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 5 of 31
Found at i:2421589 original size:147 final size:147
Alignment explanation
Indices: 2421321--2421611 Score: 483
Period size: 147 Copynumber: 2.0 Consensus size: 147
2421311 TTTAGGTGCA
* * *
2421321 TTAATAATTGATTCACAGTGTTTAGTTGATAGCTTGCATAATTCAACATACTTTCAGGCTGGTCA
1 TTAATAATTGATTCACACTGTTTAGATGATAGCTTGCATAATTCAACATACTTTCAGGCGGGTCA
* * * *
2421386 GTTGTTTAGGCACTATATATATGCAGCTTGGTATTTATAGGCTTTAATTCCCCATTCCTTTTAAG
66 GCTGTTTAGGCACTATATATACGCAGCTTGATATTTATAGGCTTTAATTCCACATTCCTTTTAAG
*
2421451 AAACCATCTTGATTGCT
131 AAACCATCTCGATTGCT
*
2421468 TTAATAATTGATTCACACTGTTTAGATGATAGCTTGCATAATTCAACCTACTTTCAGGCGGGTCA
1 TTAATAATTGATTCACACTGTTTAGATGATAGCTTGCATAATTCAACATACTTTCAGGCGGGTCA
**
2421533 GCTGTTTAGGCACTATATATACGCAGCTTGATATTTATAGGCTTTAATTCCACATTCCTTTTGGG
66 GCTGTTTAGGCACTATATATACGCAGCTTGATATTTATAGGCTTTAATTCCACATTCCTTTTAAG
2421598 AAACCATCTCGATT
131 AAACCATCTCGATT
2421612 CCGTGTTGCA
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
147 133 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (147 bp):
TTAATAATTGATTCACACTGTTTAGATGATAGCTTGCATAATTCAACATACTTTCAGGCGGGTCA
GCTGTTTAGGCACTATATATACGCAGCTTGATATTTATAGGCTTTAATTCCACATTCCTTTTAAG
AAACCATCTCGATTGCT
Found at i:2423644 original size:62 final size:62
Alignment explanation
Indices: 2423547--2423673 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
2423537 GTTCATGGAC
2423547 TTGACATATGAGTGCATGTTCCTTTTCAGGGTGCTAGGGCACAAAGAGTAGAGTATCTTTTA
1 TTGACATATGAGTGCATGTTCCTTTTCAGGGTGCTAGGGCACAAAGAGTAGAGTATCTTTTA
*
2423609 TTGACATATGAGTGCATGTTCCTTTTCAGGGTGCTAGGGCGCAAAGAGTAGAGTATCTTTTA
1 TTGACATATGAGTGCATGTTCCTTTTCAGGGTGCTAGGGCACAAAGAGTAGAGTATCTTTTA
2423671 TTG
1 TTG
2423674 CATGCATTTC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (62 bp):
TTGACATATGAGTGCATGTTCCTTTTCAGGGTGCTAGGGCACAAAGAGTAGAGTATCTTTTA
Found at i:2436904 original size:13 final size:13
Alignment explanation
Indices: 2436886--2436910 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2436876 CTCTTTTCAT
2436886 AAAAAAAAATTTG
1 AAAAAAAAATTTG
2436899 AAAAAAAAATTT
1 AAAAAAAAATTT
2436911 ATACTTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAAAAAAATTTG
Found at i:2438000 original size:52 final size:52
Alignment explanation
Indices: 2437915--2438019 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 52
2437905 CTGGCATGTC
* *
2437915 GACATGTTAGTGCCACATCAGCATTACCACGACATTATATTAGGGCCACGTG
1 GACATGTTAGTGCCACATCAGCATTACCACGACATCATATTAGAGCCACGTG
** * * * * *
2437967 GACATGTTAGTGCCATGTTAGTATTGCCTCGACATCATATTAGAGCCATGTG
1 GACATGTTAGTGCCACATCAGCATTACCACGACATCATATTAGAGCCACGTG
2438019 G
1 G
2438020 CACTGTCATG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (52 bp):
GACATGTTAGTGCCACATCAGCATTACCACGACATCATATTAGAGCCACGTG
Found at i:2439039 original size:17 final size:16
Alignment explanation
Indices: 2439014--2439049 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2439004 TATAATTAGA
2439014 ATTAATAAAAATAATAT
1 ATTAAT-AAAATAATAT
*
2439031 ATTACTAAAATAATAT
1 ATTAATAAAATAATAT
2439047 ATT
1 ATT
2439050 TGAGAATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAATAAAATAATAT
Found at i:2443019 original size:15 final size:14
Alignment explanation
Indices: 2442990--2443016 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2442980 CATAATGATT
2442990 AAAACAAAAAACCA
1 AAAACAAAAAACCA
2443004 AAAACAAAAAACC
1 AAAACAAAAAACC
2443017 CAAGACCGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAACAAAAAACCA
Found at i:2447746 original size:2 final size:2
Alignment explanation
Indices: 2447739--2447770 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2447729 CAATGGTGGG
2447739 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
2447771 GAGCAAATGT
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:2447870 original size:28 final size:28
Alignment explanation
Indices: 2447823--2447906 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 28
2447813 AAAATTTTTA
2447823 AATTTTTTATTTATATATAATATTTTTAAAT
1 AATTTTTTA-TT-TA-ATAATATTTTTAAAT
* * *
2447854 AATTTTTTATTTAATAAT-TAATATAAGT
1 AATTTTTTATTTAATAATAT-TTTTAAAT
* *
2447882 AATTATTTATTTATTATATATTTTT
1 AATTTTTTATTTAATA-ATATTTTT
2447907 CTATTATTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
27 1 0.02
28 24 0.56
29 6 0.14
30 3 0.07
31 9 0.21
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (28 bp):
AATTTTTTATTTAATAATATTTTTAAAT
Found at i:2448460 original size:10 final size:10
Alignment explanation
Indices: 2448445--2448474 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
2448435 TTATTATAAG
2448445 TTTTTTTATT
1 TTTTTTTATT
2448455 TTTTTTTATT
1 TTTTTTTATT
2448465 TTTTTATTAT
1 TTTTT-TTAT
2448475 ATAAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:2477757 original size:35 final size:35
Alignment explanation
Indices: 2477718--2477786 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
2477708 GAAGCTCAGG
*
2477718 TGAATTTATGTTCTACTATGTACGTTCAAAAAACC
1 TGAATTTATGTTCTACTACGTACGTTCAAAAAACC
2477753 TGAATTTATGTTCTACTACGTACGTTCAAAAAAC
1 TGAATTTATGTTCTACTACGTACGTTCAAAAAAC
2477787 AAAGTCTCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (35 bp):
TGAATTTATGTTCTACTACGTACGTTCAAAAAACC
Found at i:2478810 original size:20 final size:20
Alignment explanation
Indices: 2478785--2478937 Score: 73
Period size: 20 Copynumber: 7.3 Consensus size: 20
2478775 ATGTTATAAT
2478785 TAAAATAAAAAATATAAAAA
1 TAAAATAAAAAATATAAAAA
* *
2478805 TAAAATATATAATATAAAAA
1 TAAAATAAAAAATATAAAAA
2478825 TAAAAAATATAATAAA-ATAAAATA
1 T--AAAATA-AA-AAATATAAAA-A
* * *
2478849 TAAAGA-ATTAAAATTTACATAA
1 TAAA-ATA-AAAAATATA-AAAA
*
2478871 TATAGATAAACGAAAT-T-AAAA
1 TA-AAATAAA--AAATATAAAAA
* *
2478892 TAAAATATATAATATAAAAA
1 TAAAATAAAAAATATAAAAA
* * *
2478912 TATATTAAATAA-ATAAAAA
1 TAAAATAAAAAATATAAAAA
2478931 TAAAATA
1 TAAAATA
2478938 TACAAGATTA
Statistics
Matches: 101, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
18 3 0.03
19 13 0.13
20 37 0.37
21 8 0.08
22 19 0.19
23 13 0.13
24 8 0.08
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAAATAAAAAATATAAAAA
Found at i:2478830 original size:35 final size:35
Alignment explanation
Indices: 2478779--2478850 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
2478769 TTTGTAATGT
2478779 TATAATTAAAATAAAAAATAT-A-AAAATAAAATA
1 TATAATTAAAATAAAAAATATAATAAAATAAAATA
2478812 TATAATATAAAAATAAAAAATATAATAAAATAAAATA
1 TATAAT-T-AAAATAAAAAATATAATAAAATAAAATA
2478849 TA
1 TA
2478851 AAGAATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
33 6 0.17
34 1 0.03
35 14 0.40
36 1 0.03
37 13 0.37
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (35 bp):
TATAATTAAAATAAAAAATATAATAAAATAAAATA
Found at i:2478860 original size:15 final size:15
Alignment explanation
Indices: 2478785--2478939 Score: 91
Period size: 15 Copynumber: 10.6 Consensus size: 15
2478775 ATGTTATAAT
2478785 TAAAATA-AAAAATA
1 TAAAATATAAAAATA
2478799 TAAAA-AT-AAAATA
1 TAAAATATAAAAATA
*
2478812 TATAATATAAAAATA
1 TAAAATATAAAAATA
*
2478827 AAAAATATAATAAA-A
1 TAAAATATAA-AAATA
2478842 TAAAATATAAAGAAT-
1 TAAAATATAAA-AATA
* *
2478857 TAAAATTTACATAATA
1 TAAAATATA-AAAATA
*
2478873 T-AGATA-AACGAAAT-
1 TAAAATATAA--AAATA
2478887 T-AAA-AT-AAAATA
1 TAAAATATAAAAATA
*
2478899 TATAATATAAAAATA
1 TAAAATATAAAAATA
*
2478914 TATTAAATA-AATAAAAA
1 TA--AAATATAA-AAATA
2478931 TAAAATATA
1 TAAAATATA
2478940 CAAGATTATA
Statistics
Matches: 109, Mismatches: 13, Indels: 36
0.69 0.08 0.23
Matches are distributed among these distances:
11 4 0.04
12 1 0.01
13 16 0.15
14 14 0.13
15 56 0.51
16 8 0.07
17 10 0.09
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (15 bp):
TAAAATATAAAAATA
Found at i:2491127 original size:30 final size:28
Alignment explanation
Indices: 2491063--2491131 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 28
2491053 TTGAATATGA
* *
2491063 CGTGTAATAATAATATTTTTTCAACATG
1 CGTGTAACAATAATATTTTTTCAACAGG
*
2491091 CTGTGTAACAATAATATTTTTTTCAATACGG
1 C-GTGTAACAATAATA-TTTTTTCAACA-GG
2491122 CGTGTAACAA
1 CGTGTAACAA
2491132 CATTTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.03
29 13 0.37
30 19 0.54
31 2 0.06
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (28 bp):
