Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 10 of 105
Found at i:1870959 original size:19 final size:18
Alignment explanation
Indices: 1870937--1870972 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1870927 TTTTTTTCTT
*
1870937 TAAAAATTTAAATTAAAAA
1 TAAAAAATTAAA-TAAAAA
1870956 TAAAAAATTAAATAAAA
1 TAAAAAATTAAATAAAA
1870973 TAATTAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAAATTAAATAAAAA
Found at i:1870979 original size:13 final size:13
Alignment explanation
Indices: 1870953--1870985 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1870943 TTTAAATTAA
1870953 AAATAAAA-AATT
1 AAATAAAATAATT
1870965 AAATAAAATAATT
1 AAATAAAATAATT
1870978 -AATAAAAT
1 AAATAAAAT
1870986 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:1885269 original size:48 final size:48
Alignment explanation
Indices: 1885210--1885344 Score: 198
Period size: 48 Copynumber: 2.8 Consensus size: 48
1885200 TTCAATAGAT
* *
1885210 TTTTTAAGTTGTTGAGCTTCTGCTTAGAGGAGCTTTTTCAAGATGAAG
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAAG
* *
1885258 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAAT
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAAG
* * *
1885306 TTTTAAAATTGTTGAGCCTATACTTAGAGGAGCCTTTTT
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAG-CTTTTT
1885345 AATTTTTCAA
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
48 72 0.92
49 6 0.08
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.41
Consensus pattern (48 bp):
TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAAG
Found at i:1885377 original size:44 final size:43
Alignment explanation
Indices: 1885303--1885498 Score: 211
Period size: 45 Copynumber: 4.4 Consensus size: 43
1885293 TTTCAAGATG
* * *
1885303 AATTTTTAAAA-TTGTTGAGCCTATACTTAGAGGAGCCTTTTT
1 AATTTTTAAAAGTTGTTAAGCCTCTACTTAGAGGAGCCTTTTA
* *
1885345 AATTTTTCAAAAGTCGTTAAGCCTCTATTTAGAAGG-GCCTCTTTA
1 AATTTTT-AAAAGTTGTTAAGCCTCTACTTAG-AGGAGCCT-TTTA
* *
1885390 AATTTTTAAAAGTTGTTAAGCCTCTACTTAGATGAACCTTTTTTA
1 AATTTTTAAAAGTTGTTAAGCCTCTACTTAGAGGAGCC--TTTTA
*
1885435 AATTTTTAAAAGTTGTTGAA-CCTCTA-TTCAGAGGAGTCTTTTA
1 AATTTTTAAAAGTTGTT-AAGCCTCTACTT-AGAGGAGCCTTTTA
1885478 AATTTTTAAAAAAGTTGTTAA
1 AATTTTT--AAAAGTTGTTAA
1885499 CCTTCTGGAG
Statistics
Matches: 131, Mismatches: 12, Indels: 20
0.80 0.07 0.12
Matches are distributed among these distances:
42 7 0.05
43 18 0.14
44 47 0.36
45 56 0.43
46 3 0.02
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (43 bp):
AATTTTTAAAAGTTGTTAAGCCTCTACTTAGAGGAGCCTTTTA
Found at i:1885418 original size:88 final size:88
Alignment explanation
Indices: 1885303--1885498 Score: 240
Period size: 88 Copynumber: 2.2 Consensus size: 88
1885293 TTTCAAGATG
* *
1885303 AATTTTTAAAA-TTGTTGAGCCTATACTTAGAGGAGCC-TTTTT-AATTTTTCAAAAGTCGTT-A
1 AATTTTTAAAAGTTGTTAAGCCTATACTTAGAGGAACCTTTTTTAAATTTTT-AAAAGTCGTTGA
*
1885364 AGCCTCTATTTAGAAGG-GCCTCTTTA
65 A-CCTCTATTCAG-AGGAGCCT-TTTA
* * *
1885390 AATTTTTAAAAGTTGTTAAGCCTCTACTTAGATGAACCTTTTTTAAATTTTTAAAAGTTGTTGAA
1 AATTTTTAAAAGTTGTTAAGCCTATACTTAGAGGAACCTTTTTTAAATTTTTAAAAGTCGTTGAA
*
1885455 CCTCTATTCAGAGGAGTCTTTTA
66 CCTCTATTCAGAGGAGCCTTTTA
1885478 AATTTTTAAAAAAGTTGTTAA
1 AATTTTT--AAAAGTTGTTAA
1885499 CCTTCTGGAG
Statistics
Matches: 95, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
87 11 0.12
88 36 0.38
89 27 0.28
90 21 0.22
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (88 bp):
AATTTTTAAAAGTTGTTAAGCCTATACTTAGAGGAACCTTTTTTAAATTTTTAAAAGTCGTTGAA
CCTCTATTCAGAGGAGCCTTTTA
Found at i:1885435 original size:45 final size:43
Alignment explanation
Indices: 1885303--1885498 Score: 177
Period size: 44 Copynumber: 4.4 Consensus size: 43
1885293 TTTCAAGATG
* * *
1885303 AATTTTTAAAA-TTGTTGAGCCTATACTTAGAGGAGCCTTTTT-
1 AATTTTTAAAAGTTGTTAAGCCTCTACTTAGA-GAACCTTTTTA
* * ** *
1885345 AATTTTTCAAAAGTCGTTAAGCCTCTATTTAGAAGGGCCTCTTTA
1 AATTTTT-AAAAGTTGTTAAGCCTCTACTTAG-AGAACCTTTTTA
1885390 AATTTTTAAAAGTTGTTAAGCCTCTACTTAGATGAACCTTTTTTA
1 AATTTTTAAAAGTTGTTAAGCCTCTACTTAGA-GAACC-TTTTTA
* *
1885435 AATTTTTAAAAGTTGTTGAA-CCTCTA-TTCAGAGGA-GTCTTTTA
1 AATTTTTAAAAGTTGTT-AAGCCTCTACTT-AGAGAACCT-TTTTA
1885478 AATTTTTAAAAAAGTTGTTAA
1 AATTTTT--AAAAGTTGTTAA
1885499 CCTTCTGGAG
Statistics
Matches: 130, Mismatches: 13, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
42 8 0.06
43 17 0.13
44 54 0.42
45 49 0.38
46 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (43 bp):
AATTTTTAAAAGTTGTTAAGCCTCTACTTAGAGAACCTTTTTA
Found at i:1888734 original size:26 final size:28
Alignment explanation
Indices: 1888682--1888739 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 28
1888672 ATTTAAACTT
**
1888682 AAATTGATAAAATATTTTTTATAAAATA
1 AAATTGATAAAATATTTTAGATAAAATA
* *
1888710 AAATT-ATAAAAT-TTTTAGATTAAATT
1 AAATTGATAAAATATTTTAGATAAAATA
1888736 AAAT
1 AAAT
1888740 AGTATCTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 14 0.54
27 7 0.27
28 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (28 bp):
AAATTGATAAAATATTTTAGATAAAATA
Found at i:1890004 original size:59 final size:59
Alignment explanation
Indices: 1889934--1890045 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 59
1889924 TAGGATAAAA
* * *
1889934 TAATTTATTTATTAGTCAAAATTAT-TTTTTCTCAAAGTTTATACAATTTAAATATTGAG
1 TAATTTATTTATTAGTCAAAATTATCCTTCT-TCAAAATTTATACAATTTAAATATTGAG
*
1889993 TAATTTATTTATTAGTCAAAATTATCCTTCTTCAAAATTTATATAATTTAAAT
1 TAATTTATTTATTAGTCAAAATTATCCTTCTTCAAAATTTATACAATTTAAAT
1890046 TATTAATTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 45 0.94
60 3 0.06
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.49
Consensus pattern (59 bp):
TAATTTATTTATTAGTCAAAATTATCCTTCTTCAAAATTTATACAATTTAAATATTGAG
Found at i:1895380 original size:59 final size:59
Alignment explanation
Indices: 1895288--1895401 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 59
1895278 AATAGGATAA
* *
1895288 AATAATTTATTTATTAGTCAAAAATATTATTCCTCAAAGTTTATACAATTTAAATATTG
1 AATAATTTATTTATTAGTCAAAAATATCATTCCTCAAAATTTATACAATTTAAATATTG
* * * *
1895347 AATAATTTATTTATTAGTCAAAATTATCCTTCCTTAAAATTTATATAATTTAAAT
1 AATAATTTATTTATTAGTCAAAAATATCATTCCTCAAAATTTATACAATTTAAAT
1895402 TATTAATTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.46
Consensus pattern (59 bp):
AATAATTTATTTATTAGTCAAAAATATCATTCCTCAAAATTTATACAATTTAAATATTG
Found at i:1897237 original size:18 final size:18
Alignment explanation
Indices: 1897214--1897249 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1897204 TAGATTATTT
1897214 GTCAGTTAATGAATTAAA
1 GTCAGTTAATGAATTAAA
1897232 GTCAGTTAATGAATTAAA
1 GTCAGTTAATGAATTAAA
1897250 AGTAAATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (18 bp):
GTCAGTTAATGAATTAAA
Found at i:1898392 original size:13 final size:14
Alignment explanation
Indices: 1898364--1898394 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1898354 TTTCATATCA
1898364 TATTCATATCATAT
1 TATTCATATCATAT
1898378 TATT-ATATCATAT
1 TATTCATATCATAT
1898391 TATT
1 TATT
1898395 GATCGACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTCATATCATAT
Found at i:1900993 original size:17 final size:16
Alignment explanation
Indices: 1900973--1901028 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
1900963 GTTTACTTTT
1900973 TTAAAAAATAAATGAAA
1 TTAAAAAATAAAT-AAA
*
1900990 TTAAGAAATAAATAAA
1 TTAAAAAATAAATAAA
* *
1901006 TAAATAAAACAAATTAAA
1 TTAA-AAAATAAA-TAAA
1901024 TTAAA
1 TTAAA
1901029 TTAAAAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 6 0.19
17 19 0.59
18 7 0.22
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (16 bp):
TTAAAAAATAAATAAA
Found at i:1901322 original size:42 final size:43
Alignment explanation
Indices: 1901278--1901517 Score: 263
Period size: 42 Copynumber: 5.7 Consensus size: 43
1901268 CTCTTTGTAT
* * *
1901278 AGAGGCTAAACAAATTT-AAATGGGAAATGAGCTCCTCTAAAT
1 AGAGGCTAAACAACTTTAAAATAGGAAATGAGCTCCTCTAAAC
** ** *
1901320 AGAGGCTAAATGACTTTAAAATAGGAAATGAATTCCTCTATAC
1 AGAGGCTAAACAACTTTAAAATAGGAAATGAGCTCCTCTAAAC
* * *
1901363 AGAGGCTAAACAATTTTAAAATAGGAAATGTGCTACTCTAAAC
1 AGAGGCTAAACAACTTTAAAATAGGAAATGAGCTCCTCTAAAC
* * *
1901406 AGAGGCTAAATAAGTTT-AAATAGGAAATGGGCTCCTCTAAAC
1 AGAGGCTAAACAACTTTAAAATAGGAAATGAGCTCCTCTAAAC
* * * *
1901448 AGATGCTAAACAACTTT-AAATAGGAAATGAGCT-TTTTAAAT
1 AGAGGCTAAACAACTTTAAAATAGGAAATGAGCTCCTCTAAAC
** *
1901489 AGAGATTAAACAATTTTAAAATAGGAAAT
1 AGAGGCTAAACAACTTTAAAATAGGAAAT
1901518 AGGATTGAAC
Statistics
Matches: 165, Mismatches: 31, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
41 18 0.11
42 77 0.47
43 70 0.42
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (43 bp):
AGAGGCTAAACAACTTTAAAATAGGAAATGAGCTCCTCTAAAC
Found at i:1901434 original size:85 final size:85
Alignment explanation
Indices: 1901278--1901517 Score: 277
Period size: 85 Copynumber: 2.8 Consensus size: 85
1901268 CTCTTTGTAT
* * * *
1901278 AGAGGCTAAACAAATTTAAATGGGAAATGAGCTCCTCTAAATAGAGGCTAAATGACTTTAAAATA
1 AGAGGCTAAACAAATTTAAATAGGAAATGAGCTACTCTAAACAGAGGCTAAATAACTTTAAAATA
* *
1901343 GGAAATGAATTCCTCTATAC
66 GGAAATGAACTCCTCTAAAC
* * *
1901363 AGAGGCTAAACAATTTTAAAATAGGAAATGTGCTACTCTAAACAGAGGCTAAATAAGTTT-AAAT
1 AGAGGCTAAACAAATTT-AAATAGGAAATGAGCTACTCTAAACAGAGGCTAAATAACTTTAAAAT
**
1901427 AGGAAATGGGCTCCTCTAAAC
65 AGGAAATGAACTCCTCTAAAC
* * * * * ** * *
1901448 AGATGCTAAACAACTTTAAATAGGAAATGAGCT-TTTTAAATAGAGATTAAACAATTTTAAAATA
1 AGAGGCTAAACAAATTTAAATAGGAAATGAGCTACTCTAAACAGAGGCTAAATAACTTTAAAATA
1901512 GGAAAT
66 GGAAAT
1901518 AGGATTGAAC
Statistics
Matches: 132, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
83 18 0.14
84 26 0.20
85 52 0.39
86 36 0.27
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (85 bp):
AGAGGCTAAACAAATTTAAATAGGAAATGAGCTACTCTAAACAGAGGCTAAATAACTTTAAAATA
GGAAATGAACTCCTCTAAAC
Found at i:1901698 original size:59 final size:60
Alignment explanation
Indices: 1901633--1901748 Score: 164
Period size: 59 Copynumber: 1.9 Consensus size: 60
1901623 AACTGAAATT
* *
1901633 GAAGATGAGTGACCAAAATTGAA-CTGCATGCCAAAAAAT-AAATAATCTAGACCAAGATC
1 GAAGATGAGTGACCAAAATTGAATC-ACAAGCCAAAAAATAAAATAATCTAGACCAAGATC
** *
1901692 GAAGATGAGTGACCATGATTGAATCACAAGTCAAAAAATAAAATAATCTAGACCAAG
