Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 4 of 31
Found at i:1713700 original size:84 final size:87
Alignment explanation
Indices: 1713551--1713724 Score: 230
Period size: 84 Copynumber: 2.0 Consensus size: 87
1713541 CTATGGGAAA
* * *
1713551 CTATCAAATGTAACTAACCATACTGGTTAGAAGAATTGTTAGAGATCAACAAAATGAAGGAAATC
1 CTATCAAATATAACTAACCATACTAGTTAGAAGAATTATTAGAGA-CAACAAAATGAAGGAAATC
*
1713616 AAAACAAGACTAACAAGTGAACT
65 AAAACAAGACCAACAAGTGAACT
*
1713639 CTATC-AATATAAC-AACCCATACTAGTTAGAAGAATTATTAG-G-GAACAAAATGAAGGAAATC
1 CTATCAAATATAACTAA-CCATACTAGTTAGAAGAATTATTAGAGACAACAAAATGAAGGAAATC
* * *
1713700 AAAGCAAGACCAATAAGTGAGCT
65 AAAACAAGACCAACAAGTGAACT
1713723 CT
1 CT
1713725 CATAGACTAG
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
84 39 0.51
86 3 0.04
87 30 0.39
88 5 0.06
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (87 bp):
CTATCAAATATAACTAACCATACTAGTTAGAAGAATTATTAGAGACAACAAAATGAAGGAAATCA
AAACAAGACCAACAAGTGAACT
Found at i:1715214 original size:30 final size:30
Alignment explanation
Indices: 1715178--1715234 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1715168 GTTAATTATA
* * * *
1715178 TTATTTTGAGTCAATTAAGTTTTTATATTT
1 TTATTTTGAATAAAATAAATTTTTATATTT
1715208 TTATTTTGAATAAAATAAATTTTTATA
1 TTATTTTGAATAAAATAAATTTTTATA
1715235 ATTAATTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (30 bp):
TTATTTTGAATAAAATAAATTTTTATATTT
Found at i:1715501 original size:28 final size:26
Alignment explanation
Indices: 1715468--1715546 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 26
1715458 ATAATTAATT
1715468 ATAAAAATTTATTTAATTTAAAAAAA
1 ATAAAAATTTATTTAATTTAAAAAAA
* * * *
1715494 TATAAAAATATGATTAAATATGATAAAAA
1 -ATAAAAAT-TTATTTAAT-TTAAAAAAA
1715523 ATAAAAAATTTATTT--TTTAAAAAA
1 AT-AAAAATTTATTTAATTTAAAAAA
1715547 TAATTTATGA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
25 6 0.15
26 1 0.02
27 8 0.20
28 13 0.32
29 13 0.32
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (26 bp):
ATAAAAATTTATTTAATTTAAAAAAA
Found at i:1715772 original size:2 final size:2
Alignment explanation
Indices: 1715765--1715806 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1715755 AAGTTGTATG
1715765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1715807 CATTCTGAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1734105 original size:6 final size:6
Alignment explanation
Indices: 1734094--1734120 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1734084 ACTTGAGCAT
1734094 TTGAAC TTGAAC TTGAAC TTGAAC TTG
1 TTGAAC TTGAAC TTGAAC TTGAAC TTG
1734121 GTTGAGTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (6 bp):
TTGAAC
Found at i:1743821 original size:60 final size:60
Alignment explanation
Indices: 1743721--1743844 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 60
1743711 AACTTTTAAA
* * * * *
1743721 CATTTTGAGTAGTTTGAAGTGGTTTTTGATACACTAAAAAAAACTTTTGAGTATGTTGAG
1 CATTTTAAGTAGTTTGAAGTAGTTTTTAATACACTAAAAAAAACTTTTAAGCATGTTGAG
* * * *
1743781 CATTTTAAGTATTTTGAAGTAGTTTTTAATAC-TTGGAAAAAAACTTTTAAGCATTTTGAG
1 CATTTTAAGTAGTTTGAAGTAGTTTTTAATACACT-AAAAAAAACTTTTAAGCATGTTGAG
1743841 CATT
1 CATT
1743845 CTTTCCTAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 53 0.98
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (60 bp):
CATTTTAAGTAGTTTGAAGTAGTTTTTAATACACTAAAAAAAACTTTTAAGCATGTTGAG
Found at i:1744023 original size:22 final size:22
Alignment explanation
Indices: 1743982--1744029 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1743972 AGATATTATA
*
1743982 TGACTAATTTTTAGGCATTGCG
1 TGACTAATTTTTAAGCATTGCG
* * *
1744004 TGACTGATTTTTAAGTATTGTG
1 TGACTAATTTTTAAGCATTGCG
1744026 TGAC
1 TGAC
1744030 CGGTTGATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (22 bp):
TGACTAATTTTTAAGCATTGCG
Found at i:1744068 original size:22 final size:23
Alignment explanation
Indices: 1744018--1744079 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
1744008 TGATTTTTAA
* **
1744018 GTATTGTGTGACCGGTTGATATG
1 GTATTGTATGACTAGTTGATATG
1744041 GTATTGCT-TGACTAGTTGATA-G
1 GTATTG-TATGACTAGTTGATATG
1744063 GTATTGTATGACTAGTT
1 GTATTGTATGACTAGTT
1744080 AATAAGATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 1 0.03
22 16 0.46
23 17 0.49
24 1 0.03
ACGTcount: A:0.21, C:0.08, G:0.29, T:0.42
Consensus pattern (23 bp):
GTATTGTATGACTAGTTGATATG
Found at i:1773321 original size:14 final size:14
Alignment explanation
Indices: 1773302--1773328 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1773292 CTAAAATTAT
1773302 AACTTATAAAAAAG
1 AACTTATAAAAAAG
1773316 AACTTATAAAAAA
1 AACTTATAAAAAA
1773329 AAATTTACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (14 bp):
AACTTATAAAAAAG
Found at i:1774265 original size:65 final size:65
Alignment explanation
Indices: 1774196--1774334 Score: 174
Period size: 65 Copynumber: 2.1 Consensus size: 65
1774186 CTTTAGCATA
* * * *
1774196 TGACATTTGATATCTA-ACCAGACAAAGTTTAAGGTTGC-ACAAGTTTGAGTTTAAATTTCAACA
1 TGACATTTGATATC-AGACCAGACAAAGTTTAAGATTACAACAAGTTGGA-CTTAAATTTCAACA
1774259 TG
64 TG
* * * *
1774261 TGACATTTGATATCAGAGCAGACAAAGTTTAAGATTACAAGAAGTTGGACTTAAGTTTCAATATG
1 TGACATTTGATATCAGACCAGACAAAGTTTAAGATTACAACAAGTTGGACTTAAATTTCAACATG
1774326 TGACATTTG
1 TGACATTTG
1774335 GTATTAAAGC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 1 0.02
65 55 0.86
66 8 0.12
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (65 bp):
TGACATTTGATATCAGACCAGACAAAGTTTAAGATTACAACAAGTTGGACTTAAATTTCAACATG
Found at i:1774649 original size:29 final size:29
Alignment explanation
Indices: 1774617--1774674 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1774607 TTTTAGAGTT
1774617 TGGTTAGGTTTAATTATTGACCTATAACA
1 TGGTTAGGTTTAATTATTGACCTATAACA
1774646 TGGTTAGGTTTAATTATTGACCTATAACA
1 TGGTTAGGTTTAATTATTGACCTATAACA
1774675 AATGTTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (29 bp):
TGGTTAGGTTTAATTATTGACCTATAACA
Found at i:1781773 original size:29 final size:29
Alignment explanation
Indices: 1781732--1781787 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
1781722 TTTAACTAAA
*
1781732 AATAAAAATATAAA-AGCTTGATTGAATGT
1 AATAAAAATATAAAGA-CTTAATTGAATGT
1781761 AATAAAAGA-ATAAAGACTTAATTGAAT
1 AATAAAA-ATATAAAGACTTAATTGAAT
1781788 TTTCTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (29 bp):
AATAAAAATATAAAGACTTAATTGAATGT
Found at i:1793587 original size:2 final size:2
Alignment explanation
Indices: 1793574--1793620 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
1793564 ATGGACAAAA
* * *
1793574 CT CT CT CC CT CT CT CT CT CT CT CT CT CT CC CT CT CC CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1793616 CT CT C
1 CT CT C
1793621 ATATGTAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (2 bp):
CT
Found at i:1862645 original size:34 final size:34
Alignment explanation
Indices: 1862607--1862696 Score: 135
Period size: 34 Copynumber: 2.6 Consensus size: 34
1862597 GGCTGCCATC
** * *
1862607 ATTTCAGTTTTCTATAGCATTTGAGGTTGTTTTT
1 ATTTCAGTTTTCTATAGCATTACAGGCTGTCTTT
*
1862641 ATTTCAGTTTTCTATAGCATTACTGGCTGTCTTT
1 ATTTCAGTTTTCTATAGCATTACAGGCTGTCTTT
1862675 ATTTCAGTTTTCTATAGCATTA
1 ATTTCAGTTTTCTATAGCATTA
1862697 TTTGGTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.20, C:0.13, G:0.14, T:0.52
Consensus pattern (34 bp):
ATTTCAGTTTTCTATAGCATTACAGGCTGTCTTT
Found at i:1872097 original size:37 final size:37
Alignment explanation
Indices: 1872055--1872130 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
1872045 CATTAGTCAA
1872055 ACTGGCTAGAATACTTGGATAGTCTCAATCATTGCAG
1 ACTGGCTAGAATACTTGGATAGTCTCAATCATTGCAG
* *
1872092 ACTGGCTAGAATACTTGGATGGTCTCAATCATTTCAG
1 ACTGGCTAGAATACTTGGATAGTCTCAATCATTGCAG
1872129 AC
1 AC
1872131 ATCTGCACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (37 bp):
