Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 6 of 318
Found at i:1749616 original size:18 final size:17
Alignment explanation
Indices: 1749588--1749622 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1749578 ATTATTAAGA
*
1749588 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1749605 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1749623 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:1749736 original size:18 final size:17
Alignment explanation
Indices: 1749708--1749742 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1749698 ATTATTAAGA
*
1749708 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1749725 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1749743 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:1749999 original size:16 final size:16
Alignment explanation
Indices: 1749978--1750046 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
1749968 GATTAGCTAT
1749978 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1749994 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
*
1750011 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
1750027 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1750043 TACA
1 TACA
1750047 GCGAACTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 35 0.70
17 15 0.30
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1750025 original size:33 final size:32
Alignment explanation
Indices: 1749978--1750046 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
1749968 GATTAGCTAT
1749978 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
1750011 TACATCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
1750043 TACA
1 TACA
1750047 GCGAACTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:1750620 original size:21 final size:21
Alignment explanation
Indices: 1750594--1750636 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1750584 TATATATGTG
*
1750594 TATATATATA-AAAATTTTATA
1 TATATACATACAAAA-TTTATA
1750615 TATATACATACAAAATTTATA
1 TATATACATACAAAATTTATA
1750636 T
1 T
1750637 TGCATGAGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
TATATACATACAAAATTTATA
Found at i:1759818 original size:14 final size:16
Alignment explanation
Indices: 1759799--1759831 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1759789 CCATGTTTCG
1759799 TATTCTTT-A-CTTAT
1 TATTCTTTAAGCTTAT
1759813 TATTCTTTAAGCTTAT
1 TATTCTTTAAGCTTAT
1759829 TAT
1 TAT
1759832 GTGATTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.61
Consensus pattern (16 bp):
TATTCTTTAAGCTTAT
Found at i:1769389 original size:4 final size:4
Alignment explanation
Indices: 1769380--1769406 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1769370 CACCTTTGGT
1769380 TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TAT
1769407 ATGTTATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:1771843 original size:5 final size:5
Alignment explanation
Indices: 1771833--1771863 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1771823 AATAATTAAG
1771833 TATAT TATAT TATAT TATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TA-TAT TATAT
1771864 ATAAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:1773534 original size:39 final size:39
Alignment explanation
Indices: 1773427--1773561 Score: 114
Period size: 39 Copynumber: 3.4 Consensus size: 39
1773417 GACCTCGAGT
* * *
1773427 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** * ** *
1773468 CGATGAGGTACCGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
1773506 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
1773545 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
1773562 CCATATTGGT
Statistics
Matches: 74, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
38 18 0.24
39 36 0.49
40 4 0.05
41 14 0.19
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:1775407 original size:24 final size:25
Alignment explanation
Indices: 1775360--1775409 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
1775350 TTTTAGTTGA
1775360 TGACTGCAAATGCTCTGGTAATATT
1 TGACTGCAAATGCTCTGGTAATATT
*
1775385 TGACTGCTAAAT-CT-TTGTAATATT
1 TGACTGC-AAATGCTCTGGTAATATT
1775409 T
1 T
1775410 CTTTCGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 10 0.43
25 9 0.39
26 4 0.17
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (25 bp):
TGACTGCAAATGCTCTGGTAATATT
Found at i:1779337 original size:41 final size:39
Alignment explanation
Indices: 1779247--1779338 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 39
1779237 TGAAAGTAGG
* **
1779247 TGAT-GAAAGAACTTACTGTTGGAAGCGCTTTTGTTGATT
1 TGATAGAAAG-ACTTACTGTTGGAAGCACTTTTGTTGAAA
* *
1779286 TGGTAGGAAAGACTTGCTGTTGGAAGCACTTTTGTTGAAAAA
1 TGATA-GAAAGACTTACTGTTGGAAGCACTTTTGTTG--AAA
1779328 TGATAGAAAGA
1 TGATAGAAAGA
1779339 ACTTCCAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
39 3 0.07
40 24 0.56
41 11 0.26
42 5 0.12
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.33
Consensus pattern (39 bp):
TGATAGAAAGACTTACTGTTGGAAGCACTTTTGTTGAAA
Found at i:1783445 original size:41 final size:41
Alignment explanation
Indices: 1783388--1783478 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
1783378 AAATGGGGTA
*
1783388 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTGAGGTGT
1 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
1783429 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
1 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
*
1783470 TGGGGGTGG
1 TGGGAGTGG
1783479 AGAGTTTGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.22, C:0.12, G:0.42, T:0.24
Consensus pattern (41 bp):
TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
Found at i:1794583 original size:23 final size:23
Alignment explanation
Indices: 1794555--1794605 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1794545 GAATTGGTAT
1794555 ATATTGATTAAATTAAGTTAAAC
1 ATATTGATTAAATTAAGTTAAAC
1794578 ATATTGATTAAATTAAGTTAAAC
1 ATATTGATTAAATTAAGTTAAAC
1794601 A-ATTG
1 ATATTG
1794606 GTCGATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (23 bp):
ATATTGATTAAATTAAGTTAAAC
Found at i:1794661 original size:31 final size:32
Alignment explanation
Indices: 1794624--1794689 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
1794614 AGACTCAATT
* *
1794624 TTTTTAATATTTTCTTT-TTAAA-TTGTATAAA
1 TTTTTAATAATTTATTTATTAAACTTG-ATAAA
1794655 TTTTTAATAATTTATTTAATTAAACTTGATAAA
1 TTTTTAATAATTTATTT-ATTAAACTTGATAAA
1794688 TT
1 TT
1794690 AATTAAACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 15 0.50
33 12 0.40
34 3 0.10
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (32 bp):
TTTTTAATAATTTATTTATTAAACTTGATAAA
Found at i:1796513 original size:72 final size:72
Alignment explanation
Indices: 1796414--1796569 Score: 231
Period size: 72 Copynumber: 2.2 Consensus size: 72
1796404 GGATCTAGTT
* * * *
1796414 AATCATTTATGATCCGTCACTCGCATACTTCACACCACTCGTTATAAGGTACTTATTATGGATTG
1 AATCA-TTAAGATCCGTCACTCACATACTTCACACCACTCGCTATAAGATACTTATTATGGATTG
*
1796479 TCCATGAG
65 TCCATCAG
* * *
1796487 AATCATTAAGATCCGTCACTCACATACTTCATACCACTCGCTATAAGATACTTGTTGTGGATTGT
1 AATCATTAAGATCCGTCACTCACATACTTCACACCACTCGCTATAAGATACTTATTATGGATTGT
1796552 CCATCAG
66 CCATCAG
1796559 AATCATTAAGA
1 AATCATTAAGA
1796570 CATAACAACA
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
72 70 0.93
73 5 0.07
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (72 bp):
AATCATTAAGATCCGTCACTCACATACTTCACACCACTCGCTATAAGATACTTATTATGGATTGT
CCATCAG
Found at i:1804026 original size:13 final size:12
Alignment explanation
Indices: 1803986--1804027 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1803976 ATTTCTTTTA
*
1803986 TTTTCTTGAATT
1 TTTTATTGAATT
1803998 TTTTATAT-AATT
1 TTTTAT-TGAATT
1804010 TTTTATTGAATT
1 TTTTATTGAATT
1804022 CTTTTA
1 -TTTTA
1804028 AAAATGCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 1 0.04
12 19 0.73
13 6 0.23
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (12 bp):
TTTTATTGAATT
Found at i:1804160 original size:17 final size:19
Alignment explanation
Indices: 1804140--1804180 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
1804130 TTAATAAATG