1 GAAGATGAGTGACCAAAATTGAATCACAAGCCAAAAAATAAAATAATCTAGACCAAG
1901749 CCAAGGTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 32 0.64
60 18 0.36
ACGTcount: A:0.48, C:0.16, G:0.17, T:0.19
Consensus pattern (60 bp):
GAAGATGAGTGACCAAAATTGAATCACAAGCCAAAAAATAAAATAATCTAGACCAAGATC
Found at i:1901777 original size:16 final size:16
Alignment explanation
Indices: 1901756--1901788 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1901746 AAGCCAAGGT
*
1901756 AAAAAATAAGTTATTG
1 AAAAAATAAGTGATTG
1901772 AAAAAATAAGTGATTG
1 AAAAAATAAGTGATTG
1901788 A
1 A
1901789 GACTAAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (16 bp):
AAAAAATAAGTGATTG
Found at i:1902191 original size:74 final size:74
Alignment explanation
Indices: 1902096--1902255 Score: 223
Period size: 74 Copynumber: 2.2 Consensus size: 74
1902086 AAATCCCAAT
* * * *
1902096 ATTCGAAGTTTCACAAGAAATTCACAAAGATTTCAAAA-TTTGTAAAAAGTCAAGATTCACAAAT
1 ATTCCAAGTTTCACAAAAAATTCACAAAGATTTCAAAACTTT-TAAAAAGTCAAAATTCACAAAA
**
1902160 GTTTGTAAGA
65 GTTTACAAGA
* *
1902170 ATTCCAAGTTTCACAAAAAATTCACAAAGATTTGAAAACTTTTAAAAGGTCAAAATTCACAAAAG
1 ATTCCAAGTTTCACAAAAAATTCACAAAGATTTCAAAACTTTTAAAAAGTCAAAATTCACAAAAG
1902235 TTTACAAGA
66 TTTACAAGA
*
1902244 ATTCCAATTTTC
1 ATTCCAAGTTTC
1902256 GCAAGTGTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
74 73 0.96
75 3 0.04
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (74 bp):
ATTCCAAGTTTCACAAAAAATTCACAAAGATTTCAAAACTTTTAAAAAGTCAAAATTCACAAAAG
TTTACAAGA
Found at i:1903650 original size:27 final size:28
Alignment explanation
Indices: 1903620--1903678 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
1903610 TTAGTTTAAG
*
1903620 TTTTCATTTTTTTTTCTCTTTTTT-CTT
1 TTTTCATTTGTTTTTCTCTTTTTTCCTT
* * *
1903647 TTTTTATTTGTTTTTGTTTTTTTTCCTT
1 TTTTCATTTGTTTTTCTCTTTTTTCCTT
1903675 TTTT
1 TTTT
1903679 TTTTTTACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.83
Consensus pattern (28 bp):
TTTTCATTTGTTTTTCTCTTTTTTCCTT
Found at i:1903660 original size:19 final size:19
Alignment explanation
Indices: 1903620--1903684 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 19
1903610 TTAGTTTAAG
1903620 TTTTCATTTTTTTTTCTCTT
1 TTTTC-TTTTTTTTTCTCTT
*
1903640 TTTTCTTTTTTTATT-T-GT
1 TTTTCTTTTTTT-TTCTCTT
*
1903658 TTTT-GTTTTTTTTC-CTT
1 TTTTCTTTTTTTTTCTCTT
1903675 TTTT-TTTTTT
1 TTTTCTTTTTT
1903685 ACATATCTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
16 2 0.05
17 16 0.42
18 5 0.13
19 8 0.21
20 7 0.18
ACGTcount: A:0.03, C:0.09, G:0.03, T:0.85
Consensus pattern (19 bp):
TTTTCTTTTTTTTTCTCTT
Found at i:1910951 original size:19 final size:21
Alignment explanation
Indices: 1910927--1910965 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
1910917 TTAATGTTAA
1910927 AAAATAAAAA-A-ATAATTTT
1 AAAATAAAAATATATAATTTT
1910946 AAAATAAAAATATATAATTT
1 AAAATAAAAATATATAATTT
1910966 AAGGACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATAAAAATATATAATTTT
Found at i:1911916 original size:19 final size:20
Alignment explanation
Indices: 1911894--1911933 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1911884 ATATTTATAT
*
1911894 TATATTTATAT-AAAAATTA
1 TATATATATATGAAAAATTA
*
1911913 TATATATATATGATAAATTA
1 TATATATATATGAAAAATTA
1911933 T
1 T
1911934 GTTGGTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TATATATATATGAAAAATTA
Found at i:1919968 original size:3 final size:3
Alignment explanation
Indices: 1919960--1919995 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1919950 ATAAATTGTT
1919960 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1919996 AATCTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1921224 original size:26 final size:25
Alignment explanation
Indices: 1921195--1921252 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
1921185 TTGTTCTTCC
1921195 CTTTTTTCTTTCTTTT-TTTTCTTGAA
1 CTTTTTTCTTT-TTTTATTTTCTTG-A
** *
1921221 CTTTTGACTTTTTTTATTTTGTTGA
1 CTTTTTTCTTTTTTTATTTTCTTGA
1921246 CTTTTTT
1 CTTTTTT
1921253 TTAAAACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.09, C:0.12, G:0.07, T:0.72
Consensus pattern (25 bp):
CTTTTTTCTTTTTTTATTTTCTTGA
Found at i:1921225 original size:25 final size:24
Alignment explanation
Indices: 1921197--1921251 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1921187 GTTCTTCCCT
1921197 TTTTTCTTTCTTTT-TTTTCTTGAAC
1 TTTTTCTTT-TTTTATTTTCTTG-AC
* *
1921222 TTTTGACTTTTTTTATTTTGTTGAC
1 TTTT-TCTTTTTTTATTTTCTTGAC
1921247 TTTTT
1 TTTTT
1921252 TTTAAAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.09, C:0.11, G:0.07, T:0.73
Consensus pattern (24 bp):
TTTTTCTTTTTTTATTTTCTTGAC
Found at i:1921667 original size:108 final size:105
Alignment explanation
Indices: 1921494--1921711 Score: 301
Period size: 108 Copynumber: 2.0 Consensus size: 105
1921484 TAAGGATCCT
*** * * * *
1921494 CTAAACAAAAGGTATGCAATTTTTTAAAAAATAAATCAAGAAATAGGCTTCTTTAAATAAAGGCT
1 CTAAACAAAAGGTATGCAATTTAAAAAAAAAAAAACCAAGAAATAGGCTTCTCTAAACAAAGGCT
* *
1921559 AAATAACTTTAAATGATAAATGAGCTCCTTTAAACAAAGG
66 AAACAACTTTAAATGAGAAATGAGCTCCTTTAAACAAAGG
*
1921599 CTAAACAAAAGGTATGCAATTTAAAAAAAAAAAAAAAACCAAGAAATAGGCTTCTCTAAACAGAG
1 CTAAACAAAAGGTATGCAATTT---AAAAAAAAAAAAACCAAGAAATAGGCTTCTCTAAACAAAG
* *
1921664 GCTAAACAACTTTAAATGGGAAATGAGCTCCTTTAAACAGAGG
63 GCTAAACAACTTTAAATGAGAAATGAGCTCCTTTAAACAAAGG
1921707 CTAAA
1 CTAAA
1921712 TAACTTTAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
105 22 0.22
108 76 0.78
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (105 bp):
CTAAACAAAAGGTATGCAATTTAAAAAAAAAAAAACCAAGAAATAGGCTTCTCTAAACAAAGGCT
AAACAACTTTAAATGAGAAATGAGCTCCTTTAAACAAAGG
Found at i:1921747 original size:43 final size:42
Alignment explanation
Indices: 1921641--1922075 Score: 330
Period size: 43 Copynumber: 10.2 Consensus size: 42
1921631 AAAAAACCAA
*
1921641 GAAATAGGCTTCTCTAAACAGAGGCTAAACAACTTT-AAATGG
1 GAAATAGGCTT-TCTAAACAGAGGCTAAACAACTTTAAAATAG
*
1921683 GAAAT-GAGCTCCTT-TAAACAGAGGCTAAATAACTTTAAAATAG
1 GAAATAG-GCT--TTCTAAACAGAGGCTAAACAACTTTAAAATAG
* * *
1921726 GAAATAGGCTATTCTATACAGAGGCTAAATGAA-TTTAAAATAA
1 GAAATAGGCT-TTCTAAACAGAGGCTAAA-CAACTTTAAAATAG
* * * * ** *
1921769 GAAATAGACTTCTTTAAACAGATGTTAAATGACTTT-AAGTAG
1 GAAATAGGCTT-TCTAAACAGAGGCTAAACAACTTTAAAATAG
* * * *
1921811 AAAATTGAGCTTTTCTATACAGAGGCTAAACAACTCTAAAATAG
1 GAAATAG-GC-TTTCTAAACAGAGGCTAAACAACTTTAAAATAG
* * * *
1921855 GAAATGGGCTCCTCTAAACATAGGTTAAACAACTTT-AAATAG
1 GAAATAGGCT-TTCTAAACAGAGGCTAAACAACTTTAAAATAG
** *
1921897 GAAAT-GAGCTTCTCTATCCAAAGGCTAAACAACTTTAAAATAG
1 GAAATAG-GCTT-TCTAAACAGAGGCTAAACAACTTTAAAATAG
* * * * *
1921940 GAAATAAGCTCCTT-TAAACAGAGACTAAATAATTTTAAAATAA
1 GAAATAGGCT--TTCTAAACAGAGGCTAAACAACTTTAAAATAG
* * * * * *
1921983 GAAATAGACTCCTCTAAACAAAGACTAAATAA-TTTTAAATAG
1 GAAATAGGCT-TTCTAAACAGAGGCTAAACAACTTTAAAATAG
* *
1922025 GAAATGGGCTTCTCTAAATAGAGGCTAAACAACTTTAAAATAG
1 GAAATAGGCTT-TCTAAACAGAGGCTAAACAACTTTAAAATAG
*
1922068 AAAATAGG
1 GAAATAGG
1922076 ACTGAACCTC
Statistics
Matches: 309, Mismatches: 62, Indels: 43
0.75 0.15 0.10
Matches are distributed among these distances:
41 2 0.01
42 111 0.36
43 178 0.58
44 17 0.06
45 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (42 bp):
GAAATAGGCTTTCTAAACAGAGGCTAAACAACTTTAAAATAG
Found at i:1921937 original size:85 final size:85
Alignment explanation
Indices: 1921641--1922074 Score: 421
Period size: 85 Copynumber: 5.1 Consensus size: 85
1921631 AAAAAACCAA
* * *
1921641 GAAATAGGCTTCTCTAAACAGAGGCTAAACAACTTT-AAATGGGAAATGAGCTCCTTTAAACAGA
1 GAAATA-GCTTCTCTATACAGAGGCTAAACAACTTTAAAATAGGAAATGGGCTCCTTTAAACAGA
1921705 GGCTAAATAACTTTAAAATAG
65 GGCTAAATAACTTTAAAATAG
* * * * *
1921726 GAAATAGGCTAT-TCTATACAGAGGCTAAATGAA-TTTAAAATAAGAAATAGACTTCTTTAAACA
1 GAAATA-GCT-TCTCTATACAGAGGCTAAA-CAACTTTAAAATAGGAAATGGGCTCCTTTAAACA
* * * *
1921789 GATGTTAAATGACTTT-AAGTAG
63 GAGGCTAAATAACTTTAAAATAG
* * * * *
1921811 AAAATTGAGCTTTTCTATACAGAGGCTAAACAACTCTAAAATAGGAAATGGGCTCCTCTAAACAT
1 GAAA-T-AGCTTCTCTATACAGAGGCTAAACAACTTTAAAATAGGAAATGGGCTCCTTTAAACAG
* *
1921876 AGGTTAAACAACTTT-AAATAG
64 AGGCTAAATAACTTTAAAATAG
* * **
1921897 GAAATGAGCTTCTCTATCCAAAGGCTAAACAACTTTAAAATAGGAAATAAGCTCCTTTAAACAGA
1 GAAAT-AGCTTCTCTATACAGAGGCTAAACAACTTTAAAATAGGAAATGGGCTCCTTTAAACAGA
* * *
1921962 GACTAAATAATTTTAAAATAA
65 GGCTAAATAACTTTAAAATAG
* * * * * * * * *
1921983 GAAATAGACTCCTCTAAACAAAGACTAAATAA-TTTTAAATAGGAAATGGGCTTCTCTAAATAGA
1 GAAATAG-CTTCTCTATACAGAGGCTAAACAACTTTAAAATAGGAAATGGGCTCCTTTAAACAGA
*
1922047 GGCTAAACAACTTTAAAATAG
65 GGCTAAATAACTTTAAAATAG
*
1922068 AAAATAG
1 GAAATAG
1922075 GACTGAACCT
Statistics
Matches: 285, Mismatches: 55, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
85 154 0.54
86 130 0.46
87 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (85 bp):
GAAATAGCTTCTCTATACAGAGGCTAAACAACTTTAAAATAGGAAATGGGCTCCTTTAAACAGAG
GCTAAATAACTTTAAAATAG
Found at i:1922073 original size:128 final size:127
Alignment explanation
Indices: 1921641--1922073 Score: 465
Period size: 128 Copynumber: 3.4 Consensus size: 127
1921631 AAAAAACCAA
* * *
1921641 GAAATAGGCTTCTCTAAACAGAGGCTAAACAACTTTAAATGGGAAATGAGCTCCTTTAAACAGAG
1 GAAATAGGCTTCTCTAAACAGAGGCTAAACAACTTTAAATAGAAAATAAGCTCCTTTAAACAGAG
** * * * *
1921706 GCTAAATAACTTTAAAATAGGAAATAGGCTATTCTATACAGAGGCTAAATGAATTTAAAATAA
66 GCTAAATAACTTTAAAATAGGAAATAGGCTCCTCTAAACAAAGGCTAAAT-AATTTTAAATAG
* * * * ** * * * *
1921769 GAAATAGACTTCTTTAAACAGATGTTAAATGACTTTAAGTAGAAAATTGAGCT-TTTCTATACAG
1 GAAATAGGCTTCTCTAAACAGAGGCTAAACAACTTTAAATAGAAAA-TAAGCTCCTT-TAAACAG
* * * * * * *
1921833 AGGCTAAACAACTCTAAAATAGGAAATGGGCTCCTCTAAACATAGGTTAAACAACTTTAAATAG
64 AGGCTAAATAACTTTAAAATAGGAAATAGGCTCCTCTAAACAAAGGCTAAATAATTTTAAATAG
** * *
1921897 GAAAT-GAGCTTCTCTATCCAAAGGCTAAACAACTTTAAAATAGGAAATAAGCTCCTTTAAACAG
1 GAAATAG-GCTTCTCTAAACAGAGGCTAAACAACTTT-AAATAGAAAATAAGCTCCTTTAAACAG
* * * * *
1921961 AGACTAAATAATTTTAAAATAAGAAATAGACTCCTCTAAACAAAGACTAAATAATTTTAAATAG
64 AGGCTAAATAACTTTAAAATAGGAAATAGGCTCCTCTAAACAAAGGCTAAATAATTTTAAATAG
* *
1922025 GAAATGGGCTTCTCTAAATAGAGGCTAAACAACTTTAAAATAGAAAATA
1 GAAATAGGCTTCTCTAAACAGAGGCTAAACAACTTT-AAATAGAAAATA
1922074 GGACTGAACC
Statistics
