACCAAAAC
1 ATTAAGA--A-TT-TTATT-AAATT-AT-ATATT-TT--AA-TTAAA-ATAT-ATTTA--ATAA-
* * *
1997686 AAATT-TCTGCT-AAT-T-
50 TAATTATGT-TTAAATATG
*
1997701 ATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTAAATA
1 ATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATA
1997766 TG
66 TG
1997768 ATTAA
1 ATTAA
1997773 ATTATTTATT
Statistics
Matches: 114, Mismatches: 15, Indels: 44
0.66 0.09 0.25
Matches are distributed among these distances:
64 5 0.04
65 8 0.07
66 2 0.02
67 14 0.12
68 4 0.04
69 7 0.06
70 7 0.06
71 4 0.04
72 4 0.04
73 8 0.07
74 4 0.04
75 4 0.04
76 7 0.06
77 7 0.06
78 4 0.04
79 10 0.09
80 2 0.02
81 8 0.07
82 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (67 bp):
ATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATA
TG
Found at i:1997706 original size:146 final size:147
Alignment explanation
Indices: 1997550--1997817 Score: 502
Period size: 146 Copynumber: 1.8 Consensus size: 147
1997540 ATAAGAATAT
*
1997550 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
1997615 AAATATGATTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAAATAATTTA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAAATAATTTA
1997679 CCAAAACAAATTTCTGC
131 CCAAAACAAATTTCTGC
1997696 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
1997761 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAA
1997818 CAATAACAAT
Statistics
Matches: 118, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
146 91 0.77
147 27 0.23
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAAATAATTTA
CCAAAACAAATTTCTGC
Found at i:1997736 original size:18 final size:17
Alignment explanation
Indices: 1997708--1997742 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1997698 ATTATTAAGA
*
1997708 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1997725 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1997743 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1997953 original size:44 final size:45
Alignment explanation
Indices: 1997904--1997998 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
1997894 TTACACCTCT
* * *
1997904 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
** *
1997948 ATTACATTCAACCAAACAGTTGATTTGCTATTACACATCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
1997993 ATTACA
1 ATTACA
1997999 CCTCTAATCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
Found at i:1997998 original size:16 final size:16
Alignment explanation
Indices: 1997979--1998030 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
1997969 GATTTGCTAT
* * *
1997979 TACACATCTATTCCAT
1 TACACCTCTAATCCAA
1997995 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1998011 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1998027 TACA
1 TACA
1998031 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:2000640 original size:12 final size:12
Alignment explanation
Indices: 2000623--2000658 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2000613 ATATCGCAAA
*
2000623 GTGGCGGCTGCG
1 GTGGCGGCGGCG
2000635 GTGGCGGCGGCG
1 GTGGCGGCGGCG
*
2000647 GTGGAGGCGGCG
1 GTGGCGGCGGCG
2000659 ACGGCCAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.03, C:0.22, G:0.64, T:0.11
Consensus pattern (12 bp):
GTGGCGGCGGCG
Found at i:2010946 original size:57 final size:57
Alignment explanation
Indices: 2010877--2011020 Score: 261
Period size: 57 Copynumber: 2.5 Consensus size: 57