1804140 AATTATTAA-AATA-TAAT
1 AATTATTAATAATATTAAT
1804157 AA-T-TTAATAATATTAAT
1 AATTATTAATAATATTAAT
1804174 AATTATT
1 AATTATT
1804181 TTGTAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
15 4 0.20
16 5 0.25
17 8 0.40
18 1 0.05
19 2 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTATTAATAATATTAAT
Found at i:1810514 original size:21 final size:21
Alignment explanation
Indices: 1810485--1810544 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
1810475 GGTGGATCAA
* *
1810485 CTCTTACGAGCTTTTGTTCAG
1 CTCTCACGAGCTTCTGTTCAG
1810506 CTCTCACGAGCTTCTGTTCAG
1 CTCTCACGAGCTTCTGTTCAG
* * *
1810527 CTTTTATGAGCTTCTGTT
1 CTCTCACGAGCTTCTGTT
1810545 AACAATGTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.43
Consensus pattern (21 bp):
CTCTCACGAGCTTCTGTTCAG
Found at i:1811280 original size:52 final size:52
Alignment explanation
Indices: 1811223--1811327 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
1811213 GTTTTTTATA
1811223 TGTATAAATTTCATATTTGAAATGAATTGATATGATTAAAGTTTATACAAGC
1 TGTATAAATTTCATATTTGAAATGAATTGATATGATTAAAGTTTATACAAGC
1811275 TGTATAAATTTCATATTTGAAATGAATTGATATGATTAAAGTTTATACAAGC
1 TGTATAAATTTCATATTTGAAATGAATTGATATGATTAAAGTTTATACAAGC
1811327 T
1 T
1811328 TACTAAGCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (52 bp):
TGTATAAATTTCATATTTGAAATGAATTGATATGATTAAAGTTTATACAAGC
Found at i:1815753 original size:40 final size:40
Alignment explanation
Indices: 1815485--1815753 Score: 457
Period size: 40 Copynumber: 6.7 Consensus size: 40
1815475 GCAAACACAT
* * * *
1815485 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
* *
1815525 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
* *
1815565 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
*
1815605 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1815645 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1815685 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1815725 TTGCCTTCGGGTCTTAGCCCGGATATATT
1 TTGCCTTCGGGTCTTAGCCCGGATATATT
1815754 CCAATGCTCA
Statistics
Matches: 217, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 217 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
Found at i:1829540 original size:19 final size:21
Alignment explanation
Indices: 1829516--1829566 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
1829506 CCCGACCAAA
*
1829516 GTCAAAAGA-A-AAACAGCGT
1 GTCAAAAGAGAGAAAAAGCGT
1829535 GTCAAAAGACAGAGAAAAAGCGT
1 GTCAAAAG--AGAGAAAAAGCGT
1829558 GTCAAAAGA
1 GTCAAAAGA
1829567 CAGACTACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 8 0.30
21 2 0.07
22 1 0.04
23 16 0.59
ACGTcount: A:0.53, C:0.14, G:0.24, T:0.10
Consensus pattern (21 bp):
GTCAAAAGAGAGAAAAAGCGT
Found at i:1829560 original size:23 final size:24
Alignment explanation
Indices: 1829525--1829570 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
1829515 AGTCAAAAGA
1829525 AAAACAGCGTGTCAAAAGACAGAG
1 AAAACAGCGTGTCAAAAGACAGAG
1829549 AAAA-AGCGTGTCAAAAGACAGA
1 AAAACAGCGTGTCAAAAGACAGA
1829571 CTACACAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (24 bp):
AAAACAGCGTGTCAAAAGACAGAG
Found at i:1847706 original size:23 final size:23
Alignment explanation
Indices: 1847621--1847704 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
1847611 CTTAATGCCG
*
1847621 TTCTGGTGTGTCTGGGTGGATTA
1 TTCTGGTGTGTTTGGGTGGATTA
*
1847644 TTCTGGTGTGTTTGGGTGGATCA
1 TTCTGGTGTGTTTGGGTGGATTA
* * *
1847667 TTCTAGTGTGTTCGGTTGGATTA
1 TTCTGGTGTGTTTGGGTGGATTA
*
1847690 TTATGGTGTGTTTGG
1 TTCTGGTGTGTTTGG
1847705 TTAGATCCGT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.10, C:0.07, G:0.37, T:0.46
Consensus pattern (23 bp):
TTCTGGTGTGTTTGGGTGGATTA
Found at i:1864503 original size:46 final size:46
Alignment explanation
Indices: 1864448--1864586 Score: 115
Period size: 38 Copynumber: 3.2 Consensus size: 46
1864438 AACAAGTAAA
1864448 AACATATAAAAGGAATATTTGTTAAACAACGGAAAACAAAAAATAT
1 AACATATAAAAGGAATATTTGTTAAACAACGGAAAACAAAAAATAT
*
1864494 AACATAT-AAA-GAA-A-GTGTTAGAA-AAC----AACAAAAAACT-T
1 AACATATAAAAGGAATATTTGTTA-AACAACGGAAAACAAAAAA-TAT
* *
1864532 ---ATAAAAAAGGAATATTTGTTAAACAACGGAAAACAAACAAAAAT
1 AACATATAAAAGGAATATTTGTTAAACAACGGAAAACAAA-AAATAT
*
1864576 ATATATATAAA
1 A-ACATATAAA
1864587 CTTAAGATAA
Statistics
Matches: 71, Mismatches: 5, Indels: 32
0.66 0.05 0.30
Matches are distributed among these distances:
35 3 0.04
36 3 0.04
37 3 0.04
38 13 0.18
39 9 0.13
42 8 0.11
43 9 0.13
44 7 0.10
45 3 0.04
46 7 0.10
48 6 0.08
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (46 bp):
AACATATAAAAGGAATATTTGTTAAACAACGGAAAACAAAAAATAT
Found at i:1864528 original size:79 final size:83
Alignment explanation
Indices: 1864431--1864586 Score: 230
Period size: 81 Copynumber: 1.9 Consensus size: 83
1864421 AAAAAATGTA
** * *
1864431 TTAGAAGAACAAGTAAAAAC-ATATAAAAGGAATATTTGTTAAACAACGGAAAACAAA-AAATAT
1 TTAGAAGAACAACAAAAAACTATAAAAAAGGAATATTTGTTAAACAACGGAAAACAAACAAAAAT
1864494 A-ACATATAAAGAAAGTG
66 ATACATATAAAGAAAGTG
1864511 TTAGAA-AACAACAAAAAACTTATAAAAAAGGAATATTTGTTAAACAACGGAAAACAAACAAAAA
1 TTAGAAGAACAACAAAAAAC-TATAAAAAAGGAATATTTGTTAAACAACGGAAAACAAACAAAAA
*
1864575 TATATATATAAA
65 TATACATATAAA
1864587 CTTAAGATAA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
79 11 0.16
80 6 0.09
81 36 0.54
82 6 0.09
83 8 0.12
ACGTcount: A:0.60, C:0.08, G:0.11, T:0.21
Consensus pattern (83 bp):
TTAGAAGAACAACAAAAAACTATAAAAAAGGAATATTTGTTAAACAACGGAAAACAAACAAAAAT
ATACATATAAAGAAAGTG
Found at i:1887027 original size:49 final size:49
Alignment explanation
Indices: 1886972--1887117 Score: 140
Period size: 42 Copynumber: 3.2 Consensus size: 49
1886962 ACAAGTAAAA
1886972 ACATATAAAAAGGAATATTTGTTAAACAACGGAAAACAAAAAAATATAT
1 ACATATAAAAAGGAATATTTGTTAAACAACGGAAAACAAAAAAATATAT
* *
1887021 ACATAT-AAAA-GAA-A-GTGTTAGAA-AA---ACAACAAAAAAACT-TAT
1 ACATATAAAAAGGAATATTTGTTA-AACAACGGAAAACAAAAAAA-TATAT
1887063 --A-A-AAAAAGGAATATTTGTTAAACAACGGAAAACAAACAAAA-ATAT
1 ACATATAAAAAGGAATATTTGTTAAACAACGGAAAACAAA-AAAATATAT
*
1887108 ATATATAAAA
1 ACATATAAAA
1887118 CTTAAGATAA
Statistics
Matches: 77, Mismatches: 4, Indels: 32
0.68 0.04 0.28
Matches are distributed among these distances:
39 5 0.06
40 4 0.05
41 3 0.04
42 21 0.27
43 1 0.01
45 17 0.22
46 7 0.09
47 4 0.05
48 5 0.06
49 10 0.13
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.21
Consensus pattern (49 bp):
ACATATAAAAAGGAATATTTGTTAAACAACGGAAAACAAAAAAATATAT
Found at i:1905730 original size:42 final size:42
Alignment explanation
Indices: 1905682--1905809 Score: 141
Period size: 42 Copynumber: 3.0 Consensus size: 42
1905672 CTTCATTTAC
* * * *
1905682 TCGATGCTATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGTCCAGCTATGGTCTTACACATATTCACAT-A
* * *
1905725 T-GATGCCATAGCCCAGCTATAGTCTTACACATATTCATATA
1 TCGATGCCATAGTCCAGCTATGGTCTTACACATATTCACATA
* ** *
1905766 TCGATGCCATGGTCCAGCTATGGTCTTACATGTAATCACATA
1 TCGATGCCATAGTCCAGCTATGGTCTTACACATATTCACATA
1905808 TC
1 TC
1905810 ACATATCACA
Statistics
Matches: 70, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
41 2 0.03
42 67 0.96
43 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (42 bp):
TCGATGCCATAGTCCAGCTATGGTCTTACACATATTCACATA
Found at i:1905843 original size:56 final size:56
Alignment explanation
Indices: 1905752--1905864 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 56
1905742 TATAGTCTTA
* * * *
1905752 CACATATTCATATATCGATGCCATGGTCCAGCTATGGTCTTACATGTAATCACATAT
1 CACATATTCACATATCGATGCCATGGCCCAACTATGGTCTTACACG-AATCACATAT
*
1905809 CACATA-TCACATATCGATGCCATTGCCCAACTATGGTCTTACACGAATCACATAT
1 CACATATTCACATATCGATGCCATGGCCCAACTATGGTCTTACACGAATCACATAT
1905864 C
1 C
1905865 TCACTGATGC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 11 0.22
56 34 0.67
57 6 0.12
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (56 bp):
CACATATTCACATATCGATGCCATGGCCCAACTATGGTCTTACACGAATCACATAT
Found at i:1905890 original size:46 final size:47
Alignment explanation
Indices: 1905809--1905942 Score: 121
Period size: 47 Copynumber: 2.8 Consensus size: 47
1905799 AATCACATAT
* *
1905809 CACATATCACATATCGATGCCAT-TGCCCA-ACTATGGTCTTACAC-GAAT
1 CACATATCACACA--GATGCCATAT-CCCAGA-TATGGTCTTACACAGAAG