Matches: 245, Mismatches: 54, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
127 1 0.00
128 178 0.73
129 66 0.27
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.27
Consensus pattern (127 bp):
GAAATAGGCTTCTCTAAACAGAGGCTAAACAACTTTAAATAGAAAATAAGCTCCTTTAAACAGAG
GCTAAATAACTTTAAAATAGGAAATAGGCTCCTCTAAACAAAGGCTAAATAATTTTAAATAG
Found at i:1922385 original size:65 final size:64
Alignment explanation
Indices: 1922316--1922519 Score: 212
Period size: 65 Copynumber: 3.1 Consensus size: 64
1922306 ACCAAGGTCG
* * * *
1922316 AAGATGAGTGATTAGGATTGAACCATAAGTAAAAAAAATAAATGATCTAGATTGAACAAAGATCA
1 AAGATGAGTAACTAGGATTGAATCATAGGTAAAAAAAATAAAT-ATCTAGATTGAACAAAGATCA
* ** ** * *
1922381 AAGATAAGTAACCGGGATTGAATCATAGGTTGAAAAAATAAATACTTTAGATTGAACCAAGATTC
1 AAGATGAGTAACTAGGATTGAATCATAGGTAAAAAAAATAAATA-TCTAGATTGAACAAAGA-TC
1922446 A
64 A
* ** * *
1922447 AA-ATGAGTAACTAAGATTGAATCGCAGGTCAAAAAAATAAATAATCTAGATTGAACTAAGATCA
1 AAGATGAGTAACTAGGATTGAATCATAGGTAAAAAAAATAAAT-ATCTAGATTGAACAAAGATCA
*
1922511 AATATGAGT
1 AAGATGAGT
1922520 GACTGGGACT
Statistics
Matches: 114, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
64 6 0.05
65 102 0.89
66 6 0.05
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.25
Consensus pattern (64 bp):
AAGATGAGTAACTAGGATTGAATCATAGGTAAAAAAAATAAATATCTAGATTGAACAAAGATCA
Found at i:1922547 original size:65 final size:64
Alignment explanation
Indices: 1922348--1922552 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 64
1922338 CCATAAGTAA
* * * ** *
1922348 AAAAAATAAATGATCTAGATTGAACAAAGATCAAAGATAAGTAACCGGGATTGAATCATAGGTTG
1 AAAAAATAAATAATCTAGATTGAACAAAGATCAAA-ATGAGTAACTGGGATTGAATCGCAGGTCG
* * * ** *
1922413 AAAAAATAAATACTTTAGATTGAACCAAGATTCAAAATGAGTAACTAAGATTGAATCGCAGGTCA
1 AAAAAATAAATAATCTAGATTGAACAAAGA-TCAAAATGAGTAACTGGGATTGAATCGCAGGTCG
* * * * *
1922478 AAAAAATAAATAATCTAGATTGAACTAAGATCAAATATGAGTGACTGGGACTGAACCGCAAGTCG
1 AAAAAATAAATAATCTAGATTGAACAAAGATCAAA-ATGAGTAACTGGGATTGAATCGCAGGTCG
1922543 AAAAAATAAA
1 AAAAAATAAA
1922553 ATTCAAAATT
Statistics
Matches: 116, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
64 5 0.04
65 106 0.91
66 5 0.04
ACGTcount: A:0.49, C:0.11, G:0.18, T:0.22
Consensus pattern (64 bp):
AAAAAATAAATAATCTAGATTGAACAAAGATCAAAATGAGTAACTGGGATTGAATCGCAGGTCG
Found at i:1923008 original size:23 final size:23
Alignment explanation
Indices: 1922929--1923008 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 23
1922919 ATATCTACAG
1922929 AATTTAAAGATTCTTATTTG-AA
1 AATTTAAAGATTCTTATTTGAAA
* ** *
1922951 AATTTAAGAAATTC--ACATCAAA
1 AATTTAA-AGATTCTTATTTGAAA
* *
1922973 AAGTTAAATATTCTTATTTGAAA
1 AATTTAAAGATTCTTATTTGAAA
*
1922996 AATTTAAGGATTC
1 AATTTAAAGATTC
1923009 ACATCCAAAT
Statistics
Matches: 42, Mismatches: 12, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
21 7 0.17
22 15 0.36
23 20 0.48
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (23 bp):
AATTTAAAGATTCTTATTTGAAA
Found at i:1923098 original size:22 final size:22
Alignment explanation
Indices: 1923039--1923098 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
1923029 AAAATTTTAG
* *
1923039 AGATTCACATT-ATAAAGTTAA
1 AGATTCACATTGAAAAACTTAA
***
1923060 AGATTTTTAGTTGAAAAACTTAA
1 AGATTCACA-TTGAAAAACTTAA
1923083 AGATTCACATTGAAAA
1 AGATTCACATTGAAAA
1923099 TTTCAAAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (22 bp):
AGATTCACATTGAAAAACTTAA
Found at i:1923196 original size:114 final size:114
Alignment explanation
Indices: 1922996--1923224 Score: 458
Period size: 114 Copynumber: 2.0 Consensus size: 114
1922986 TTATTTGAAA
1922996 AATTTAAGGATTCACATCCAAATTTTATATTAAAAAATTTTAGAGATTCACATTATAAAGTTAAA
1 AATTTAAGGATTCACATCCAAATTTTATATTAAAAAATTTTAGAGATTCACATTATAAAGTTAAA
1923061 GATTTTTAGTTGAAAAACTTAAAGATTCACATTGAAAATTTCAAAATTC
66 GATTTTTAGTTGAAAAACTTAAAGATTCACATTGAAAATTTCAAAATTC
1923110 AATTTAAGGATTCACATCCAAATTTTATATTAAAAAATTTTAGAGATTCACATTATAAAGTTAAA
1 AATTTAAGGATTCACATCCAAATTTTATATTAAAAAATTTTAGAGATTCACATTATAAAGTTAAA
1923175 GATTTTTAGTTGAAAAACTTAAAGATTCACATTGAAAATTTCAAAATTC
66 GATTTTTAGTTGAAAAACTTAAAGATTCACATTGAAAATTTCAAAATTC
1923224 A
1 A
1923225 CCTTCATAAA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.37
Consensus pattern (114 bp):
AATTTAAGGATTCACATCCAAATTTTATATTAAAAAATTTTAGAGATTCACATTATAAAGTTAAA
GATTTTTAGTTGAAAAACTTAAAGATTCACATTGAAAATTTCAAAATTC
Found at i:1923212 original size:22 final size:22
Alignment explanation
Indices: 1923153--1923212 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
1923143 AAAATTTTAG
* *
1923153 AGATTCACATT-ATAAAGTTAA
1 AGATTCACATTGAAAAACTTAA
***
1923174 AGATTTTTAGTTGAAAAACTTAA
1 AGATTCACA-TTGAAAAACTTAA
1923197 AGATTCACATTGAAAA
1 AGATTCACATTGAAAA
1923213 TTTCAAAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (22 bp):
AGATTCACATTGAAAAACTTAA
Found at i:1924248 original size:25 final size:27
Alignment explanation
Indices: 1924220--1924274 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 27
1924210 AGATTTTCAA
*
1924220 TTTAAGTCTT-TTTTTTATC-TTATTT
1 TTTAAGTCTTATTTTTTACCTTTATTT
* *
1924245 TTT-ATTTTTATTTTTTACCTTTATTT
1 TTTAAGTCTTATTTTTTACCTTTATTT
1924271 TTTA
1 TTTA
1924275 CATTTTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
24 4 0.17
25 11 0.46
26 9 0.38
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTAAGTCTTATTTTTTACCTTTATTT
Found at i:1924274 original size:13 final size:13
Alignment explanation
Indices: 1924230--1924275 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
1924220 TTTAAGTCTT
*
1924230 TTTTTTATC-TTA
1 TTTTTTACCTTTA
**
1924242 TTTTTTATTTTTA
1 TTTTTTACCTTTA
1924255 TTTTTTACCTTTA
1 TTTTTTACCTTTA
1924268 TTTTTTAC
1 TTTTTTAC
1924276 ATTTTTTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 8 0.27
13 22 0.73
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTACCTTTA
Found at i:1924572 original size:6 final size:6
Alignment explanation
Indices: 1924561--1924617 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
1924551 ACCTCATCAA
* * * *
1924561 TTTCTT TTTCTTT TTTCTT ATTATT CTTTCTT TCTCTT ATTCTT TTT-TT
1 TTTCTT TTTC-TT TTTCTT TTTCTT -TTTCTT TTTCTT TTTCTT TTTCTT
1924610 TTTCTT TT
1 TTTCTT TT
1924618 CATCATTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
5 5 0.12
6 25 0.62
7 10 0.25
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:1924589 original size:16 final size:15
Alignment explanation
Indices: 1924568--1924608 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
1924558 CAATTTCTTT
1924568 TTCTTTTTTCTTATTA
1 TTCTTTTTTC-TATTA
*
1924584 TTCTTTCTTTCTCTTA
1 TTCTTT-TTTCTATTA
1924600 TTCTTTTTT
1 TTCTTTTTT
1924609 TTTTCTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 3 0.13
16 16 0.70
17 4 0.17
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTTTTTCTATTA
Found at i:1924613 original size:19 final size:19
Alignment explanation
Indices: 1924562--1924614 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1924552 CCTCATCAAT
1924562 TTCTTTTTCTTTTT-TCTTA
1 TTCTTTTT-TTTTTCTCTTA
* * *
1924581 TTATTCTTTCTTTCTCTTA
1 TTCTTTTTTTTTTCTCTTA
1924600 TTCTTTTTTTTTTCT
1 TTCTTTTTTTTTTCT
1924615 TTTCATCATT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (19 bp):
TTCTTTTTTTTTTCTCTTA
Found at i:1928583 original size:3 final size:3
Alignment explanation
Indices: 1928575--1928617 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1928565 TAATGAGTAA
1928575 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1928618 TCTAAACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1932582 original size:59 final size:59
Alignment explanation
Indices: 1932512--1932623 Score: 170
Period size: 59 Copynumber: 1.9 Consensus size: 59
1932502 TAAGATAAAA
** * * *
1932512 TAATTTATTTATTAGTCAAAATTATTTTTTCTTAAAGTTTATACAATTTAAATATTGAG
1 TAATTTATTTATTAGTCAAAATTATCCTTACTCAAAATTTATACAATTTAAATATTGAG
*
1932571 TAATTTATTTATTAGTCAAAATTATCCTTACTCAAAATTTATATAATTTAAAT
1 TAATTTATTTATTAGTCAAAATTATCCTTACTCAAAATTTATACAATTTAAAT
1932624 TATTAATTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.49
Consensus pattern (59 bp):
TAATTTATTTATTAGTCAAAATTATCCTTACTCAAAATTTATACAATTTAAATATTGAG
Found at i:1937971 original size:59 final size:60
Alignment explanation
Indices: 1937874--1937988 Score: 187
Period size: 59 Copynumber: 1.9 Consensus size: 60
1937864 GATAAAATAA
*
1937874 TTTATTTATTAGTCAAAAATATCATTCCTCAAAGTTTATATAATTTAAA-TATTGAGTAG
1 TTTATTTATTAGTCAAAAATATCATTCCTCAAAATTTATATAATTTAAATTATTGAGTAG
* * *
1937933 TTTATTTATTAGTCAAAATTATCCTTCCTTAAAATTTATATAATTTAAATTATTGA
1 TTTATTTATTAGTCAAAAATATCATTCCTCAAAATTTATATAATTTAAATTATTGA
1937989 TATAATTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 45 0.88
60 6 0.12
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (60 bp):
TTTATTTATTAGTCAAAAATATCATTCCTCAAAATTTATATAATTTAAATTATTGAGTAG
Found at i:1939822 original size:18 final size:17
Alignment explanation
Indices: 1939799--1939865 Score: 91
Period size: 17 Copynumber: 3.9 Consensus size: 17
1939789 TTTGATTTAA
1939799 GGGTTTGGATTTTAGAGG
1 GGGTTTGGATTTTA-AGG
1939817 GGGTTTGGA-TTTAAGG
1 GGGTTTGGATTTTAAGG
** *
1939833 GATTTTGGATTTTTAGG
1 GGGTTTGGATTTTAAGG
1939850 GGGTTTGGATTTTAAG
1 GGGTTTGGATTTTAAG
1939866 AATTTTGGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
16 10 0.24
17 23 0.55
18 9 0.21
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.43
Consensus pattern (17 bp):
GGGTTTGGATTTTAAGG
Found at i:1939856 original size:17 final size:17
Alignment explanation
Indices: 1939799--1939884 Score: 77
Period size: 16 Copynumber: 5.1 Consensus size: 17
1939789 TTTGATTTAA
*
1939799 GGGTTTGGATTTTAGAGG
1 GGGTTTGGATTTT-TAGG
*
1939817 GGGTTTGGA-TTTAAGG
1 GGGTTTGGATTTTTAGG
**
1939833 GATTTTGGATTTTTAGG
1 GGGTTTGGATTTTTAGG
*
1939850 GGGTTTGGA-TTTTAAG
1 GGGTTTGGATTTTTAGG
***
1939866 AATTTTGGATTTTTAGG
1 GGGTTTGGATTTTTAGG
1939883 GG
1 GG
1939885 TTTTAAAAAC
Statistics
Matches: 53, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
16 22 0.42
17 22 0.42
18 9 0.17
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (17 bp):
GGGTTTGGATTTTTAGG
Found at i:1939856 original size:33 final size:33
Alignment explanation