2010867 ACCATTGCGA
*
2010877 TCACCATCAGCATCACAATTGTCATCACCACTATCAACATCCCTATTGCCATCACCG
1 TCACCATCAGCATCACAATTGCCATCACCACTATCAACATCCCTATTGCCATCACCG
2010934 TCACCATCAGCATCACAATTGCCATCACCACTATCAACATCCCTATTGCCATCACCG
1 TCACCATCAGCATCACAATTGCCATCACCACTATCAACATCCCTATTGCCATCACCG
* *
2010991 TCACCTTCAGCATCACCATTGCCATCACCA
1 TCACCATCAGCATCACAATTGCCATCACCA
2011021 TCAGCGTCAC
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 84 1.00
ACGTcount: A:0.29, C:0.40, G:0.07, T:0.24
Consensus pattern (57 bp):
TCACCATCAGCATCACAATTGCCATCACCACTATCAACATCCCTATTGCCATCACCG
Found at i:2010961 original size:24 final size:24
Alignment explanation
Indices: 2010853--2011043 Score: 112
Period size: 24 Copynumber: 7.2 Consensus size: 24
2010843 GCCGTCACCG
* *
2010853 TCACCATCAGCATCACCATTGCGA
1 TCACCATCAGCATCACAATTGCCA
*
2010877 TCACCATCAGCATCACAATTGTCA
1 TCACCATCAGCATCACAATTGCCA
* * *
2010901 TCACCACTATCAACATCCCTATTGCCATCA
1 TCA-C-C-ATCAGCATCACAATTG-C--CA
2010931 CCGTCACCATCAGCATCACAATTGCCA
1 ---TCACCATCAGCATCACAATTGCCA
* * *
2010958 TCACCACTATCAACATCCCTATTGCCA
1 TCA-C-C-ATCAGCATCACAATTGCCA
*
2010985 TCACCGTCACCTTCAGCATCACCATTGCCA
1 TCA-C--CA---TCAGCATCACAATTGCCA
* *
2011015 TCACCATCAGCGTCACAATTACCA
1 TCACCATCAGCATCACAATTGCCA
2011039 TCACC
1 TCACC
2011044 GTCACCACTA
Statistics
Matches: 131, Mismatches: 20, Indels: 32
0.72 0.11 0.17
Matches are distributed among these distances:
24 47 0.36
25 2 0.02
26 2 0.02
27 39 0.30
28 1 0.01
29 2 0.02
30 33 0.25
31 1 0.01
32 1 0.01
33 3 0.02
ACGTcount: A:0.29, C:0.40, G:0.08, T:0.23
Consensus pattern (24 bp):
TCACCATCAGCATCACAATTGCCA
Found at i:2011049 original size:30 final size:30
Alignment explanation
Indices: 2010828--2011050 Score: 158
Period size: 30 Copynumber: 8.0 Consensus size: 30
2010818 CATCACCACT
* * *
2010828 ATCAGCATCCCTATTGCCGTCACCGTCACC
1 ATCAGCATCACAATTGCCATCACCGTCACC
* *
2010858 ATCAGCATCACCATTG-C--GA---TCACC
1 ATCAGCATCACAATTGCCATCACCGTCACC
* *
2010882 ATCAGCATCACAATTGTCATCA-C--CACT
1 ATCAGCATCACAATTGCCATCACCGTCACC
* * *
2010909 ATCAACATCCCTATTGCCATCACCGTCACC
1 ATCAGCATCACAATTGCCATCACCGTCACC
*
2010939 ATCAGCATCACAATTGCCATCA-C--CACT
1 ATCAGCATCACAATTGCCATCACCGTCACC
* * *
2010966 ATCAACATCCCTATTGCCATCACCGTCACC
1 ATCAGCATCACAATTGCCATCACCGTCACC
* *
2010996 TTCAGCATCACCATTG-C--CA---TCACC
1 ATCAGCATCACAATTGCCATCACCGTCACC
* *
2011020 ATCAGCGTCACAATTACCATCACCGTCACC
1 ATCAGCATCACAATTGCCATCACCGTCACC
2011050 A
1 A
2011051 CTATCAGAAA
Statistics
Matches: 150, Mismatches: 27, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
24 37 0.25
25 2 0.01
27 49 0.33
28 2 0.01
29 3 0.02
30 57 0.38
ACGTcount: A:0.28, C:0.40, G:0.09, T:0.23
Consensus pattern (30 bp):
ATCAGCATCACAATTGCCATCACCGTCACC
Found at i:2016998 original size:18 final size:17
Alignment explanation
Indices: 2016956--2017029 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 17
2016946 TTAAATGTTC
*
2016956 TATTACATTTAGTTTAATT
1 TATTA-ATTTA-TTTTATT
2016975 TATTAAATTTATTTTATT
1 TATT-AATTTATTTTATT
* *
2016993 TTTTAATTTAATTTAATAT
1 TATTAATTT-ATTTTAT-T
* *
2017012 AATTAATTTCTTTTATT
1 TATTAATTTATTTTATT
2017029 T
1 T
2017030 TGATTATTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
17 6 0.14
18 20 0.45
19 17 0.39
20 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (17 bp):
TATTAATTTATTTTATT