CGTGTAACAATAATATTTTTTCAACAGG
Found at i:2491306 original size:76 final size:75
Alignment explanation
Indices: 2491138--2491308 Score: 225
Period size: 76 Copynumber: 2.3 Consensus size: 75
2491128 ACAACATTTT
* * * *
2491138 TTAATTATGGTATGTAACATGTTTTTCTGCATGACATATAATAATAGTATTTTTTTTCAACATAA
1 TTAATCATGGTATGTAACATATTTTTCTACATGACATATAACAATAGTATTTTTTTTCAACATAA
*
2491203 CGTACAACAA
66 CATACAACAA
* * * * *
2491213 TCTAACCATAGTGTGTAACATATTTTTGTACATGACATATAACAATAGTATTTTTTTTCAACATG
1 T-TAATCATGGTATGTAACATATTTTTCTACATGACATATAACAATAGTATTTTTTTTCAACATA
2491278 ACATACAACAA
65 ACATACAACAA
*
2491289 CTTAATCATGGCATGTAACA
1 -TTAATCATGGTATGTAACA
2491309 ACATAAACAT
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
75 1 0.01
76 78 0.98
77 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (75 bp):
TTAATCATGGTATGTAACATATTTTTCTACATGACATATAACAATAGTATTTTTTTTCAACATAA
CATACAACAA
Found at i:2491308 original size:21 final size:21
Alignment explanation
Indices: 2491272--2491329 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
2491262 ATTTTTTTTC
** *
2491272 AACATGACATACAACAACTTA
1 AACATGACATGTAACAACATA
* *
2491293 ATCATGGCATGTAACAACATA
1 AACATGACATGTAACAACATA
*
2491314 AACATGATATGTAACA
1 AACATGACATGTAACA
2491330 TATTTTTATA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.22
Consensus pattern (21 bp):
AACATGACATGTAACAACATA
Found at i:2503483 original size:11 final size:12
Alignment explanation
Indices: 2503466--2503490 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2503456 TTAAAATTTC
2503466 ATAAAAAATGTA
1 ATAAAAAATGTA
2503478 ATAAAAAATGTA
1 ATAAAAAATGTA
2503490 A
1 A
2503491 CAATCAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
ATAAAAAATGTA
Found at i:2503730 original size:17 final size:16
Alignment explanation
Indices: 2503692--2503734 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
2503682 TAAATTTAAT
2503692 ATATTTTTAAAATATA
1 ATATTTTTAAAATATA
* * *
2503708 AAATTTTATATAATATC
1 ATATTTT-TAAAATATA
2503725 ATATTTTTAA
1 ATATTTTTAA
2503735 TAAATATAGT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATTTTTAAAATATA
Found at i:2503737 original size:17 final size:16
Alignment explanation
Indices: 2503690--2503742 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
2503680 TGTAAATTTA
2503690 ATATATTTTTAA-AAT
1 ATATATTTTTAATAAT
* *
2503705 ATAAAATTTTATATAAT
1 ATATATTTTTA-ATAAT
2503722 ATCATATTTTTAATAA-
1 AT-ATATTTTTAATAAT
2503738 ATATA
1 ATATA
2503743 GTTATTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 12 0.39
16 3 0.10
17 9 0.29
18 7 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATATTTTTAATAAT
Found at i:2512320 original size:2 final size:2
Alignment explanation
Indices: 2512313--2512344 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2512303 TTTAAATACA
2512313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2512345 ACAGCATGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2520373 original size:2 final size:2
Alignment explanation
Indices: 2520366--2520399 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2520356 AAATACTTAA
* *
2520366 AT AT AT AT AT AC AT AT GT 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
2520400 CCCATAATGG
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:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2526406 original size:27 final size:29
Alignment explanation
Indices: 2526372--2526438 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
2526362 ATAGAAGTAT
*
2526372 ATTTAATTAAAAAT-A-AAAAATATAAGA
1 ATTTAATTAAAAATGATAAAAATATAAAA
**
2526399 ATTTAATTAAAGGTGATAAAAATATAAAA
1 ATTTAATTAAAAATGATAAAAATATAAAA
*
2526428 ATTTATTTAAA
1 ATTTAATTAAA
2526439 GTTTTTAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 12 0.35
28 1 0.03
29 21 0.62
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (29 bp):
ATTTAATTAAAAATGATAAAAATATAAAA
Found at i:2531969 original size:33 final size:32
Alignment explanation
Indices: 2531931--2532006 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 32
2531921 CACCACTGGG
*
2531931 TGGTCCCAAAACCCCCTAAACTCATCAATACAA
1 TGGTCCCAAAAACCCCTAAACTCATCAAT-CAA
* * *
2531964 TGGTCCCAAAAACCCCTAAATTCATCACTCTA
1 TGGTCCCAAAAACCCCTAAACTCATCAATCAA
2531996 TGGTCCCAAAA
1 TGGTCCCAAAA
2532007 TCCTAGTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 13 0.33
33 26 0.67
ACGTcount: A:0.37, C:0.34, G:0.08, T:0.21
Consensus pattern (32 bp):
TGGTCCCAAAAACCCCTAAACTCATCAATCAA
Found at i:2532004 original size:32 final size:32
Alignment explanation
Indices: 2531899--2532006 Score: 108
Period size: 32 Copynumber: 3.3 Consensus size: 32
2531889 ACAAAATATG
* * * * ***
2531899 TGGTCCTAAAAACTCCTAAAGTCACCACTGGG
1 TGGTCCCAAAAACCCCTAAACTCATCACTCAA
* *
2531931 TGGTCCCAAAACCCCCTAAACTCATCAATACAA
1 TGGTCCCAAAAACCCCTAAACTCATCACT-CAA
* *
2531964 TGGTCCCAAAAACCCCTAAATTCATCACTCTA
1 TGGTCCCAAAAACCCCTAAACTCATCACTCAA
2531996 TGGTCCCAAAA
1 TGGTCCCAAAA
2532007 TCCTAGTGAA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
32 36 0.58
33 26 0.42
ACGTcount: A:0.35, C:0.32, G:0.11, T:0.21
Consensus pattern (32 bp):
TGGTCCCAAAAACCCCTAAACTCATCACTCAA
Found at i:2533822 original size:21 final size:21
Alignment explanation
Indices: 2533773--2533823 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 21
2533763 TATTGATATA
2533773 ATATTTTTAAAAAATTTCTAAAT
1 ATATTTTT--AAAATTTCTAAAT
* *
2533796 -TA-TTTTAAATTTTTTAAAT
1 ATATTTTTAAAATTTCTAAAT
2533815 ATATTTTTA
1 ATATTTTTA
2533824 TTTTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 11 0.46
20 2 0.08
21 9 0.38
22 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTTTTAAAATTTCTAAAT
Found at i:2534595 original size:15 final size:16
Alignment explanation
Indices: 2534568--2534610 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2534558 ATATATATTA
*
2534568 AATA-TAATAAAATTT
1 AATATTAATAAATTTT
2534583 AATATTAATAAATTTT
1 AATATTAATAAATTTT
2534599 AATTATT-ATAAA
1 AA-TATTAATAAA
2534611 GATATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 4 0.16
16 17 0.68
17 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATTAATAAATTTT
Found at i:2534829 original size:17 final size:16
Alignment explanation
Indices: 2534787--2534817 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2534777 TATAAAATAT
*
2534787 AATTAATTTAAATCTA
1 AATTTATTTAAATCTA
2534803 AATTTATTTAAATCT
1 AATTTATTTAAATCT
2534818 GTATCTTATT
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:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTATTTAAATCTA
Found at i:2543029 original size:18 final size:18
Alignment explanation
Indices: 2543006--2543046 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2542996 CAATGTTTAG
2543006 TATAATATGA-AACTAATT
1 TATAATATGATAAC-AATT
*
2543024 TATAATATGATAACATTT
1 TATAATATGATAACAATT
2543042 TATAA
1 TATAA
2543047 CTTTTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (18 bp):
TATAATATGATAACAATT
Found at i:2549361 original size:15 final size:15
Alignment explanation
Indices: 2549338--2549370 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2549328 CTCAAAAATC
*
2549338 TTATCACTTTAGTGG
1 TTATAACTTTAGTGG
2549353 TTATAACTTTAGTGG
1 TTATAACTTTAGTGG
2549368 TTA
1 TTA
2549371 GCACGGCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (15 bp):
TTATAACTTTAGTGG
Found at i:2549444 original size:7 final size:7
Alignment explanation
Indices: 2549432--2549461 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2549422 TCCCTCCCTG
2549432 CCTCTTC
1 CCTCTTC
2549439 CCTCTTC
1 CCTCTTC
2549446 CCTCTTC
1 CCTCTTC
*
2549453 CCTCCTC
1 CCTCTTC
2549460 CC
1 CC
2549462 CACTCCCATC
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:0.63, G:0.00, T:0.37
Consensus pattern (7 bp):
CCTCTTC
Found at i:2549451 original size:14 final size:14
Alignment explanation
Indices: 2549422--2549461 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2549412 GCCTGTTCCC
*
2549422 TCCCTCCCTGCCTCT
1 TCCCT-CCTCCCTCT
*
2549437 TCCCTCTTCCCTCT
1 TCCCTCCTCCCTCT
2549451 TCCCTCCTCCC
1 TCCCTCCTCCC
2549462 CACTCCCATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.00, C:0.62, G:0.03, T:0.35
Consensus pattern (14 bp):
TCCCTCCTCCCTCT
Found at i:2550346 original size:21 final size:21