Indices: 1939784--1939884 Score: 136
Period size: 33 Copynumber: 3.1 Consensus size: 33
1939774 TTTGAGGTTT
* *
1939784 GGGGTTTTGATTTAAGGG--TTTGGATTTTAGAG
1 GGGGTTTGGATTTAAGGGATTTTGGATTTT-TAG
1939816 GGGGTTTGGATTTAAGGGATTTTGGATTTTTAG
1 GGGGTTTGGATTTAAGGGATTTTGGATTTTTAG
*
1939849 GGGGTTTGGATTTTAA-GAATTTTGGATTTTTAG
1 GGGGTTTGGA-TTTAAGGGATTTTGGATTTTTAG
1939882 GGG
1 GGG
1939885 TTTTAAAAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
32 17 0.27
33 31 0.49
34 15 0.24
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.45
Consensus pattern (33 bp):
GGGGTTTGGATTTAAGGGATTTTGGATTTTTAG
Found at i:1939888 original size:17 final size:17
Alignment explanation
Indices: 1939802--1939888 Score: 79
Period size: 17 Copynumber: 5.2 Consensus size: 17
1939792 GATTTAAGGG
* *
1939802 TTTGGATTTTAGAGGGGG
1 TTTGGATTTT-TAGGGGT
* *
1939820 TTTGGA-TTTAAGGGAT
1 TTTGGATTTTTAGGGGT
*
1939836 TTTGGATTTTTAGGGGG
1 TTTGGATTTTTAGGGGT
* **
1939853 TTTGGA-TTTTAAGAAT
1 TTTGGATTTTTAGGGGT
1939869 TTTGGATTTTTAGGGGT
1 TTTGGATTTTTAGGGGT
1939886 TTT
1 TTT
1939889 AAAAACTTAG
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
16 22 0.41
17 26 0.48
18 6 0.11
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.48
Consensus pattern (17 bp):
TTTGGATTTTTAGGGGT
Found at i:1939904 original size:33 final size:33
Alignment explanation
Indices: 1939827--1939905 Score: 79
Period size: 33 Copynumber: 2.4 Consensus size: 33
1939817 GGGTTTGGAT
** **
1939827 TTAAGGGATTTTGGATTTTTAGGGGGTTTGGATT
1 TTAA-GGATTTTGGATTTTTAGGGGGTTTAAAAC
* *
1939861 TTAAGAATTTTGGATTTTTAGGGGTTTTAAAAAC
1 TTAAGGATTTTGGATTTTTAGGGGGTTT-AAAAC
1939895 TT-AGGATTTTG
1 TTAAGGATTTTG
1939906 AAAATTAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
33 30 0.81
34 7 0.19
ACGTcount: A:0.24, C:0.01, G:0.28, T:0.47
Consensus pattern (33 bp):
TTAAGGATTTTGGATTTTTAGGGGGTTTAAAAC
Found at i:1941329 original size:18 final size:18
Alignment explanation
Indices: 1941306--1941342 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1941296 CTACTTTCTG
1941306 TTTTTTTCTATTTTTTTA
1 TTTTTTTCTATTTTTTTA
* *
1941324 TTTTTTTGTGTTTTTTTA
1 TTTTTTTCTATTTTTTTA
1941342 T
1 T
1941343 ATAATTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.03, G:0.05, T:0.84
Consensus pattern (18 bp):
TTTTTTTCTATTTTTTTA
Found at i:1941628 original size:23 final size:22
Alignment explanation
Indices: 1941597--1941640 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1941587 AATCGAATTT
*
1941597 ATGCTCAAAAGTCTTACAAAATC
1 ATGCCCAAAAGTCTTA-AAAATC
*
1941620 ATGCCCAAAGGTCTTAAAAAT
1 ATGCCCAAAAGTCTTAAAAAT
1941641 TATGTCCGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.25
Consensus pattern (22 bp):
ATGCCCAAAAGTCTTAAAAATC
Found at i:1941754 original size:22 final size:22
Alignment explanation
Indices: 1941728--1941796 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
1941718 CGAATCAAAT
*
1941728 TTATGCTTGGAGGTCTTAAGAA
1 TTATGCCTGGAGGTCTTAAGAA
* *
1941750 TTATGCCCGGAGGTCTTAAAAA
1 TTATGCCTGGAGGTCTTAAGAA
*
1941772 TCATGCCTGGAGGTCTTATAGAA
1 TTATGCCTGGAGGTCTTA-AGAA
1941795 TT
1 TT
1941797 GACTGGGATA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (22 bp):
TTATGCCTGGAGGTCTTAAGAA
Found at i:1941804 original size:132 final size:131
Alignment explanation
Indices: 1941628--1941927 Score: 440
Period size: 132 Copynumber: 2.3 Consensus size: 131
1941618 TCATGCCCAA
* * * *
1941628 AGGTCTTAAAAATTATGTCCGGAGGTCTTACAGAATTGATTGGGATAACATCGCAAGTCAAAAGA
1 AGGTCTTAAAAATCATG-CCGGAGGTCTTATAGAATTGACTGGGATAACACCGCAAGTCAAAAGA
* * *
1941693 TAAAAAATTGATCGGGATAACACCACGAATCAAATTTATGCTTGGAGGTCTTA-AGAATTATGCC
65 TAAAAAATTGATCGGGATAACACCACGAATCAAATTTATGCCTGGAGGTCTTAGA-AATCATACC
1941757 CGG
129 CGG
*
1941760 AGGTCTTAAAAATCATGCCTGGAGGTCTTATAGAATTGACTGGGATAACACCGTAAGTCAAAAGA
1 AGGTCTTAAAAATCATGCC-GGAGGTCTTATAGAATTGACTGGGATAACACCGCAAGTCAAAAGA
* * *
1941825 TAAAGAATTGATCGGGATAACACCGCGAATCAAATTTATGCCTGGAGGTCTTAGAAATCATACCT
65 TAAAAAATTGATCGGGATAACACCACGAATCAAATTTATGCCTGGAGGTCTTAGAAATCATACCC
1941890 GG
130 GG
* *
1941892 AGGTCTTAGAAATCATGCCCGAAGGTCTTATAGAAT
1 AGGTCTTAAAAATCATG-CCGGAGGTCTTATAGAAT
1941928 CATGCCCGGA
Statistics
Matches: 152, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
131 2 0.01
132 147 0.97
133 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (131 bp):
AGGTCTTAAAAATCATGCCGGAGGTCTTATAGAATTGACTGGGATAACACCGCAAGTCAAAAGAT
AAAAAATTGATCGGGATAACACCACGAATCAAATTTATGCCTGGAGGTCTTAGAAATCATACCCG
G
Found at i:1941932 original size:23 final size:22
Alignment explanation
Indices: 1941862--1941994 Score: 131
Period size: 22 Copynumber: 6.0 Consensus size: 22
1941852 AATCAAATTT
*
1941862 ATGCCTGGAGGTCTTAGAAATC
1 ATGCCCGGAGGTCTTAGAAATC
* *
1941884 ATACCTGGAGGTCTTAGAAATC
1 ATGCCCGGAGGTCTTAGAAATC
* *
1941906 ATGCCCGAAGGTCTTATAGAATC
1 ATGCCCGGAGGTCTTAGA-AATC
* * *
1941929 ATGCCCGGAGGTCTTACAGATT
1 ATGCCCGGAGGTCTTAGAAATC
* ** * *
1941951 ATGTCAAGAGGTCTTAGAGATT
1 ATGCCCGGAGGTCTTAGAAATC
*
1941973 ATGCCCGGAGGTCTTACAAATC
1 ATGCCCGGAGGTCTTAGAAATC
1941995 TCAAAATCTT
Statistics
Matches: 91, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
22 71 0.78
23 20 0.22
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (22 bp):
ATGCCCGGAGGTCTTAGAAATC
Found at i:1941941 original size:45 final size:45
Alignment explanation
Indices: 1941869--1941994 Score: 141
Period size: 45 Copynumber: 2.8 Consensus size: 45
1941859 TTTATGCCTG
* * * *
1941869 GAGGTCTTAGA-AATCATACCTGGAGGTCTTAGAAATCATGCC-C
1 GAGGTCTTAGAGAATCATGCCCGGAGGTCTTACAAATCATGCCAA
* * * *
1941912 GAAGGTCTTATAGAATCATGCCCGGAGGTCTTACAGATTATGTCAA
1 G-AGGTCTTAGAGAATCATGCCCGGAGGTCTTACAAATCATGCCAA
*
1941958 GAGGTCTTAGAG-ATTATGCCCGGAGGTCTTACAAATC
1 GAGGTCTTAGAGAATCATGCCCGGAGGTCTTACAAATC
1941995 TCAAAATCTT
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
43 1 0.01
44 31 0.46
45 35 0.51
46 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (45 bp):
GAGGTCTTAGAGAATCATGCCCGGAGGTCTTACAAATCATGCCAA
Found at i:1942739 original size:33 final size:33
Alignment explanation
Indices: 1942671--1942933 Score: 268
Period size: 33 Copynumber: 8.1 Consensus size: 33
1942661 CTTTTTTTGG
* * *
1942671 GGCCAAATAAATTGGGCTT-AAA-TTCATTGAA
1 GGCCAGATAAACTGGGCTTAAAACTTCATTGAT
* *
1942702 GGCCA-ACTAAATTGGGCTTAAAACCTCATTGAT
1 GGCCAGA-TAAACTGGGCTTAAAACTTCATTGAT
* * *
1942735 GGCCAGATAAATTGGGCTTAAAATTTTATTGAT
1 GGCCAGATAAACTGGGCTTAAAACTTCATTGAT
* *
1942768 GGCCAGACAAACTGGGCTT-AAA-TGTCATTAAT
1 GGCCAGATAAACTGGGCTTAAAACT-TCATTGAT
* * *
1942800 GGCCAGATAAACTGGG-TTTAAGCTTCATTAAT
1 GGCCAGATAAACTGGGCTTAAAACTTCATTGAT
* ** * *
1942832 GGTCAGATAAACTAAGCTTAAAACTTCATTTAA
1 GGCCAGATAAACTGGGCTTAAAACTTCATTGAT
* *
1942865 GGCCAGATAAACTGGGCTTAAAGCTTCATTGTT
1 GGCCAGATAAACTGGGCTTAAAACTTCATTGAT
* *
1942898 GGCCAGATAAACTGGACTTAAAACTTCATTAAT
1 GGCCAGATAAACTGGGCTTAAAACTTCATTGAT
1942931 GGC
1 GGC
1942934 TTAAAACTTC
Statistics
Matches: 195, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.01
31 20 0.10
32 50 0.26
33 123 0.63
34 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (33 bp):
GGCCAGATAAACTGGGCTTAAAACTTCATTGAT
Found at i:1942938 original size:19 final size:19
Alignment explanation
Indices: 1942914--1942952 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1942904 ATAAACTGGA
1942914 CTTAAAACTTCATTAATGG
1 CTTAAAACTTCATTAATGG
*
1942933 CTTAAAACTTCATTGATGG
1 CTTAAAACTTCATTAATGG
1942952 C
1 C
1942953 CAGATAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (19 bp):
CTTAAAACTTCATTAATGG
Found at i:1942968 original size:33 final size:33
Alignment explanation
Indices: 1942931--1943570 Score: 838
Period size: 33 Copynumber: 19.4 Consensus size: 33
1942921 CTTCATTAAT
*
1942931 GGCTTAAAACTTCATTGATGGCCAGATAAACTG
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
* ** *
1942964 GGCTTAAAGTTTCATTGATGATCAGATAAACTA
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
*
1942997 GGCTTAAAGCTTCATTGATGGCTAGATAAACTG
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
* * *
1943030 GGCTTAAAGCTTCATTGATGGGCAAATAAACTA
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
* * *
1943063 GACTTAAATCTTTATTTGA-GGCCAGATAAACTG
1 GGCTTAAAGCTTCA-TTGATGGCCAGATAAACTG
* *
1943096 GGTTTAAAGCCTCATTGATGGCCAGATAAACTG
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
*
1943129 GGCTTAAAGCTTCATTGATGGCCAAATAAACTG
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
*
1943162 GGCTTAAATCTTCATTTGA-GGCCAGATAAACTG
1 GGCTTAAAGCTTCA-TTGATGGCCAGATAAACTG
* * * * *
1943195 GGTTTAAAACCTCATTGATGGCCAAATAAGCT-
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
*
1943227 GGCTTAAAGCTTCATTAATGGCCAGATAAACTG
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
*
1943260 GGCTTAAAGTTTCATTGATGGCCAGATAAACTG
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
* *
1943293 AGCTTAAAGCTTCATTGATGGCCAAATAAACTG
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
* * *
1943326 GGCTTAAATCTTTATTTGA-GGTCAGATAAACTG
1 GGCTTAAAGCTTCA-TTGATGGCCAGATAAACTG
* * * *
1943359 GGTTTAAAGCCTCATTGATGGCCAGATAAGCTA
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
* * *
1943392 GGCTTAAAGCTTTATTAATGGCCAGATAAACTA
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
* * *
1943425 GGCTTAAAGTTTCATTGATGGCCAGAAAAATTG
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
* *
1943458 GGCTTAAAGCTTCATTAATGGCCAGATAAACTA
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
* *
1943491 GGCTTAAAGTTTCATTGATGGCCAGAAAAACTG
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
1943524 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
1 GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
1943557 GGCTTAAATGCTTC
1 GGCTTAAA-GCTTC
1943571 TGAGCTTAAA
Statistics
Matches: 519, Mismatches: 80, Indels: 15
0.85 0.13 0.02
Matches are distributed among these distances:
32 38 0.07
33 464 0.89
34 17 0.03
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (33 bp):
GGCTTAAAGCTTCATTGATGGCCAGATAAACTG
Found at i:1942990 original size:85 final size:85
Alignment explanation
Indices: 1942847--1943019 Score: 258
Period size: 85 Copynumber: 2.0 Consensus size: 85
1942837 GATAAACTAA