Found at i:2017002 original size:36 final size:36
Alignment explanation
Indices: 2016962--2017030 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
2016952 GTTCTATTAC
* *
2016962 ATTTAGTTTAAT-TTATTAAATTTATTTTATTTTTTA
1 ATTTAATTTAATATAATT-AATTTATTTTATTTTTTA
*
2016998 ATTTAATTTAATATAATTAATTTCTTTTATTTT
1 ATTTAATTTAATATAATTAATTTATTTTATTTT
2017031 GATTATTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 25 0.86
37 4 0.14
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (36 bp):
ATTTAATTTAATATAATTAATTTATTTTATTTTTTA
Found at i:2020523 original size:27 final size:27
Alignment explanation
Indices: 2020493--2020570 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
2020483 AGCCAATCAC
2020493 ATTGGCGGTACCAAAT-GTGCCAAAGAG
1 ATTGGCGGTACC-AATGGTGCCAAAGAG
* * *
2020520 ATTGGTGGCACCAATGGTGCCAAAGTG
1 ATTGGCGGTACCAATGGTGCCAAAGAG
*
2020547 ATTGGCCGTACCAATGGTGCCAAA
1 ATTGGCGGTACCAATGGTGCCAAA
2020571 TGACTAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 3 0.07
27 41 0.93
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (27 bp):
ATTGGCGGTACCAATGGTGCCAAAGAG
Found at i:2020672 original size:19 final size:19
Alignment explanation
Indices: 2020645--2020714 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
2020635 TCAACTCATT
*
2020645 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
2020664 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
2020682 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
2020701 TTTTAATTTAATAA
1 TTTTAATTTAATAA
2020715 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:2020695 original size:37 final size:37
Alignment explanation
Indices: 2020650--2020720 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
2020640 TCATTTTTTT
2020650 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
2020687 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
2020721 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:2020939 original size:19 final size:18
Alignment explanation
Indices: 2020915--2020973 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 18
2020905 TCTAATTAAG
2020915 TAATAATTCTATTTTAATT
1 TAATAA-TCTATTTTAATT
* * *
2020934 TAATAAACTATTCTCATT
1 TAATAATCTATTTTAATT
2020952 TAATAACTCTATTTTAATT
1 TAATAA-TCTATTTTAATT
2020971 TAA
1 TAA
2020974 ATGAGAATAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATAATCTATTTTAATT
Found at i:2020944 original size:18 final size:19
Alignment explanation
Indices: 2020923--2020973 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
2020913 AGTAATAATT
2020923 CTATTTTAATTTAATAA-A
1 CTATTTTAATTTAATAACA
* * *
2020941 CTATTCTCATTTAATAACT
1 CTATTTTAATTTAATAACA
2020960 CTATTTTAATTTAA
1 CTATTTTAATTTAA
2020974 ATGAGAATAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (19 bp):
CTATTTTAATTTAATAACA
Found at i:2020993 original size:18 final size:19
Alignment explanation
Indices: 2020970--2021016 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
2020960 CTATTTTAAT
* *
2020970 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
2020988 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
2021007 TTAAAT-AAAA
1 TTAAATGAAAA
2021017 AAATGAGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:2021024 original size:20 final size:19
Alignment explanation
Indices: 2020985--2021025 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2020975 TGAGAATAGT
* *