ACTGGCTAGAATACTTGGATAGTCTCAATCATTGCAG
Found at i:1876909 original size:2 final size:2
Alignment explanation
Indices: 1876866--1876895 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1876856 TAGTCTTTCA
1876866 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1876896 GTCTTTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1894830 original size:7 final size:7
Alignment explanation
Indices: 1894814--1894846 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
1894804 CCTTGGATGG
*
1894814 TGCTGCC
1 TGCTGAC
1894821 TGCTGAC
1 TGCTGAC
1894828 TGCTGAC
1 TGCTGAC
1894835 TGCTGAC
1 TGCTGAC
1894842 TGCTG
1 TGCTG
1894847 GAGCTAATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.09, C:0.30, G:0.30, T:0.30
Consensus pattern (7 bp):
TGCTGAC
Found at i:1905624 original size:2 final size:2
Alignment explanation
Indices: 1905617--1905650 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1905607 TTCAGTCAAC
* *
1905617 AT AT AT AT AC AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1905651 TTATGTGTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1910871 original size:28 final size:28
Alignment explanation
Indices: 1910831--1910888 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
1910821 TCCTAATAGA
1910831 TGAGGATTGTTTTGACCCAATATGACTT
1 TGAGGATTGTTTTGACCCAATATGACTT
*
1910859 TGAGGATTGTTTTGACCCAATATTACTT
1 TGAGGATTGTTTTGACCCAATATGACTT
1910887 TG
1 TG
1910889 TGTGTGATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (28 bp):
TGAGGATTGTTTTGACCCAATATGACTT
Found at i:1918434 original size:31 final size:30
Alignment explanation
Indices: 1918354--1918436 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 30
1918344 CGCCCTAAAA
* * *
1918354 TTTTAAAAATTTATA-AATTTTTTCTTATT
1 TTTTTAAAATTTTTATAATTTTTTCTTAAT
* * * *
1918383 TTGTTTTAAATATTTGTAATTTTTCTTTTAAT
1 TT-TTTAAAATTTTTATAATTTTT-TCTTAAT
1918415 TTTTTAAAATTTTTATAATTTT
1 TTTTTAAAATTTTTATAATTTT
1918437 ATTATCTCAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
29 2 0.05
30 8 0.20
31 24 0.59
32 7 0.17
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (30 bp):
TTTTTAAAATTTTTATAATTTTTTCTTAAT
Found at i:1918475 original size:30 final size:31
Alignment explanation
Indices: 1918421--1918478 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1918411 TAATTTTTTA
1918421 AAATTTTTATAATTTTATTATCTCAAATATT
1 AAATTTTTATAATTTTATTATCTCAAATATT
*
1918452 AAATTTTT-TATTTTTATCT-TCTCAAAT
1 AAATTTTTATAATTTTAT-TATCTCAAAT
1918479 TTGAAACCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (31 bp):
AAATTTTTATAATTTTATTATCTCAAATATT
Found at i:1921510 original size:17 final size:15
Alignment explanation
Indices: 1921484--1921533 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
1921474 AATTCATTAA
1921484 TTTTATTTTTATATTT
1 TTTTATTTTTAT-TTT
1921500 TTTTAATTTTTA-TTT
1 TTTT-ATTTTTATTTT
1921515 TTTTA-TTTTATTTT
1 TTTTATTTTTATTTT
1921529 ATTTT
1 -TTTT
1921534 TTATTCTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.16
14 4 0.13
15 11 0.35
16 4 0.13
17 7 0.23
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTATTTTTATTTT
Found at i:1921514 original size:23 final size:24
Alignment explanation
Indices: 1921480--1921534 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
1921470 TCCTAATTCA
1921480 TTAA-TTTTATTTTTATATTTT-T
1 TTAATTTTTATTTTTATATTTTAT
*
1921502 TTAATTTTTATTTTTTTATTTTAT
1 TTAATTTTTATTTTTATATTTTAT
*
1921526 TTTATTTTT
1 TTAATTTTT
1921535 TATTCTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 4 0.14
23 16 0.55
24 9 0.31
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (24 bp):
TTAATTTTTATTTTTATATTTTAT
Found at i:1921517 original size:25 final size:25
Alignment explanation
Indices: 1921480--1921538 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
1921470 TCCTAATTCA
*
1921480 TTAA-TTTTATTTTTATA-TTT-TT
1 TTAATTTTTATTTTTTTATTTTATT
1921502 TTAATTTTTATTTTTTTATTTTATT
1 TTAATTTTTATTTTTTTATTTTATT
*
1921527 TTATTTTTTATT
1 TTAATTTTTATT
1921539 CTATTAACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 4 0.12
23 12 0.38
24 3 0.09
25 13 0.41
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (25 bp):
TTAATTTTTATTTTTTTATTTTATT
Found at i:1921528 original size:12 final size:12
Alignment explanation
Indices: 1921500--1921543 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1921490 TTTTATATTT
*
1921500 TTTTAATTTTTA
1 TTTTATTTTTTA
*
1921512 TTTTTTTATTTTA
1 TTTTATT-TTTTA
1921525 TTTTATTTTTTA
1 TTTTATTTTTTA
*
1921537 TTCTATT
1 TTTTATT
1921544 AACAAATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:1921534 original size:17 final size:18
Alignment explanation
Indices: 1921483--1921543 Score: 72
Period size: 17 Copynumber: 3.4 Consensus size: 18
1921473 TAATTCATTA
*
1921483 ATTTTATTTTTATATTTT
1 ATTTTATTTTTATTTTTT
*
1921501 -TTTAATTTTTATTTTTTT
1 ATTTTATTTTTA-TTTTTT
1921519 ATTTTA-TTTTATTTTTT
1 ATTTTATTTTTATTTTTT
*
1921536 ATTCTATT
1 ATTTTATT
1921544 AACAAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 21 0.58
18 11 0.31
19 4 0.11
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.79
Consensus pattern (18 bp):
ATTTTATTTTTATTTTTT
Found at i:1924784 original size:16 final size:16
Alignment explanation
Indices: 1924763--1924841 Score: 63
Period size: 16 Copynumber: 4.9 Consensus size: 16
1924753 TATTATTATA
1924763 ATATTTTATATTTAAT
1 ATATTTTATATTTAAT
* *
1924779 ATATTTT-TAATGATAT
1 ATATTTTATATTTA-AT
*
1924795 ATATTTTAT-TTTTAT
1 ATATTTTATATTTAAT
* *
1924810 TTATTATTATAATTTTAT
1 ATATT-TTAT-ATTTAAT
*
1924828 ATATTTTATTTTTA
1 ATATTTTATATTTA
1924842 TTTCTTTAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
15 10 0.20
16 24 0.49
17 5 0.10
18 10 0.20
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (16 bp):
ATATTTTATATTTAAT
Found at i:1924795 original size:91 final size:87
Alignment explanation
Indices: 1924699--1924873 Score: 194
Period size: 91 Copynumber: 1.9 Consensus size: 87
1924689 TATGAATTTT
*
1924699 TATATAATATTATTTCTTAAATATATT-TT-TAATATCATATATTTTATTTTTA-TCTATTATTA
1 TATAT-ATATTATTT-TT--ATATATTATTATAATATCATATATTTTATTTTTATTCT-TTAATA
1924761 TAATATTTTATATTTAATATATTTTTAATGA
61 T-AT-TTTTATA-TT-ATATATTTTTAATGA
* * * *
1924792 TATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTTTATTTCTTTAATATATT
1 TATATATATTATTTTTATATATTATTATAATATCATATATTTTATTTTTA-TTCTTTAATATATT
1924857 TTTATATTATATATTTT
65 TTTATATTATATATTTT
1924874 ATTTTAATTT
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
88 9 0.12
89 8 0.11
90 9 0.12
91 25 0.34
92 14 0.19
93 8 0.11
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (87 bp):
TATATATATTATTTTTATATATTATTATAATATCATATATTTTATTTTTATTCTTTAATATATTT
TTATATTATATATTTTTAATGA
Found at i:1924833 original size:58 final size:58
Alignment explanation
Indices: 1924701--1924833 Score: 191
Period size: 58 Copynumber: 2.3 Consensus size: 58
1924691 TGAATTTTTA
* *
1924701 TATAATATTATT-TCTTAAATATATTTTTAATATCATATATTTTATTTTTATCTATTAT
1 TATAATATT-TTATATTTAATATATTTTTAATATCATATATTTTATTTTTATCTATTAT
*
1924759 TATAATATTTTATATTTAATATATTTTTAATGAT-ATATATTTTATTTTTATTTATTAT
1 TATAATATTTTATATTTAATATATTTTTAAT-ATCATATATTTTATTTTTATCTATTAT
1924817 TATAAT-TTTATATATTT
1 TATAATATTT-TATATTT
1924834 TATTTTTATT
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
57 5 0.07
58 62 0.90
59 2 0.03
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (58 bp):
TATAATATTTTATATTTAATATATTTTTAATATCATATATTTTATTTTTATCTATTAT
Found at i:1924841 original size:39 final size:39
Alignment explanation
Indices: 1924773--1924964 Score: 114
Period size: 39 Copynumber: 4.8 Consensus size: 39
1924763 ATATTTTATA
*
1924773 TTTAATATATTTTTAATGA-TATATATTTTATTTTTA----
1 TTTAATATA-TTATAAT-ATTATATATTTTATTTTTATTTC
*
1924809 TTT-AT-TATTATAATTTTATATATTTTATTTTTATTTC
1 TTTAATATATTATAATATTATATATTTTATTTTTATTTC