* * *
1942847 GCTTAAAACTTCATTTAAGGCCAGATAAACTGGGCTTAAAGCTTCATTGTTGGCCAGATAAACT-
1 GCTTAAAACTTCATTGAAGGCCAGATAAACTGGGCTTAAAGCTTCATTGATGACCAGATAAACTA
1942911 GGACTTAAAACTTCATTAATG
66 GG-CTTAAAACTTCATTAATG
* * *
1942932 GCTTAAAACTTCATTGATGGCCAGATAAACTGGGCTTAAAGTTTCATTGATGATCAGATAAACTA
1 GCTTAAAACTTCATTGAAGGCCAGATAAACTGGGCTTAAAGCTTCATTGATGACCAGATAAACTA
* *
1942997 GGCTTAAAGCTTCATTGATG
66 GGCTTAAAACTTCATTAATG
1943017 GCT
1 GCT
1943020 AGATAAACTG
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
85 77 0.97
86 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (85 bp):
GCTTAAAACTTCATTGAAGGCCAGATAAACTGGGCTTAAAGCTTCATTGATGACCAGATAAACTA
GGCTTAAAACTTCATTAATG
Found at i:1951205 original size:33 final size:32
Alignment explanation
Indices: 1951134--1951211 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 32
1951124 TTTGAGGTTT
*
1951134 GGGGTTTTGATTTAAGGGTTTGGATTTTATAG
1 GGGGTTTGGATTTAAGGGTTTGGATTTTATAG
1951166 GGGGTTTGGATTTAAGGGATTTTGGATTTT-TAG
1 GGGGTTTGGATTTAAGGG--TTTGGATTTTATAG
1951199 GGGGTTTGGATTT
1 GGGGTTTGGATTT
1951212 TTAGATGTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
32 17 0.40
33 16 0.37
34 10 0.23
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.46
Consensus pattern (32 bp):
GGGGTTTGGATTTAAGGGTTTGGATTTTATAG
Found at i:1951213 original size:18 final size:17
Alignment explanation
Indices: 1951149--1951215 Score: 91
Period size: 17 Copynumber: 3.9 Consensus size: 17
1951139 TTTGATTTAA
1951149 GGGTTTGGATTTTATAGG
1 GGGTTTGGATTTT-TAGG
*
1951167 GGGTTTGGA-TTTAAGG
1 GGGTTTGGATTTTTAGG
**
1951183 GATTTTGGATTTTTAGG
1 GGGTTTGGATTTTTAGG
1951200 GGGTTTGGATTTTTAG
1 GGGTTTGGATTTTTAG
1951216 ATGTTTTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
16 10 0.24
17 23 0.55
18 9 0.21
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.46
Consensus pattern (17 bp):
GGGTTTGGATTTTTAGG
Found at i:1952299 original size:21 final size:20
Alignment explanation
Indices: 1952252--1952301 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
1952242 TTTTTATATA
1952252 ATTAATAATTATTATTTTATT
1 ATTAA-AATTATTATTTTATT
1952273 -TT-AAATTATTATTATTATT
1 ATTAAAATTATTATT-TTATT
1952292 ATTAAAATTA
1 ATTAAAATTA
1952302 AAATAGTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 10 0.38
19 6 0.23
20 4 0.15
21 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTAAAATTATTATTTTATT
Found at i:1954470 original size:32 final size:32
Alignment explanation
Indices: 1954404--1954471 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
1954394 TAGATTTGAT
*
1954404 AATTGATATATTTATATCATGTAAAATATTAA
1 AATTGATATATTTATATCATGTAAAATATAAA
* * ***
1954436 AATTTATATATTTATGTCATGTGTTATATAAA
1 AATTGATATATTTATATCATGTAAAATATAAA
1954468 AATT
1 AATT
1954472 ATGTATCATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (32 bp):
AATTGATATATTTATATCATGTAAAATATAAA
Found at i:1954596 original size:13 final size:12
Alignment explanation
Indices: 1954580--1954622 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
1954570 TTTCATATTT
1954580 TATTTTCATATCA
1 TATTTT-ATATCA
1954593 TA-TTTATATCA
1 TATTTTATATCA
*
1954604 TATTATTATATTA
1 TATT-TTATATCA
1954617 TATTTT
1 TATTTT
1954623 TGATCGACAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 8 0.30
12 6 0.22
13 13 0.48
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTTATATCA
Found at i:1955899 original size:3 final size:3
Alignment explanation
Indices: 1955891--1955925 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1955881 TAATGAGTAA
1955891 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1955926 AGATAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1957169 original size:24 final size:23
Alignment explanation
Indices: 1957126--1957171 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
1957116 TTTTTTCTTT
1957126 CTTTTTTTTTTTTTGAACTTTTGA
1 CTTTTTTTTTTTTT-AACTTTTGA
1957150 CTTTTTTGTTTTGTTT-ACTTTT
1 CTTTTTT-TTTT-TTTAACTTTT
1957172 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
24 13 0.65
25 4 0.20
26 3 0.15
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (23 bp):
CTTTTTTTTTTTTTAACTTTTGA
Found at i:1957512 original size:42 final size:43
Alignment explanation
Indices: 1957468--1957707 Score: 263
Period size: 42 Copynumber: 5.7 Consensus size: 43
1957458 CTCTTTGTAT
* * *
1957468 AGAGGCTAAACAAATTT-AAATGGGAAATGAGCTCCTCTAAAT
1 AGAGGCTAAACAACTTTAAAATAGGAAATGAGCTCCTCTAAAC
** ** *
1957510 AGAGGCTAAATGACTTTAAAATAGGAAATGAATTCCTCTATAC
1 AGAGGCTAAACAACTTTAAAATAGGAAATGAGCTCCTCTAAAC
* * *
1957553 AGAGGCTAAACAATTTTAAAATAGGAAATGTGCTACTCTAAAC
1 AGAGGCTAAACAACTTTAAAATAGGAAATGAGCTCCTCTAAAC
* * *
1957596 AGAGGCTAAATAAGTTT-AAATAGGAAATGGGCTCCTCTAAAC
1 AGAGGCTAAACAACTTTAAAATAGGAAATGAGCTCCTCTAAAC
* * * *
1957638 AGATGCTAAACAACTTT-AAATAGGAAATGAGCT-TTTTAAAT
1 AGAGGCTAAACAACTTTAAAATAGGAAATGAGCTCCTCTAAAC
** *
1957679 AGAGATTAAACAATTTTAAAATAGGAAAT
1 AGAGGCTAAACAACTTTAAAATAGGAAAT
1957708 AGGATTGAAC
Statistics
Matches: 165, Mismatches: 31, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
41 18 0.11
42 77 0.47
43 70 0.42
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (43 bp):
AGAGGCTAAACAACTTTAAAATAGGAAATGAGCTCCTCTAAAC
Found at i:1957624 original size:85 final size:85
Alignment explanation
Indices: 1957468--1957707 Score: 277
Period size: 85 Copynumber: 2.8 Consensus size: 85
1957458 CTCTTTGTAT
* * * *
1957468 AGAGGCTAAACAAATTTAAATGGGAAATGAGCTCCTCTAAATAGAGGCTAAATGACTTTAAAATA
1 AGAGGCTAAACAAATTTAAATAGGAAATGAGCTACTCTAAACAGAGGCTAAATAACTTTAAAATA
* *
1957533 GGAAATGAATTCCTCTATAC
66 GGAAATGAACTCCTCTAAAC
* * *
1957553 AGAGGCTAAACAATTTTAAAATAGGAAATGTGCTACTCTAAACAGAGGCTAAATAAGTTT-AAAT
1 AGAGGCTAAACAAATTT-AAATAGGAAATGAGCTACTCTAAACAGAGGCTAAATAACTTTAAAAT
**
1957617 AGGAAATGGGCTCCTCTAAAC
65 AGGAAATGAACTCCTCTAAAC
* * * * * ** * *
1957638 AGATGCTAAACAACTTTAAATAGGAAATGAGCT-TTTTAAATAGAGATTAAACAATTTTAAAATA
1 AGAGGCTAAACAAATTTAAATAGGAAATGAGCTACTCTAAACAGAGGCTAAATAACTTTAAAATA
1957702 GGAAAT
66 GGAAAT
1957708 AGGATTGAAC
Statistics
Matches: 132, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
83 18 0.14
84 26 0.20
85 52 0.39
86 36 0.27
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (85 bp):
AGAGGCTAAACAAATTTAAATAGGAAATGAGCTACTCTAAACAGAGGCTAAATAACTTTAAAATA
GGAAATGAACTCCTCTAAAC
Found at i:1957893 original size:59 final size:60
Alignment explanation
Indices: 1957823--1957938 Score: 155
Period size: 59 Copynumber: 1.9 Consensus size: 60
1957813 AACTGAAATT
* * *
1957823 GAAGATGAGTGACCAAAATTGAA-CTGCATGCCAAAAAAT-AAATAATCTGGACCAAGATC
1 GAAGATGAGTGACCAAAATTGAATC-ACAGGCCAAAAAATAAAATAATCTAGACCAAGATC
** *
1957882 GAAGATGAGTGACCATGATTGAATCACAGGTCAAAAAATAAAATAATCTAGACCAAG
1 GAAGATGAGTGACCAAAATTGAATCACAGGCCAAAAAATAAAATAATCTAGACCAAG
1957939 CCAAGGTAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 32 0.65
60 17 0.35
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (60 bp):
GAAGATGAGTGACCAAAATTGAATCACAGGCCAAAAAATAAAATAATCTAGACCAAGATC
Found at i:1957969 original size:16 final size:16
Alignment explanation
Indices: 1957948--1957978 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1957938 GCCAAGGTAG
*
1957948 AAAATAAGTTATTGAA
1 AAAATAAGTGATTGAA
1957964 AAAATAAGTGATTGA
1 AAAATAAGTGATTGA
1957979 GACTAAACCA
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:0.55, C:0.00, G:0.16, T:0.29
Consensus pattern (16 bp):
AAAATAAGTGATTGAA
Found at i:1958381 original size:74 final size:74
Alignment explanation
Indices: 1958286--1958445 Score: 223
Period size: 74 Copynumber: 2.2 Consensus size: 74
1958276 AAATCCCAAT
* * * *
1958286 ATTCGAAGTTTCACAAGAAATTCACAAAGATTTCAAAA-TTTGTAAAAAGTCAAGATTCACAAAT
1 ATTCCAAGTTTCACAAAAAATTCACAAAGATTTCAAAACTTT-TAAAAAGTCAAAATTCACAAAA
**
1958350 GTTTGTAAGA
65 GTTTACAAGA
* *
1958360 ATTCCAAGTTTCACAAAAAATTCACAAAGATTTGAAAACTTTTAAAAGGTCAAAATTCACAAAAG
1 ATTCCAAGTTTCACAAAAAATTCACAAAGATTTCAAAACTTTTAAAAAGTCAAAATTCACAAAAG
1958425 TTTACAAGA
66 TTTACAAGA
*
1958434 ATTCCAATTTTC
1 ATTCCAAGTTTC
1958446 GCAAGTGTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
74 73 0.96
75 3 0.04
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (74 bp):
ATTCCAAGTTTCACAAAAAATTCACAAAGATTTCAAAACTTTTAAAAAGTCAAAATTCACAAAAG
TTTACAAGA
Found at i:1959824 original size:1 final size:1
Alignment explanation
Indices: 1959820--1959877 Score: 62
Period size: 1 Copynumber: 58.0 Consensus size: 1
1959810 TAAGTTTTCA
* * * * * *
1959820 TTTTTTTTTCTCTTTTTTCTTTTTTTATTTTTTTTGTTTTTTTTCTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1959878 ACATATCTTG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.02, C:0.07, G:0.02, T:0.90
Consensus pattern (1 bp):
T
Found at i:1959843 original size:26 final size:25
Alignment explanation
Indices: 1959821--1959877 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 25
1959811 AAGTTTTCAT
* *
1959821 TTTTTTTTCTCTTTTTTCTTTTTTTA
1 TTTTTTTTGTTTTTTTTC-TTTTTTA
1959847 TTTTTTTTGTTTTTTTTCTTTTTT-
1 TTTTTTTTGTTTTTTTTCTTTTTTA
1959871 TTTTTTT
1 TTTTTTT
1959878 ACATATCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 7 0.24
25 6 0.21
26 16 0.55
ACGTcount: A:0.02, C:0.07, G:0.02, T:0.89
Consensus pattern (25 bp):
TTTTTTTTGTTTTTTTTCTTTTTTA
Found at i:1964160 original size:25 final size:25
Alignment explanation
Indices: 1964132--1964197 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 25
1964122 AGGTAATGAG
*
1964132 TAAAATAATAATAATAAACAAAATC
1 TAAAAAAATAATAATAAACAAAATC
1964157 TAAAAAAATAATAATAAACAAAA--
1 TAAAAAAATAATAATAAACAAAATC
1964180 TAAACAAAATAA-AATAAA
1 TAAA-AAAATAATAATAAA
1964198 AATGAAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
23 10 0.26
24 7 0.18
25 22 0.56
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (25 bp):
TAAAAAAATAATAATAAACAAAATC
Found at i:1974339 original size:22 final size:22
Alignment explanation
Indices: 1974309--1974355 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
1974299 CCTAAACTAA
* *
1974309 AAAAAAAAAAAAAAAAGTGGATTG
1 AAAAAAACAAAGAAAA-T-GATTG
1974333 AAAAAAACAAAGAAAATGATTG
1 AAAAAAACAAAGAAAATGATTG
1974355 A
1 A
1974356 GTGGAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 1 0.05