2020985 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
2021004 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
2021024 TT
1 TT
2021026 GAAGGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:2021178 original size:27 final size:27
Alignment explanation
Indices: 2021092--2021169 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
2021082 ATTTTAGTCA
* *
2021092 TTTGGCATCATTGGTGCCGCCAATCAC
1 TTTGGCACCATTGGTGCCGCCAATCTC
*
2021119 TTTGGCACCATTGGTGCCACCAATCTC
1 TTTGGCACCATTGGTGCCGCCAATCTC
*
2021146 TTTGGCACCTTTGGTGCCGCCAAT
1 TTTGGCACCATTGGTGCCGCCAAT
2021170 GTGATTGGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.17, C:0.31, G:0.22, T:0.31
Consensus pattern (27 bp):
TTTGGCACCATTGGTGCCGCCAATCTC
Found at i:2025213 original size:30 final size:31
Alignment explanation
Indices: 2025179--2025236 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
2025169 AGATGATTCT
*
2025179 TGTGATGATG-ATCTTATGGGCC-TATGTACA
1 TGTGATGATGCA-CCTATGGGCCTTATGTACA
*
2025209 TGTGATTATGCACCTATGGGCCTTATGT
1 TGTGATGATGCACCTATGGGCCTTATGT
2025237 GTGAAGATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.38
Consensus pattern (31 bp):
TGTGATGATGCACCTATGGGCCTTATGTACA
Found at i:2026774 original size:21 final size:20
Alignment explanation
Indices: 2026744--2026786 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
2026734 TGGTTTGATC
*
2026744 TTTTATTTTTTATATTAATT
1 TTTTATTTTTTAAATTAATT
*
2026764 TTTTAATTTTTTAAATTTATT
1 TTTT-ATTTTTTAAATTAATT
2026785 TT
1 TT
2026787 GATAAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATTTTTTAAATTAATT
Found at i:2026878 original size:15 final size:15
Alignment explanation
Indices: 2026850--2026880 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2026840 ATATTTTCAT
2026850 AAATATTTTAAAAAA
1 AAATATTTTAAAAAA
2026865 AAATAATTTTAAAAAA
1 AAAT-ATTTTAAAAAA
2026881 TTTTAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATATTTTAAAAAA
Found at i:2026884 original size:10 final size:10
Alignment explanation
Indices: 2026823--2026889 Score: 52
Period size: 10 Copynumber: 6.8 Consensus size: 10
2026813 TCTAATATTA
2026823 TTTAACAAAAT
1 TTTAA-AAAAT
*
2026834 TTTAAAATAT
1 TTTAAAAAAT
*
2026844 TTTCATAAATAT
1 TTT-A-AAAAAT
2026856 TTTAAAAAA-
1 TTTAAAAAAT
*
2026865 ---AAATAAT
1 TTTAAAAAAT
2026872 TTTAAAAAAT
1 TTTAAAAAAT
2026882 TTTAAAAA
1 TTTAAAAA
2026890 TTATTTTTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
6 5 0.11
10 25 0.54
11 7 0.15
12 9 0.20
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (10 bp):
TTTAAAAAAT
Found at i:2026889 original size:27 final size:27
Alignment explanation
Indices: 2026837--2026889 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
2026827 ACAAAATTTT
*
2026837 AAAATATTTTCATAAATATTTTAAAAA
1 AAAATATTTTCATAAAAATTTTAAAAA
2026864 AAAATAATTTT-A-AAAAATTTTAAAAA
1 AAAAT-ATTTTCATAAAAATTTTAAAAA
2026890 TTATTTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 13 0.54
27 6 0.25
28 5 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
AAAATATTTTCATAAAAATTTTAAAAA
Found at i:2029502 original size:28 final size:28
Alignment explanation
Indices: 2029471--2029530 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
2029461 ACTGTTACGT
* * *
2029471 AACTACTTTAGAACTAACCACACCTAAC
1 AACTACTCTACAACTAACCACAACTAAC
* * *
2029499 AACTGCTCTACAACTGACTACAACTAAC
1 AACTACTCTACAACTAACCACAACTAAC