* * * *
1924846 TTTAATATATTTTTATATTATATATTTTATTTTAATTTGT
1 TTTAATATATTATAATATTATATATTTTATTTTTATTT-C
* *
1924886 TTTACCTATATTATATAAATATTA-AT-TTTTATATTTTATTTTAT
1 TTTA-ATATA-T-TAT-AATATTATATATTTTAT-TTTTA-TTT-C
* * *
1924930 TTTAATTTTTATTCTTATATTATATATTTTATTTT
1 TTTAA--TATATTATAATATTATATATTTTATTTT
1924965 AATTATAATA
Statistics
Matches: 122, Mismatches: 16, Indels: 29
0.73 0.10 0.17
Matches are distributed among these distances:
33 23 0.19
34 2 0.02
35 2 0.02
36 3 0.02
37 3 0.02
38 2 0.02
39 27 0.22
40 4 0.03
41 4 0.03
42 13 0.11
43 15 0.12
44 21 0.17
45 3 0.02
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (39 bp):
TTTAATATATTATAATATTATATATTTTATTTTTATTTC
Found at i:1924843 original size:33 final size:33
Alignment explanation
Indices: 1924736--1924877 Score: 125
Period size: 33 Copynumber: 4.4 Consensus size: 33
1924726 TTTAATATCA
*
1924736 TATATTTTATTT-TTATCTATTATTATA-ATATTT
1 TATATTTTATTTATT-T-TATAATTATATATATTT
* * *
1924769 TATATTTAATATATTTT-TAATGATATATATTT
1 TATATTTTATTTATTTTATAATTATATATATTT
*
1924801 TAT-TTTTATTTATTATTATAATTTTATATATTT
1 TATATTTTATTTATT-TTATAATTATATATATTT
* * * *
1924834 TAT-TTTTATTTCTTTAATATATT-TTTATATTA
1 TATATTTTATTTATTTTATA-ATTATATATATTT
1924866 TATATTTTATTT
1 TATATTTTATTT
1924878 TAATTTGTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
31 15 0.16
32 26 0.29
33 48 0.53
34 2 0.02
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (33 bp):
TATATTTTATTTATTTTATAATTATATATATTT
Found at i:1924936 original size:24 final size:24
Alignment explanation
Indices: 1924796--1924941 Score: 75
Period size: 24 Copynumber: 5.6 Consensus size: 24
1924786 TAATGATATA
1924796 TATTTT-ATTTTTAT-TTATTATTAT
1 TATTTTAATTTTTATATT-TTATT-T
*
1924820 AATTTTATATATTTTAT-TTTTATTT
1 TATTTTA-AT-TTTTATATTTTATTT
*
1924845 CT-TTAATATATTTTTATATTATATATTT
1 -TATT-TTA-ATTTTTATATT-T-TATTT
* *
1924873 TATTTTAATTTGTTTTACCTATATTATATA
1 TATTTTAA--T-TTTTA--TATTTTAT-TT
* *
1924903 AATATTAATTTTTATATTTTATTT
1 TATTTTAATTTTTATATTTTATTT
1924927 TATTTTAATTTTTAT
1 TATTTTAATTTTTAT
1924942 TCTTATATTA
Statistics
Matches: 95, Mismatches: 12, Indels: 30
0.69 0.09 0.22
Matches are distributed among these distances:
24 19 0.20
25 16 0.17
26 15 0.16
27 17 0.18
28 9 0.09
29 8 0.08
30 8 0.08
31 3 0.03
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (24 bp):
TATTTTAATTTTTATATTTTATTT
Found at i:1924975 original size:26 final size:27
Alignment explanation
Indices: 1924927--1924979 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
1924917 TATTTTATTT
* * *
1924927 TATTTTAATTTTTATTCTTATATTATA
1 TATTTTAATTTTAATTATAATATTATA
1924954 TATTTT-ATTTTAATTATAATATTATA
1 TATTTTAATTTTAATTATAATATTATA
1924980 AAATATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (27 bp):
TATTTTAATTTTAATTATAATATTATA
Found at i:1930060 original size:17 final size:18
Alignment explanation
Indices: 1930040--1930076 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1930030 ATTTTAAAAG
1930040 TTTTTTAAA-TATAAATA
1 TTTTTTAAATTATAAATA
*
1930057 -TTTTTAAATTATGAATA
1 TTTTTTAAATTATAAATA
1930074 TTT
1 TTT
1930077 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 3
0.81 0.05 0.14
Matches are distributed among these distances:
16 8 0.47
17 7 0.41
18 2 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTTTAAATTATAAATA
Found at i:1930062 original size:16 final size:17
Alignment explanation
Indices: 1930041--1930076 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1930031 TTTTAAAAGT
1930041 TTTTTAAA-TATAAATA
1 TTTTTAAATTATAAATA
*
1930057 TTTTTAAATTATGAATA
1 TTTTTAAATTATAAATA
1930074 TTT
1 TTT
1930077 ATTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTTAAATTATAAATA
Found at i:1940867 original size:2 final size:2
Alignment explanation
Indices: 1940854--1940893 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
1940844 ATCTAATGCA
*
1940854 AG AG AG ATG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG A
1 AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1940894 ATTATTGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
AG
Found at i:1941089 original size:6 final size:6
Alignment explanation
Indices: 1941078--1941104 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1941068 CCTATAGAAT
1941078 GTGGGA GTGGGA GTGGGA GTGGGA GTG
1 GTGGGA GTGGGA GTGGGA GTGGGA GTG
1941105 CATCAGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.67, T:0.19
Consensus pattern (6 bp):
GTGGGA
Found at i:1941900 original size:1 final size:1
Alignment explanation
Indices: 1941894--1941928 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
1941884 GGGCAAGCCA
*
1941894 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1941929 TTTCTTGCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:1953042 original size:14 final size:14
Alignment explanation
Indices: 1953025--1953124 Score: 62
Period size: 14 Copynumber: 7.3 Consensus size: 14
1953015 CCCCACCCAC
1953025 TTTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
*** *
1953039 TTTTTAATTCAAA-
1 TTTTCCCTCCAAAG
*
1953052 ATTTCCC-CCAAAAG
1 TTTTCCCTCC-AAAG
*
1953066 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
** *
1953080 -TTTCAATTCAAAG
1 TTTTCCCTCCAAAG
* *
1953093 TATTCCCCCCAAAG
1 TTTTCCCTCCAAAG
*
1953107 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
1953121 TTTT
1 TTTT
1953125 GGAAGGTTCT
Statistics
Matches: 61, Mismatches: 21, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
12 1 0.02
13 16 0.26
14 42 0.69
15 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.35
Consensus pattern (14 bp):
TTTTCCCTCCAAAG
Found at i:1953071 original size:41 final size:42
Alignment explanation
Indices: 1953026--1953124 Score: 157
Period size: 41 Copynumber: 2.4 Consensus size: 42
1953016 CCCACCCACT
*
1953026 TTTCCCTCCAAAGTTTTTAATTCAAAAT-TTCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTCAATTCAAAATATTCCCCCAAAAGA
* *
1953067 TTTCCCTCCAAAG-TTTCAATTCAAAGTATTCCCCCCAAAGA
1 TTTCCCTCCAAAGTTTTCAATTCAAAATATTCCCCCAAAAGA
1953108 TTTCCCTCCAAAGTTTT
1 TTTCCCTCCAAAGTTTT
1953125 GGAAGGTTCT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 12 0.23
41 38 0.72
42 3 0.06
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.34
Consensus pattern (42 bp):
TTTCCCTCCAAAGTTTTCAATTCAAAATATTCCCCCAAAAGA
Found at i:1958336 original size:42 final size:43
Alignment explanation
Indices: 1958288--1958389 Score: 170
Period size: 42 Copynumber: 2.4 Consensus size: 43
1958278 CCCACCCACT
* *
1958288 TTTCCTCCAAAGTTTTTAATTCAAAGTATT-CTCCCCAAAAGA
1 TTTCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCCAAAAGA
1958330 TTTCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCCAAAAGA
1 TTTCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCCAAAAGA
1958373 TTTCCCTCCAAAGTTTT
1 TTT-CCTCCAAAGTTTT
1958390 GGAAGGTTCT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
42 29 0.52
43 14 0.25
44 13 0.23
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.35
Consensus pattern (43 bp):
TTTCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCCAAAAGA
Found at i:1958828 original size:12 final size:13
Alignment explanation
Indices: 1958811--1958861 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 13
1958801 ATAGATAAAA
1958811 TTTTTATTTA-AT
1 TTTTTATTTACAT
1958823 TTTTTATTTACAT
1 TTTTTATTTACAT
*
1958836 TATTATTATTTATAT
1 T-TT-TTATTTACAT
1958851 TTATTTATTTA
1 TT-TTTATTTA
1958862 TTTTAATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
12 10 0.29
13 3 0.09
14 10 0.29
15 11 0.32
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTATTTACAT
Found at i:1960145 original size:15 final size:15
Alignment explanation
Indices: 1960125--1960158 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1960115 CTTCAACTCA
1960125 ATAAACCTTTTTATT