24 14 0.67
ACGTcount: A:0.70, C:0.02, G:0.15, T:0.13
Consensus pattern (22 bp):
AAAAAAACAAAGAAAATGATTG
Found at i:1975127 original size:20 final size:19
Alignment explanation
Indices: 1975102--1975145 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
1975092 TCGAATCAAA
*
1975102 TTATATATTTTTATTAATTT
1 TTATATATTTTT-TAAATTT
1975122 TTATATATTTTTTAAATTT
1 TTATATATTTTTTAAATTT
1975141 TTATA
1 TTATA
1975146 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATATATTTTTTAAATTT
Found at i:1975149 original size:11 final size:10
Alignment explanation
Indices: 1975102--1975147 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
1975092 TCGAATCAAA
*
1975102 TTATATATTT
1 TTATAAATTT
*
1975112 TTATTAATTT
1 TTATAAATTT
*
1975122 TTATATATTT
1 TTATAAATTT
1975132 TT-TAAATTT
1 TTATAAATTT
1975141 TTATAAA
1 TTATAAA
1975148 ATAAAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTATAAATTT
Found at i:1975206 original size:18 final size:19
Alignment explanation
Indices: 1975170--1975204 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1975160 ATTTTATATA
1975170 TAAATTTATTTAAATAAAT
1 TAAATTTATTTAAATAAAT
1975189 TAAATTT-TTT-AATAAA
1 TAAATTTATTTAAATAAA
1975205 ATAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTTATTTAAATAAAT
Found at i:1976161 original size:104 final size:106
Alignment explanation
Indices: 1976017--1976221 Score: 303
Period size: 104 Copynumber: 2.0 Consensus size: 106
1976007 TTAAACTTTT
* *
1976017 TAAAATTTTAATTCCAAAAATATTAAAAGTGATTGGTTAAAATAT-ACTTAATAA-ATGTTTTTA
1 TAAAATTTTAATTCCAAAAAAATTAAAAGTGATTGATTAAAATATCA-TTAATAATAT-TTTTTA
1976080 TAAATTTTAATTTAAATGAATTTTTT-ATTATTAGACTCTTAA
64 TAAATTTTAATTTAAATGAATTTTTTAATTATTAGACTCTTAA
* *
1976122 TAAAATTTTAATT-TAAAAAAATCT-AAAGTGATTGATTAAAATATCATTAGTAATATTTTTTAT
1 TAAAATTTTAATTCCAAAAAAAT-TAAAAGTGATTGATTAAAATATCATTAATAATATTTTTTAT
*
1976185 AAATTTTAATTTAAATGATTTTTTTAATTATTAGACT
65 AAATTTTAATTTAAATGAATTTTTTAATTATTAGACT
1976222 TTTTTTTATA
Statistics
Matches: 91, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
104 63 0.69
105 28 0.31
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (106 bp):
TAAAATTTTAATTCCAAAAAAATTAAAAGTGATTGATTAAAATATCATTAATAATATTTTTTATA
AATTTTAATTTAAATGAATTTTTTAATTATTAGACTCTTAA
Found at i:1978345 original size:18 final size:19
Alignment explanation
Indices: 1978297--1978346 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
1978287 TGACCCAAAA
1978297 TTAATA-AAATATTATTTT
1 TTAATATAAATATTATTTT
1978315 TTAAATATAAAATATTA-TTT
1 TT-AATAT-AAATATTATTTT
1978335 TTAATATAAATA
1 TTAATATAAATA
1978347 CAAAATTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.24
19 9 0.31
20 5 0.17
21 8 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATATAAATATTATTTT
Found at i:1978346 original size:25 final size:21
Alignment explanation
Indices: 1978300--1978344 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1978290 CCCAAAATTA
1978300 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
1978321 ATAAAATATTA-TTTTT-AAT
1 ATAAAATATTATTTTTTAAAT
1978340 ATAAA
1 ATAAA
1978345 TACAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 8 0.33
20 5 0.21
21 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:1978359 original size:18 final size:18
Alignment explanation
Indices: 1978338--1978372 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1978328 ATTATTTTTA
1978338 ATATAAATACAAAATTAT
1 ATATAAATACAAAATTAT
*
1978356 ATATAAATATAAAATTA
1 ATATAAATACAAAATTA
1978373 AATAATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATAAATACAAAATTAT
Found at i:1978971 original size:16 final size:16
Alignment explanation
Indices: 1978952--1978985 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1978942 TATTTAATAG
1978952 TTTAATTATTTTA-AAT
1 TTTAATT-TTTTATAAT
1978968 TTTAATTTTTTATAAT
1 TTTAATTTTTTATAAT
1978984 TT
1 TT
1978986 CGAATTGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTAATTTTTTATAAT
Found at i:1980286 original size:24 final size:25
Alignment explanation
Indices: 1980241--1980288 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
1980231 TTATTATGAA
1980241 TTTAATATTTTAAAATTGTTATTTG
1 TTTAATATTTTAAAATTGTTATTTG
1980266 TTTAAT-TTTTATAAATT-TTATTT
1 TTTAATATTTTA-AAATTGTTATTT
1980289 AGTAAATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (25 bp):
TTTAATATTTTAAAATTGTTATTTG
Found at i:1980296 original size:24 final size:24
Alignment explanation
Indices: 1980248--1980296 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
1980238 GAATTTAATA
*
1980248 TTTTAAAATTGTTATTTGTTTAAT
1 TTTTAAAATTGTTATTTGTTAAAT
1980272 TTTTATAAATT-TTATTTAG-TAAAT
1 TTTTA-AAATTGTTATTT-GTTAAAT
1980296 T
1 T
1980297 AGTTCTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTTAAAATTGTTATTTGTTAAAT
Found at i:1980843 original size:11 final size:11
Alignment explanation
Indices: 1980829--1980872 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
1980819 TTACTTGTTG
*
1980829 ATAACTTAGTA
1 ATAACTTAATA
* *
1980840 ATAAATTAATG
1 ATAACTTAATA
1980851 ATAACTTAATA
1 ATAACTTAATA
*
1980862 ATAATTTAATA
1 ATAACTTAATA
1980873 GTAAATCAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (11 bp):
ATAACTTAATA
Found at i:1980852 original size:22 final size:22
Alignment explanation
Indices: 1980827--1980871 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1980817 AGTTACTTGT
*
1980827 TGATAACTTAGTAATAAATTAA
1 TGATAACTTAATAATAAATTAA
*
1980849 TGATAACTTAATAATAATTTAA
1 TGATAACTTAATAATAAATTAA
1980871 T
1 T
1980872 AGTAAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (22 bp):
TGATAACTTAATAATAAATTAA
Found at i:1981208 original size:22 final size:22
Alignment explanation
Indices: 1981089--1981258 Score: 75
Period size: 22 Copynumber: 7.9 Consensus size: 22
1981079 GTGAATCATA
* * *
1981089 AATAATTTAATGGTAAATCAAT
1 AATAATGTAATAGTAAATTAAT
* *
1981111 AAT-A-GTAAGCAGTAAATCAAT
1 AATAATGTAA-TAGTAAATTAAT
* **
1981132 TATAACATAATAGTAAA-TATAT
1 AATAATGTAATAGTAAATTA-AT
* * ** * *
1981154 AAAAATATAACGGTAAATCATT
1 AATAATGTAATAGTAAATTAAT
* *
1981176 GATAATTTAATAGTAAATTAAT
1 AATAATGTAATAGTAAATTAAT
*
1981198 AAT-ATAGT-A-A-TAAATTATT
1 AATAAT-GTAATAGTAAATTAAT
*
1981217 AATAATGTAATAGTAAATTACT
1 AATAATGTAATAGTAAATTAAT
* * *
1981239 AATAATTTAGTTGTAAATTA
1 AATAATGTAATAGTAAATTA
1981259 GTGATAATTT
Statistics
Matches: 110, Mismatches: 28, Indels: 20
0.70 0.18 0.13
Matches are distributed among these distances:
19 13 0.12
20 7 0.06
21 18 0.16
22 68 0.62
23 4 0.04
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (22 bp):
AATAATGTAATAGTAAATTAAT
Found at i:1981236 original size:19 final size:19
Alignment explanation
Indices: 1981177--1981242 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
1981167 TAAATCATTG
*
1981177 ATAATTTAATAGTAAATTA
1 ATAATATAATAGTAAATTA
* *
1981196 ATAATATAGTAATAAATTATTA
1 ATAATATAATAGT-AA--ATTA
*
1981218 ATAATGTAATAGTAAATTA
1 ATAATATAATAGTAAATTA
*
1981237 CTAATA
1 ATAATA
1981243 ATTTAGTTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 18 0.50
20 2 0.06
21 2 0.06
22 14 0.39
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (19 bp):
ATAATATAATAGTAAATTA
Found at i:1981249 original size:19 final size:20
Alignment explanation
Indices: 1981186--1981249 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 20
1981176 GATAATTTAA
*
1981186 TAGTAAATTAATAAT-ATAG
1 TAGTAAATTAATAATAATAT
* * *
1981205 TAATAAATTATTAATAATGTAA
1 TAGTAAATTAATAATAA--TAT
*
1981227 TAGTAAATTACTAATAAT-T
1 TAGTAAATTAATAATAATAT
1981246 TAGT
1 TAGT
1981250 TGTAAATTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
19 17 0.47
20 2 0.06
22 17 0.47
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.41
Consensus pattern (20 bp):
TAGTAAATTAATAATAATAT
Found at i:1981265 original size:22 final size:22
Alignment explanation
Indices: 1981177--1981282 Score: 101
Period size: 22 Copynumber: 5.0 Consensus size: 22
1981167 TAAATCATTG
*
1981177 ATAATTTAATAGTAAA-T--TA
1 ATAATTTAGTAGTAAATTAGTA
* * *
1981196 ATAATATAGTAATAAATTATTA
1 ATAATTTAGTAGTAAATTAGTA
* * *
1981218 ATAATGTAATAGTAAATTACTA
1 ATAATTTAGTAGTAAATTAGTA
* *
1981240 ATAATTTAGTTGTAAATTAGTG
1 ATAATTTAGTAGTAAATTAGTA
*
1981262 ATAATTTAGTAATAAATTAGT
1 ATAATTTAGTAGTAAATTAGT
1981283 TAATTATTGA
Statistics
Matches: 70, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
19 13 0.19
20 1 0.01
22 56 0.80
ACGTcount: A:0.48, C:0.01, G:0.09, T:0.42
Consensus pattern (22 bp):
ATAATTTAGTAGTAAATTAGTA
Found at i:1981476 original size:22 final size:22
Alignment explanation
Indices: 1981344--1981492 Score: 122
Period size: 22 Copynumber: 6.8 Consensus size: 22
1981334 TTATAAATTT
* *
1981344 ATAATAAATCATCAATAATTTA
1 ATAATAAATCATTAATAACTTA
*
1981366 AT-AGAAATCATTAATAACTTA
1 ATAATAAATCATTAATAACTTA
* * *
1981387 AGAATATATCATTCATAACTTA
1 ATAATAAATCATTAATAACTTA
*** * *
1981409 ATGGCAAATCATTCATAAATTA
1 ATAATAAATCATTAATAACTTA
*
1981431 GA-AATAAATCATTAATAATTTA
1 -ATAATAAATCATTAATAACTTA
* *
1981453 ATAATAAATCAATGATAACTTA
1 ATAATAAATCATTAATAACTTA
* * *
1981475 ATAGTAAATAATTGATAA
1 ATAATAAATCATTAATAA
1981493 TGTAATTGTC
Statistics
Matches: 100, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
21 18 0.18
22 81 0.81
23 1 0.01
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (22 bp):
ATAATAAATCATTAATAACTTA
Found at i:1981483 original size:44 final size:42
Alignment explanation
Indices: 1981346--1981517 Score: 137
Period size: 44 Copynumber: 4.0 Consensus size: 42
1981336 ATAAATTTAT
* * *
1981346 AATAAATCATCAATAATTTAATAGAAATCATTAATAACTTAA
1 AATAAATCATTAATAATTTAATATAAATCATTGATAACTTAA
* * * ** * *
1981388 GAATATATCATTCATAACTTAATGGCAAATCATTCATAAATTAGA
1 -AATAAATCATTAATAATTTAAT-ATAAATCATTGATAACTTA-A
*
1981433 AATAAATCATTAATAATTTAATAATAAATCAATGATAACTTAA
1 AATAAATCATTAATAATTTAAT-ATAAATCATTGATAACTTAA
* * * * * *
1981476 TAGTAAATAATTGATAATGTAATTGTCAATCATTGATAACTT
1 -AATAAATCATTAATAATTTAA-TATAAATCATTGATAACTT
1981518 TTTATACTTA
Statistics
Matches: 101, Mismatches: 24, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
43 19 0.19
44 80 0.79
45 2 0.02
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.35
