Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009460.1 Hibiscus syriacus cultivar Beakdansim tig00113722_pilon, 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: 2853300
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 10 of 14
Found at i:1830517 original size:3 final size:3
Alignment explanation
Indices: 1830495--1830566 Score: 61
Period size: 3 Copynumber: 25.7 Consensus size: 3
1830485 CCTACAAAAG
1830495 TAA TAA -AA TAA -AA GTAA TAA TAA TAA TAA TAA TAAA TAAA TAA -AA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA
1830540 T-A TAA T-A TAA T-A TAA T-A TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1830567 TTTTTGTAGA
Statistics
Matches: 59, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
2 16 0.27
3 34 0.58
4 9 0.15
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1830527 original size:15 final size:14
Alignment explanation
Indices: 1830490--1830566 Score: 72
Period size: 14 Copynumber: 5.4 Consensus size: 14
1830480 TGGGGCCTAC
1830490 AAAAGTAATAA-AAT
1 AAAA-TAATAATAAT
1830504 AAAAGTAATAATAAT
1 AAAA-TAATAATAAT
1830519 AATAATAATAAATAAAT
1 AA-AATAAT-AAT-AAT
1830536 AAAAT-ATAAT-AT
1 AAAATAATAATAAT
*
1830548 AATATAAT-ATAAT
1 AAAATAATAATAAT
1830561 AAAATA
1 AAAATA
1830567 TTTTTGTAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
12 8 0.15
13 9 0.16
14 14 0.25
15 11 0.20
16 8 0.15
17 5 0.09
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:1830567 original size:15 final size:15
Alignment explanation
Indices: 1830495--1830567 Score: 69
Period size: 15 Copynumber: 4.7 Consensus size: 15
1830485 CCTACAAAAG
*
1830495 TAATAAAATAAAAGTAA
1 TAATAAAATATAA-T-A
1830512 TAATAATAATAATAATA
1 TAATAA-AAT-ATAATA
*
1830529 -AAT-AAATAAAATA
1 TAATAAAATATAATA
*
1830542 TAATATAATATAATA
1 TAATAAAATATAATA
1830557 TAATAAAATAT
1 TAATAAAATAT
1830568 TTTTGTAGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
13 5 0.11
14 6 0.13
15 19 0.40
16 3 0.06
17 7 0.15
18 4 0.09
19 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (15 bp):
TAATAAAATATAATA
Found at i:1832849 original size:3 final size:3
Alignment explanation
Indices: 1832841--1832886 Score: 65
Period size: 3 Copynumber: 14.3 Consensus size: 3
1832831 TCGCCCGGTG
1832841 TTC TTC TTC TTCC TTC TTTC TTTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TT-C TTC -TTC -TTC TTC TTC TTC TTC TTC TTC TTC T
1832887 GCTTGCACAG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 31 0.76
4 10 0.24
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1833802 original size:4 final size:4
Alignment explanation
Indices: 1833793--1833823 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1833783 GAAGAAGAAT
*
1833793 AAAG AAAG AAAG AAAG AAAG AAAG AAGG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1833824 AGAAGACGGG
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:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1837207 original size:19 final size:19
Alignment explanation
Indices: 1837185--1837221 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1837175 CCATTTCCAA
1837185 AGGAATCCCACATTCCCCG
1 AGGAATCCCACATTCCCCG
1837204 AGGAATCCCACATTCCCC
1 AGGAATCCCACATTCCCC
1837222 ATCCAAACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.43, G:0.14, T:0.16
Consensus pattern (19 bp):
AGGAATCCCACATTCCCCG
Found at i:1838659 original size:3 final size:3
Alignment explanation
Indices: 1838651--1838678 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1838641 TTTTTCCTAT
1838651 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1838679 AACATGTGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1841091 original size:19 final size:19
Alignment explanation
Indices: 1841054--1841091 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1841044 ATGGGAGGTT
*
1841054 TGGTAAAATGAAATTAAAA
1 TGGTAAAATGAAATAAAAA
1841073 TGGTAAAAAT-AAATAAAAA
1 TGGT-AAAATGAAATAAAAA
1841092 GCAATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (19 bp):
TGGTAAAATGAAATAAAAA
Found at i:1843807 original size:6 final size:6
Alignment explanation
Indices: 1843797--1843873 Score: 100
Period size: 6 Copynumber: 12.2 Consensus size: 6
1843787 TTGTCGAAAC
*
1843797 AAAAACT AAAATT AAAAAT AAAAACAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAA-T AAAAAT AAAAAT --AAA-AAT AAAAAT AAAAAT AAAAAT AAAAAT
*
1843849 AAAAAT TAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
1843874 TAGCAGAATC
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
6 50 0.79
7 7 0.11
8 3 0.05
9 3 0.05
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:1849914 original size:21 final size:21
Alignment explanation
Indices: 1849890--1849930 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1849880 TCGGCTTATG
1849890 AAAAGTTTAGCTAAGCATGAC
1 AAAAGTTTAGCTAAGCATGAC
1849911 AAAAGTTTAGCTAAGCATGA
1 AAAAGTTTAGCTAAGCATGA
1849931 TAATAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (21 bp):
AAAAGTTTAGCTAAGCATGAC
Found at i:1852641 original size:23 final size:23
Alignment explanation