1 ATAAACCTTTTTATT
1960140 ATAAACCTTTTTATT
1 ATAAACCTTTTTATT
1960155 ATAA
1 ATAA
1960159 TTTGATGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAAACCTTTTTATT
Found at i:1966629 original size:21 final size:21
Alignment explanation
Indices: 1966590--1966631 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1966580 TGAAATATAT
1966590 AACATATGCATTATATTTATTC
1 AACATAT-CATTATATTTATTC
1966612 AACATAT-ATTATTATTTATT
1 AACATATCATTA-TATTTATT
1966632 AAGTGAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (21 bp):
AACATATCATTATATTTATTC
Found at i:1974078 original size:20 final size:20
Alignment explanation
Indices: 1974053--1974096 Score: 74
Period size: 18 Copynumber: 2.3 Consensus size: 20
1974043 TAAATTTTTT
1974053 TTATAAAATTTTTTAATAAA
1 TTATAAAATTTTTTAATAAA
1974073 TTAT--AATTTTTTAATAAA
1 TTATAAAATTTTTTAATAAA
1974091 TTATAA
1 TTATAA
1974097 TTTTTGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 18 0.82
20 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATAAAATTTTTTAATAAA
Found at i:1974112 original size:18 final size:18
Alignment explanation
Indices: 1974059--1974101 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1974049 TTTTTTATAA
1974059 AATTTTTTAATAAATTAT
1 AATTTTTTAATAAATTAT
1974077 AATTTTTTAATAAATTAT
1 AATTTTTTAATAAATTAT
1974095 AATTTTT
1 AATTTTT
1974102 GTTAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AATTTTTTAATAAATTAT
Found at i:1974261 original size:16 final size:16
Alignment explanation
Indices: 1974242--1974292 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
1974232 GAGCTTTTCC
1974242 TAAAATCTTT-TTTTTT
1 TAAAAT-TTTATTTTTT
1974258 T-AAATTTTATTTTTT
1 TAAAATTTTATTTTTT
* *
1974273 TAAAAAATTTAATTTTT
1 T-AAAATTTTATTTTTT
1974290 TAA
1 TAA
1974293 GAACTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 3 0.10
15 11 0.37
16 3 0.10
17 13 0.43
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TAAAATTTTATTTTTT
Found at i:2007063 original size:17 final size:19
Alignment explanation
Indices: 2007027--2007067 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
2007017 TTAATAATTT
2007027 TAAATAAAATTAAAATAAA
1 TAAATAAAATTAAAATAAA
*
2007046 TAAAT-AAA-TAATATAAA
1 TAAATAAAATTAAAATAAA
2007063 TAAAT
1 TAAAT
2007068 TTTTAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.62
18 3 0.14
19 5 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAATAAAATTAAAATAAA
Found at i:2013697 original size:4 final size:4
Alignment explanation
Indices: 2013683--2013717 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2013673 TATTTTTAAT
*
2013683 TATC CATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TAT
2013718 ACATACATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (4 bp):
TATC
Found at i:2019854 original size:25 final size:25
Alignment explanation
Indices: 2019806--2019854 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2019796 CAAATTAGGT
* * **
2019806 AATAAAAAATTATTTTTTTTAAAAA
1 AATAAAAAACTATTTATTACAAAAA
2019831 AATAAAAAACTATTTATTACAAAA
1 AATAAAAAACTATTTATTACAAAA
2019855 TTTAATGTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
AATAAAAAACTATTTATTACAAAAA
Found at i:2021278 original size:3 final size:3
Alignment explanation
Indices: 2021270--2021295 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2021260 TTATGTTTTA
2021270 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
2021296 AAGGGAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2023849 original size:12 final size:11
Alignment explanation
Indices: 2023834--2023876 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
2023824 TTGCTGTTGC
2023834 TGCTGCTGATTT
1 TGCTG-TGATTT
*
2023846 TGCTGTGCTTGT
1 TGCTGTGATT-T
2023858 TGCTGTTGATTT
1 TGCTG-TGATTT
2023870 TGCTGTG
1 TGCTGTG
2023877 CCGGTTGCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 6 0.22
12 17 0.63
13 4 0.15
ACGTcount: A:0.05, C:0.14, G:0.30, T:0.51
Consensus pattern (11 bp):
TGCTGTGATTT
Found at i:2023867 original size:24 final size:24
Alignment explanation
Indices: 2023834--2023887 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2023824 TTGCTGTTGC
* **
2023834 TGCTGCTGATTTTGCTGTGCTTGT
1 TGCTGTTGATTTTGCTGTGCCGGT
2023858 TGCTGTTGATTTTGCTGTGCCGGT
1 TGCTGTTGATTTTGCTGTGCCGGT
2023882 TGCTGT
1 TGCTGT
2023888 GGTTGCACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.04, C:0.17, G:0.31, T:0.48
Consensus pattern (24 bp):
TGCTGTTGATTTTGCTGTGCCGGT
Found at i:2044665 original size:15 final size:15
Alignment explanation
Indices: 2044645--2044674 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2044635 GCCCTTGGTT
2044645 CAAATTTAAAAGGTA
1 CAAATTTAAAAGGTA
2044660 CAAATTTAAAAGGTA
1 CAAATTTAAAAGGTA
2044675 TCTTATAGCA
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:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (15 bp):
CAAATTTAAAAGGTA
Found at i:2052793 original size:7 final size:7
Alignment explanation
Indices: 2052778--2052807 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2052768 AGCTGCTAAA
*
2052778 CCCGTTC
1 CCCGCTC
2052785 CCCGCTC
1 CCCGCTC
2052792 CCCGCTC
1 CCCGCTC
2052799 CCCGCTC
1 CCCGCTC
2052806 CC
1 CC
2052808 TCCTCCCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.70, G:0.13, T:0.17
Consensus pattern (7 bp):
CCCGCTC
Found at i:2065589 original size:18 final size:18
Alignment explanation
Indices: 2065566--2065608 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2065556 TAAAAACTTA
*
2065566 TTTGATTTAAAAGAAACT
1 TTTGATTTAAAAGAAAAT
2065584 TTTGATTTAAAAGAAAAT
1 TTTGATTTAAAAGAAAAT
2065602 TTTGATT
1 TTTGATT
2065609 GAATGTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (18 bp):
TTTGATTTAAAAGAAAAT
Found at i:2081677 original size:24 final size:24
Alignment explanation
Indices: 2081650--2081698 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2081640 ATCGATCTCA
2081650 AACAAAATGTCAACACCGGAATGC
1 AACAAAATGTCAACACCGGAATGC
2081674 AACAAAATGTCAACACCGGAATGC
1 AACAAAATGTCAACACCGGAATGC
2081698 A
1 A
2081699 CCACTCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.12
Consensus pattern (24 bp):
AACAAAATGTCAACACCGGAATGC
Found at i:2098721 original size:20 final size:21
Alignment explanation
Indices: 2098686--2098730 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2098676 TAGCATCTTA
*
2098686 TTCTCTTTTTAGTTGTTTTGT
1 TTCTCTTTTTAGTTGTTTTGC
*
2098707 TTCTC-TTTTATTTGTTTTGC
1 TTCTCTTTTTAGTTGTTTTGC
2098727 TTCT
1 TTCT
2098731 TCCTACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.04, C:0.13, G:0.11, T:0.71
Consensus pattern (21 bp):
TTCTCTTTTTAGTTGTTTTGC
Found at i:2125827 original size:14 final size:14
Alignment explanation
Indices: 2125804--2125833 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2125794 ATGTTGAGTC
*
2125804 TTAAATATTAAAAT
1 TTAAAGATTAAAAT
2125818 TTAAAGATTAAAAT
1 TTAAAGATTAAAAT
2125832 TT
1 TT
2125834 TTAAATATTA
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:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
TTAAAGATTAAAAT
Found at i:2130544 original size:23 final size:23
Alignment explanation
Indices: 2130524--2130575 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2130514 AAATAATATT
* *
2130524 ATAATATTTAATATATAAATAAA
1 ATAATAATTAAAATATAAATAAA
2130547 ATAATAATTAAAATATAAA-AAA
1 ATAATAATTAAAATATAAATAAA
2130569 A-AATAAT
1 ATAATAAT
2130576 ATTACACTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 6 0.22
22 4 0.15
23 17 0.63
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAATAATTAAAATATAAATAAA
Found at i:2130579 original size:23 final size:24
Alignment explanation
Indices: 2130524--2130579 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
2130514 AAATAATATT
* *
2130524 ATAATATT-TAATATATAAATAAA
1 ATAATATTAAAATATATAAAAAAA
2130547 ATAATAATTAAAATATA-AAAAAAA