* * * *
1905857 CACATATCTCACTGATGCCATATCCCAGATATGGTCTTATACAGTAG
1 CACATATCACACAGATGCCATATCCCAGATATGGTCTTACACAGAAG
* * **
1905904 CATATATCACACAGATGTCATATCTTAGATATGGTCTTA
1 CACATATCACACAGATGCCATATCCCAGATATGGTCTTA
1905943 TACGGAAATC
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
46 24 0.34
47 37 0.52
48 10 0.14
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (47 bp):
CACATATCACACAGATGCCATATCCCAGATATGGTCTTACACAGAAG
Found at i:1906013 original size:31 final size:31
Alignment explanation
Indices: 1905975--1906042 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
1905965 TAGCCGAATA
*
1905975 TTCACTGATCAGGTAGCCGAAGCTACCATTT
1 TTCACTGATCAGGTAGCCGAAGCTACCACTT
1906006 TTCACTGATCAGGTAGCCGAAGCTACCACTT
1 TTCACTGATCAGGTAGCCGAAGCTACCACTT
1906037 TTCACT
1 TTCACT
1906043 TTCACTTGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (31 bp):
TTCACTGATCAGGTAGCCGAAGCTACCACTT
Found at i:1908783 original size:13 final size:13
Alignment explanation
Indices: 1908765--1908815 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
1908755 TATGAGAAGA
1908765 GAGAAAAATAAAG
1 GAGAAAAATAAAG
1908778 GAGAAAAATAAGAG
1 GAGAAAAATAA-AG
*
1908792 AATG-AAAATAAA-
1 GA-GAAAAATAAAG
*
1908804 GAAAAAAATAAA
1 GAGAAAAATAAA
1908816 AAAAGTACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 9 0.28
13 12 0.38
14 10 0.31
15 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.10
Consensus pattern (13 bp):
GAGAAAAATAAAG
Found at i:1908790 original size:26 final size:25
Alignment explanation
Indices: 1908761--1908814 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
1908751 AGAATATGAG
*
1908761 AAGAG-AGAAAAATAAAGGAGAAAAAT
1 AAGAGAAG-AAAATAAA-GAAAAAAAT
1908787 AAGAGAATGAAAATAAAGAAAAAAAT
1 AAGAGAA-GAAAATAAAGAAAAAAAT
1908813 AA
1 AA
1908815 AAAAAGTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 15 0.60
27 9 0.36
28 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (25 bp):
AAGAGAAGAAAATAAAGAAAAAAAT
Found at i:1946745 original size:24 final size:24
Alignment explanation
Indices: 1946718--1946763 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1946708 TTTAAATGTG
* *
1946718 ATTTTTTTACTATTTTTAATTAGA
1 ATTTATTTACAATTTTTAATTAGA
1946742 ATTTATTTACAATTTTTAATTA
1 ATTTATTTACAATTTTTAATTA
1946764 TAGTGTCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTTATTTACAATTTTTAATTAGA
Found at i:1952020 original size:34 final size:32
Alignment explanation
Indices: 1951976--1952044 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
1951966 TTTTTATTCT
*
1951976 TTTTGACAAAATACTTAAAATTATTAATAGCCTC
1 TTTTGAC-AAA-ACTTAAAACTATTAATAGCCTC
*
1952010 TTTTGTCAAAACTTAAAACTATTAATAGCCTC
1 TTTTGACAAAACTTAAAACTATTAATAGCCTC
1952042 TTT
1 TTT
1952045 CAACTCGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 24 0.73
33 3 0.09
34 6 0.18
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (32 bp):
TTTTGACAAAACTTAAAACTATTAATAGCCTC
Found at i:1978927 original size:13 final size:14
Alignment explanation
Indices: 1978911--1978946 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1978901 CAATCTCATA
1978911 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
1978924 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
1978937 TCTC-ATTTCA
1 TCTCAATTTCA
1978947 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:1978936 original size:18 final size:19
Alignment explanation
Indices: 1978898--1978938 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
1978888 TGGTTCATGT
1978898 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
1978917 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
1978935 TTTC
1 TTTC
1978939 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:1979070 original size:23 final size:23
Alignment explanation
Indices: 1979043--1979100 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1979033 GCAGATTCCT
*
1979043 CCCAAACACGCCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
*
1979066 TCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
1979089 CCCAAACACACC
1 CCCAAACACACC
1979101 CGGAATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.45, C:0.41, G:0.05, T:0.09
Consensus pattern (23 bp):
CCCAAACACACCAGAATATCCAA
Found at i:1979491 original size:15 final size:15
Alignment explanation
Indices: 1979471--1979517 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
1979461 TATTATATAT
1979471 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
1979486 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
1979501 TTCAATCAATATAAA
1 TTCAATCAATATAAA
1979516 TT
1 TT
1979518 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:1980221 original size:19 final size:19
Alignment explanation
Indices: 1980199--1980239 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1980189 CAAACCCTAA
1980199 TTCTCCCTT-TTTCTTTTCT
1 TTCTCCCTTCTTTC-TTTCT
*
1980218 TTCTCCTTTCTTTCTTTCT
1 TTCTCCCTTCTTTCTTTCT
1980237 TTC
1 TTC
1980240 CTTCCCCTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (19 bp):
TTCTCCCTTCTTTCTTTCT
Found at i:1980500 original size:31 final size:32
Alignment explanation
Indices: 1980442--1980505 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
1980432 CATACATTTG
*
1980442 TCATAATTTAATATATTTATTACATAAAAATC
1 TCATAATATAATATATTTATTACATAAAAATC
*
1980474 TCATAATATAAT-TATTTAATTA-ATAAATATC
1 TCATAATATAATATATTT-ATTACATAAAAATC
1980505 T
1 T
1980506 TATTTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 14 0.48
32 15 0.52
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (32 bp):
TCATAATATAATATATTTATTACATAAAAATC
Found at i:1981036 original size:13 final size:14
Alignment explanation
Indices: 1981018--1981046 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1981008 GATTAACTTC
1981018 ATAAATATTTT-TA
1 ATAAATATTTTCTA
1981031 ATAAATATTTTCTA
1 ATAAATATTTTCTA
1981045 AT
1 AT
1981047 CTATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:1986607 original size:15 final size:15
Alignment explanation
Indices: 1986587--1986616 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1986577 GATTTTATAG
1986587 GATGACCAAATGCAT
1 GATGACCAAATGCAT
*
1986602 GATGACCAATTGCAT
1 GATGACCAAATGCAT
1986617 TTACTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (15 bp):
GATGACCAAATGCAT
Found at i:1993643 original size:22 final size:23
Alignment explanation
Indices: 1993613--1993657 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1993603 AATGAGCTTC
*
1993613 TTATATATAT-TTTTTGAATTTT
1 TTATATATATCTTTTTCAATTTT
*
1993635 TTATTTATATCTTTTTCAATTTT
1 TTATATATATCTTTTTCAATTTT
1993658 AAATTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (23 bp):
TTATATATATCTTTTTCAATTTT
Found at i:1996325 original size:4 final size:4
Alignment explanation
Indices: 1996316--1996340 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1996306 AAAATAGGAA
1996316 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
1996341 CAAATTAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2002609 original size:23 final size:22
Alignment explanation
Indices: 2002564--2002609 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
2002554 TTTGAAAATA
2002564 AATTTAAATTTCAAGTTAATTG
1 AATTTAAATTTCAAGTTAATTG
*
2002586 AATTTAATTATTT-AAGTTATTTG
1 AATTTAA--ATTTCAAGTTAATTG
2002609 A
1 A
2002610 TTTTTTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 10 0.48
24 4 0.19
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (22 bp):
AATTTAAATTTCAAGTTAATTG
Found at i:2004634 original size:22 final size:22
Alignment explanation
Indices: 2004600--2004654 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
2004590 TTAAACATAA
* *
2004600 AATATATAAATTTTTCATATTTT
1 AATA-ATATATTTTTAATATTTT
* * *
2004623 ATTATTATATTTTTAATTTTTT
1 AATAATATATTTTTAATATTTT
2004645 AATAATATAT
1 AATAATATAT
2004655 ATATAAATAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
AATAATATATTTTTAATATTTT
Found at i:2010669 original size:8 final size:8
Alignment explanation
Indices: 2010656--2010702 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
2010646 GACAATAACC
2010656 ATTATTTA
1 ATTATTTA
2010664 ATTATTTA
1 ATTATTTA
2010672 ATTATTT-
1 ATTATTTA
2010679 -TTATTT-