Alignment explanation
Indices: 2550320--2550364 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2550310 AATTATGACC
*
2550320 ATGATGAAGGTGGTGGTGGTG
1 ATGATGAAGATGGTGGTGGTG
*
2550341 ATGATGATGATGGTGGTGGTG
1 ATGATGAAGATGGTGGTGGTG
2550362 ATG
1 ATG
2550365 CTGAGCTGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.49, T:0.31
Consensus pattern (21 bp):
ATGATGAAGATGGTGGTGGTG
Found at i:2554098 original size:2 final size:2
Alignment explanation
Indices: 2554088--2554121 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2554078 ACACACACAC
*
2554088 AT AT GT 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
2554122 GTACATTCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2591493 original size:211 final size:213
Alignment explanation
Indices: 2591071--2591506 Score: 619
Period size: 211 Copynumber: 2.0 Consensus size: 213
2591061 TACGTATGAA
* * **
2591071 TATATATAATATATTACTTTATTATATATATGAAATTAATGATACAACTTATATGTATAATATTT
1 TATATATAATATATTACTTTATTATACATATAAAATTAATGATACAACTTATA-GTAT-ATATAA
* * *
2591136 TAATTTTATATCAAAATTTGTATAAATAATAACTAATTATAAATAATATGTTATAAAAACTAAGG
64 TAATTTTATATCAAAATTTGTATAAATAATAACTAATTAAAAACAATATGTTATAAAAACTAAAG
** *
2591201 CAATAACTAATAAAATTATTAAGTGTAATCATATAAATAAAGTTTATTATAAGTTATAGTAATGC
129 CAATAAC--ATAAAATTATTAAACGTAATCATATAAATAAAGTTTATTATAAGTTATAGTAATAC
* *
2591266 TTATGTATAAATTAAATATATG
192 TTATATAAAAATTAAATATATG
2591288 TATATATAATATATTACTTTATTATGTACATATAAAATTAATGATACAACTTATA-TAT-TATAA
1 TATATATAATATATTACTTTATTA--TACATATAAAATTAATGATACAACTTATAGTATATATAA
* *
2591351 T-ATTTTATATCAAAGTTTGTATAAATAATAATTAATTAAAAACAATATGTTATAAAAACTAAAG
64 TAATTTTATATCAAAATTTGTATAAATAATAACTAATTAAAAACAATATGTTATAAAAACTAAAG
** * * *
2591415 TGATAAC-TAAAGTTATTAAACGTAGTTATATAAATAAAGTTTATTATAAGTTATAGTAATACTT
129 CAATAACATAAAATTATTAAACGTAATCATATAAATAAAGTTTATTATAAGTTATAGTAATACTT
2591479 ATATAAAAATTAAATATATG
194 ATATAAAAATTAAATATATG
2591499 TATATATA
1 TATATATA
2591507 TTTATATAAT
Statistics
Matches: 198, Mismatches: 19, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
211 77 0.39
214 63 0.32
215 4 0.02
217 27 0.14
219 27 0.14
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (213 bp):
TATATATAATATATTACTTTATTATACATATAAAATTAATGATACAACTTATAGTATATATAATA
ATTTTATATCAAAATTTGTATAAATAATAACTAATTAAAAACAATATGTTATAAAAACTAAAGCA
ATAACATAAAATTATTAAACGTAATCATATAAATAAAGTTTATTATAAGTTATAGTAATACTTAT
ATAAAAATTAAATATATG
Found at i:2593549 original size:16 final size:17
Alignment explanation
Indices: 2593534--2593585 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
2593524 AAATTTTAAT
2593534 TTTA-ATTC-AATCTAA
1 TTTACATTCAAATCTAA
2593549 TTTACATTCAAATCTAAA
1 TTTACATTCAAATCT-AA
*
2593567 TATACATAATCAAATCTAA
1 TTTACAT--TCAAATCTAA
2593586 AAGTTCAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 5 0.16
18 8 0.26
19 2 0.06
20 8 0.26
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTACATTCAAATCTAA
Found at i:2594277 original size:43 final size:43
Alignment explanation
Indices: 2594230--2594319 Score: 135
Period size: 43 Copynumber: 2.1 Consensus size: 43
2594220 AATTCTAAGC
* *
2594230 ATTTCAAGTTTGTGAAACAATGACCACCGGTGTCGTTTACTTA
1 ATTTCAAGTTTGTGAAACAATAACCACCGGTGTCATTTACTTA
* * *
2594273 ATTTCAAGTTTGTGAAACGATAACTACTGGTGTCATTTACTTA
1 ATTTCAAGTTTGTGAAACAATAACCACCGGTGTCATTTACTTA
2594316 ATTT
1 ATTT
2594320 TTTAAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (43 bp):
ATTTCAAGTTTGTGAAACAATAACCACCGGTGTCATTTACTTA
Found at i:2611908 original size:28 final size:28
Alignment explanation
Indices: 2611867--2611920 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
2611857 ATACCCAAAT
* *
2611867 ATAAAATATGACATGGCATGTTGATTGG
1 ATAAAATATAACATGGCATATTGATTGG
2611895 ATAAAATATAACATGGCATATTGATT
1 ATAAAATATAACATGGCATATTGATT
2611921 AGACACAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (28 bp):
ATAAAATATAACATGGCATATTGATTGG
Found at i:2620578 original size:12 final size:11
Alignment explanation
Indices: 2620555--2620591 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2620545 TCATAAAGAT
2620555 ATATTTTTTTA
1 ATATTTTTTTA
2620566 ATATTTTTATTA
1 ATATTTTT-TTA
2620578 A-ATTTTTTT-
1 ATATTTTTTTA
2620587 ATATT
1 ATATT
2620592 ATTGTATCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 1 0.04
10 5 0.21
11 14 0.58
12 4 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATATTTTTTTA
Found at i:2640742 original size:2 final size:2
Alignment explanation
Indices: 2640735--2640765 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2640725 CCATCAAGTG
2640735 TC TC TC 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 TC TC TC T
2640766 TTCTTTCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2644607 original size:26 final size:26
Alignment explanation
Indices: 2644573--2644630 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
2644563 TTATTTATTA
2644573 TATTTAATTAA-ATT-ATTATTAAATAT
1 TATTTAATTAATATTAATTA--AAATAT
*
2644599 TATTTAATTAATATTAATTAAAATTT
1 TATTTAATTAATATTAATTAAAATAT
2644625 TATTTA
1 TATTTA
2644631 TTATTTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 22 0.76
27 3 0.10
28 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTTAATTAATATTAATTAAAATAT
Found at i:2644628 original size:36 final size:35
Alignment explanation
Indices: 2644539--2644628 Score: 96
Period size: 35 Copynumber: 2.6 Consensus size: 35
2644529 AAATTTAAAT
* * * *
2644539 TATTT-ATAAAAATTATATAAAATTTTATTTATTA
1 TATTTAATTAAAATTTTATTAAATATTATTTATTA
2644573 TATTTAATT-AAATTATTATTAAATATTATTTAATTA
1 TATTTAATTAAAATT-TTATTAAATATTATTT-ATTA
2644609 -ATATTAATTAAAATTTTATT
1 TAT-TTAATTAAAATTTTATT
2644629 TATTATTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
34 10 0.21
35 17 0.36
36 15 0.32
37 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
TATTTAATTAAAATTTTATTAAATATTATTTATTA
Found at i:2644725 original size:26 final size:27
Alignment explanation
Indices: 2644669--2644725 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
2644659 CAAGAGTAAA
2644669 AATATCATTTTATAATATTAATATGTT
1 AATATCATTTTATAATATTAATATGTT
*
2644696 -ATATCATTATT-TATTA-TAATATGTT
1 AATATCATT-TTATAATATTAATATGTT
2644721 AATAT
1 AATAT
2644726 GCTATATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 9 0.33
26 16 0.59
27 2 0.07
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (27 bp):
AATATCATTTTATAATATTAATATGTT
Found at i:2661843 original size:15 final size:16
Alignment explanation
Indices: 2661823--2661852 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2661813 AATCACCACG
2661823 TCAACA-CCGTATTTT
1 TCAACAGCCGTATTTT
2661838 TCAACAGCCGTATTT
1 TCAACAGCCGTATTT
2661853 AACAGAGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.37
Consensus pattern (16 bp):
TCAACAGCCGTATTTT
Found at i:2675226 original size:2 final size:2
Alignment explanation
Indices: 2675219--2675248 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2675209 NNNNNNNNNN
2675219 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
2675249 AAAGACACAA
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):
TA
Found at i:2680344 original size:4 final size:4
Alignment explanation
Indices: 2680335--2680365 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2680325 TATGTACTAT
*
2680335 TTTA TTTA TTTA TTTA TTTA TTTA TATA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2680366 CTTATCGTAT
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:2681739 original size:2 final size:2
Alignment explanation
Indices: 2681734--2681761 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2681724 TACAAAAAAT
2681734 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
2681762 CACACACATA
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):
TA
Found at i:2682990 original size:4 final size:4
Alignment explanation
Indices: 2682981--2683007 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2682971 GCGTGACAAG
2682981 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
2683008 CACATAGATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:2683438 original size:66 final size:66
Alignment explanation
Indices: 2683320--2683818 Score: 301
Period size: 66 Copynumber: 7.6 Consensus size: 66