1 ATAAT-ATTAAAATATATAAAAAAA
2130571 ATAATATTA
1 ATAATATTA
2130580 CACTGTTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 9 0.31
24 14 0.48
25 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
ATAATATTAAAATATATAAAAAAA
Found at i:2130742 original size:6 final size:6
Alignment explanation
Indices: 2130731--2130780 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
2130721 ATATTATATA
* *
2130731 TTTTAT TTTTAT TTATTAT TATAAT TTTATAT ATTTTAT TTTTAT TTTTA
1 TTTTAT TTTTAT TT-TTAT TTTTAT TTT-TAT -TTTTAT TTTTAT TTTTA
2130781 ATATAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
6 24 0.65
7 10 0.27
8 3 0.08
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTAT
Found at i:2130742 original size:15 final size:15
Alignment explanation
Indices: 2130710--2130775 Score: 69
Period size: 15 Copynumber: 4.1 Consensus size: 15
2130700 CATCTCTTAA
* *
2130710 ATATATTTTTAATATT
1 ATATA-TTTTATTTTT
2130726 ATATATTTTATTTTT
1 ATATATTTTATTTTT
*
2130741 ATTTATTATTATAATTTT
1 ATATATT-TTAT--TTTT
2130759 ATATATTTTATTTTT
1 ATATATTTTATTTTT
2130774 AT
1 AT
2130776 TTTTAATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
15 20 0.47
16 9 0.21
17 4 0.09
18 10 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATATATTTTATTTTT
Found at i:2130743 original size:18 final size:18
Alignment explanation
Indices: 2130722--2130776 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 18
2130712 ATATTTTTAA
2130722 TATTATATATTTTATTTT
1 TATTATATATTTTATTTT
* **
2130740 TATT-TAT-TATTATAAT
1 TATTATATATTTTATTTT
2130756 T-TTATATATTTTATTTT
1 TATTATATATTTTATTTT
2130773 TATT
1 TATT
2130777 TTTAATATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
15 2 0.07
16 10 0.36
17 10 0.36
18 6 0.21
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTATATATTTTATTTT
Found at i:2130763 original size:33 final size:33
Alignment explanation
Indices: 2130632--2130796 Score: 128
Period size: 33 Copynumber: 5.0 Consensus size: 33
2130622 ATTTTAAAAA
* *
2130632 TTATTTTTATTTATTAAAATATAAATTTA-ATATAT
1 TTATTTTTATTTATT--ATTATAATTTTATATAT-T
* * *
2130667 TTATATTT-TTTATTATTA-ATTTTTATATAATA
1 TTATTTTTATTTATTATTATAATTTTATAT-ATT
* * * *
2130699 TCATCTCTTAAATATATT-TT-TAATATTATATATT
1 TTAT-T-TT-TATTTATTATTATAATTTTATATATT
2130733 TTATTTTTATTTATTATTATAATTTTATATATT
1 TTATTTTTATTTATTATTATAATTTTATATATT
*
2130766 TTATTTTTATTT-TTAATATAATTTT-TATATT
1 TTATTTTTATTTATTATTATAATTTTATATATT
2130797 ATATATTATA
Statistics
Matches: 104, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
31 17 0.16
32 24 0.23
33 28 0.27
34 13 0.12
35 17 0.16
36 5 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (33 bp):
TTATTTTTATTTATTATTATAATTTTATATATT
Found at i:2130791 original size:18 final size:19
Alignment explanation
Indices: 2130713--2130802 Score: 60
Period size: 20 Copynumber: 4.7 Consensus size: 19
2130703 CTCTTAAATA
2130713 TATTTTTA-ATATTATATATTT
1 TATTTTTATATA-TA-AT-TTT
* * *
2130734 TATTTTTATTTATTATTAT
1 TATTTTTATATATAATTTT
* * *
2130753 AATTTTATATATTTTATTTT
1 TATTTT-TATATATAATTTT
2130773 TATTTTTA-ATATAATTTT
1 TATTTTTATATATAATTTT
*
2130791 TA-TATTATATAT
1 TATTTTTATATAT
2130803 TATATTTTAA
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
17 4 0.07
18 14 0.25
19 9 0.16
20 17 0.31
21 9 0.16
22 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTTTATATATAATTTT
Found at i:2130799 original size:38 final size:39
Alignment explanation
Indices: 2130709--2130818 Score: 128
Period size: 33 Copynumber: 3.0 Consensus size: 39
2130699 TCATCTCTTA
2130709 AATAT-ATTTTTAATATTATATATTTTATTTTTATTTATT
1 AATATAATTTTT-ATATTATATATTTTATTTTTATTTATT
*
2130748 ATTATAA----T-T-TTATATATTTTATTTTTATTT-TT
1 AATATAATTTTTATATTATATATTTTATTTTTATTTATT
* *
2130780 AATATAATTTTTATATTATATATTATATTTTAATTTATT
1 AATATAATTTTTATATTATATATTTTATTTTTATTTATT
2130819 TTACTTATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
32 8 0.14
33 21 0.36
34 1 0.02
36 2 0.03
37 1 0.02
38 19 0.32
39 6 0.10
40 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (39 bp):
AATATAATTTTTATATTATATATTTTATTTTTATTTATT
Found at i:2130921 original size:21 final size:21
Alignment explanation
Indices: 2130880--2130932 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
2130870 TTTGATTTTT
*
2130880 ATATTAT-ATATATTATTATA
1 ATATTATAAAATATTATTATA
2130900 ATATTATAAAATATT-TTAATA
1 ATATTATAAAATATTATT-ATA
* *
2130921 AAATAATAAAAT
1 ATATTATAAAAT
2130933 TGAAAGGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATTATAAAATATTATTATA
Found at i:2134388 original size:27 final size:25
Alignment explanation
Indices: 2134260--2134399 Score: 79
Period size: 27 Copynumber: 5.4 Consensus size: 25
2134250 TGGTTTGTCA
* * *
2134260 TAATTTTTTCATTATAATGTAATAAT
1 TAATTTTTT-AATATATTATAATAAT
* *
2134286 TAAATTTTTCA-ATA-TATAAT-AT
1 TAATTTTTTAATATATTATAATAAT
* * *
2134308 CTAAATCTTTAATATTATGTATAACAAT
1 -TAATTTTTTAATA-TAT-TATAATAAT
*
2134336 TATATTTTTTAATATATTTTAAAATAAT
1 TA-ATTTTTTAATATA--TTATAATAAT
*
2134364 TAATTTTTTAATATGATATGTAATAAT
1 TAATTTTTTAATAT-AT-TATAATAAT
*
2134391 TAAATTTTT
1 TAATTTTTT
2134400 CAACACAATA
Statistics
Matches: 89, Mismatches: 14, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
22 2 0.02
23 14 0.16
24 4 0.04
25 2 0.02
26 9 0.10
27 36 0.40
28 21 0.24
29 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (25 bp):
TAATTTTTTAATATATTATAATAAT
Found at i:2134479 original size:27 final size:27
Alignment explanation
Indices: 2134358--2134483 Score: 112
Period size: 27 Copynumber: 4.6 Consensus size: 27
2134348 TATATTTTAA
* * *
2134358 AATAATTAATTTTTTAATATGATATGT
1 AATAATTAAATTTTTAACATAATATGT
* *
2134385 AATAATTAAATTTTTCAACACAATATAT
1 AATAATTAAATTTTT-AACATAATATGT
* * *
2134413 AACAATAAAATTTTCAACATGTAATA--T
1 AATAATTAAATTTTTAACA--TAATATGT
*
2134440 AATAACTAAATTTTTAACATAATATGT
1 AATAATTAAATTTTTAACATAATATGT
* *
2134467 AAAAATTATATTTTTAA
1 AATAATTAAATTTTTAA
2134484 TTTAATTTTT
Statistics
Matches: 78, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
25 5 0.06
27 49 0.63
28 20 0.26
29 4 0.05
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (27 bp):
AATAATTAAATTTTTAACATAATATGT
Found at i:2136028 original size:7 final size:7
Alignment explanation
Indices: 2136016--2136059 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
2136006 GCTGCGACAC
2136016 TAAAATA
1 TAAAATA
2136023 TAAAATA
1 TAAAATA
*
2136030 CAAAATA
1 TAAAATA
2136037 TAAAATA
1 TAAAATA
2136044 TAAAATA
1 TAAAATA
2136051 TAAAATA
1 TAAAATA
2136058 TA
1 TA
2136060 TACATGGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAATA
Found at i:2142708 original size:52 final size:51
Alignment explanation
Indices: 2142639--2142742 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 51
2142629 TATAATGATC
2142639 CATGTTGGAACCATGACATCTTTCCCCATTCTAAC-AAAGTTTCATTATCTTT
1 CATGTTGGAACCATGACATCTTTCCCCATTCTAACAAAAG-TTCATTAT-TTT
* **
2142691 CATGTTGGAACCGTGACATCTTTTTCCATTCTAACAAAAGTTCATTATTTT
1 CATGTTGGAACCATGACATCTTTCCCCATTCTAACAAAAGTTCATTATTTT
2142742 C
1 C
2142743 GGTAGTACAT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
51 4 0.08
52 40 0.83
53 4 0.08
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (51 bp):
CATGTTGGAACCATGACATCTTTCCCCATTCTAACAAAAGTTCATTATTTT
Found at i:2146990 original size:2 final size:2
Alignment explanation
Indices: 2146946--2146971 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2146936 TAGCTGAACC
2146946 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2146972 CACACACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2148370 original size:27 final size:27
Alignment explanation
Indices: 2148326--2148500 Score: 92
Period size: 29 Copynumber: 6.3 Consensus size: 27
2148316 AGACATTAAA
2148326 GTGTAACAA-AATGTTTTTAAATATGAC
1 GTGTAACAATAAT-TTTTTAAATATGAC