1 ATTATTTA
2010685 -TTATTTA
1 ATTATTTA
*
2010692 ATTATTCA
1 ATTATTTA
2010700 ATT
1 ATT
2010703 TTTTGAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
6 12 0.33
8 24 0.67
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (8 bp):
ATTATTTA
Found at i:2014522 original size:17 final size:16
Alignment explanation
Indices: 2014500--2014547 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
2014490 TTTTTGTAAA
2014500 ATTATATTTTAAATAT
1 ATTATATTTTAAATAT
* *
2014516 GATTATATGTAAAATAT
1 -ATTATATTTTAAATAT
2014533 ATTTAATATTTTAAA
1 A-TT-ATATTTTAAA
2014548 CATAAGTCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 1 0.04
17 16 0.64
18 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (16 bp):
ATTATATTTTAAATAT
Found at i:2017030 original size:14 final size:13
Alignment explanation
Indices: 2016999--2017040 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2016989 TTACGGTTAG
2016999 TTATTTTTTTAAT
1 TTATTTTTTTAAT
* *
2017012 ATATTTTTATTTAT
1 TTATTTTT-TTAAT
2017026 TTA-TTTTTTAAT
1 TTATTTTTTTAAT
2017038 TTA
1 TTA
2017041 ATCGTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 7 0.29
13 11 0.46
14 6 0.25
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTTTTTAAT
Found at i:2017336 original size:48 final size:48
Alignment explanation
Indices: 2017247--2017338 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
2017237 TTTCTTGGCT
* * *
2017247 TAAAAACGCCTAAGTCAGCCTAACTTCCACCGATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
2017295 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCA
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCA
2017339 GCAGAATTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
47 4 0.10
48 35 0.90
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:2019851 original size:48 final size:48
Alignment explanation
Indices: 2019762--2019855 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
2019752 TTTCTTGGCT
* * *
2019762 TAAAAACGCCTAAGTCAGCCTAACTTCCACCGATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
* *
2019810 TAAAAATGCCTAAGTCAGCTTAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCTAACTTC-CAACAATAAAGGATTCAAC
2019856 AGAATTCCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 2 0.05
48 38 0.95
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.21
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:2032950 original size:14 final size:14
Alignment explanation
Indices: 2032928--2032967 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2032918 AACCATAAAA
* *
2032928 AAATACAAAACTTT
1 AAATCCAAAACCTT
2032942 AAATCCAAAACCTT
1 AAATCCAAAACCTT
*
2032956 AAATCTAAAACC
1 AAATCCAAAACC
2032968 CAAAAACCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATCCAAAACCTT
Found at i:2039267 original size:2 final size:2
Alignment explanation
Indices: 2039262--2039288 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2039252 TCTCTCTTAA
2039262 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
2039289 GATAAAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2047591 original size:3 final size:3
Alignment explanation
Indices: 2047583--2047607 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2047573 CATTAAAAGA
2047583 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
2047608 GATCGGACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2053770 original size:24 final size:25
Alignment explanation
Indices: 2053743--2053789 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2053733 TAATTAAATT
*
2053743 TTATAAATAATTAATATT-TATTAG
1 TTATAAATAATTAAAATTATATTAG
*
2053767 TTATAAATATTTAAAATTATATT
1 TTATAAATAATTAAAATTATATT
2053790 TCATATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTATAAATAATTAAAATTATATTAG
Found at i:2053881 original size:20 final size:20
Alignment explanation
Indices: 2053828--2053881 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 20
2053818 ATAATAATTT
2053828 TTTAAATATT-TTT-ACTAA
1 TTTAAATATTATTTAACTAA
** *
2053846 AATACAATAATA-TTAACTAA
1 TTTA-AATATTATTTAACTAA
2053866 TTTAAATATTATTTAA
1 TTTAAATATTATTTAA
2053882 ATACATATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
18 2 0.08
19 13 0.50
20 11 0.42
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTAAATATTATTTAACTAA
Found at i:2056228 original size:5 final size:5
Alignment explanation
Indices: 2056218--2056250 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
2056208 AATAATTAAG
2056218 TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TAT
2056251 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:2065696 original size:20 final size:19
Alignment explanation
Indices: 2065647--2065698 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2065637 TCTTTCAACA
*
2065647 AAAAATACAAAATAATTTT
1 AAAAATTCAAAATAATTTT
*
2065666 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
2065685 AAAAATTTCAAAAT
1 AAAAA-TTCAAAAT
2065699 TTGTGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.14
19 16 0.57
20 8 0.29
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:2065885 original size:16 final size:16
Alignment explanation
Indices: 2065866--2065896 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2065856 TTGAAAAAGT
2065866 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
2065882 TTTCAAATTTATATG
1 TTTCAAATATATATG
2065897 CTAATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:2071475 original size:14 final size:14
Alignment explanation
Indices: 2071456--2071500 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
2071446 CCTGCAAGCC
*
2071456 ATATATGTCAATAT
1 ATATATGTCTATAT
2071470 ATATATGTCTATAT
1 ATATATGTCTATAT
*
2071484 ATATGTGTCTATAT
1 ATATATGTCTATAT
2071498 ATA
1 ATA
2071501 ATTTTAAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (14 bp):
ATATATGTCTATAT
Found at i:2074647 original size:21 final size:21
Alignment explanation
Indices: 2074615--2074662 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
2074605 CTTTAATGCA
2074615 TTCAAT-TCATTTTCGTTGAC
1 TTCAATATCATTTTCGTTGAC
2074635 TTCAATATCATTTTCGTTGAC
1 TTCAATATCATTTTCGTTGAC
2074656 TTCAATA
1 TTCAATA
2074663 AACTACGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (21 bp):
TTCAATATCATTTTCGTTGAC
Found at i:2090166 original size:2 final size:2
Alignment explanation
Indices: 2090159--2090183 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2090149 TTATACATGT
2090159 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2090184 TTAAGGGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2115835 original size:36 final size:36
Alignment explanation
Indices: 2115789--2115980 Score: 156
Period size: 36 Copynumber: 5.5 Consensus size: 36
2115779 GGGGGTGACA
2115789 GTGGTGGTGGTGGAGGTGAATGGTAAATAACTGAAG
1 GTGGTGGTGGTGGAGGTGAATGGTAAATAACTGAAG
* * *
2115825 GTGGTGGTGGTGGTGGTG-A-GG-AATATGTTAC--AAC
1 GTGGTGGTGGTGGAGGTGAATGGTAA-A--TAACTGAAG
2115859 G-GGTGGTGGTGGAGGTGAATGGTAAATAACTGAAG
1 GTGGTGGTGGTGGAGGTGAATGGTAAATAACTGAAG
* * *
2115894 GTGGTGGTGGTGGTGGTG-A-GG-AATATGTTAC--AAC
1 GTGGTGGTGGTGGAGGTGAATGGTAA-A--TAACTGAAG
* *
2115928 G-GGTGGTGGTGGAGGCGAATGGTAAATAACTGGAG
1 GTGGTGGTGGTGGAGGTGAATGGTAAATAACTGAAG
* *
2115963 GCGGTGGTGGTGGTGGTG
1 GTGGTGGTGGTGGAGGTG
2115981 GTGAGGAATA
Statistics
Matches: 122, Mismatches: 16, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
33 39 0.32
34 14 0.11
35 13 0.11
36 56 0.46
ACGTcount: A:0.22, C:0.05, G:0.47, T:0.26
Consensus pattern (36 bp):
GTGGTGGTGGTGGAGGTGAATGGTAAATAACTGAAG
Found at i:2115910 original size:72 final size:69
Alignment explanation
Indices: 2115791--2116011 Score: 379
Period size: 69 Copynumber: 3.2 Consensus size: 69
2115781 GGGTGACAGT
2115791 GGTGGTGGTGGAGGTGAATGGTAAATAACTGAAGGTGGTGGTGGTGGTGGTGAGGAATATGTTAC
1 GGTGGTGGTGGAGGTGAATGGTAAATAACTGAAGGTGGTGGTGGTGGTGGTGAGGAATATGTTAC
2115856 AACG
66 AACG
2115860 GGTGGTGGTGGAGGTGAATGGTAAATAACTGAAGGTGGTGGTGGTGGTGGTGAGGAATATGTTAC
1 GGTGGTGGTGGAGGTGAATGGTAAATAACTGAAGGTGGTGGTGGTGGTGGTGAGGAATATGTTAC
2115925 AACG
66 AACG
* *
2115929 GGTGGTGGTGGAGGCGAATGGTAAATAACTGGAGGCGGTGGTGGTGGTGGTGGTGAGGAATATGT
1 GGTGGTGGTGGAGGTGAATGGTAAATAACT-GA--AGGTGGTGGTGGTGGTGGTGAGGAATATGT
*