2683310 GTTTCCTTGT
* * * ** * * *
2683320 CCAGGGCTCGGACCAGAGTCCTTCATGTCGCCATTAGTCT-GGTTGTCTGTTAATTTATTTCCCA
1 CCAGGGCTCGGACCAGAGTCCTTAATGCCTCCAAGAGT-TAGGCTGTCAGTTAACTTATTTCCCA
2683384 CA
65 CA
* * * * *
2683386 CCAGGGCTTGGACCAGAGTCCTTGATGCCTCCAAGGGTTTGGCTGTCAGTTAACTTGTTTCCCAC
1 CCAGGGCTCGGACCAGAGTCCTTAATGCCTCCAAGAGTTAGGCTGTCAGTTAACTTATTTCCCAC
2683451 A
66 A
* * * * * *
2683452 CCAGGACTCGGGCCTGAATCCTTAATGCCTCCGAGA-TTAGAGCTGTCAGTGAACTTATTTCCCA
1 CCAGGGCTCGGACCAGAGTCCTTAATGCCTCCAAGAGTTAG-GCTGTCAGTTAACTTATTTCCCA
2683516 CA
65 CA
* * * * * * * *
2683518 CC-GGGACTTGGACCAGAGTCCTTAATGCCTCCTAGAGTGAAGCTATCGGTTAACTTGTTTCCTA
1 CCAGGG-CTCGGACCAGAGTCCTTAATGCCTCCAAGAGTTAGGCTGTCAGTTAACTTATTTCCCA
*
2683582 CC
65 CA
* * * * * * * *
2683584 CCAGGGCTCGGCCCGGAGTCCTTGATACCTCCAAGAG-TCGAGCTGTC-GATTAACATGTGTCCC
1 CCAGGGCTCGGACCAGAGTCCTTAATGCCTCCAAGAGTTAG-GCTGTCAG-TTAACTTATTTCCC
**
2683647 TGA
64 ACA
* * * * * * * * * *
2683650 CCAGGACTTGGCCCGGAGTCCTTTATACCTCCAAGAG-TCGAGCTATC-GATTAACTTGTGTCCC
1 CCAGGGCTCGGACCAGAGTCCTTAATGCCTCCAAGAGTTAG-GCTGTCAG-TTAACTTATTTCCC
*
2683713 TCA
64 ACA
* * * * ** * * * * * *
2683716 CCAGGACTCGGACCGGAGTCCTTTATACCTCCAAGAGGCAAGCTGTCGGTAAACTTGTGTCCCTC
1 CCAGGGCTCGGACCAGAGTCCTTAATGCCTCCAAGAGTTAGGCTGTCAGTTAACTTATTTCCCAC
2683781 A
66 A
* * * *
2683782 CCAGGACTCGGACCGGAGTCCTTTATACCTCCAAGAG
1 CCAGGGCTCGGACCAGAGTCCTTAATGCCTCCAAGAG
2683819 GCAAGCTGTT
Statistics
Matches: 359, Mismatches: 65, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
65 7 0.02
66 346 0.96
67 6 0.02
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.26
Consensus pattern (66 bp):
CCAGGGCTCGGACCAGAGTCCTTAATGCCTCCAAGAGTTAGGCTGTCAGTTAACTTATTTCCCAC
A
Found at i:2683819 original size:66 final size:66
Alignment explanation
Indices: 2683427--2683850 Score: 422
Period size: 66 Copynumber: 6.4 Consensus size: 66
2683417 CAAGGGTTTG
* * * * * * * * * **
2683427 GCTGTCAGTTAACTTGTTTCCCACACCAGGACTCGGGCCTGAATCCTTAATGCCTCCGAGA-TTA
1 GCTGTCGGTTAACTTGTGTCCCTCACCAGGACTCGGACCGGAGTCCTTTATACCTCCAAGAGGCA
2683491 GA
66 -A
* * * * * * * * * * *
2683493 GCTGTCAGTGAACTTATTTCCCACACCGGGACTTGGACCAGAGTCCTTAATGCCTCCTAGAGTG-
1 GCTGTCGGTTAACTTGTGTCCCTCACCAGGACTCGGACCGGAGTCCTTTATACCTCCAAGAG-GC
2683557 AA
65 AA
* * * * * * *
2683559 GCTATCGGTTAACTTGT-TTCCTACCCCAGGGCTCGGCCCGGAGTCCTTGATACCTCCAAGAGTC
1 GCTGTCGGTTAACTTGTGTCCCT-CACCAGGACTCGGACCGGAGTCCTTTATACCTCCAAGAGGC
*
2683623 GA
65 AA
* * * * * * *
2683625 GCTGTCGATTAACATGTGTCCCTGACCAGGACTTGGCCCGGAGTCCTTTATACCTCCAAGAGTCG
1 GCTGTCGGTTAACTTGTGTCCCTCACCAGGACTCGGACCGGAGTCCTTTATACCTCCAAGAGGCA
2683690 A
66 A
* *
2683691 GCTATCGATTAACTTGTGTCCCTCACCAGGACTCGGACCGGAGTCCTTTATACCTCCAAGAGGCA
1 GCTGTCGGTTAACTTGTGTCCCTCACCAGGACTCGGACCGGAGTCCTTTATACCTCCAAGAGGCA
2683756 A
66 A
*
2683757 GCTGTCGGTAAACTTGTGTCCCTCACCAGGACTCGGACCGGAGTCCTTTATACCTCCAAGAGGCA
1 GCTGTCGGTTAACTTGTGTCCCTCACCAGGACTCGGACCGGAGTCCTTTATACCTCCAAGAGGCA
2683822 A
66 A
* *
2683823 GCTGTTGGTAAACTTGTGTCCCTCACCA
1 GCTGTCGGTTAACTTGTGTCCCTCACCA
2683851 CCAGAGCTTG
Statistics
Matches: 307, Mismatches: 46, Indels: 10
0.85 0.13 0.03
Matches are distributed among these distances:
65 3 0.01
66 299 0.97
67 5 0.02
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (66 bp):
GCTGTCGGTTAACTTGTGTCCCTCACCAGGACTCGGACCGGAGTCCTTTATACCTCCAAGAGGCA
A
Found at i:2683837 original size:132 final size:132
Alignment explanation
Indices: 2683379--2683850 Score: 448
Period size: 132 Copynumber: 3.6 Consensus size: 132
2683369 TTAATTTATT
* * * * * *** * *
2683379 TCCCACACCAGGGCTTGGACCAGAGTCCTTGATGCCTCCAAG-GGTTTGGCTGTCAGTTAACTTG
1 TCCCTCACCAGGACTTGGACCGGAGTCCTTTATACCTCCAAGAGG-CAAGCTATCGGTTAACTTG
* * * * * * * * * *
2683443 TTTCCCACACCAGGACTCGGGCCTGAATCCTTAATGCCTCCGAGA-TTAGAGCTGTCAGTGAACT
65 TGTCCCTCACCAGGACTCGGACCGGAGTCCTTAATACCTCCAAGAGTCA-AGCTGTCGGTAAACT
* *
2683507 TATT
129 TGTG
* * * * * *
2683511 TCCCACACCGGGACTTGGACCAGAGTCCTTAATGCCTCCTAGAGTG-AAGCTATCGGTTAACTTG
1 TCCCTCACCAGGACTTGGACCGGAGTCCTTTATACCTCCAAGAG-GCAAGCTATCGGTTAACTTG
* * * * * * * * *
2683575 T-TTCCTACCCCAGGGCTCGGCCCGGAGTCCTTGATACCTCCAAGAGTCGAGCTGTCGATTAACA
65 TGTCCCT-CACCAGGACTCGGACCGGAGTCCTTAATACCTCCAAGAGTCAAGCTGTCGGTAAACT
2683639 TGTG
129 TGTG
* * * * *
2683643 TCCCTGACCAGGACTTGGCCCGGAGTCCTTTATACCTCCAAGAGTCGAGCTATCGATTAACTTGT
1 TCCCTCACCAGGACTTGGACCGGAGTCCTTTATACCTCCAAGAGGCAAGCTATCGGTTAACTTGT
* *
2683708 GTCCCTCACCAGGACTCGGACCGGAGTCCTTTATACCTCCAAGAGGCAAGCTGTCGGTAAACTTG
66 GTCCCTCACCAGGACTCGGACCGGAGTCCTTAATACCTCCAAGAGTCAAGCTGTCGGTAAACTTG
2683773 TG
131 TG
* * * *
2683775 TCCCTCACCAGGACTCGGACCGGAGTCCTTTATACCTCCAAGAGGCAAGCTGTTGGTAAACTTGT
1 TCCCTCACCAGGACTTGGACCGGAGTCCTTTATACCTCCAAGAGGCAAGCTATCGGTTAACTTGT
2683840 GTCCCTCACCA
66 GTCCCTCACCA
2683851 CCAGAGCTTG
Statistics
Matches: 278, Mismatches: 56, Indels: 12
0.80 0.16 0.03
Matches are distributed among these distances:
131 3 0.01
132 268 0.96
133 6 0.02
134 1 0.00
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.25
Consensus pattern (132 bp):
TCCCTCACCAGGACTTGGACCGGAGTCCTTTATACCTCCAAGAGGCAAGCTATCGGTTAACTTGT
GTCCCTCACCAGGACTCGGACCGGAGTCCTTAATACCTCCAAGAGTCAAGCTGTCGGTAAACTTG
TG
Found at i:2684851 original size:2 final size:2
Alignment explanation
Indices: 2684846--2684877 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
2684836 TTTTTAAGTC
2684846 AT AT AT AT GAT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A
2684878 GTTTTAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2697750 original size:17 final size:17
Alignment explanation
Indices: 2697728--2697760 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2697718 ACTAAAATAT
*
2697728 TTTTAATATATATATAC
1 TTTTAATATAAATATAC
2697745 TTTTAATATAAATATA
1 TTTTAATATAAATATA
2697761 TTTACTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTAATATAAATATAC
Found at i:2697764 original size:15 final size:15
Alignment explanation
Indices: 2697722--2697764 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
2697712 ATATATACTA
*
2697722 AAATATTTTTAATAT
1 AAATATATTTAATAT
*
2697737 ATATATACTTTTAATAT
1 AAATATA--TTTAATAT
2697754 AAATATATTTA
1 AAATATATTTA
2697765 CTTTCTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 9 0.39
17 14 0.61
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATATATTTAATAT
Found at i:2697804 original size:15 final size:15
Alignment explanation
Indices: 2697784--2697834 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
2697774 TTGTGTAACA
2697784 TTATAAAATTATAAT
1 TTATAAAATTATAAT
2697799 TTATAAAATTATTAA-
1 TTATAAAATTA-TAAT
*
2697814 TTATAATATATATAACT
1 TTATAAAAT-TATAA-T
2697831 TTAT
1 TTAT
2697835 TTATATAAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 22 0.71
16 5 0.16
17 4 0.13
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATAAAATTATAAT
Found at i:2713000 original size:18 final size:19
Alignment explanation
Indices: 2712963--2713037 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 19
2712953 CATCATTATT
*
2712963 ATATTATTAAATTTAATATC
1 ATATTATTAAA-TAAATATC
2712983 ATATTATTAAA-AAATATC
1 ATATTATTAAATAAATATC
* *
2713001 ATATTAATACAATTAAATATT
1 ATATTATTA-AA-TAAATATC
2713022 ATATTAATATAAATAA
1 ATATT-AT-TAAATAA
2713038 TTAAAAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
18 14 0.30
19 2 0.04
20 11 0.24
21 14 0.30
22 3 0.07
23 2 0.04
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATTATTAAATAAATATC
Found at i:2713020 original size:21 final size:20
Alignment explanation
Indices: 2712963--2713030 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 20
2712953 CATCATTATT
* *
2712963 ATATTATTAAATTTAATATC
1 ATATTAATAAATTAAATATC
*
2712983 ATATTATTAAA--AAATATC
1 ATATTAATAAATTAAATATC
*
2713001 ATATTAATACAATTAAATATT
1 ATATTAATA-AATTAAATATC
2713022 ATATTAATA
1 ATATTAATA
2713031 TAAATAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 14 0.33
19 2 0.05
20 11 0.26
21 15 0.36
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTAATAAATTAAATATC
Found at i:2713059 original size:35 final size:34
Alignment explanation
Indices: 2713013--2713079 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
2713003 ATTAATACAA
2713013 TTAAATATTATATTAATATAAATAA-TTAAAAATT
1 TTAAATATTATATTAATAT-AATAATTTAAAAATT
* *