2029527 AACT
1 AACT
2029531 GACAACTTCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.42, C:0.32, G:0.05, T:0.22
Consensus pattern (28 bp):
AACTACTCTACAACTAACCACAACTAAC
Found at i:2039504 original size:22 final size:23
Alignment explanation
Indices: 2039467--2039515 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
2039457 AAATTTAAAA
2039467 TTATTTAAATAATAAAAAATAATT
1 TTATTTAAAT-ATAAAAAATAATT
* *
2039491 TTATTTAAAT-TAAATAATATTT
1 TTATTTAAATATAAAAAATAATT
2039513 TTA
1 TTA
2039516 ATTATTCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 13 0.57
24 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATTTAAATATAAAAAATAATT
Found at i:2039920 original size:9 final size:9
Alignment explanation
Indices: 2039908--2040075 Score: 211
Period size: 9 Copynumber: 18.9 Consensus size: 9
2039898 ATTTTTACTA
*
2039908 TTTTAATAT
1 TTTTAAAAT
*
2039917 TTTTACAAT
1 TTTTAAAAT
**
2039926 ATTTTATGAT
1 -TTTTAAAAT
*
2039936 TTCTAATAAT
1 TTTTAA-AAT
2039946 TTTT--AAT
1 TTTTAAAAT
2039953 TTTTAAAA-
1 TTTTAAAAT
2039961 TTTTAAAAT
1 TTTTAAAAT
2039970 TTTTAAAAT
1 TTTTAAAAT
2039979 TTTTAAAAT
1 TTTTAAAAT
2039988 TTTTAAAAT
1 TTTTAAAAT
2039997 TTTTAAAAT
1 TTTTAAAAT
2040006 TTTTAAAAT
1 TTTTAAAAT
2040015 TTTTAAAAT
1 TTTTAAAAT
2040024 TTTTAAAAT
1 TTTTAAAAT
2040033 TTTTAAAA-
1 TTTTAAAAT
2040041 TTTTAAAA-
1 TTTTAAAAT
*
2040049 TTTTAACAT
1 TTTTAAAAT
*
2040058 TTTTACAATT
1 TTTTA-AAAT
2040068 TTTTAAAA
1 TTTTAAAA
2040076 AAATTCCAAC
Statistics
Matches: 140, Mismatches: 12, Indels: 14
0.84 0.07 0.08
Matches are distributed among these distances:
7 7 0.05
8 23 0.16
9 91 0.65
10 19 0.14
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:2043330 original size:31 final size:31
Alignment explanation
Indices: 2043282--2043350 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
2043272 TTTAAACTTT
*
2043282 TTTATCC-ATGTTAATCCTCAAACTTATAAC
1 TTTATCCAATATTAATCCTCAAACTTATAAC
2043312 TTTATCCAATATTAATCCTCAAACTTATAAC
1 TTTATCCAATATTAATCCTCAAACTTATAAC
2043343 TTTATCCA
1 TTTATCCA
2043351 GGTTTGATCC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 7 0.19
31 30 0.81
ACGTcount: A:0.35, C:0.23, G:0.01, T:0.41
Consensus pattern (31 bp):
TTTATCCAATATTAATCCTCAAACTTATAAC
Found at i:2048103 original size:28 final size:28
Alignment explanation
Indices: 2048054--2048109 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2048044 TTTAATTAAA
*
2048054 AAAATTAAAGTTGATCGGAAAATTCAAT
1 AAAATTAAAGTTGATCGCAAAATTCAAT
*
2048082 AAAATTAAAGTTTAGT-GCAAAATTCAAT
1 AAAATTAAAGTTGA-TCGCAAAATTCAAT
2048110 CACATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (28 bp):
AAAATTAAAGTTGATCGCAAAATTCAAT
Found at i:2048650 original size:70 final size:70
Alignment explanation
Indices: 2048569--2048703 Score: 243
Period size: 70 Copynumber: 1.9 Consensus size: 70
2048559 GTGAAGAGTG
* *
2048569 ATGAATGATTCATAAAAAAGAATATATTGACCGTACGTGGATGTACAATCGCTCATTAAAAAGTA
1 ATGAATAATTCATAAAAAAGAATACATTGACCGTACGTGGATGTACAATCGCTCATTAAAAAGTA
2048634 CTGTC
66 CTGTC
*
2048639 ATGAATAATTCATAAAAAAGAATACATTGACCGTACGTGGATGTACGATCGCTCATTAAAAAGTA
1 ATGAATAATTCATAAAAAAGAATACATTGACCGTACGTGGATGTACAATCGCTCATTAAAAAGTA
2048704 GTGTGAACGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (70 bp):
ATGAATAATTCATAAAAAAGAATACATTGACCGTACGTGGATGTACAATCGCTCATTAAAAAGTA
CTGTC
Found at i:2060559 original size:18 final size:18