2115994 TACAAAG
63 TACAACG
*
2116001 GGTGGCGGTGG
1 GGTGGTGGTGG
2116012 TGAAGGTGAT
Statistics
Matches: 145, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
69 98 0.68
70 2 0.01
72 45 0.31
ACGTcount: A:0.23, C:0.05, G:0.47, T:0.25
Consensus pattern (69 bp):
GGTGGTGGTGGAGGTGAATGGTAAATAACTGAAGGTGGTGGTGGTGGTGGTGAGGAATATGTTAC
AACG
Found at i:2116262 original size:21 final size:21
Alignment explanation
Indices: 2116235--2116311 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
2116225 GGAGTGGGGA
*
2116235 GGCGGTGGTGGAGAATG-TGGT
1 GGCGGTGGGGGAGAATGAT-GT
* *
2116256 GGGGGTGGGGGTGAATGATGT
1 GGCGGTGGGGGAGAATGATGT
*
2116277 GGCGGTGGGGGTGAATGATGT
1 GGCGGTGGGGGAGAATGATGT
* *
2116298 GGTGGTGGAGGAGA
1 GGCGGTGGGGGAGA
2116312 GTTATAGTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 47 0.98
22 1 0.02
ACGTcount: A:0.16, C:0.03, G:0.60, T:0.22
Consensus pattern (21 bp):
GGCGGTGGGGGAGAATGATGT
Found at i:2116518 original size:15 final size:15
Alignment explanation
Indices: 2116494--2116590 Score: 70
Period size: 15 Copynumber: 6.5 Consensus size: 15
2116484 GATATGTAGG
* *
2116494 GGTGGGGGTGAAGGA
1 GGTGGAGGTGATGGA
2116509 GGTGGAGGTGATGGA
1 GGTGGAGGTGATGGA
** * * *
2116524 TATGTAGGGGGTGG-
1 GGTGGAGGTGATGGA
* *
2116538 GGTGGGGGTGAAGGA
1 GGTGGAGGTGATGGA
* * *
2116553 GGTGGTGGTGAGGGC
1 GGTGGAGGTGATGGA
*
2116568 GGTGGAGGTGATGGT
1 GGTGGAGGTGATGGA
2116583 GGTGGAGG
1 GGTGGAGG
2116591 AGGTGGAGAG
Statistics
Matches: 61, Mismatches: 20, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
14 7 0.11
15 54 0.89
ACGTcount: A:0.15, C:0.01, G:0.64, T:0.20
Consensus pattern (15 bp):
GGTGGAGGTGATGGA
Found at i:2116554 original size:38 final size:38
Alignment explanation
Indices: 2116444--2116556 Score: 111
Period size: 38 Copynumber: 2.9 Consensus size: 38
2116434 CGGTGGTAAC
* * * **
2116444 GGATAAGTAGGTGGCGGGGGTGAAGGCGGTGGAGGTGAT
1 GGATATGTAGG-GGTGGGGGTGAAGGAGAAGGAGGTGAT
**
2116483 GGATATGTAGGGGTGGGGGTGAAGGAGGTGGAGGTGAT
1 GGATATGTAGGGGTGGGGGTGAAGGAGAAGGAGGTGAT
** *
2116521 GGATATGTAGGGG-GTGGGGTGGGGGTGAAGGAGGTG
1 GGATATGTAGGGGTG-GGGGTGAAGGAGAAGGAGGTG
2116557 GTGGTGAGGG
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
37 1 0.02
38 54 0.83
39 10 0.15
ACGTcount: A:0.19, C:0.02, G:0.59, T:0.19
Consensus pattern (38 bp):
GGATATGTAGGGGTGGGGGTGAAGGAGAAGGAGGTGAT
Found at i:2116563 original size:44 final size:38
Alignment explanation
Indices: 2116418--2116539 Score: 147
Period size: 38 Copynumber: 3.2 Consensus size: 38
2116408 TGGCGCAGGT
* * * * * *
2116418 GGTGAGGGTGAAGG-GGCGGTGGTAACGGATAAGTAGG
1 GGTGGGGGTGAAGGAGGTGGAGGTGATGGATATGTAGG
* *
2116455 TGGCGGGGGTGAAGGCGGTGGAGGTGATGGATATGTAGG
1 -GGTGGGGGTGAAGGAGGTGGAGGTGATGGATATGTAGG
2116494 GGTGGGGGTGAAGGAGGTGGAGGTGATGGATATGTAGGG
1 GGTGGGGGTGAAGGAGGTGGAGGTGATGGATATGTA-GG
2116533 GGTGGGG
1 GGTGGGG
2116540 TGGGGGTGAA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
38 46 0.63
39 27 0.37
ACGTcount: A:0.20, C:0.03, G:0.58, T:0.19
Consensus pattern (38 bp):
GGTGGGGGTGAAGGAGGTGGAGGTGATGGATATGTAGG
Found at i:2116722 original size:33 final size:30
Alignment explanation
Indices: 2116664--2116724 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 30
2116654 TGGGGGAGGT
* *
2116664 GAATAAACTGGTGGTGGAGGGGGAGGGGGA
1 GAATAAACGGGTGGTGGAGGAGGAGGGGGA
2116694 GAATAAACGGGTGGTGGGAGTGAAGGAGGGG
1 GAATAAACGGGTGGT-GGAG-G-AGGAGGGG
2116725 AGGCGGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 14 0.54
31 4 0.15
32 1 0.04
33 7 0.27
ACGTcount: A:0.28, C:0.03, G:0.56, T:0.13
Consensus pattern (30 bp):
GAATAAACGGGTGGTGGAGGAGGAGGGGGA
Found at i:2118388 original size:99 final size:99
Alignment explanation
Indices: 2118217--2118412 Score: 347
Period size: 99 Copynumber: 2.0 Consensus size: 99
2118207 GTTTGAGGAG
* *
2118217 AGAGACAAGGGGATGAAAGGGTGTTTTTCTAGTAGGAATTGTAGGGCATGTGCTTGTGTGAGAGA
1 AGAGACAAAGGGATGAAAGGGTGTTTTTCTAGTAGGAATTGTAGGGCATGTGCTTGTGTAAGAGA
* *
2118282 AATGAAAATAACAATAATAAAAAGGAGAAGAAAA
66 AAGGAAAAAAACAATAATAAAAAGGAGAAGAAAA
2118316 AGAGACAAAGGGATGAAAGGGTGTTTTTCTAGTAGGAATTGTAGGGCATGTGCTTGTGTAAGAGA
1 AGAGACAAAGGGATGAAAGGGTGTTTTTCTAGTAGGAATTGTAGGGCATGTGCTTGTGTAAGAGA
*
2118381 AAGGAAAAAAACAATAATAAAAAGGAGGAGAA
66 AAGGAAAAAAACAATAATAAAAAGGAGAAGAA
2118413 GAAAAAAAGA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.43, C:0.05, G:0.31, T:0.21
Consensus pattern (99 bp):
AGAGACAAAGGGATGAAAGGGTGTTTTTCTAGTAGGAATTGTAGGGCATGTGCTTGTGTAAGAGA
AAGGAAAAAAACAATAATAAAAAGGAGAAGAAAA
Found at i:2122803 original size:19 final size:20
Alignment explanation
Indices: 2122765--2122803 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2122755 AAATATTTAC
*
2122765 AAATATCAAATAATAAAATT
1 AAATATCAAAAAATAAAATT
*
2122785 AAATAT-AAAAAATATAATT
1 AAATATCAAAAAATAAAATT
2122804 TTGGTTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATATCAAAAAATAAAATT
Found at i:2130785 original size:15 final size:15
Alignment explanation
Indices: 2130765--2130793 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2130755 TCTATTTCCA
2130765 AAAATATATTATTAC
1 AAAATATATTATTAC
2130780 AAAATATATTATTA
1 AAAATATATTATTA
2130794 ATACTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATATATTATTAC
Found at i:2143351 original size:20 final size:19
Alignment explanation
Indices: 2143317--2143354 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2143307 AAATTATAGT
2143317 ATAAAAATTAAATTTAAAA
1 ATAAAAATTAAATTTAAAA
*
2143336 ATAAAATTTCAAATTTAAA
1 ATAAAAATT-AAATTTAAA
2143355 TACCAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAAATTAAATTTAAAA
Found at i:2144575 original size:20 final size:20
Alignment explanation
Indices: 2144523--2144565 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2144513 ATTAGTATTC
2144523 TTATCCTGAATTTTAGAATT
1 TTATCCTGAATTTTAGAATT
*
2144543 TTATCCTGAATTTTAGTATT
1 TTATCCTGAATTTTAGAATT
2144563 TTA
1 TTA
2144566 ATTTGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (20 bp):
TTATCCTGAATTTTAGAATT
Found at i:2152720 original size:17 final size:17
Alignment explanation
Indices: 2152698--2152731 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2152688 ATCCACTAAT
*
2152698 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2152715 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2152732 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:2157359 original size:17 final size:17
Alignment explanation
Indices: 2157337--2157370 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2157327 ATCCACTAAT
*
2157337 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2157354 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2157371 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:2158871 original size:23 final size:23
Alignment explanation
Indices: 2158845--2158888 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2158835 TCTAGTAGTG
*
2158845 ATTTAATTAACATGCATGAATAT
1 ATTTAATTAAAATGCATGAATAT
* *
2158868 ATTTATTTAAAATGCGTGAAT
1 ATTTAATTAAAATGCATGAAT
2158889 GTAATAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (23 bp):
ATTTAATTAAAATGCATGAATAT
Found at i:2159045 original size:22 final size:22
Alignment explanation
Indices: 2158999--2159045 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2158989 GCTTCCAACA
* * * *
2158999 ATATATTTTGATTTTTTTATTC
1 ATATATTTTGAATCTTTGATGC
2159021 ATATATTTTGAATCTTTGATGC
1 ATATATTTTGAATCTTTGATGC
2159043 ATA
1 ATA
2159046 CATAATTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (22 bp):
ATATATTTTGAATCTTTGATGC
Found at i:2159407 original size:33 final size:33
Alignment explanation
Indices: 2159365--2159435 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2159355 GTTGAAATAC
* *
2159365 TAATCTTAAATATACCCTCTAATTAAATGCCTA
1 TAATTTTAAATATACCCTCGAATTAAATGCCTA
2159398 TAATTTTAAATATACCCTCGAATTAAATGCCTA
1 TAATTTTAAATATACCCTCGAATTAAATGCCTA
2159431 TAATT
1 TAATT
2159436 AGGGTTGGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.38
Consensus pattern (33 bp):
TAATTTTAAATATACCCTCGAATTAAATGCCTA
Found at i:2163937 original size:30 final size:31
Alignment explanation
Indices: 2163901--2163964 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 31