2713047 TTAACATATTATATTTATATTATAATTTAAAAA
1 TTAA-ATATTATATTAATATAATAATTTAAAAA
2713080 AAAATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.28
35 21 0.72
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
TTAAATATTATATTAATATAATAATTTAAAAATT
Found at i:2716431 original size:12 final size:12
Alignment explanation
Indices: 2716414--2716456 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
2716404 AAAAATAAAA
2716414 TTTTTATTTAAT
1 TTTTTATTTAAT
2716426 TTTTTATTTATAT
1 TTTTTATTTA-AT
2716439 TATTATTATTT-AT
1 T-TT-TTATTTAAT
2716452 TTTTT
1 TTTTT
2716457 TCAATTCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 2 0.07
12 12 0.43
13 6 0.21
14 2 0.07
15 6 0.21
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATTTAAT
Found at i:2716621 original size:15 final size:16
Alignment explanation
Indices: 2716601--2716634 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2716591 TATTATGTGG
*
2716601 ATTTT-ATTTTTAATA
1 ATTTTAATTTTTAAAA
2716616 ATTTTAATTTTTAAAA
1 ATTTTAATTTTTAAAA
2716632 ATT
1 ATT
2716635 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAATTTTTAAAA
Found at i:2719462 original size:11 final size:11
Alignment explanation
Indices: 2719446--2719477 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2719436 AAAGTATTTA
2719446 AAAATAATAAT
1 AAAATAATAAT
2719457 AAAATAATAAT
1 AAAATAATAAT
*
2719468 AAAATGATAA
1 AAAATAATAA
2719478 AATAAGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:2719716 original size:21 final size:21
Alignment explanation
Indices: 2719672--2719723 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
2719662 TTAAGTAATT
*
2719672 ATATAATAAAATCTAAGAAAA
1 ATATAATAAAATATAAGAAAA
* *
2719693 ATATGATAAAATATAA-AAAT
1 ATATAATAAAATATAAGAAAA
2719713 A-ATAA-AAAATA
1 ATATAATAAAATA
2719724 ACTTACTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 6 0.22
19 3 0.11
20 4 0.15
21 14 0.52
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (21 bp):
ATATAATAAAATATAAGAAAA
Found at i:2724765 original size:19 final size:19
Alignment explanation
Indices: 2724741--2724781 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2724731 ACTGAGAGTC
2724741 CTTTTCCAAATCATCTTAT
1 CTTTTCCAAATCATCTTAT
2724760 CTTTTCCAAATCATCTTAT
1 CTTTTCCAAATCATCTTAT
2724779 CTT
1 CTT
2724782 CATACCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (19 bp):
CTTTTCCAAATCATCTTAT
Found at i:2730286 original size:39 final size:41
Alignment explanation
Indices: 2730206--2730286 Score: 94
Period size: 42 Copynumber: 2.0 Consensus size: 41
2730196 AAATATTTTC
* * * *
2730206 TAATATTATAATTAAAAATAAAAAATATTAAAATAATATATA
1 TAATATAAGAATTAAAAATAAAAAATA-TAAAAGAAAATATA
*
2730248 TAATATAAGAATTAAAACT-AAAAATA-AAAAGAAAATATA
1 TAATATAAGAATTAAAAATAAAAAATATAAAAGAAAATATA
2730287 AGAAATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
39 11 0.32
41 7 0.21
42 16 0.47
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (41 bp):
TAATATAAGAATTAAAAATAAAAAATATAAAAGAAAATATA
Found at i:2730366 original size:6 final size:6
Alignment explanation
Indices: 2730344--2730404 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
2730334 ATGTAATATA
* * * *
2730344 AAAAAT AATATT AAAAAT AAAAAT AAAATAT ATAAAAT GATAAT AATAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-AT A-AAAAT AAAAAT AA-AAAT
*
2730395 GAAAAT AAAA
1 AAAAAT AAAA
2730405 TATATGACAT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
6 30 0.71
7 9 0.21
8 3 0.07
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (6 bp):
AAAAAT
Found at i:2730374 original size:32 final size:33
Alignment explanation
Indices: 2730338--2730408 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 33
2730328 TAAAATATGT
*
2730338 AATATAAAAAATAATATTAA-AAATAAAAATAA
1 AATATAAAAAATAATAATAATAAATAAAAATAA
* * *
2730370 AATATATAAAATGATAATAATAAATGAAAATAA
1 AATATAAAAAATAATAATAATAAATAAAAATAA
2730403 AATATA
1 AATATA
2730409 TGACATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.50
33 17 0.50
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (33 bp):
AATATAAAAAATAATAATAATAAATAAAAATAA
Found at i:2730386 original size:23 final size:20
Alignment explanation
Indices: 2730328--2730380 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
2730318 GAAATTAAAT
*
2730328 TAAAATATGT-AATATAAAAA
1 TAAAATAT-TAAAAATAAAAA
*
2730348 -ATAATATTAAAAATAAAAA
1 TAAAATATTAAAAATAAAAA
2730367 TAAAATATATAAAA
1 TAAAATAT-TAAAA
2730381 TGATAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 1 0.04
19 15 0.56
20 6 0.22
21 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (20 bp):
TAAAATATTAAAAATAAAAA
Found at i:2730396 original size:13 final size:13
Alignment explanation
Indices: 2730357--2730402 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2730347 AATAATATTA
2730357 AAAATAA-AAAT-
1 AAAATAATAAATG
2730368 AAAATATATAAAATG
1 AAAATA-AT-AAATG
*
2730383 ATAATAATAAATG
1 AAAATAATAAATG
2730396 AAAATAA
1 AAAATAA
2730403 AATATATGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 6 0.21
12 1 0.03
13 11 0.38
14 6 0.21
15 5 0.17
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAATAATAAATG
Found at i:2730405 original size:33 final size:32
Alignment explanation
Indices: 2730338--2730409 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 32
2730328 TAAAATATGT
* *
2730338 AATATAAAAAATAATATTAAAAATAAAAATAA
1 AATATATAAAATAATAATAAAAATAAAAATAA
* *
2730370 AATATATAAAATGATAATAATAAATGAAAATAA
1 AATATATAAAATAATAATAA-AAATAAAAATAA
2730403 AATATAT
1 AATATAT
2730410 GACATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
32 17 0.49
33 18 0.51
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (32 bp):
AATATATAAAATAATAATAAAAATAAAAATAA
Found at i:2730411 original size:15 final size:15
Alignment explanation
Indices: 2730363--2730425 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
2730353 ATTAAAAATA
*
2730363 AAAATAAAATATATA
1 AAAATAAAATATATG
*
2730378 AAATGATAATAATAAATG
1 AAA--ATAA-AATATATG
2730396 AAAATAAAATATATG
1 AAAATAAAATATATG
* *
2730411 ACATTAAAAATATAT
1 AAAAT-AAAATATAT
2730426 TTAAGAGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
15 13 0.33
16 13 0.33
17 4 0.10
18 9 0.23
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAATAAAATATATG
Found at i:2730580 original size:21 final size:23
Alignment explanation
Indices: 2730550--2730594 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
2730540 TGTAAACCAA
2730550 ACATTGTAAT-ATTATTTT-CTT
1 ACATTGTAATCATTATTTTACTT
*
2730571 ACATTTTAATCATTATTTTACTT
1 ACATTGTAATCATTATTTTACTT
2730594 A
1 A
2730595 TATACCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 8 0.38
23 4 0.19
ACGTcount: A:0.31, C:0.11, G:0.02, T:0.56
Consensus pattern (23 bp):
ACATTGTAATCATTATTTTACTT
Found at i:2731111 original size:14 final size:14
Alignment explanation
Indices: 2731092--2731119 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2731082 TTGTGGACCG
2731092 TGACAAATTGACAA
1 TGACAAATTGACAA
2731106 TGACAAATTGACAA
1 TGACAAATTGACAA
2731120 CGGATCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
TGACAAATTGACAA
Found at i:2732850 original size:24 final size:24
Alignment explanation
Indices: 2732820--2732925 Score: 176
Period size: 24 Copynumber: 4.4 Consensus size: 24
2732810 AAGACATGAG
2732820 AGGGAGAAGGAACGTGAAAAGGAA
1 AGGGAGAAGGAACGTGAAAAGGAA
* *
2732844 AGAGAGAAGGATCGTGAAAAGGAA
1 AGGGAGAAGGAACGTGAAAAGGAA
*
2732868 AGGGAGAAGGAACATGAAAAGGAA
1 AGGGAGAAGGAACGTGAAAAGGAA
*
2732892 AGGGAGAAGGAACGCGAAAAGGAA
1 AGGGAGAAGGAACGTGAAAAGGAA
2732916 AGGGAGAAGG
1 AGGGAGAAGG
2732926 TTGAAAGGGA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 75 1.00
ACGTcount: A:0.50, C:0.05, G:0.42, T:0.04
Consensus pattern (24 bp):
AGGGAGAAGGAACGTGAAAAGGAA
Found at i:2732925 original size:12 final size:12
Alignment explanation
Indices: 2732820--2732925 Score: 79
Period size: 12 Copynumber: 8.8 Consensus size: 12
2732810 AAGACATGAG
2732820 AGGGAGAAGGAA
1 AGGGAGAAGGAA
* * *
2732832 CGTGAAAAGGAA
1 AGGGAGAAGGAA
* *
2732844 AGAGAGAAGGAT
1 AGGGAGAAGGAA
* * *
2732856 CGTGAAAAGGAA
1 AGGGAGAAGGAA
2732868 AGGGAGAAGGAA
1 AGGGAGAAGGAA
* *
2732880 CA-TGAAAAGGAA
1 -AGGGAGAAGGAA
2732892 AGGGAGAAGGAA
1 AGGGAGAAGGAA
* * *
2732904 CGCGAAAAGGAA