Consensus pattern (42 bp):
AATAAATCATTAATAATTTAATATAAATCATTGATAACTTAA
Found at i:1981510 original size:22 final size:22
Alignment explanation
Indices: 1981348--1981517 Score: 121
Period size: 22 Copynumber: 7.8 Consensus size: 22
1981338 AAATTTATAA
** *
1981348 TAAATCATCAATAATTTAATAG
1 TAAATCATTGATAACTTAATAG
* * *
1981370 -AAATCATTAATAACTTAAGAA
1 TAAATCATTGATAACTTAATAG
* * *
1981391 TATATCATTCATAACTTAATGG
1 TAAATCATTGATAACTTAATAG
* * * *
1981413 CAAATCATTCATAAATTAGA-AA
1 TAAATCATTGATAACTTA-ATAG
* * *
1981435 TAAATCATTAATAATTTAATAA
1 TAAATCATTGATAACTTAATAG
*
1981457 TAAATCAATGATAACTTAATAG
1 TAAATCATTGATAACTTAATAG
* *
1981479 TAAATAATTGATAA-TGTAATTG
1 TAAATCATTGATAACT-TAATAG
*
1981501 TCAATCATTGATAACTT
1 TAAATCATTGATAACTT
1981518 TTTATACTTA
Statistics
Matches: 117, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
21 19 0.16
22 96 0.82
23 2 0.02
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (22 bp):
TAAATCATTGATAACTTAATAG
Found at i:1983491 original size:22 final size:22
Alignment explanation
Indices: 1983465--1983507 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1983455 GTTAATCATT
1983465 ATAACCTAATAGTAAATTAGTA
1 ATAACCTAATAGTAAATTAGTA
*
1983487 ATAACTTAATAGTAAATTAGT
1 ATAACCTAATAGTAAATTAGT
1983508 TTTAGTCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (22 bp):
ATAACCTAATAGTAAATTAGTA
Found at i:1983650 original size:46 final size:45
Alignment explanation
Indices: 1983538--1983673 Score: 143
Period size: 46 Copynumber: 3.0 Consensus size: 45
1983528 TTGATAAATT
* * * *
1983538 TAGTAGTAAATAATAAATAACTTAATAGTAAATCAATGATAGTTTA
1 TAGTAGTTAATCATAAATAACTTAATAGTAAATTAAT-ATAATTTA
* *
1983584 -A-TTGTTAATCATTAAA-AACTTAAAAGTAAATTAATATAATTTA
1 TAGTAGTTAATCA-TAAATAACTTAATAGTAAATTAATATAATTTA
* *
1983627 CTAGTAGTTAATCATCAATAACTTAATAGTAAATTATAGATAATTTA
1 -TAGTAGTTAATCATAAATAACTTAATAGTAAATTA-ATATAATTTA
1983674 ATATAAATTA
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
43 7 0.09
44 24 0.32
45 9 0.12
46 25 0.34
47 9 0.12
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.38
Consensus pattern (45 bp):
TAGTAGTTAATCATAAATAACTTAATAGTAAATTAATATAATTTA
Found at i:1983682 original size:21 final size:22
Alignment explanation
Indices: 1983471--1983693 Score: 80
Period size: 22 Copynumber: 10.0 Consensus size: 22
1983461 CATTATAACC
* *
1983471 TAATAGTAAATTAGTAATAACT
1 TAATAGTAAATTAGTGATAATT
** * *
1983493 TAATAGTAAATTAGTTTTAGTC
1 TAATAGTAAATTAGTGATAATT
* *
1983515 TAGTAGT-AATTAATTGATAAATT
1 TAATAGTAAATT-AGTGAT-AATT
* * * *
1983538 TAGTAGTAAA-TAATAAATAACT
1 TAATAGTAAATTAGT-GATAATT
* * *
1983560 TAATAGTAAATCAATGATAGTT
1 TAATAGTAAATTAGTGATAATT
* * * * * * *
1983582 TAATTGTTAATCATTAAAAACT
1 TAATAGTAAATTAGTGATAATT
* *
1983604 TAAAAGTAAATTAAT-ATAATT
1 TAATAGTAAATTAGTGATAATT
* * * *
1983625 TACTAGTAGTTAATCA-TCAATAACT
1 TA--A-TAGTAAATTAGT-GATAATT
1983650 TAATAGTAAATTA-TAGATAATT
1 TAATAGTAAATTAGT-GATAATT
1983672 TAATA-TAAATTAGTGATAATT
1 TAATAGTAAATTAGTGATAATT
1983693 T
1 T
1983694 GATAATGCAT
Statistics
Matches: 148, Mismatches: 42, Indels: 23
0.69 0.20 0.11
Matches are distributed among these distances:
21 25 0.17
22 89 0.60
23 18 0.12
24 9 0.06
25 7 0.05
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.39
Consensus pattern (22 bp):
TAATAGTAAATTAGTGATAATT
Found at i:1983735 original size:22 final size:22
Alignment explanation
Indices: 1983665--1983737 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
1983655 GTAAATTATA
1983665 GATAATTTAAT-ATAAAT-TAGT
1 GATAATTTAATAATAAATAT-GT
* **
1983686 GATAATTTGATAATGCATCATG-
1 GATAATTTAATAATAAAT-ATGT
*
1983708 GTTAATTTAATAATAAATATGT
1 GATAATTTAATAATAAATATGT
1983730 GATAATTT
1 GATAATTT
1983738 TGTAGTATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
21 13 0.32
22 25 0.62
23 1 0.03
24 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (22 bp):
GATAATTTAATAATAAATATGT
Found at i:1983966 original size:22 final size:22
Alignment explanation
Indices: 1983936--1983991 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1983926 TATATTAGTT
* *
1983936 ATAACTTTATTAAAAAATTATCA
1 ATAA-TTTAGTAAAAAATAATCA
* *
1983959 GTAATTTAGTAATAAATAATCA
1 ATAATTTAGTAAAAAATAATCA
1983981 ATAATTTAGTA
1 ATAATTTAGTA
1983992 GTAAATCATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (22 bp):
ATAATTTAGTAAAAAATAATCA
Found at i:1984105 original size:22 final size:22
Alignment explanation
Indices: 1983960--1984139 Score: 180
Period size: 22 Copynumber: 8.2 Consensus size: 22
1983950 AAATTATCAG
* * **
1983960 TAATTTAGTAATAAATAATCAA
1 TAATTTAGTAGTAAATCATTGA
*
1983982 TAATTTAGTAGTAAATCATTCA
1 TAATTTAGTAGTAAATCATTGA
* *
1984004 TAATTTAATAGTAAATCATTCA
1 TAATTTAGTAGTAAATCATTGA
* * *
1984026 TAATTTAGTAGCAAATCAATGC
1 TAATTTAGTAGTAAATCATTGA
*
1984048 TAATTTAGTAGTAAATCATTAA
1 TAATTTAGTAGTAAATCATTGA
* *
1984070 TAATTTAGTAGTATATTATTGA
1 TAATTTAGTAGTAAATCATTGA
* *
1984092 TAATTTAGTAGTATATTATTGA
1 TAATTTAGTAGTAAATCATTGA
* * * * *
1984114 CAACTTAATAGTAAATAACTGA
1 TAATTTAGTAGTAAATCATTGA
1984136 TAAT
1 TAAT
1984140 ATAATAATAA
Statistics
Matches: 133, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 133 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (22 bp):
TAATTTAGTAGTAAATCATTGA
Found at i:1984546 original size:21 final size:21
Alignment explanation
Indices: 1984522--1984612 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 21
1984512 TCAATGGTTG
*
1984522 CCAAAATTATATTATAAGTTA
1 CCAAAATTATATTAAAAGTTA
* *
1984543 CCAAACTAATA-TAGAAAGTTA
1 CCAAAATTATATTA-AAAGTTA
* *
1984564 CCAAAATTATATTGAAGGTTA
1 CCAAAATTATATTAAAAGTTA
* * *
1984585 TCAAAATTTTATTAAAACTTA
1 CCAAAATTATATTAAAAGTTA
*
1984606 TCAAAAT
1 CCAAAAT
1984613 CAAAATTATA
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
20 2 0.04
21 53 0.95
22 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (21 bp):
CCAAAATTATATTAAAAGTTA
Found at i:1984614 original size:27 final size:27
Alignment explanation
Indices: 1984584--1984637 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1984574 ATTGAAGGTT
*
1984584 ATCAAAATTTTATTA-AAACTTATCAAA
1 ATCAAAATTATA-TAGAAACTTATCAAA
*
1984611 ATCAAAATTATATAGAAAGTTATCAAA
1 ATCAAAATTATATAGAAACTTATCAAA
1984638 TTTTACTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (27 bp):
ATCAAAATTATATAGAAACTTATCAAA
Found at i:1984666 original size:48 final size:48
Alignment explanation
Indices: 1984566--1984668 Score: 122
Period size: 48 Copynumber: 2.1 Consensus size: 48
1984556 GAAAGTTACC
* * *
1984566 AAAATTATATTGAAGGTTATCAAAATTTTATTAAAACTTATCAAAATC
1 AAAATTATATAGAAAGTTATCAAAATTTTATTAAAACTTATCAAAATA
*
1984614 AAAATTATATAGAAAGTTATC-AAATTTTACTT-ATA-TTATACTAAAATA
1 AAAATTATATAGAAAGTTATCAAAATTTTA-TTAAAACTTAT-C-AAAATA
1984662 AAAATTA
1 AAAATTA
1984669 AATTATTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
46 4 0.08
47 11 0.23
48 33 0.69
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (48 bp):
AAAATTATATAGAAAGTTATCAAAATTTTATTAAAACTTATCAAAATA
Found at i:1985088 original size:45 final size:45
Alignment explanation
Indices: 1985037--1985123 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
1985027 AAAAAAAGTA
1985037 TATATATCAATATCATGATGAAATATTAAAAGTTTTGTTCAAAAG
1 TATATATCAATATCATGATGAAATATTAAAAGTTTTGTTCAAAAG
* * *
1985082 TATATATCAATATTATGGTGAAATATTGAAAGTTTTGTTCAA
1 TATATATCAATATCATGATGAAATATTAAAAGTTTTGTTCAA
1985124 TACTATAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (45 bp):
TATATATCAATATCATGATGAAATATTAAAAGTTTTGTTCAAAAG
Found at i:1989636 original size:18 final size:19
Alignment explanation
Indices: 1989592--1989637 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1989582 ATTAATTTGC
*
1989592 TAATTTTAATGTATTAAAA
1 TAATTTTAATGTAATAAAA
*
1989611 -AATGTTTACT-TAATAAAA
1 TAAT-TTTAATGTAATAAAA
1989629 TAATTTTAA
1 TAATTTTAA
1989638 AGATTGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
TAATTTTAATGTAATAAAA
Found at i:1991389 original size:15 final size:14
Alignment explanation
Indices: 1991369--1991399 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1991359 ATCTAATTAT
1991369 AAAATTATAATATAA
1 AAAATTATAA-ATAA
1991384 AAAATTATAAATAA
1 AAAATTATAAATAA
1991398 AA
1 AA
1991400 TACTCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATTATAAATAA
Found at i:1998519 original size:357 final size:354
Alignment explanation
Indices: 1997991--1999230 Score: 1351
Period size: 357 Copynumber: 3.5 Consensus size: 354
1997981 TATAACAAAT
* * * *
1997991 TATTAAAGGCGTTTTATAATAACAGACGT-CTTTAATAATCCGAAAAAAA-ATTTTTAAGAAAAT
1 TATTGAAGGCGTTTCATAATAAAAGAC-TCCTTTAATAAT---AAAAAAATTTTTTTAAGAAAAT
* * ** * * *
1998054 TATTGAAAGCGTTGTTATCTGCAACCACATTCACTAATTATATACAAACTGTGATAGGAATTATT
62 TATTGAAGGCGTTATTATCTGCAACTGCTTTCACTAATTATCTACAAACTGTGATAAGAATTATT
* * * *
1998119 AAATGCATCTTTCTTGGATATATGCCTTTAATAACTATGTTAAAATTTATGTGACGGTATATAGA
127 AAATGCGTCTTTCTTGGATATACGCCTTCAATAACCATGTTAAAATTTATGTGACGGTATATAGA
* * * *
1998184 ACGTATTTTACAGTAGAAAACGCCTTTAGTGATTCCCAAAAATTTTAGTGAAAAAACTTTAAAAG
192 ATGCATTTTACAGTAGAAAACGCCTTTAATGATTCCCAAAATTTTTAGTGAAAAAA-TTTAAAAG
* * * *
1998249 CGTCTGTTATTGACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAAGTATATTAAAGGTACTT
256 CGTCTGTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAAGTATATTGAAGGTGCCT
** *
1998314 TTTTGAATAAACACCTTCTATAACTATCATGGTA
321 TTTTGAATAAATGCCTTCTATAACCATCATGGTA
* *
1998348 AATTGAAGGCGTTTCATAATAAAAGACTCTTTTAATAATAAAAAAATTTTTTTTTAAGAAAATTA
1 TATTGAAGGCGTTTCATAATAAAAGACTCCTTTAATAATAAAAAAA--TTTTTTTAAGAAAATTA
* * * *
1998413 TTGAAGGCATTATTATCTGCAACTGCTTTCACTAATTATCTACAAACTATAATAAAAATTATTAA
64 TTGAAGGCGTTATTATCTGCAACTGCTTTCACTAATTATCTACAAACTGTGATAAGAATTATTAA
* * **
1998478 ATGCGTCTTTCTTTGATATACGCCTTCAATAACCGTGTTAAAATTTATGTGGTGGTATATAGAAT
129 ATGCGTCTTTCTTGGATATACGCCTTCAATAACCATGTTAAAATTTATGTGACGGTATATAGAAT
** * * *
1998543 GCATTTTACAGTA-AAAGATACCTTTAATGATTTCTAAAATTTTTAGTGAAAAAATTTTAAAGGC
194 GCATTTTACAGTAGAAA-ACGCCTTTAATGATTCCCAAAATTTTTAGTGAAAAAA-TTTAAAAGC
* * * **
1998607 GTCTATTATTAACAAATGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAATATGCCTT
257 GTCTGTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAAGTATATTGAAGGTGCCTT
* * *
1998672 TTTGAATAAATGTCTTCCATAACCATCGTGGTA
322 TTTGAATAAATGCCTTCTATAACCATCATGGTA
* * * ***
1998705 TATTGAAGGCATTTCATAATAGAAGACGCCTTTAATAATTTAAAAAAA--AAATT-A-AAAATTA
1 TATTGAAGGCGTTTCATAATAAAAGACTCCTTTAATAA--TAAAAAAATTTTTTTAAGAAAATTA
* * * * *
1998766 TTAAAGGTGTTATTATCTGTAACTAGCTTT-ATTAATTATCTACAAATTGTGATAAGAATTATTA
64 TTGAAGGCGTTATTATCTGCAACT-GCTTTCACTAATTATCTACAAACTGTGATAAGAATTATTA
* * ** *
1998830 TAGAT--GACTTTCTTGGATATACACCTTCAATAACTGTGTTAAAATTTGTGTGACGGTATATAG
128 -A-ATGCGTCTTTCTTGGATATACGCCTTCAATAACCATGTTAAAATTTATGTGACGGTATATAG
* * * * **
1998893 AATGCATTTTACAATAGAAGACGCCTTTAATGATTTCTC-AAATTTTTAGTGAGAAAATTTTGAA
191 AATGCATTTTACAGTAGAAAACGCCTTTAATGA-TTCCCAAAATTTTTAGTGAAAAAATTTAAAA
* * * *
1998957 GACATTTGTTAATAACAAACACCTTCAGTAATGGATTACTAAGTTTAAAAGTATATTGAAGGTGC
255 G-CGTCTGTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAAGTATATTGAAGGTGC
* *
1999022 CTTTTCGAATAAATGCCTTCTATAACCATCATAGTA
319 CTTTTTGAATAAATGCCTTCTATAACCATCATGGTA
* * * * *
1999058 TATTGAAGGTGTTTCATAATAAAAGA-TGCCTTTAATAATCTGAAAAACTTTTGTTAAGCAAATT
1 TATTGAAGGCGTTTCATAATAAAAGACT-CCTTTAATAA--TAAAAAAATTTTTTTAAGAAAATT
* ** * * *
1999122 ATTGAA-GC--TATTAACGTAAAAAATGCCTTCACTAATTATCTACAAATTGTGATAAGAATTAT
63 ATTGAAGGCGTTATTATC-T-GCAACTGCTTTCACTAATTATCTACAAACTGTGATAAGAATTAT
* * *
1999184 TAAAGGTGT-TGTTCTTAGATATACGCCTTCAATAACCATGTTAAAAT
126 TAAATGCGTCT-TTCTTGGATATACGCCTTCAATAACCATGTTAAAAT
1999231 CCATGTGATG
Statistics
Matches: 735, Mismatches: 124, Indels: 49
0.81 0.14 0.05
Matches are distributed among these distances:
352 5 0.01
353 275 0.37
354 25 0.03
355 13 0.02
356 75 0.10
357 334 0.45
359 8 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (354 bp):
TATTGAAGGCGTTTCATAATAAAAGACTCCTTTAATAATAAAAAAATTTTTTTAAGAAAATTATT
GAAGGCGTTATTATCTGCAACTGCTTTCACTAATTATCTACAAACTGTGATAAGAATTATTAAAT
GCGTCTTTCTTGGATATACGCCTTCAATAACCATGTTAAAATTTATGTGACGGTATATAGAATGC
ATTTTACAGTAGAAAACGCCTTTAATGATTCCCAAAATTTTTAGTGAAAAAATTTAAAAGCGTCT
GTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAAGTATATTGAAGGTGCCTTTTTG
AATAAATGCCTTCTATAACCATCATGGTA
Found at i:2001321 original size:22 final size:21
Alignment explanation
Indices: 2001296--2001337 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2001286 AGAAAGTTCT
*
2001296 GTTATATGAGACATCATCGATG
1 GTTAGATGAGA-ATCATCGATG
*
2001318 GTTAGATGATAATCATCGAT
1 GTTAGATGAGAATCATCGAT
2001338 TTAGATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (21 bp):
GTTAGATGAGAATCATCGATG
Found at i:2005663 original size:9 final size:9
Alignment explanation
Indices: 2005649--2005680 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
2005639 TTTGTGAGAT
2005649 AAAATCATA
1 AAAATCATA
2005658 AAAATCATA
1 AAAATCATA
2005667 AAAATCATA
1 AAAATCATA
2005676 AAAAT
1 AAAAT
2005681 TCCGAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAATCATA
Found at i:2005730 original size:38 final size:38
Alignment explanation
Indices: 2005688--2005766 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
2005678 AATTCCGAAT
2005688 CAAAATGACAAAACCTTGCAGGTTAGTATAAATCTTCA
1 CAAAATGACAAAACCTTGCAGGTTAGTATAAATCTTCA
*
2005726 CAAAATGACAATACCTTGCAGGTTAGTATAAATCTTCA
1 CAAAATGACAAAACCTTGCAGGTTAGTATAAATCTTCA
2005764 CAA
1 CAA
2005767 TATATGTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.27
Consensus pattern (38 bp):
CAAAATGACAAAACCTTGCAGGTTAGTATAAATCTTCA
Found at i:2009771 original size:24 final size:22
Alignment explanation
Indices: 2009744--2009798 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
2009734 TTTAATAAAA
2009744 AATTAATTTAAAATTATAATATTT
1 AATTAATTT-AAATTAT-ATATTT
* *
2009768 AATTTCATTTAAATTATATTTTT
1 AA-TTAATTTAAATTATATATTT
*
2009791 ATTTAATT
1 AATTAATT
2009799 CGAATCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 5 0.19
23 6 0.23
24 9 0.35
25 6 0.23
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTAATTTAAATTATATATTT
Found at i:2009879 original size:18 final size:20
Alignment explanation
Indices: 2009845--2009888 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
2009835 TATGATTGAA
2009845 TTATATATTTTTATTAATTT
1 TTATATATTTTTATTAATTT
2009865 TTATATA-TTTT-TTAATTT
1 TTATATATTTTTATTAATTT
2009883 TT-TATA
1 TTATATA
2009889 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.17
18 9 0.38
19 4 0.17
20 7 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATATATTTTTATTAATTT
Found at i:2010223 original size:15 final size:15
Alignment explanation
Indices: 2010197--2010241 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
2010187 ACTTATCATC
2010197 TAAA-TATAAAAATG
1 TAAACTATAAAAATG
* * *
2010211 TAAATTTTAAAAATA
1 TAAACTATAAAAATG
2010226 TAAACTATAAAAATG
1 TAAACTATAAAAATG
2010241 T
1 T
2010242 TAACAATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (15 bp):
TAAACTATAAAAATG
Found at i:2010572 original size:104 final size:107
Alignment explanation
Indices: 2010381--2010589 Score: 295
Period size: 106 Copynumber: 2.0 Consensus size: 107
2010371 TTAAACTTTT
* * *
2010381 TAAAATTTTAATTTCAAAAAAATTAAAAGTGATTGGTTAAAATATACTTAATAAATGTTTTTATA
1 TAAAATTTTAATTTCAAAAAAATCAAAAATGATTGATTAAAATATACTTAATAAATGTTTTTATA
2010446 AATTTTAATTTAAAAGAATTTTTATT-ATTATTAG-CTCTTAA
66 AATTTTAATTTAAAAGAATTTTT-TTAATTATTAGACTCTTAA
*
2010487 TAAAATTTTAATTT-AAAAAATATCAAAAATGATTGATTAAAATAT-CATTAGT-AAT-TTTTTA
1 TAAAATTTTAATTTCAAAAAA-ATCAAAAATGATTGATTAAAATATAC-TTAATAAATGTTTTTA
* *
2010548 TAAATTTTAATTTAAATGATTTTTTTTAATTATTAGACTCTT
64 TAAATTTTAATTTAAAAGAATTTTTTTAATTATTAGACTCTT
2010590 TTTTTATAAG
Statistics
Matches: 93, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
103 2 0.02
104 37 0.40
105 15 0.16
106 39 0.42
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (107 bp):
TAAAATTTTAATTTCAAAAAAATCAAAAATGATTGATTAAAATATACTTAATAAATGTTTTTATA
AATTTTAATTTAAAAGAATTTTTTTAATTATTAGACTCTTAA
Found at i:2011738 original size:16 final size:15
Alignment explanation
Indices: 2011717--2011751 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
2011707 CTTTGATTTT
*
2011717 AAAAAATTAATTATAA
1 AAAAAATTAA-AATAA
2011733 AAAAAATTAAAATAA
1 AAAAAATTAAAATAA
2011748 AAAA
1 AAAA
2011752 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAAATTAAAATAA
Found at i:2012688 original size:16 final size:17
Alignment explanation
Indices: 2012653--2012685 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2012643 ATAAAATATT
2012653 TATTTTTTAATATAAAA
1 TATTTTTTAATATAAAA
2012670 TATTTTTTAATATAAA
1 TATTTTTTAATATAAA
2012686 TATAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTTTTAATATAAAA
Found at i:2015193 original size:22 final size:22
Alignment explanation
Indices: 2015174--2015218 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2015164 AGTTAATTGT
*
2015174 TGATAACTTAATAATAAATTAA
1 TGATAACTTAACAATAAATTAA
*
2015196 TGATAACTTAACAATAATTTAA
1 TGATAACTTAACAATAAATTAA
2015218 T
1 T
2015219 AGTAAATCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (22 bp):
TGATAACTTAACAATAAATTAA
Found at i:2015334 original size:22 final size:22
Alignment explanation
Indices: 2015274--2015335 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
2015264 TCATAAAAAC
* *
2015274 TTAGTAGTAAGTAAATGATAAT
1 TTAGTAGTAAATAATTGATAAT
*
2015296 TTAGTAGTAAAAAATTGATAAT
1 TTAGTAGTAAATAATTGATAAT
*
2015318 TTAGTAGTAAATCATTGA
1 TTAGTAGTAAATAATTGA
2015336 AAACATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.37
Consensus pattern (22 bp):
TTAGTAGTAAATAATTGATAAT
Found at i:2015565 original size:22 final size:21
Alignment explanation
Indices: 2015517--2015652 Score: 91
Period size: 22 Copynumber: 6.4 Consensus size: 21
2015507 TATAACATAA
* *
2015517 TAGTAAATATATAAAAATATAAG
1 TAGTAAATAT-TAATAAT-TTAG
*
2015540 -AGTAAATCATTGATAATTTAG
1 TAGTAAAT-ATTAATAATTTAG
2015561 TAGT-AA-ATTAATAATTTAG
1 TAGTAAATATTAATAATTTAG
**
2015580 TAGTAAATTATTAATAACATA-
1 TAGTAAA-TATTAATAATTTAG
*
2015601 TAGTAAAGTACTAATAATTTAG
1 TAGTAAA-TATTAATAATTTAG
* * * *
2015623 TTGTAAACCAGTGATAATTTAG
1 TAGTAAA-TATTAATAATTTAG
*
2015645 TAATAAAT
1 TAGTAAAT
2015653 TAGTTAATCA
Statistics
Matches: 89, Mismatches: 18, Indels: 14
0.74 0.15 0.12
Matches are distributed among these distances:
19 16 0.18
20 2 0.02
21 22 0.25
22 47 0.53
23 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.37
Consensus pattern (21 bp):
TAGTAAATATTAATAATTTAG
Found at i:2015574 original size:19 final size:19
Alignment explanation
Indices: 2015552--2015594 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
2015542 TAAATCATTG
2015552 ATAATTTAGTAGTAAATTA
1 ATAATTTAGTAGTAAATTA
2015571 ATAATTTAGTAGTAAATTA
1 ATAATTTAGTAGTAAATTA
*
2015590 TTAAT
1 ATAAT
2015595 AACATATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (19 bp):
ATAATTTAGTAGTAAATTA
Found at i:2015756 original size:22 final size:22
Alignment explanation
Indices: 2015713--2015783 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 22
2015703 ATTAGTTATA
*
2015713 AATTT-ATAATAAATCATAAAT
1 AATTTAATAATAAATCACAAAT
* *
2015734 AATTTAATGATAAATCACCAAT
1 AATTTAATAATAAATCACAAAT
* *
2015756 AATTTAA-AAGAAATCACTAAT
1 AATTTAATAATAAATCACAAAT
*
2015777 AACTTAA
1 AATTTAA
2015784 GGATATATCA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 22 0.52
22 20 0.48
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.32
Consensus pattern (22 bp):
AATTTAATAATAAATCACAAAT
Found at i:2015800 original size:22 final size:22
Alignment explanation
Indices: 2015766--2015888 Score: 95
Period size: 22 Copynumber: 5.6 Consensus size: 22
2015756 AATTTAAAAG
* * *
2015766 AAATCACTAATAACTTAAGGAT
1 AAATCATTGATAACTTAAGAAT
* * **
2015788 ATATCATTTATAACTTAATG-GC
1 AAATCATTGATAACTTAA-GAAT
* * *
2015810 AAATCATTCATAAATTAAAAAT
1 AAATCATTGATAACTTAAGAAT
* *
2015832 AAATCATTGATAATTTAATAAT
1 AAATCATTGATAACTTAAGAAT
* *
2015854 AAATCATTGATAACTTAATAGT
1 AAATCATTGATAACTTAAGAAT
*
2015876 AAATAATTGATAA
1 AAATCATTGATAA
2015889 TATAATTGTT
Statistics
Matches: 82, Mismatches: 17, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
22 81 0.99
23 1 0.01
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.35
Consensus pattern (22 bp):
AAATCATTGATAACTTAAGAAT
Done.