2163891 AAATAGAAGC
2163901 CTGGAATCATCGAGGT-ATTACTAATATCGG
1 CTGGAATCATCGAGGTAATTACTAATATCGG
*
2163931 CTGGAATCATCGAGGTGAAATTACTCATATCGG
1 CTGGAATCATCGAGGT--AATTACTAATATCGG
2163964 C
1 C
2163965 AATAAATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 16 0.53
33 14 0.47
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (31 bp):
CTGGAATCATCGAGGTAATTACTAATATCGG
Found at i:2170380 original size:30 final size:30
Alignment explanation
Indices: 2170323--2170380 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
2170313 AAGAACATAC
* * *
2170323 AGAAAACAGTTTAAAACTTTCCCAATTTAA
1 AGAAAACAGTTAAAAACTTTACAAATTTAA
2170353 AGAAAA-AGTTAAAAACTTTAACAAATTT
1 AGAAAACAGTTAAAAACTTT-ACAAATTT
2170381 CAGCATCAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (30 bp):
AGAAAACAGTTAAAAACTTTACAAATTTAA
Found at i:2175012 original size:15 final size:16
Alignment explanation
Indices: 2174992--2175030 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2174982 AATTTTCTAA
*
2174992 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAC
*
2175007 AAATTATTAAAATAAC
1 AAATTATAAAAATAAC
2175023 AAATTATA
1 AAATTATA
2175031 TTTTTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATTATAAAAATAAC
Found at i:2175060 original size:24 final size:24
Alignment explanation
Indices: 2174999--2175060 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 24
2174989 TAAAAATTAT
2174999 AAAAATATA-AA-TTATTAAAATA
1 AAAAATATATAATTTATTAAAATA
* * **
2175021 ACAAAT-TATATTTTTATTATCATA
1 AAAAATATATA-ATTTATTAAAATA
2175045 AAAAATATATAATTTA
1 AAAAATATATAATTTA
2175061 ATTTCTACTG
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
21 2 0.07
22 6 0.20
24 18 0.60
25 4 0.13
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAAATATATAATTTATTAAAATA
Found at i:2176230 original size:20 final size:20
Alignment explanation
Indices: 2176201--2176245 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
2176191 GTTCAATTTA
*
2176201 AAATTTAAGATTC-AGAGTTT
1 AAATTCAAGATTCAAG-GTTT
2176221 AAATTCAAGATTCAAGGTTT
1 AAATTCAAGATTCAAGGTTT
2176241 AAATT
1 AAATT
2176246 AAAAAACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (20 bp):
AAATTCAAGATTCAAGGTTT
Found at i:2185494 original size:22 final size:22
Alignment explanation
Indices: 2185412--2185496 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 22
2185402 TATAACTCTA
2185412 AAAATGAAAATATATTT--TAAT
1 AAAAT-AAAATATATTTAATAAT
* * *
2185433 AAAAACAAAATATTTTTTATAAT
1 -AAAATAAAATATATTTAATAAT
*
2185456 AAAATAAAATCTATTTAATAAT
1 AAAATAAAATATATTTAATAAT
*
2185478 AAAATAAAATCTATTTAAT
1 AAAATAAAATATATTTAAT
2185497 CTTTAGAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
21 10 0.18
22 41 0.75
23 4 0.07
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.38
Consensus pattern (22 bp):
AAAATAAAATATATTTAATAAT
Found at i:2186016 original size:30 final size:30
Alignment explanation
Indices: 2185982--2186041 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2185972 CCACAACACA
*
2185982 GTCAACAAACAAATGAACCCAGGAGAACCT
1 GTCAACAAACAAATGAACCCAAGAGAACCT
2186012 GTCAACAAACAAATGAACCCAAGAGAACCT
1 GTCAACAAACAAATGAACCCAAGAGAACCT
2186042 TTCTGCTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.27, G:0.15, T:0.10
Consensus pattern (30 bp):
GTCAACAAACAAATGAACCCAAGAGAACCT
Found at i:2190656 original size:16 final size:16
Alignment explanation
Indices: 2190635--2190671 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2190625 TAACTATGAA
*
2190635 AATAAAAATATATTTT
1 AATAAAAATAAATTTT
2190651 AATAAAAATAAATTTT
1 AATAAAAATAAATTTT
*
2190667 TATAA
1 AATAA
2190672 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAAAAATAAATTTT
Found at i:2190691 original size:19 final size:18
Alignment explanation
Indices: 2190633--2190692 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 18
2190623 TATAACTATG
2190633 AAAATAAAAATATATTTTAAT
1 AAAAT-AAAAT-TA-TTTAAT
*
2190654 AAAA-ATAAATTTTTATAAT
1 AAAATA-AAATTATT-TAAT
2190673 AAAATAAAATCTATTTAAT
1 AAAATAAAAT-TATTTAAT
2190692 A
1 A
2190693 TTTAGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
18 2 0.06
19 19 0.58
20 8 0.24
21 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATAAAATTATTTAAT
Found at i:2199188 original size:21 final size:21
Alignment explanation
Indices: 2199136--2199190 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
2199126 TTCAAAACAA
2199136 AATTAACTTA-TT-AATTATT
1 AATTAACTTATTTAAATTATT
*
2199155 AATTAA-TAAATTTAAATTATT
1 AATTAACT-TATTTAAATTATT
2199176 AATTAACTTATTTAA
1 AATTAACTTATTTAA
2199191 GTATGAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 7 0.23
20 2 0.07
21 19 0.63
22 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTAACTTATTTAAATTATT
Found at i:2199260 original size:14 final size:14
Alignment explanation
Indices: 2199241--2199270 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2199231 TTGAACTCAA
2199241 AATTTAAATAATTT
1 AATTTAAATAATTT
*
2199255 AATTTAATTAATTT
1 AATTTAAATAATTT
2199269 AA
1 AA
2199271 AATTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTAAATAATTT
Found at i:2201366 original size:7 final size:7
Alignment explanation
Indices: 2201354--2201389 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
2201344 TTCTTCTGCT
2201354 TTTTAAA
1 TTTTAAA
2201361 TTTTAAA
1 TTTTAAA
2201368 TTTTAAA
1 TTTTAAA
*
2201375 GTTTAAA
1 TTTTAAA
2201382 TTTTAAA
1 TTTTAAA
2201389 T
1 T
2201390 ATAATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (7 bp):
TTTTAAA
Found at i:2209602 original size:40 final size:40
Alignment explanation
Indices: 2209558--2209809 Score: 346
Period size: 40 Copynumber: 6.3 Consensus size: 40
2209548 GACTTAAGGT
*
2209558 CCGCAGGCTTTGTGCTGGAATTGTATCTGGGCTTAAAGAC
1 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
* * *
2209598 CCGCAGGCTATATGCTGGAATTATATCCGGGCTTAAAGAC
1 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
* **
2209638 CCGCAGGCTTTGTGCTGGAATTGTATCCGGACTT-AAGGT
1 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
2209677 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
1 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
* * * *
2209717 CCACAGGCTTCGTGCTGGAATTGTATCTGAGCTTAAAGAC
1 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
* * * *
2209757 CCGCAGGCTTCGTGCTGGAATTGTATTCAGACTT-AAGAC
1 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
*
2209796 CCGTAGGCTTTGTG
1 CCGCAGGCTTTGTG
2209810 AATTCGGGGT
Statistics
Matches: 186, Mismatches: 25, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
39 53 0.28
40 133 0.72
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (40 bp):
CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
Found at i:2209693 original size:79 final size:79
Alignment explanation
Indices: 2209540--2209809 Score: 328
Period size: 79 Copynumber: 3.4 Consensus size: 79
2209530 ATATTTGATG
** * *
2209540 TATATCCGGACTTAAGGTCCGCAGGCTTTGTGCTGGAATTGTATCTGGGCTTAAAGACCCGCAGG
1 TATATCCGGACTTAAGACCCGCAGGCTTTGTGCTGGAATTGTATCCGGACTTAAAGACCCGCAGG
* *
2209605 CTATATGCTGGAAT
66 CTTTGTGCTGGAAT
* **
2209619 TATATCCGGGCTTAAAGACCCGCAGGCTTTGTGCTGGAATTGTATCCGGACTT-AAGGTCCGCAG
1 TATATCCGGACTT-AAGACCCGCAGGCTTTGTGCTGGAATTGTATCCGGACTTAAAGACCCGCAG
2209683 GCTTTGTGCTGGAAT
65 GCTTTGTGCTGGAAT
* * * * *
2209698 TGTATCCGGGCTTAAAGACCCACAGGCTTCGTGCTGGAATTGTAT-CTGAGCTTAAAGACCCGCA
1 TATATCCGGACTT-AAGACCCGCAGGCTTTGTGCTGGAATTGTATCCGGA-CTTAAAGACCCGCA
*
2209762 GGCTTCGTGCTGGAAT
64 GGCTTTGTGCTGGAAT
* * * *
2209778 TGTATTCAGACTTAAGACCCGTAGGCTTTGTG
1 TATATCCGGACTTAAGACCCGCAGGCTTTGTG
2209810 AATTCGGGGT
Statistics
Matches: 166, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
78 3 0.02
79 95 0.57
80 68 0.41
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (79 bp):
TATATCCGGACTTAAGACCCGCAGGCTTTGTGCTGGAATTGTATCCGGACTTAAAGACCCGCAGG
CTTTGTGCTGGAAT
Found at i:2209753 original size:119 final size:119
Alignment explanation
Indices: 2209542--2209809 Score: 412
Period size: 119 Copynumber: 2.3 Consensus size: 119
2209532 ATTTGATGTA
* *
2209542 TATCCGGACTTAAGGTCCGCAGGCTTTGTGCTGGAATTGTATCTGGGCTTAAAGACCCGCAGGCT
1 TATCCGGACTTAAGGTCCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGACCCACAGGCT
* *
2209607 ATATGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTTTGTGCTGGAATTG
66 ATATGCTGGAATTATATCCGAGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
2209661 TATCCGGACTTAAGGTCCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGACCCACAGGCT
1 TATCCGGACTTAAGGTCCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGACCCACAGGCT
* * *
2209726 -TCGTGCTGGAATTGTATCTGAGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
66 AT-ATGCTGGAATTATATCCGAGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
* * ** *
2209780 TATTCAGACTTAAGACCCGTAGGCTTTGTG
1 TATCCGGACTTAAGGTCCGCAGGCTTTGTG
2209810 AATTCGGGGT
Statistics
Matches: 136, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
118 1 0.01
119 135 0.99
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (119 bp):
TATCCGGACTTAAGGTCCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGACCCACAGGCT
ATATGCTGGAATTATATCCGAGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
Found at i:2211541 original size:53 final size:53
Alignment explanation
Indices: 2211408--2211564 Score: 190
Period size: 53 Copynumber: 2.9 Consensus size: 53
2211398 GTTACATTTC
* * * *
2211408 TAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACCA
1 TAAGGCAAGG-TACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTA-CA
* * * *
2211463 TAAGGTAAAGGTCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTT-CA
1 TAAGG-CAAGGTACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTACA
*
2211516 TAAGGCAAGGCTACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG
1 TAAGGCAAGG-TACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
2211565 CAAAAGGATA
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
52 4 0.05
53 41 0.47
55 38 0.44
56 4 0.05
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (53 bp):
TAAGGCAAGGTACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTACA
Found at i:2211600 original size:46 final size:46
Alignment explanation
Indices: 2211522--2211610 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
2211512 TTCATAAGGC
* * *
2211522 AAGGCTACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGCAA
1 AAGGATACCACGTAAGACCATGACAAGACATGGCAATGGTAAGCAA
*
2211568 AAGGATACCACGTAAGACCATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCACGTAAGACCATGACAAGACATGGCAATGGTAAG
2211611 GTACCCGTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (46 bp):
AAGGATACCACGTAAGACCATGACAAGACATGGCAATGGTAAGCAA
Found at i:2214817 original size:47 final size:48
Alignment explanation
Indices: 2214710--2214900 Score: 208
Period size: 47 Copynumber: 3.9 Consensus size: 48
2214700 AATGTGATTT
* * *
2214710 CCGTATAAGACCATAGCTGGGCTATGGCTTCGAAGAAATGTGATATGTGCTT
1 CCGTATAAGACCATAGCTGGGATATGGCATCG--G--ATGTGATATGTGCTA
*
2214762 CCGTATAAGACCATATCTGGGATATGGCATCGG-TGTGATATGTGCTA
1 CCGTATAAGACCATAGCTGGGATATGGCATCGGATGTGATATGTGCTA
* * * *
2214809 CTGTATAAGACCATATCTGGGATATGGCATCAG-TGTGATATGTGAT-
1 CCGTATAAGACCATAGCTGGGATATGGCATCGGATGTGATATGTGCTA
* * * *
2214855 CCGTGTAAGACCATGGCTGGGCTATGGCCTCGGTATGTGATATGTG
1 CCGTATAAGACCATAGCTGGGATATGGCATCGG-ATGTGATATGTG
2214901 ACTATGTGCA
Statistics
Matches: 123, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
46 26 0.21
47 56 0.46
48 11 0.09
50 1 0.01
52 29 0.24
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (48 bp):
CCGTATAAGACCATAGCTGGGATATGGCATCGGATGTGATATGTGCTA
Found at i:2214881 original size:93 final size:97
Alignment explanation
Indices: 2214712--2214919 Score: 237
Period size: 93 Copynumber: 2.1 Consensus size: 97
2214702 TGTGATTTCC
* * *
2214712 GTATAAGACCATAGCTGGGCTATGGCTTCGAAGAAATGTGATATGTGCTTCCGTATAAGACCATA
1 GTATAAGACCATAGCTGGGATATGGCATC-AAG--ATGTGATATGTGCATCCGTATAAGACCATA
*
2214777 TCTGGGATATGGCATCGG-TGTGATATGTG-CTACT
63 GCTGGGATATGGCATCGGATGTGATATGTGACTA-T
* * *
2214811 GTATAAGACCATATCTGGGATATGGCATC-AG-TGTGATATGTG-ATCCGTGTAAGACCATGGCT
1 GTATAAGACCATAGCTGGGATATGGCATCAAGATGTGATATGTGCATCCGTATAAGACCATAGCT
* *
2214873 GGGCTATGGCCTCGGTATGTGATATGTGACTAT
66 GGGATATGGCATCGG-ATGTGATATGTGACTAT
**
2214906 GTGCAAGACCATAG
1 GTATAAGACCATAG
2214920 TTTTACTATG
Statistics
Matches: 94, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
93 29 0.31
94 11 0.12
95 23 0.24
96 3 0.03
97 2 0.02
99 26 0.28
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (97 bp):
GTATAAGACCATAGCTGGGATATGGCATCAAGATGTGATATGTGCATCCGTATAAGACCATAGCT
GGGATATGGCATCGGATGTGATATGTGACTAT
Found at i:2226026 original size:50 final size:50
Alignment explanation
Indices: 2225911--2226057 Score: 204
Period size: 50 Copynumber: 2.9 Consensus size: 50
2225901 GATAATAACA
** * *
2225911 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * *
2225962 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
2226012 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
2226058 CATGGGACCT
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 51 0.61
51 33 0.39
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:2226063 original size:16 final size:16
Alignment explanation
Indices: 2226042--2226074 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2226032 CATGGTCTTA
2226042 CATGGGACCTCTCATC
1 CATGGGACCTCTCATC
*
2226058 CATGGGACCTCTTATC
1 CATGGGACCTCTCATC
2226074 C
1 C
2226075 CGGTGCCAAT
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:0.18, C:0.36, G:0.18, T:0.27
Consensus pattern (16 bp):
CATGGGACCTCTCATC
Found at i:2226082 original size:66 final size:66
Alignment explanation
Indices: 2225995--2226119 Score: 223
Period size: 66 Copynumber: 1.9 Consensus size: 66
2225985 GGTCTTATAG
*
2225995 GGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCCA
1 GGGACCTCTCATCCCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCCA
2226060 T
66 T
* *
2226061 GGGACCTCTTATCCCGGTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 GGGACCTCTCATCCCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
2226120 TTACCCAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.19, C:0.34, G:0.22, T:0.25
Consensus pattern (66 bp):
GGGACCTCTCATCCCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCCA
T
Found at i:2226235 original size:13 final size:13
Alignment explanation
Indices: 2226214--2226244 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2226204 GCTTAGATCA
*
2226214 TCATCAAATAAAT
1 TCATAAAATAAAT
2226227 TCATAAAATAAAT
1 TCATAAAATAAAT
2226240 TCATA
1 TCATA
2226245 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:2226492 original size:30 final size:30
Alignment explanation
Indices: 2226457--2226514 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2226447 CCTCGACTCT
*
2226457 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* * *
2226487 AACTTTTACATAATTACATTTTTTCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
2226515 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.02, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:2236976 original size:41 final size:41
Alignment explanation
Indices: 2236810--2236965 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
2236800 TTTATCGTTA
* * * *
2236810 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
2236851 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
2236892 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
2236933 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
2236966 AAGAGCCGGT
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 102 0.95
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:2237239 original size:33 final size:32
Alignment explanation
Indices: 2237179--2237241 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
2237169 GATAGATATG
2237179 TATATATATATGTTGCACTCGGCATAGGTGGA
1 TATATATATATGTTGCACTCGGCATAGGTGGA
* * *
2237211 TATATTTATGTGTATGCATTCGGCATAGGTG
1 TATATATATATGT-TGCACTCGGCATAGGTG
2237242 AAAATAAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.38
Consensus pattern (32 bp):
TATATATATATGTTGCACTCGGCATAGGTGGA
Found at i:2241292 original size:22 final size:22
Alignment explanation
Indices: 2241267--2241322 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
2241257 ACTGAACGCT
2241267 ATGTCGCAACATGGGGGATCCA