1 AGGGAGAAGGAA
2732916 AGGGAGAAGG
1 AGGGAGAAGG
2732926 TTGAAAGGGA
Statistics
Matches: 68, Mismatches: 24, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
11 1 0.01
12 66 0.97
13 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.42, T:0.04
Consensus pattern (12 bp):
AGGGAGAAGGAA
Found at i:2735999 original size:28 final size:28
Alignment explanation
Indices: 2735957--2736013 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
2735947 ATATATTCAC
*
2735957 TTGACAATTCTTGATTAAATTTTATAAT
1 TTGACAATTCATGATTAAATTTTATAAT
*
2735985 TTGACAATTCATGATTATATTTTATAAT
1 TTGACAATTCATGATTAAATTTTATAAT
2736013 T
1 T
2736014 AATTTGTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (28 bp):
TTGACAATTCATGATTAAATTTTATAAT
Found at i:2739787 original size:25 final size:25
Alignment explanation
Indices: 2739757--2739808 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
2739747 TGAAGAAGAT
2739757 CATCTTCAACTTTGCAACTTCATCA
1 CATCTTCAACTTTGCAACTTCATCA
2739782 CATCTTCAACTTTGCAACTTCATCA
1 CATCTTCAACTTTGCAACTTCATCA
2739807 CA
1 CA
2739809 ACCAAAACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.33, G:0.04, T:0.35
Consensus pattern (25 bp):
CATCTTCAACTTTGCAACTTCATCA
Found at i:2743003 original size:20 final size:20
Alignment explanation
Indices: 2742978--2743017 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2742968 CATCTAGTTC
2742978 TTTCTTGCCATCCTAAAAAT
1 TTTCTTGCCATCCTAAAAAT
2742998 TTTCTTGCCATCCTAAAAAT
1 TTTCTTGCCATCCTAAAAAT
2743018 AGAGATGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (20 bp):
TTTCTTGCCATCCTAAAAAT
Found at i:2743268 original size:44 final size:44
Alignment explanation
Indices: 2743228--2743314 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
2743218 AGTTTTTGGA
* * *
2743228 TATTGTGAAATTAATTTTTAAGTATTACGTGACCGATTTTTAAG
1 TATTGTGAAACTAAATTTTAAGCATTACGTGACCGATTTTTAAG
* ** *
2743272 TATTGTGTAACTAAATTTTAAGCATTGTGTGACTGATTTTTAA
1 TATTGTGAAACTAAATTTTAAGCATTACGTGACCGATTTTTAA
2743315 ACAATGCTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (44 bp):
TATTGTGAAACTAAATTTTAAGCATTACGTGACCGATTTTTAAG
Found at i:2743312 original size:22 final size:22
Alignment explanation
Indices: 2743241--2743314 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 22
2743231 TGTGAAATTA
** *
2743241 ATTTTTAAGTATTACGTGACCG
1 ATTTTTAAGTATTGTGTGACTG
* *
2743263 ATTTTTAAGTATTGTGTAACTA
1 ATTTTTAAGTATTGTGTGACTG
* *
2743285 AATTTTAAGCATTGTGTGACTG
1 ATTTTTAAGTATTGTGTGACTG
2743307 ATTTTTAA
1 ATTTTTAA
2743315 ACAATGCTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (22 bp):
ATTTTTAAGTATTGTGTGACTG
Found at i:2743372 original size:23 final size:23
Alignment explanation
Indices: 2743346--2743406 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
2743336 GCCTAAAAAT
*
2743346 TAGTCACATAATATTTTACTAAC
1 TAGTCACAAAATATTTTACTAAC
** * *
2743369 TAGTCACGCAATACTTTATTAAC
1 TAGTCACAAAATATTTTACTAAC
2743392 TAGTC-CAAAATATTT
1 TAGTCACAAAATATTT
2743407 AACATGCTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (23 bp):
TAGTCACAAAATATTTTACTAAC
Found at i:2743769 original size:27 final size:28
Alignment explanation
Indices: 2743734--2743798 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
2743724 ATAAAGATTT
* * *
2743734 AAAATTAATACTTCTG-AATTTTTTTTA
1 AAAAATAATACTTCTGAAATATTTTTAA
*
2743761 AAAAATAATACTTGTGAAATATTTTTAA
1 AAAAATAATACTTCTGAAATATTTTTAA
2743789 ACAAAATAAT
1 A-AAAATAAT
2743799 GAAATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 14 0.44
28 10 0.31
29 8 0.25
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.42
Consensus pattern (28 bp):
AAAAATAATACTTCTGAAATATTTTTAA
Found at i:2743810 original size:22 final size:24
Alignment explanation
Indices: 2743775--2743821 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2743765 ATAATACTTG
*
2743775 TGAAATATTTTTAAA-CAAAATAA
1 TGAAATATTTTTAAATAAAAATAA
2743798 TGAAAT-TTTTTAAATAAAAATAA
1 TGAAATATTTTTAAATAAAAATAA
2743821 T
1 T
2743822 CAATACCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (24 bp):
TGAAATATTTTTAAATAAAAATAA
Found at i:2745880 original size:29 final size:27
Alignment explanation
Indices: 2745828--2745897 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 27
2745818 ATTTTTAATT
*
2745828 AAAAATATTAATAGTTTTAATAAATTATC
1 AAAAAT-TTAATAGTTTTAATAAA-AATC
2745857 AAAAATTTAATA-TTTTATATTAAAAATC
1 AAAAATTTAATAGTTTTA-A-TAAAAATC
*
2745885 ATAAATTATAATA
1 AAAAATT-TAATA
2745898 AAGAGTATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 5 0.14
28 16 0.44
29 15 0.42
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (27 bp):
AAAAATTTAATAGTTTTAATAAAAATC
Found at i:2745885 original size:28 final size:28
Alignment explanation
Indices: 2745823--2745897 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 28
2745813 ATTAAATTTT
*
2745823 TAATTAAAAATATTAATAGTTTTAATAAA
1 TAATCAAAAAT-TTAATAGTTTTAATAAA
*
2745852 TTATCAAAAATTTAATA-TTTTATATTAAA
1 TAATCAAAAATTTAATAGTTTTA-A-TAAA
*
2745881 -AATCATAAATTATAATA
1 TAATCAAAAATT-TAATA
2745898 AAGAGTATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.13
28 16 0.41
29 18 0.46
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (28 bp):
TAATCAAAAATTTAATAGTTTTAATAAA
Found at i:2750599 original size:85 final size:85
Alignment explanation
Indices: 2750187--2750600 Score: 551
Period size: 85 Copynumber: 4.9 Consensus size: 85
2750177 TTTTTCAGAT
* * * * *
2750187 ATATATATTTGTTTAGATCGATCCAATTATGCATTTAAGTTTCAATCGAATTAGTATATTTGAAA
1 ATATATATTTATTCAGATCGATCCAATTATGCATTTAAGTTCCAACCGAACTAGTATATTTGAAA
*
2750252 T-AGAAATACCGTTTTTTCTG
66 TGA-AAATACTGTTTTTTCTG
* * * *
2750272 ATATATATTTACTCGGATCGATCCAATTATGCATTTAAGTTCCAATCGAACTACTATATTTGAAA
1 ATATATATTTATTCAGATCGATCCAATTATGCATTTAAGTTCCAACCGAACTAGTATATTTGAAA
*
2750337 TGAAAATATTGTTTTTTCTG
66 TGAAAATACTGTTTTTTCTG
* **********
2750357 ATATATATTTATTCAGATCAATCCAATTATGCATNNNNNNNNNNACCGAACTAGTATATTTGAAA
1 ATATATATTTATTCAGATCGATCCAATTATGCATTTAAGTTCCAACCGAACTAGTATATTTGAAA
* *
2750422 TGAAAATACTATTTTTTCTT
66 TGAAAATACTGTTTTTTCTG
* *
2750442 ATATATATTTGTTCAGATCAATCCAATTATGCATTTAAGTTCCAACCGAACTAGTATATTTGAAA
1 ATATATATTTATTCAGATCGATCCAATTATGCATTTAAGTTCCAACCGAACTAGTATATTTGAAA
* *
2750507 TGGAAATACTGTTTTTCCTG
66 TGAAAATACTGTTTTTTCTG
*
2750527 ATGTATATTTATTCAGATCGATCCAATTATGCATTTAAGTTCCAACCGAACTAGTATATTTGAAA
1 ATATATATTTATTCAGATCGATCCAATTATGCATTTAAGTTCCAACCGAACTAGTATATTTGAAA
2750592 TGAAAATAC
66 TGAAAATAC
2750601 ACCAAACTAG
Statistics
Matches: 282, Mismatches: 46, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
85 281 1.00
86 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.39
Consensus pattern (85 bp):
ATATATATTTATTCAGATCGATCCAATTATGCATTTAAGTTCCAACCGAACTAGTATATTTGAAA
TGAAAATACTGTTTTTTCTG
Found at i:2755334 original size:18 final size:18
Alignment explanation
Indices: 2755287--2755339 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
2755277 GATTTTAACG
* *
2755287 TTTTTTTATAATATATAAA
1 TTTTTTTATATTAT-TTAA
2755306 TTTTTTTATATTATTTAA
1 TTTTTTTATATTATTTAA
2755324 TTTTTTTATATT-TTTA
1 TTTTTTTATATTATTTA
2755340 TTATATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.12
18 15 0.47
19 13 0.41
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTTTATATTATTTAA
Found at i:2755337 original size:26 final size:27
Alignment explanation
Indices: 2755308--2755370 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
2755298 TATATAAATT
* *
2755308 TTTTTA-TATTATTTAATTTTTTTA-TA
1 TTTTTATTA-TATTTAATTATTTTTATA
2755334 TTTTTATTATATTTAATTAAATTTTTATA
1 TTTTTATTATATTTAATT--ATTTTTATA
2755363 TTTTTATT
1 TTTTTATT
2755371 GTAAGTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 15 0.48
27 2 0.06
28 4 0.13
29 10 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTTTATTATATTTAATTATTTTTATA
Found at i:2755347 original size:21 final size:20
Alignment explanation
Indices: 2755304--2755361 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 20
2755294 ATAATATATA
*
2755304 AATTTTTTTATA-TTAT-TT
1 AATTTTTTTATATTTTTATT
2755322 AATTTTTTTATATTTTTATT
1 AATTTTTTTATATTTTTATT
** *
2755342 ATATTTAATTAAATTTTTAT
1 A-ATTTTTTTATATTTTTAT
2755362 ATTTTTATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 12 0.36
19 3 0.09