* *
2148353 GTGTAACAATAATATTTTTTCAATAT-AGT
1 GTGTAACAAT-A-ATTTTTTAAATATGA-C
* * *
2148382 GTGTAATAATAATTTTTTTTTAACATGAC
1 GTGTAACAATAA--TTTTTTAAATATGAC
* ** *
2148411 GTATAACAATTTTTTTTTAACTATGAC
1 GTGTAACAATAATTTTTTAAATATGAC
* *
2148438 GTGTAAC-AT-ATTTTTATACATA--AA
1 GTGTAACAATAATTTTT-TAAATATGAC
* *
2148462 GTGTAACAATAGTATTTTTTTTAACATGAC
1 GTGTAACAATA--A-TTTTTTAAATATGAC
*
2148492 TTGTAACAA
1 GTGTAACAA
2148501 CTTAACGTAA
Statistics
Matches: 110, Mismatches: 23, Indels: 27
0.69 0.14 0.17
Matches are distributed among these distances:
24 8 0.07
25 7 0.06
26 6 0.05
27 28 0.25
28 6 0.05
29 43 0.39
30 12 0.11
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (27 bp):
GTGTAACAATAATTTTTTAAATATGAC
Found at i:2148416 original size:26 final size:27
Alignment explanation
Indices: 2148387--2148452 Score: 98
Period size: 26 Copynumber: 2.4 Consensus size: 27
2148377 ATAGTGTGTA
*
2148387 ATAATAATTTTTTTTTAAC-ATGACGT
1 ATAACAATTTTTTTTTAACTATGACGT
2148413 ATAACAATTTTTTTTTAACTATGACGT
1 ATAACAATTTTTTTTTAACTATGACGT
*
2148440 GTAACATATTTTT
1 ATAACA-ATTTTT
2148453 ATACATAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 18 0.50
27 12 0.33
28 6 0.17
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.50
Consensus pattern (27 bp):
ATAACAATTTTTTTTTAACTATGACGT
Found at i:2148512 original size:13 final size:13
Alignment explanation
Indices: 2148494--2148519 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2148484 AACATGACTT
2148494 GTAACAACTTAAC
1 GTAACAACTTAAC
2148507 GTAACAACTTAAC
1 GTAACAACTTAAC
2148520 CATAACGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
GTAACAACTTAAC
Found at i:2148637 original size:30 final size:32
Alignment explanation
Indices: 2148603--2148665 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
2148593 AAAATTATAA
2148603 AAAAATTA-TTTTT-AAATATATCTTATTTTT
1 AAAAATTATTTTTTAAAATATATCTTATTTTT
* *
2148633 AAAAATTATTTTTTAAAATATCTCTTTTTTTT
1 AAAAATTATTTTTTAAAATATATCTTATTTTT
2148665 A
1 A
2148666 TGAAGAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 8 0.28
31 5 0.17
32 16 0.55
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (32 bp):
AAAAATTATTTTTTAAAATATATCTTATTTTT
Found at i:2148643 original size:13 final size:13
Alignment explanation
Indices: 2148603--2148651 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
2148593 AAAATTATAA
2148603 AAAAATTATTTTT
1 AAAAATTATTTTT
2148616 AAATATATCTTATTTTT
1 AAA-A-A--TTATTTTT
2148633 AAAAATTATTTTT
1 AAAAATTATTTTT
*
2148646 TAAAAT
1 AAAAAT
2148652 ATCTCTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
13 16 0.52
14 1 0.03
15 2 0.06
16 1 0.03
17 11 0.35
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:2150644 original size:26 final size:27
Alignment explanation
Indices: 2150591--2150644 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
2150581 CAAGCGTACG
* **
2150591 TGTTGAAGAAAATATTATTACATGTCA
1 TGTTGAAGAAAAAATTATTACACATCA
2150618 TGTTGAA-AAAAAATTATTACACATCA
1 TGTTGAAGAAAAAATTATTACACATCA
2150644 T
1 T
2150645 ATTTAAAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (27 bp):
TGTTGAAGAAAAAATTATTACACATCA
Found at i:2151205 original size:58 final size:58
Alignment explanation
Indices: 2151115--2151230 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
2151105 TTTAAGAAAG
* *
2151115 GAGATCATGCACCAACTAATGAGTCAAAGTTCAGGTACAATAGATTTGTTACATGTTA
1 GAGATCATGCACCAACCAATGAGTCAAAGTTCAAGTACAATAGATTTGTTACATGTTA
2151173 GAGATCATGCACCAACCAATGAGTCAAAGTTCAAGTACAATAGATTTGTTACATGTTA
1 GAGATCATGCACCAACCAATGAGTCAAAGTTCAAGTACAATAGATTTGTTACATGTTA
2151231 AATGTATTGG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (58 bp):
GAGATCATGCACCAACCAATGAGTCAAAGTTCAAGTACAATAGATTTGTTACATGTTA
Found at i:2154350 original size:15 final size:15
Alignment explanation
Indices: 2154330--2154359 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2154320 ATTGATTGGG
2154330 CATCAAAATATGAGT
1 CATCAAAATATGAGT
2154345 CATCAAAATATGAGT
1 CATCAAAATATGAGT
2154360 GACAGCTTCA
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:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (15 bp):
CATCAAAATATGAGT
Found at i:2155779 original size:62 final size:62
Alignment explanation
Indices: 2155682--2155805 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
2155672 ATCTATATGC
2155682 ATAGTTGATGCTTTTGTAAGAAACAGATACTCTTGGTATTTGGTGTGATCGATTGTTTGTCT
1 ATAGTTGATGCTTTTGTAAGAAACAGATACTCTTGGTATTTGGTGTGATCGATTGTTTGTCT
2155744 ATAGTTGATGCTTTTGTAAGAAACAGATACTCTTGGTATTTGGTGTGATCGATTGTTTGTCT
1 ATAGTTGATGCTTTTGTAAGAAACAGATACTCTTGGTATTTGGTGTGATCGATTGTTTGTCT
2155806 TGCTCTTACC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.23, C:0.10, G:0.24, T:0.44
Consensus pattern (62 bp):
ATAGTTGATGCTTTTGTAAGAAACAGATACTCTTGGTATTTGGTGTGATCGATTGTTTGTCT
Found at i:2164968 original size:2 final size:2
Alignment explanation
Indices: 2164961--2164985 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2164951 AGAACAGCCT
2164961 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2164986 GTGTCTTCTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2169878 original size:110 final size:110
Alignment explanation
Indices: 2169679--2169895 Score: 271
Period size: 110 Copynumber: 2.0 Consensus size: 110
2169669 TTTTTAATGA
* * * * * * *
2169679 TTTCATCGATGCTTTCTACTTTTGATATAAAGGGTTAGAACTTAGGTTTATTTTACTGATGCTAA
1 TTTCATCAATGCTTTCTACTATTGATATAAAGGGTTAAAACTTAAGTTCATTCTACTAATGCTAA
2169744 AATATTATAATACATGGTACTACATTTGTATAAAACTTATACCCG
66 AATATTATAATACATGGTACTACATTTGTATAAAACTTATACCCG
**
2169789 TTTCATCAATGCTTTCTACTATTGATATTGAGGGTTAAAACTTAAGTTCATTCTA-TCAAT-CTT
1 TTTCATCAATGCTTTCTACTATTGATATAAAGGGTTAAAACTTAAGTTCATTCTACT-AATGC-T
* *
2169852 AAAATGTTATAATACAT-G-ACCATACATTTGTATAAAAGTTATAC
64 AAAATATTATAATACATGGTA-C-TACATTTGTATAAAACTTATAC
2169896 TTGAGCATAC
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
108 1 0.01
109 4 0.04
110 87 0.95
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (110 bp):
TTTCATCAATGCTTTCTACTATTGATATAAAGGGTTAAAACTTAAGTTCATTCTACTAATGCTAA
AATATTATAATACATGGTACTACATTTGTATAAAACTTATACCCG
Found at i:2174303 original size:14 final size:14
Alignment explanation
Indices: 2174284--2174310 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2174274 AAAAAAAAAG
2174284 AAAGGCACTTGATT
1 AAAGGCACTTGATT
2174298 AAAGGCACTTGAT
1 AAAGGCACTTGAT
2174311 GAGACCGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (14 bp):
AAAGGCACTTGATT
Found at i:2193957 original size:4 final size:4
Alignment explanation
Indices: 2193948--2193984 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
2193938 CAACAATGAG
*
2193948 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
2193985 TGTGTGTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:2196331 original size:21 final size:21
Alignment explanation
Indices: 2196281--2196332 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
2196271 AATGAGAAAA
*
2196281 CTTCCTTCCTCCCCTTTATTT
1 CTTCCTTCCTCCCCTTTATTC
* * *
2196302 TTTCTTTCCTCGCCTTT-TTCC
1 CTTCCTTCCTCCCCTTTATT-C
2196323 CTTCCTTCCT
1 CTTCCTTCCT
2196333 ACCAAACATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.02, C:0.42, G:0.02, T:0.54
Consensus pattern (21 bp):
CTTCCTTCCTCCCCTTTATTC
Found at i:2207541 original size:118 final size:113
Alignment explanation
Indices: 2207336--2207650 Score: 375
Period size: 118 Copynumber: 2.8 Consensus size: 113
2207326 AAAAGTAGCC
* * *
2207336 TTTTTATAATAATTATTCGTATAAATTT-TTTTTATTTTAATATTTAAGTTATTGTAATTCACTT
1 TTTTTATAATAATTATACGTATAAATTTATTTTTA-TTTAATATTTAAGTTACTGTAATTTACTT
*
2207400 GATCACATCTTTTGAATTCGAATTTCAAAAGAAGTCA-ATCATTTAAATTT
65 GATCACATCTCTTGAATTCGAATTTCAAAAGAAGT-AGATCATTTAAA-TT
* * * *
2207450 TTTTTATAACAATTATACGTATGATTTATTTATTTTTATTTGAATATATAAATTACTGTAATTTA