1 ATGTCGCAACATGGGGGATCCA
2241289 ATGTCGCAACATGGGGGATCCA
1 ATGTCGCAACATGGGGGATCCA
2241311 ATGTCGCAACAT
1 ATGTCGCAACAT
2241323 AGAAAGTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.20
Consensus pattern (22 bp):
ATGTCGCAACATGGGGGATCCA
Found at i:2249708 original size:6 final size:6
Alignment explanation
Indices: 2249697--2249759 Score: 112
Period size: 6 Copynumber: 10.8 Consensus size: 6
2249687 AATATAATAT
2249697 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATAT--
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
2249743 ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATA
2249760 TATGTTTACT
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.07
6 51 0.93
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAC
Found at i:2249760 original size:18 final size:18
Alignment explanation
Indices: 2249688--2249762 Score: 102
Period size: 18 Copynumber: 4.3 Consensus size: 18
2249678 CAACCACGTA
*
2249688 ATATA-ATATATATACAT
1 ATATATATACATATACAT
*
2249705 ATACATATACATATACAT
1 ATATATATACATATACAT
*
2249723 ATACATATACATATAC--
1 ATATATATACATATACAT
2249739 ATATATATACATATACAT
1 ATATATATACATATACAT
2249757 ATATAT
1 ATATAT
2249763 GTTTACTTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
16 15 0.29
17 4 0.08
18 33 0.63
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATATATACATATACAT
Found at i:2261601 original size:50 final size:50
Alignment explanation
Indices: 2261408--2261600 Score: 269
Period size: 50 Copynumber: 3.8 Consensus size: 50
2261398 AATAATAACA
* * ** * *
2261408 TGCCAAAGCCATGTCTCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * *
2261459 TGCCCATGCCATGTCCCAAACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
2261509 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
2261559 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
2261601 TTACCCAAAT
Statistics
Matches: 125, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 94 0.75
51 31 0.25
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:2261716 original size:13 final size:13
Alignment explanation
Indices: 2261695--2261725 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2261685 GCTTAGATCA
*
2261695 TCATCAAATAAAT
1 TCATAAAATAAAT
2261708 TCATAAAATAAAT
1 TCATAAAATAAAT
2261721 TCATA
1 TCATA
2261726 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:2261973 original size:30 final size:30
Alignment explanation
Indices: 2261938--2261995 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2261928 CCTCGACTCT
*
2261938 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
2261968 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
2261996 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:2268555 original size:30 final size:30
Alignment explanation
Indices: 2268521--2268580 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2268511 ATTTAATACG
*
2268521 AACTTTGGTAAAATTACAATTTTGCCCCTA
1 AACTTTGGCAAAATTACAATTTTGCCCCTA
* * *
2268551 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACAATTTTGCCCCTA
2268581 GACTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACAATTTTGCCCCTA
Found at i:2271309 original size:22 final size:22
Alignment explanation
Indices: 2271275--2271316 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2271265 ATAGCTAAAG
2271275 TTAAATTTAAAATATAAAAAAA
1 TTAAATTTAAAATATAAAAAAA
*
2271297 TTAAATATT-AAATATTAAAA
1 TTAAAT-TTAAAATATAAAAA
2271317 TTATGAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAAATTTAAAATATAAAAAAA
Found at i:2282800 original size:33 final size:34
Alignment explanation
Indices: 2282728--2282803 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 34
2282718 ATGTTTAAAT
* *
2282728 GTAAGACCATACCTGGGTTATGGCATTTCAGTGAA
1 GTAAGACCATAACTGAGTTATGGCATTT-AGTGAA
2282763 --AAGACCATAACTGAGTTATGGCA-TT-GTGAA
1 GTAAGACCATAACTGAGTTATGGCATTTAGTGAA
2282793 CGTAAGACCAT
1 -GTAAGACCAT
2282804 GGTTGGACCA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
30 5 0.14
32 2 0.06
33 29 0.81
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (34 bp):
GTAAGACCATAACTGAGTTATGGCATTTAGTGAA
Found at i:2282871 original size:103 final size:97
Alignment explanation
Indices: 2282708--2282957 Score: 248
Period size: 103 Copynumber: 2.5 Consensus size: 97
2282698 ACCATGTTTA
* * * *
2282708 GACCATGGCAATGTTTAAATGTAAGACCATACCTGGGTTATGGCATTTCAGTGAAAAGACCATAA
1 GACCATGGCAAT-ATT-CATGTAAGACCATAGCTGGGCTATGGCA--TCAGTGAAAAGACCATAA
* ** **
2282773 CTGAGTTATGGCATTGTGAACGTAAGACCATGGTTG
62 CTGAGTTATGGCACTACGAACGTAAGACCATGGCAG
*
2282809 GACCATGGCAATAAATATTCATGTAAGACCATAGCTGGGCTATGGCATCATGATGATAAGACCAT
1 GACCATGGC----AATATTCATGTAAGACCATAGCTGGGCTATGGCATCA-G-TGAAAAGACCAT
* **
2282874 AACTGGGTTATGGCACTACGAGTGTAAGACCATGGCAG
60 AACTGAGTTATGGCACTACGAACGTAAGACCATGGCAG
* * * * *
2282912 GGCCATGGCAATATTCGTGTAAGACTATAGTTGGACTATGGCATCA
1 GACCATGGCAATATTCATGTAAGACCATAGCTGGGCTATGGCATCA
2282958 AGTAAACGAT
Statistics
Matches: 125, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
99 33 0.26
101 12 0.10
102 1 0.01
103 74 0.59
104 2 0.02
105 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (97 bp):
GACCATGGCAATATTCATGTAAGACCATAGCTGGGCTATGGCATCAGTGAAAAGACCATAACTGA
GTTATGGCACTACGAACGTAAGACCATGGCAG
Found at i:2282902 original size:33 final size:32
Alignment explanation
Indices: 2282829--2282906 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
2282819 ATAAATATTC
* *
2282829 ATGTAAGACCATAGCTGGGCTATGGCATCATG
1 ATGTAAGACCATAACTGGGCTATGGCATCACG
*
2282861 ATGATAAGACCATAACTGGGTTATGGCA-CTACG
1 ATG-TAAGACCATAACTGGGCTATGGCATC-ACG
2282894 AGTGTAAGACCAT
1 A-TGTAAGACCAT
2282907 GGCAGGGCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
32 4 0.10
33 34 0.85
34 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (32 bp):
ATGTAAGACCATAACTGGGCTATGGCATCACG
Found at i:2285183 original size:61 final size:61
Alignment explanation
Indices: 2285100--2285215 Score: 196
Period size: 61 Copynumber: 1.9 Consensus size: 61
2285090 TCAAAATCAG
* *
2285100 TGTGTAATTATTTGTCAGGTATCAGTCACTCTTTGTATATGTATTGATGCTTCTTATACCA
1 TGTGTAATTATTTGTCAAGTATCAGTCACTCTTTGTATATCTATTGATGCTTCTTATACCA
* *
2285161 TGTGTAGTTATTTTTCAAGTATCAGTCACTCTTTGTATATCTATTGATGCTTCTT
1 TGTGTAATTATTTGTCAAGTATCAGTCACTCTTTGTATATCTATTGATGCTTCTT
2285216 GTCATTTGGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.48
Consensus pattern (61 bp):
TGTGTAATTATTTGTCAAGTATCAGTCACTCTTTGTATATCTATTGATGCTTCTTATACCA
Found at i:2286307 original size:23 final size:23
Alignment explanation
Indices: 2286281--2286353 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 23
2286271 TGCTGTTATG
*
2286281 GGTGTTGTTTTGGTGTTGTAATA
1 GGTGCTGTTTTGGTGTTGTAATA
**
2286304 GGTGCTGTCATGGTGTTGTAATA
1 GGTGCTGTTTTGGTGTTGTAATA
* * * * *
2286327 GCTACTGGTTTGGTGGTGTTATA
1 GGTGCTGTTTTGGTGTTGTAATA
2286350 GGTG
1 GGTG
2286354 TCATTTTGTT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.14, C:0.05, G:0.37, T:0.44
Consensus pattern (23 bp):
GGTGCTGTTTTGGTGTTGTAATA
Found at i:2307681 original size:24 final size:24
Alignment explanation
Indices: 2307654--2307712 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
2307644 CCCATCAGCT
*
2307654 CCTCCTCCTTCTACCA-CTCCATCC
1 CCTCCTCCTTCTACCACCT-CATCA
* *
2307678 CCTCCTCCTCCTTCCACCTCATCA
1 CCTCCTCCTTCTACCACCTCATCA
*
2307702 CCTCCGCCTTC
1 CCTCCTCCTTC
2307713 ATCCTCTGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.10, C:0.59, G:0.02, T:0.29
Consensus pattern (24 bp):
CCTCCTCCTTCTACCACCTCATCA
Found at i:2307890 original size:36 final size:36
Alignment explanation
Indices: 2307801--2307892 Score: 103
Period size: 36 Copynumber: 2.6 Consensus size: 36
2307791 CTCATCAACA
* * * * *
2307801 CCATCTCCGCCGCCGCCACCGAGGAGTCCCGGTACT
1 CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT
* *
2307837 GCATCTCCACCACCGCCTCCGAGGAATTCCGGGACT
1 CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT
* *
2307873 CCATCTCCTCCTCCGCCTCC
1 CCATCTCCACCACCGCCTCC
2307893 TTCTGATTCC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.14, C:0.49, G:0.20, T:0.17
Consensus pattern (36 bp):
CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT
Done.