20 3 0.09
21 15 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
AATTTTTTTATATTTTTATT
Found at i:2755358 original size:29 final size:28
Alignment explanation
Indices: 2755305--2755395 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 28
2755295 TAATATATAA
* *
2755305 ATTTTT-TTATATTATTTAATTTTTTTAT
1 ATTTTTATTATATTAATTAA-ATTTTTAT
2755333 ATTTTTATTATATTTAATTAAATTTTTAT
1 ATTTTTATTATA-TTAATTAAATTTTTAT
* *
2755362 ATTTTTATTGTAAGTTAAATAAATTTTTAT
1 ATTTTTATTAT-A-TTAATTAAATTTTTAT
2755392 ATTT
1 ATTT
2755396 GTTAAAATTA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 6 0.11
29 22 0.40
30 27 0.49
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
ATTTTTATTATATTAATTAAATTTTTAT
Found at i:2755385 original size:30 final size:29
Alignment explanation
Indices: 2755326--2755395 Score: 104
Period size: 30 Copynumber: 2.4 Consensus size: 29
2755316 TTATTTAATT
* *
2755326 TTTTTATATTTTTATTATATTTAATTAAA
1 TTTTTATATTTTTATTATAGTTAAATAAA
*
2755355 TTTTTATATTTTTATTGTAAGTTAAATAAA
1 TTTTTATATTTTTATTAT-AGTTAAATAAA
2755385 TTTTTATATTT
1 TTTTTATATTT
2755396 GTTAAAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 17 0.46
30 20 0.54
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (29 bp):
TTTTTATATTTTTATTATAGTTAAATAAA
Found at i:2755510 original size:33 final size:33
Alignment explanation
Indices: 2755467--2755554 Score: 104
Period size: 33 Copynumber: 2.7 Consensus size: 33
2755457 TTATATCATA
* *
2755467 TGATATTAATATAATATATTAAAATATTATATT
1 TGATAATAATATAATATATTAAAATATTATAAT
* * * **
2755500 TTATAATAATATGATATACTAGTATATTATAAT
1 TGATAATAATATAATATATTAAAATATTATAAT
*
2755533 TGATAATAATATAACATATTAA
1 TGATAATAATATAATATATTAA
2755555 TTTAACATGA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (33 bp):
TGATAATAATATAATATATTAAAATATTATAAT
Found at i:2761773 original size:25 final size:24
Alignment explanation
Indices: 2761739--2761785 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
2761729 CAATCTTGTT
2761739 TTCATTTATAGTTCTGCA-ACTGATC
1 TTCATTTATA--TCTGCAGACTGATC
2761764 TTCATTTATATCTGCAGACTGA
1 TTCATTTATATCTGCAGACTGA
2761786 GGATAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.29
24 5 0.24
25 10 0.48
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (24 bp):
TTCATTTATATCTGCAGACTGATC
Found at i:2768828 original size:15 final size:15
Alignment explanation
Indices: 2768810--2768840 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2768800 GTGTGATTAT
2768810 AAGTAATATGATTGC
1 AAGTAATATGATTGC
*
2768825 AAGTAATGTGATTGC
1 AAGTAATATGATTGC
2768840 A
1 A
2768841 GGAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (15 bp):
AAGTAATATGATTGC
Found at i:2769086 original size:21 final size:21
Alignment explanation
Indices: 2769027--2769086 Score: 50
Period size: 26 Copynumber: 2.7 Consensus size: 21
2769017 TATCATCTCC
*
2769027 TATATTTATTTT-TAATGTGA
1 TATATTTATTTTATAATCTGA
*
2769047 TATACTTTATTTTTATTATAATCTTA
1 TATA-TTTA---TT-TTATAATCTGA
2769073 TATATTTATTTTAT
1 TATATTTATTTTAT
2769087 TTTTTATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
20 4 0.12
21 8 0.25
22 2 0.06
24 2 0.06
25 6 0.19
26 10 0.31
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (21 bp):
TATATTTATTTTATAATCTGA
Found at i:2775721 original size:4 final size:4
Alignment explanation
Indices: 2775712--2775742 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2775702 ACCAGCAGAA
2775712 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
2775743 AGGCACCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:2796443 original size:95 final size:94
Alignment explanation
Indices: 2796275--2796468 Score: 248
Period size: 95 Copynumber: 2.1 Consensus size: 94
2796265 TCAATTAATG
* * * * * **
2796275 AATTTTGCCACTGTAATTTTAATTTTGTTGATTTTTGGACAAAATGTAATGAAATTATAATATTT
1 AATTTTACCACTATAATTTTAATCTTGTTCATTTTTGAACAAAACATAATGAAATTATAATATTT
*
2796340 CACAGAATATTTTGTTAAATGGA-ATAGGCA
66 CACAGAATATTTTGTT-AATGCAGAT-GGCA
*
2796370 AATTTTACCACTATACTTTTAATCTTGTTCATTTTTGAACAAAACATAATGAAATTGA-AATATT
1 AATTTTACCACTATAATTTTAATCTTGTTCATTTTTGAACAAAACATAATGAAATT-ATAATATT
**
2796434 TCATGGAATATTTTGTTAATGCAGATGGCA
65 TCACAGAATATTTTGTTAATGCAGATGGCA
2796464 AATTT
1 AATTT
2796469 CCATCAATTC
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
94 14 0.16
95 71 0.83
96 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (94 bp):
AATTTTACCACTATAATTTTAATCTTGTTCATTTTTGAACAAAACATAATGAAATTATAATATTT
CACAGAATATTTTGTTAATGCAGATGGCA
Found at i:2797162 original size:77 final size:77
Alignment explanation
Indices: 2797035--2797190 Score: 258
Period size: 77 Copynumber: 2.0 Consensus size: 77
2797025 TTTTCCAAGC
* ** *
2797035 CTCACCAGCTGATGGTTTTGATTGAATAGCCTAAATGAAAAATTAATCATATGGAGCATAGAAAT
1 CTCACCAGCAGATGGTTTTGATTGAATAGCCTAAACAAAAAATTAATCATATGGAGCATAAAAAT
2797100 TAGAAGCCATCA
66 TAGAAGCCATCA
*
2797112 CTCACCGGCAGATGGTTTTGATTGAATAGCCTAAACAAAAAATTAATCATATGGAGCATAAAAAT
1 CTCACCAGCAGATGGTTTTGATTGAATAGCCTAAACAAAAAATTAATCATATGGAGCATAAAAAT
*
2797177 TAGAAGTCATCA
66 TAGAAGCCATCA
2797189 CT
1 CT
2797191 TTTTTTAGAC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (77 bp):
CTCACCAGCAGATGGTTTTGATTGAATAGCCTAAACAAAAAATTAATCATATGGAGCATAAAAAT
TAGAAGCCATCA
Found at i:2801229 original size:20 final size:21
Alignment explanation
Indices: 2801201--2801241 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2801191 GTCACATAAA
* *
2801201 TATGTCATGTTATCAT-TTAT
1 TATGGCATGTCATCATATTAT
2801221 TATGGCATGTCATCATATTAT
1 TATGGCATGTCATCATATTAT
2801242 GTCAATGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (21 bp):
TATGGCATGTCATCATATTAT
Found at i:2801355 original size:26 final size:27
Alignment explanation
Indices: 2801308--2801361 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
2801298 AACTATTAAT
*
2801308 TATAAAATTATTTAATTTAAAATAAAAA
1 TATAAAA-TATTTAATTAAAAATAAAAA
2801336 TATAAAA-ATTTAATTAAAAATAAAAA
1 TATAAAATATTTAATTAAAAATAAAAA
2801362 ATTATTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 18 0.72
28 7 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
TATAAAATATTTAATTAAAAATAAAAA
Found at i:2817112 original size:13 final size:14
Alignment explanation
Indices: 2817096--2817127 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2817086 ACTAAAACCC
2817096 AAAAAAAAAGAAA-
1 AAAAAAAAAGAAAG
2817109 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
2817123 AAAAA
1 AAAAA
2817128 GAAGTGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:2817832 original size:18 final size:18
Alignment explanation
Indices: 2817789--2817835 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2817779 AATTGGCTTT
*
2817789 GACTTGGAATTGGAAGTA
1 GACTTGGAATTCGAAGTA
* *
2817807 GAAC-TGGAATTCGAATTC
1 G-ACTTGGAATTCGAAGTA
2817825 GACTTGGAATT
1 GACTTGGAATT
2817836 GAAATTTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.30
Consensus pattern (18 bp):
GACTTGGAATTCGAAGTA
Found at i:2818254 original size:3 final size:3
Alignment explanation
Indices: 2818246--2818270 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2818236 AATGACAATG
2818246 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
2818271 AGCTTCCCAT
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:2819090 original size:38 final size:39
Alignment explanation
Indices: 2819010--2819106 Score: 160
Period size: 38 Copynumber: 2.5 Consensus size: 39
2819000 AGACACAGCA
*
2819010 GGGTTTGTGTTGTTTTTAATCTTCAAAAAAAAAAAAAAGG
1 GGGTTGGTGTTG-TTTTAATCTTCAAAAAAAAAAAAAAGG
*
2819050 GGGTTGGTGTTGTTTTAATCTTC-AAAAAAAAAAAAGGG
1 GGGTTGGTGTTGTTTTAATCTTCAAAAAAAAAAAAAAGG
2819088 GGGTTGGTGTTGTTTTAAT
1 GGGTTGGTGTTGTTTTAAT
2819107 TATATAAAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
38 33 0.60
39 11 0.20
40 11 0.20
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (39 bp):
GGGTTGGTGTTGTTTTAATCTTCAAAAAAAAAAAAAAGG
Found at i:2820327 original size:3 final size:3
Alignment explanation
Indices: 2820319--2820363 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2820309 TTAAAGACTA
2820319 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2820364 TTAAAAGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2824546 original size:2 final size:2
Alignment explanation