1 TTTTTATAATAATTATACGTAT-A--AATTTATTTTTATTT-AATATTTAAGTTACTGTAATTTA
* * * *
2207515 TTTGGTCACATCTCTTGAATTTGAATTTCAAAAGGAGTAGATCATTTAAATT
62 CTTGATCACATCTCTTGAATTCGAATTTCAAAAGAAGTAGATCATTTAAATT
* * * * * *
2207567 TTCTTAAAATAATTATACGTATAAATTAATATTT-TTTAATATTTAAGTTACTGTAACTTACTAG
1 TTTTTATAATAATTATACGTATAAATTTATTTTTATTTAATATTTAAGTTACTGTAATTTACTTG
*
2207631 CTCACATCTCTTGAATTCGA
66 ATCACATCTCTTGAATTCGA
2207651 TCATTTAAAT
Statistics
Matches: 170, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
112 40 0.24
113 3 0.02
114 28 0.16
115 1 0.01
116 1 0.01
117 29 0.17
118 68 0.40
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.48
Consensus pattern (113 bp):
TTTTTATAATAATTATACGTATAAATTTATTTTTATTTAATATTTAAGTTACTGTAATTTACTTG
ATCACATCTCTTGAATTCGAATTTCAAAAGAAGTAGATCATTTAAATT
Found at i:2211146 original size:98 final size:98
Alignment explanation
Indices: 2210969--2211163 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
2210959 TTACATATGC
* *
2210969 AGCTTTCTATAATTTCATGCTATACTTCTTCAGGGCAGGAAGTTGATACCATAGAGTTGCATCTA
1 AGCTCTCTATAATTTCATGCTATACTTCTTCAGGGAAGGAAGTTGATACCATAGAGTTGCATCTA
2211034 GCTATGTCCCGCTTCTCTGAAGCATGTGCAACT
66 GCTATGTCCCGCTTCTCTGAAGCATGTGCAACT
2211067 AGCTCTCTATAATTTCATGCTATACTTCTTCAGGGAAGGAAGTTGATACCATAGAGTTGCATCTA
1 AGCTCTCTATAATTTCATGCTATACTTCTTCAGGGAAGGAAGTTGATACCATAGAGTTGCATCTA
* *
2211132 GCTATGTCCTGCTTCTCTGAAGCGTGTGCAAC
66 GCTATGTCCCGCTTCTCTGAAGCATGTGCAAC
2211164 CATGTCCTTC
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (98 bp):
AGCTCTCTATAATTTCATGCTATACTTCTTCAGGGAAGGAAGTTGATACCATAGAGTTGCATCTA
GCTATGTCCCGCTTCTCTGAAGCATGTGCAACT
Found at i:2214162 original size:20 final size:20
Alignment explanation
Indices: 2214137--2214179 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2214127 GAAATGTTCA
*
2214137 AAGTTCAAATAAAAAGTCTT
1 AAGTTCAAACAAAAAGTCTT
2214157 AAGTTCAAACAAAAAGTCTT
1 AAGTTCAAACAAAAAGTCTT
2214177 AAG
1 AAG
2214180 AGAGAGAATC
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:0.51, C:0.12, G:0.12, T:0.26
Consensus pattern (20 bp):
AAGTTCAAACAAAAAGTCTT
Found at i:2231209 original size:2 final size:2
Alignment explanation
Indices: 2231202--2231233 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2231192 CCCTACACTG
2231202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2231234 TTGTAGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2233486 original size:4 final size:4
Alignment explanation
Indices: 2233477--2233507 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2233467 TTTGAATTTC
*
2233477 CTTT CTTT CTTT CTAT CTTT CTTT CTTT CTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
2233508 CCTCCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:2243080 original size:106 final size:106
Alignment explanation
Indices: 2242891--2243104 Score: 392
Period size: 106 Copynumber: 2.0 Consensus size: 106
2242881 TAATATATTC
*
2242891 TAGATATTGGAAGCACTGAGTGTCATGTAATATTGTGTACTAATGGTTGATATGTACGAACTCAT
1 TAGATATTGGAAGCACTAAGTGTCATGTAATATTGTGTACTAATGGTTGATATGTACGAACTCAT
* *
2242956 CTTGAATGGTTAATGTATGATCTTATGATAATTGTATGAAT
66 CTTGAATGGTTAAGGTATGATCTTATGATAATTCTATGAAT
*
2242997 TAGATATTGGAAGCACTAAGTGTCATGTAATATTGTGTACTAATGGTTGTTATGTACGAACTCAT
1 TAGATATTGGAAGCACTAAGTGTCATGTAATATTGTGTACTAATGGTTGATATGTACGAACTCAT
2243062 CTTGAATGGTTAAGGTATGATCTTATGATAATTCTATGAAT
66 CTTGAATGGTTAAGGTATGATCTTATGATAATTCTATGAAT
2243103 TA
1 TA
2243105 TGTGCTAAGG
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (106 bp):
TAGATATTGGAAGCACTAAGTGTCATGTAATATTGTGTACTAATGGTTGATATGTACGAACTCAT
CTTGAATGGTTAAGGTATGATCTTATGATAATTCTATGAAT
Found at i:2246477 original size:16 final size:17
Alignment explanation
Indices: 2246456--2246493 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2246446 ATGCGTCCTC
*
2246456 AATTGCAATTGGGAA-G
1 AATTGCAATTGGCAATG
*
2246472 AATTGCTATTGGCAATG
1 AATTGCAATTGGCAATG
2246489 AATTG
1 AATTG
2246494 AGTGAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (17 bp):
AATTGCAATTGGCAATG
Found at i:2257361 original size:20 final size:19
Alignment explanation
Indices: 2257338--2257384 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
2257328 TTGATTAAAA
*
2257338 TTTTAAATAAATATATTAAT
1 TTTTAAATAAACATATT-AT
*
2257358 TTTTAAAATAAACATCTTAT
1 TTTT-AAATAAACATATTAT
2257378 TTTTAAA
1 TTTTAAA
2257385 ATTTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTAAATAAACATATTAT
Found at i:2257385 original size:20 final size:21
Alignment explanation
Indices: 2257338--2257386 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
2257328 TTGATTAAAA
*
2257338 TTTT-AAATAAATATATTAAT
1 TTTTAAAATAAACATATTAAT
*
2257358 TTTTAAAATAAACATCTT-AT
1 TTTTAAAATAAACATATTAAT
2257378 TTTTAAAAT
1 TTTTAAAAT
2257387 TTTTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAAAATAAACATATTAAT
Found at i:2257607 original size:22 final size:23
Alignment explanation
Indices: 2257564--2257607 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
2257554 TTTTTTCAAA
*
2257564 AAATTAGATAATAATAATTTTTG
1 AAATTAGATAATAAAAATTTTTG
2257587 AAATTA-ATAA-AAAAATATTTT
1 AAATTAGATAATAAAAAT-TTTT
2257608 AATTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (23 bp):
AAATTAGATAATAAAAATTTTTG
Found at i:2264741 original size:16 final size:17
Alignment explanation
Indices: 2264703--2264742 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2264693 TAGAAATTAC
2264703 ATATTT-ATTTAATAAT
1 ATATTTAATTTAATAAT
*
2264719 -TAATTAATTTAA-AAT
1 ATATTTAATTTAATAAT
2264734 ATATTTAAT
1 ATATTTAAT
2264743 GAGATACAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTTAATTTAATAAT
Found at i:2268746 original size:13 final size:12
Alignment explanation
Indices: 2268728--2268766 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
2268718 TGATCAAACC
2268728 TAAAAAAAAAAA
1 TAAAAAAAAAAA
2268740 GTAAAAAATAAAAA
1 -TAAAAAA-AAAAA
*
2268754 TAAAAAAAGAAA
1 TAAAAAAAAAAA
2268766 T
1 T
2268767 TCTAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 5 0.21
13 14 0.58
14 5 0.21
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (12 bp):
TAAAAAAAAAAA
Found at i:2272784 original size:76 final size:77
Alignment explanation
Indices: 2272694--2272842 Score: 205
Period size: 77 Copynumber: 1.9 Consensus size: 77
2272684 TTTTTCTTAT
* *
2272694 AGAGTAAACTCAAATTTTACAATTATTTTTCTTATTTTTTT-TCT-TTATA-AAGTAAAAGATGC
1 AGAGTAAACCCAAATTTTACAATTA-TTTTCATATTTTTTTATCTCTTATAGAA-TAAAAGATGC
2272756 ATTGCTTAACTATA
64 ATTGCTTAACTATA
* ** *
2272770 AGAGTAAGCCCAAATTTTGTAATTATTTTCATATTTTTTTATTTCTTATAGAATAAAAGATGCAT
1 AGAGTAAACCCAAATTTTACAATTATTTTCATATTTTTTTATCTCTTATAGAATAAAAGATGCAT
2272835 TGCTTAAC
66 TGCTTAAC
2272843 CATGTTTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
75 14 0.22
76 23 0.36
77 25 0.39
78 2 0.03
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (77 bp):
AGAGTAAACCCAAATTTTACAATTATTTTCATATTTTTTTATCTCTTATAGAATAAAAGATGCAT
TGCTTAACTATA
Found at i:2275586 original size:3 final size:3
Alignment explanation
Indices: 2275578--2275618 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2275568 TCTCTCACAA
2275578 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2275619 CGTGATAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2282295 original size:19 final size:20
Alignment explanation
Indices: 2282250--2282298 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
2282240 TACAAATTTA
*
2282250 TTAATTTTTAAATAAATATAT
1 TTAATTATTAAAT-AATATAT
2282271 TT--TTATTAAAT-ATATAT
1 TTAATTATTAAATAATATAT
2282288 TTAATTATTAA
1 TTAATTATTAA
2282299 TTTATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 8 0.32
19 15 0.60
21 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATTATTAAATAATATAT
Found at i:2282391 original size:26 final size:27
Alignment explanation