Alignment explanation
Indices: 2060536--2060574 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2060526 CCGCTCCAGC
2060536 AAAGGACACTAAAGATGG
1 AAAGGACACTAAAGATGG
**
2060554 AAAGGATGCTAAAGATGG
1 AAAGGACACTAAAGATGG
2060572 AAA
1 AAA
2060575 AGACTCGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.28, T:0.13
Consensus pattern (18 bp):
AAAGGACACTAAAGATGG
Found at i:2061097 original size:38 final size:38
Alignment explanation
Indices: 2061046--2061118 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
2061036 TTGCTTATAT
* * *
2061046 ATCATTTTCGTGGTTTTATCTATGATTGTGTTTAAAAC
1 ATCATTTTCGTGGTTATATCGATGATTGTGCTTAAAAC
2061084 ATCATATTT-GTGGTTATATCGATGATTGTGCTTAA
1 ATCAT-TTTCGTGGTTATATCGATGATTGTGCTTAA
2061119 CATAGCATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
38 28 0.90
39 3 0.10
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.48
Consensus pattern (38 bp):
ATCATTTTCGTGGTTATATCGATGATTGTGCTTAAAAC
Found at i:2070356 original size:24 final size:23
Alignment explanation
Indices: 2070323--2070369 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
2070313 TGATCATTTA
2070323 ATTATTGAAAAGTTTAATTTAAG
1 ATTATTGAAAAGTTTAATTTAAG
* *
2070346 ATTATTTGAAAATTTTTATTTAAG
1 ATTA-TTGAAAAGTTTAATTTAAG
2070370 TCATTAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (23 bp):
ATTATTGAAAAGTTTAATTTAAG
Found at i:2074099 original size:5 final size:5
Alignment explanation
Indices: 2074077--2074142 Score: 62
Period size: 5 Copynumber: 13.2 Consensus size: 5
2074067 TTTATTTAAT
* * * * *
2074077 ATATA AT-TA ATATT ATATA ATATA ATATA TTATA TTATA TTATA TTATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
*
2074126 AAATA ATATA TATATA A
1 ATATA ATATA -ATATA A
2074143 AACATAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
4 4 0.08
5 44 0.83
6 5 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (5 bp):
ATATA
Found at i:2074104 original size:15 final size:15
Alignment explanation
Indices: 2074076--2074142 Score: 68
Period size: 14 Copynumber: 4.5 Consensus size: 15
2074066 GTTTATTTAA
2074076 TATATAAT-TAATAT
1 TATATAATATAATAT
2074090 TATATAATATAATATAT
1 TATATAATAT-A-ATAT
* *
2074107 TATATTATATTATAT
1 TATATAATATAATAT
2074122 TATA-AA-ATAATAT
1 TATATAATATAATAT
2074135 ATATATAA
1 -TATATAA
2074143 AACATAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
13 6 0.14
14 13 0.30
15 11 0.25
16 1 0.02
17 13 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATAATATAATAT
Found at i:2094007 original size:31 final size:30
Alignment explanation
Indices: 2093972--2094034 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
2093962 TACAAAATGA
2093972 TCATTGAACTATTC-AAAAGTTTTCATTTAAG
1 TCATTGAACTATTCGAAAA-TTTT-ATTTAAG
**
2094003 TCATTGAGTTATTCGGAAAATTTTATTTAAG
1 TCATTGAACTATTC-GAAAATTTTATTTAAG
2094034 T
1 T
2094035 TACCGGGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 20 0.71
32 4 0.14
33 4 0.14
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (30 bp):
TCATTGAACTATTCGAAAATTTTATTTAAG
Found at i:2094409 original size:15 final size:15
Alignment explanation
Indices: 2094389--2094418 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2094379 TAATTTTAAG
2094389 GGGTCAAAGTTAAAT
1 GGGTCAAAGTTAAAT
2094404 GGGTCAAAGTTAAAT
1 GGGTCAAAGTTAAAT
2094419 TTTAACTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (15 bp):
GGGTCAAAGTTAAAT
Done.