Indices: 2824539--2824568 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2824529 TTGCAAACGA
2824539 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2824569 GGACGTGTTA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2825325 original size:29 final size:30
Alignment explanation
Indices: 2825291--2825364 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
2825281 TTGCATTTTT
*
2825291 TAATTAAAAGTTAAATGTTTT-AATTATAA
1 TAATTAAAAGTTAAATATTTTAAATTATAA
* * *
2825320 TAATTAAGAGTTAAATATTTTCAAATTTTTA
1 TAATTAAAAGTTAAATATTTT-AAATTATAA
2825351 TAATTAAAAGTTAA
1 TAATTAAAAGTTAA
2825365 GGTAAGAGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 19 0.50
31 19 0.50
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (30 bp):
TAATTAAAAGTTAAATATTTTAAATTATAA
Found at i:2825531 original size:55 final size:55
Alignment explanation
Indices: 2825454--2825636 Score: 154
Period size: 55 Copynumber: 3.3 Consensus size: 55
2825444 ACAGTTTTTT
**
2825454 TAATATGTAATAATTAAATTTTTCAACATGATGTA-TAATAACTAAAATTTTAATA
1 TAATATGTAATAATTAAATTTTTCAACATG-TCAAGTAATAACTAAAATTTTAATA
* ** * * *
2825509 TAATGTGTAATAATTATCTTTTTTAATATGTCAAGTAATAATTAAAATTTTAATA
1 TAATATGTAATAATTAAATTTTTCAACATGTCAAGTAATAACTAAAATTTTAATA
* * * * * * * * * * *
2825564 TGACATGTAACAATTACATTTTT-AACTTGACATGAAATAATTATATTTTTAATA
1 TAATATGTAATAATTAAATTTTTCAACATGTCAAGTAATAACTAAAATTTTAATA
**
2825618 TAATATACAATAATTAAAT
1 TAATATGTAATAATTAAAT
2825637 ATTCAACCTG
Statistics
Matches: 100, Mismatches: 27, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
54 39 0.39
55 61 0.61
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (55 bp):
TAATATGTAATAATTAAATTTTTCAACATGTCAAGTAATAACTAAAATTTTAATA
Found at i:2825573 original size:27 final size:27
Alignment explanation
Indices: 2825458--2825636 Score: 126
Period size: 27 Copynumber: 6.6 Consensus size: 27
2825448 TTTTTTTAAT
* *
2825458 ATGTAATAATTAAATTTTTCAACATGAT
1 ATGTAATAATTAAATTTTT-AATATGAC
* * * * * *
2825486 GTATAATAACTAAAATTTTAATATAAT
1 ATGTAATAATTAAATTTTTAATATGAC
* ** *
2825513 GTGTAATAATTATCTTTTTTAATATGTC
1 ATGTAATAATTA-AATTTTTAATATGAC
* *
2825541 AAGTAATAATTAAAATTTTAATATGAC
1 ATGTAATAATTAAATTTTTAATATGAC
* *
2825568 ATGTAACAATTACATTTTTAACT-TGAC
1 ATGTAATAATTAAATTTTTAA-TATGAC
* * * *
2825595 ATGAAATAATTATATTTTTAATATAAT
1 ATGTAATAATTAAATTTTTAATATGAC
**
2825622 ATACAATAATTAAAT
1 ATGTAATAATTAAAT
2825637 ATTCAACCTG
Statistics
Matches: 116, Mismatches: 32, Indels: 7
0.75 0.21 0.05
Matches are distributed among these distances:
26 1 0.01
27 80 0.69
28 35 0.30
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (27 bp):
ATGTAATAATTAAATTTTTAATATGAC
Found at i:2828512 original size:26 final size:24
Alignment explanation
Indices: 2828483--2828544 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 24
2828473 ATTTATAAAA
*
2828483 TTTAAATAAATCATTATTTTTATCAT
1 TTTAAATAAATCATTATATTT-T-AT
* **
2828509 TTTAATTAAATTTTTATATTTTAT
1 TTTAAATAAATCATTATATTTTAT
2828533 TTTAAATTAAAT
1 TTTAAA-TAAAT
2828545 TAATTTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 7 0.23
25 6 0.20
26 17 0.57
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTAAATAAATCATTATATTTTAT
Found at i:2828560 original size:13 final size:14
Alignment explanation
Indices: 2828542--2828574 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2828532 TTTTAAATTA
*
2828542 AATTAATTTTTA-T
1 AATTAATTATTATT
2828555 AATTAATTATTATT
1 AATTAATTATTATT
2828569 AATTAA
1 AATTAA
2828575 AATATCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTAATTATTATT
Found at i:2831363 original size:16 final size:15
Alignment explanation
Indices: 2831325--2831368 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
2831315 AAAAATTATG
*
2831325 AAAAAATTAATAAATT
1 AAAAAATT-ATTAATT
*
2831341 AATAAATTATTAATT
1 AAAAAATTATTAATT
2831356 AAAAAAATTATTA
1 -AAAAAATTATTA
2831369 TCATATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAAAATTATTAATT
Found at i:2831614 original size:18 final size:18
Alignment explanation
Indices: 2831584--2831632 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
2831574 TGTATAACAA
2831584 AAAATATTTTTTTAAAAT
1 AAAATATTTTTTTAAAAT
2831602 AAAAT-TTTATTTTAAAAATT
1 AAAATATTT-TTTT-AAAA-T
*
2831622 AATATATTTTT
1 AAAATATTTTT
2831633 GTGTAATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 3 0.12
18 9 0.35
19 4 0.15
20 7 0.27
21 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAAATATTTTTTTAAAAT
Found at i:2857722 original size:2 final size:2
Alignment explanation
Indices: 2857715--2857743 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2857705 GCTATGTGTC
2857715 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
2857744 TGGGGTAGAG
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:2868760 original size:22 final size:21
Alignment explanation
Indices: 2868726--2868772 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
2868716 TTCGGGGGCA
*
2868726 TTTTTTTCCTTGGAGCT-GTTGC
1 TTTTTTACCTTGG-GCTAGTT-C
*
2868748 TTTTTTACGTTGGGCTAGTTC
1 TTTTTTACCTTGGGCTAGTTC
2868769 TTTT
1 TTTT
2868773 AGGAGTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.06, C:0.15, G:0.21, T:0.57
Consensus pattern (21 bp):
TTTTTTACCTTGGGCTAGTTC
Found at i:2871986 original size:6 final size:6
Alignment explanation
Indices: 2871975--2872001 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2871965 TATGTTGCAA
2871975 TGTGCC TGTGCC TGTGCC TGTGCC TGT
1 TGTGCC TGTGCC TGTGCC TGTGCC TGT
2872002 ATCATATACT
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:0.00, C:0.30, G:0.33, T:0.37
Consensus pattern (6 bp):
TGTGCC
Found at i:2882111 original size:2 final size:2
Alignment explanation
Indices: 2882104--2882150 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2882094 CTTCCTGATT
2882104 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2882146 TC TC T
1 TC TC T
2882151 ATATATATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2882155 original size:2 final size:2
Alignment explanation
Indices: 2882150--2882174 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2882140 TCTCTCTCTC
2882150 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
2882175 TTGTTAAATG
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:2887547 original size:25 final size:24
Alignment explanation
Indices: 2887494--2887553 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 24
2887484 TTATTGCTCA
* *
2887494 AATG-AAGAAAAAATAATAATTAT
1 AATGCAAGAAAAAATAACAATAAT
**
2887517 TGTGCAAGAAAACAATAACAATAAT
1 AATGCAAGAAAA-AATAACAATAAT
*
2887542 AATGCAATAAAA
1 AATGCAAGAAAA
2887554 GAAAAGGCAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
23 2 0.07
24 7 0.25
25 19 0.68
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.22
Consensus pattern (24 bp):
AATGCAAGAAAAAATAACAATAAT
Found at i:2889922 original size:3 final size:3
Alignment explanation
Indices: 2889908--2889939 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2889898 CATGGTGGAA
*
2889908 AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2889940 AAGGGAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2891177 original size:17 final size:17
Alignment explanation
Indices: 2891133--2891179 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
2891123 TTTTTTTAAT
2891133 TTATATATTA-TATAAAA
1 TTAT-TATTATTATAAAA
*
2891150 TTATTACTTATTATAAAT
1 TTATTA-TTATTATAAAA
*
2891168 TTTTTATTATTA
1 TTATTATTATTA
2891180 ATTAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 2 0.08
17 13 0.50
18 11 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATTATTATTATAAAA
Found at i:2901375 original size:57 final size:57
Alignment explanation
Indices: 2901306--2901419 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
2901296 GGAACCTGGG
* *
2901306 CCAGACAGCCCAACAACCTTTATGTTGACACCATTGCTTGCATATTACAACCAGACA
1 CCAGACAGCCCAACAACCTTTATGCTGACACCATTGCTTGCAGATTACAACCAGACA
*
2901363 CCAGACAGCCCAATAACCTTTATGCTGACACCATTGCTTGCAGATTACAACCAGACA
1 CCAGACAGCCCAACAACCTTTATGCTGACACCATTGCTTGCAGATTACAACCAGACA
2901420 GATGCAGTCT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.33, C:0.32, G:0.13, T:0.22
Consensus pattern (57 bp):
CCAGACAGCCCAACAACCTTTATGCTGACACCATTGCTTGCAGATTACAACCAGACA
Done.