Indices: 2282339--2282391 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
2282329 TATAATAATA
* * *
2282339 TTAAAAATAATTTTATTTTTATTAATT
1 TTAAAAATAATTGTATTTATATAAATT
*
2282366 TTAAAAATTATTGTA-TTATATAAATT
1 TTAAAAATAATTGTATTTATATAAATT
2282392 ATAATTTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
TTAAAAATAATTGTATTTATATAAATT
Found at i:2283613 original size:28 final size:28
Alignment explanation
Indices: 2283577--2283632 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
2283567 TTCAAAATAT
2283577 TTAAATAAATTTTGAT-TTTTTATTTTA
1 TTAAATAAATTTTGATATTTTTATTTTA
*
2283604 TTAAATTAAATTTTTATATTTTTATTTTA
1 TTAAA-TAAATTTTGATATTTTTATTTTA
2283633 ATTTAAGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 5 0.19
28 10 0.38
29 11 0.42
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (28 bp):
TTAAATAAATTTTGATATTTTTATTTTA
Found at i:2296174 original size:21 final size:21
Alignment explanation
Indices: 2296148--2296189 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2296138 TTAGGTCTAG
2296148 GTGCTCGTATTCTACAATGTA
1 GTGCTCGTATTCTACAATGTA
2296169 GTGCTCGTATTCTACAATGTA
1 GTGCTCGTATTCTACAATGTA
2296190 TTACAAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (21 bp):
GTGCTCGTATTCTACAATGTA
Found at i:2298533 original size:76 final size:76
Alignment explanation
Indices: 2298399--2298556 Score: 201
Period size: 76 Copynumber: 2.1 Consensus size: 76
2298389 CTTTAATGAA
* * * * * *
2298399 ATTACATGTCATGTACAAAAATATGTTACACGTCATGGTTAGATTGTTATACATCATGTTTAAAA
1 ATTACATGTCATGAACAAAAACATGTTACACGTCATAGTTAGATTGTTACACACCATGTTGAAAA
2298464 AAAATACTATT
66 AAAATACTATT
* * *
2298475 ATTACCTGTCATGAATAAAAACATGTTACACG-CTATAGTTAGATTGTTACACGCCATGTTGAAA
1 ATTACATGTCATGAACAAAAACATGTTACACGTC-ATAGTTAGATTGTTACACACCATGTTGAAA
*
2298539 AAAAATACTGTT
65 AAAAATACTATT
*
2298551 GTTACA
1 ATTACA
2298557 CGTTATAATT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
75 1 0.01
76 68 0.99
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (76 bp):
ATTACATGTCATGAACAAAAACATGTTACACGTCATAGTTAGATTGTTACACACCATGTTGAAAA
AAAATACTATT
Found at i:2298574 original size:52 final size:52
Alignment explanation
Indices: 2298498--2298614 Score: 153
Period size: 52 Copynumber: 2.2 Consensus size: 52
2298488 AATAAAAACA
* **
2298498 TGTTACACGCTATAGTTAGATTGTTACACGCCATGTTGAAAAAAAATACTGT
1 TGTTACACGCTATAATTAGATTGTTACACGCCATACTGAAAAAAAATACTGT
* * * * *
2298550 TGTTACACGTTATAATTAGGTTGTTACACGTCATACTGAAGAAAAATATTGT
1 TGTTACACGCTATAATTAGATTGTTACACGCCATACTGAAAAAAAATACTGT
*
2298602 TGTTATACGCTAT
1 TGTTACACGCTAT
2298615 GCACAAAAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (52 bp):
TGTTACACGCTATAATTAGATTGTTACACGCCATACTGAAAAAAAATACTGT
Found at i:2298663 original size:25 final size:25
Alignment explanation
Indices: 2298619--2298673 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
2298609 CGCTATGCAC
* *
2298619 AAAAATATGTTACATACCATAATT-A
1 AAAAAGATGTTACACACCAT-ATTGA
*
2298644 AAAAAGATGTTACACGCCATATTGA
1 AAAAAGATGTTACACACCATATTGA
2298669 AAAAA
1 AAAAA
2298674 AATATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 3 0.12
25 23 0.88
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.25
Consensus pattern (25 bp):
AAAAAGATGTTACACACCATATTGA
Found at i:2346413 original size:40 final size:40
Alignment explanation
Indices: 2346354--2346447 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 40
2346344 AGTTAATTGA
** *
2346354 TTAGGCCGAGTCGGGCACTGCCATTACAAGGGATAACTGT
1 TTAGGCCGAGTTTGACACTGCCATTACAAGGGATAACTGT
* * *
2346394 TTAGGCCGAGTTTGACACTGCCATTGCAATGGATAGCTGT
1 TTAGGCCGAGTTTGACACTGCCATTACAAGGGATAACTGT
*
2346434 TTAGGCCAAGTTTG
1 TTAGGCCGAGTTTG
2346448 GCATAGATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
TTAGGCCGAGTTTGACACTGCCATTACAAGGGATAACTGT
Found at i:2361522 original size:2 final size:2
Alignment explanation
Indices: 2361515--2361539 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2361505 TGTTTTTGCT
2361515 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2361540 TGAAATTAAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2363278 original size:2 final size:2
Alignment explanation
Indices: 2363271--2363295 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2363261 AAACAGTAAG
2363271 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2363296 GGGCTGAGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2368946 original size:19 final size:19
Alignment explanation
Indices: 2368924--2368961 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2368914 CATTTTCGGG
*
2368924 TTTTTTCTCAATTGCTTTT
1 TTTTTTCTCAATTACTTTT
2368943 TTTTTTCTCAATTACTTTT
1 TTTTTTCTCAATTACTTTT
2368962 GTGTTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.16, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTTTCTCAATTACTTTT
Found at i:2369717 original size:2 final size:2
Alignment explanation
Indices: 2369710--2369737 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2369700 TGTTTTACTA
2369710 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2369738 GCGCGTATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2380562 original size:2 final size:2
Alignment explanation
Indices: 2380555--2380579 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2380545 CATGAAATGT
2380555 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2380580 TAAAAAAGCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2384027 original size:14 final size:14
Alignment explanation
Indices: 2384005--2384045 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2383995 TGGTTATTAA
2384005 TTAATAATTTATTT
1 TTAATAATTTATTT
*
2384019 TTCATAA-TT-TTT
1 TTAATAATTTATTT
*
2384031 TTAAAAATTTATTT
1 TTAATAATTTATTT
2384045 T
1 T
2384046 ATATTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
12 8 0.36
13 4 0.18
14 10 0.45
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TTAATAATTTATTT
Found at i:2385771 original size:2 final size:2
Alignment explanation
Indices: 2385764--2385792 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2385754 CATGAAATGT
2385764 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2385793 GAGTAATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2390197 original size:2 final size:2
Alignment explanation
Indices: 2390190--2390227 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2390180 TTCATATACC
2390190 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2390228 TTCAGAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2402222 original size:18 final size:18
Alignment explanation
Indices: 2402169--2402222 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
2402159 TAATCGTGTT
* *
2402169 ATCGTATTTAAACATATA
1 ATCGTGTTTAAACATGTA
* *
2402187 AACGTGTTTAATA-GTGTA
1 ATCGTGTTTAA-ACATGTA
2402205 ATCGTGTTTAAACATGTA
1 ATCGTGTTTAAACATGTA
2402223 TACATAACAC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (18 bp):
ATCGTGTTTAAACATGTA
Found at i:2403025 original size:16 final size:17
Alignment explanation
Indices: 2403006--2403045 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
2402996 GAAAAAACTC
*
2403006 AAATTTAAAATTAATT-
1 AAATTTAAAAATAATTA
2403022 AAA-TTAAAAATAATTA
1 AAATTTAAAAATAATTA
2403038 AAATTTAA
1 AAATTTAA
2403046 TATAATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 11 0.52
16 6 0.29
17 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTAAAAATAATTA
Found at i:2403050 original size:16 final size:15
Alignment explanation
Indices: 2403006--2403052 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
2402996 GAAAAAACTC
2403006 AAATTTAAAATTAATT
1 AAATTTAAAA-TAATT
*
2403022 AAATTAAAAATAATT
1 AAATTTAAAATAATT
*
2403037 AAAATTTAATATAATT
1 -AAATTTAAAATAATT
2403053 TTGACCGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATTTAAAATAATT
Done.