Indices: 1852595--1852641 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1852585 ATGACTAGTT
* *
1852595 TTTTTTTTAATTTTAAAATTTAA
1 TTTTTTGTAATTTTAAAATATAA
1852618 TTTTTTGTAATATTTAAAA-ATAA
1 TTTTTTGTAAT-TTTAAAATATAA
1852641 T
1 T
1852642 AATAACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTTTGTAATTTTAAAATATAA
Found at i:1854640 original size:17 final size:19
Alignment explanation
Indices: 1854608--1854643 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1854598 CATATATCTC
1854608 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
1854627 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
1854644 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:1855238 original size:64 final size:65
Alignment explanation
Indices: 1855127--1855275 Score: 196
Period size: 64 Copynumber: 2.3 Consensus size: 65
1855117 TCTTTCAATG
* * * *
1855127 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TTTATTTTA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTATTTATTTT-
1855191 A
65 A
* * *
1855192 AAGG-ATGCATCGATGCATTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTATTTCTTTT
1 AAGGAATGCATCGATGCACTA-CTTATGCATCGATGCATAAAAGGCATTCGATGTTATTTATTTT
1855255 A
65 A
1855256 AAGGAATGCATCGATGCACT
1 AAGGAATGCATCGATGCACT
1855276 TATGAATGTG
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
64 48 0.65
65 26 0.35
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (65 bp):
AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTATTTATTTTA
Found at i:1859418 original size:64 final size:65
Alignment explanation
Indices: 1859307--1859455 Score: 196
Period size: 64 Copynumber: 2.3 Consensus size: 65
1859297 TCTTTCAATG
* * * *
1859307 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TTTATTTTA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTTT-
1859371 A
65 A
* * *
1859372 AAGG-ATGCATCGATGCATTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTTCTTTT
1 AAGGAATGCATCGATGCACTA-CTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTTT
1859435 A
65 A
1859436 AAGGAATGCATCGATGCACT
1 AAGGAATGCATCGATGCACT
1859456 TATGAATGTG
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
64 48 0.65
65 26 0.35
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (65 bp):
AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTTTA
Found at i:1862044 original size:2 final size:2
Alignment explanation
Indices: 1862037--1862069 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1862027 AATATTATGA
1862037 AT AT AT AT AT AT 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 AT A
1862070 GAACTAGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1864794 original size:37 final size:37
Alignment explanation
Indices: 1864742--1864815 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
1864732 TTCGTTTCTC
* *
1864742 CTTTTTCAGGGAGAATTAAGATTAGATTTAAAATTTT
1 CTTTTTCAAGGAGAATTAAGATTAAATTTAAAATTTT
* *
1864779 CTTTTTCAAGTAGAATTAAGATTAAATTTAAATTTTT
1 CTTTTTCAAGGAGAATTAAGATTAAATTTAAAATTTT
1864816 TTAAAAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.46
Consensus pattern (37 bp):
CTTTTTCAAGGAGAATTAAGATTAAATTTAAAATTTT
Found at i:1870088 original size:13 final size:13
Alignment explanation
Indices: 1870061--1870099 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1870051 TACATAAAAA
1870061 TCCTAAAATATAAT
1 TCCTAAAA-ATAAT
* *
1870075 TCTTTAAAATAAT
1 TCCTAAAAATAAT
1870088 TCCTAAAAATAA
1 TCCTAAAAATAA
1870100 AGATAAACCC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (13 bp):
TCCTAAAAATAAT
Found at i:1870626 original size:19 final size:19
Alignment explanation
Indices: 1870602--1870640 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1870592 TCGAATGCAT
1870602 TCCATGCACCGATACACTC
1 TCCATGCACCGATACACTC
* *
1870621 TCCATGCATCGATGCACTC
1 TCCATGCACCGATACACTC
1870640 T
1 T
1870641 GAATATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATACACTC
Found at i:1870732 original size:64 final size:65
Alignment explanation
Indices: 1870588--1870748 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 65
1870578 GAATTAATTG
* * * *** *
1870588 AACATCGAATGCATTCCATGCACCGATACACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
1870653 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTTA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
1870717 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1870749 CTTGGTGCGC
Statistics
Matches: 83, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 40 0.48
65 43 0.52
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1877800 original size:19 final size:19
Alignment explanation
Indices: 1877776--1877814 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1877766 TCGAATGCAT
1877776 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1877795 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1877814 T
1 T
1877815 GAATATTTTC
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:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1877831 original size:65 final size:64
Alignment explanation
Indices: 1877713--1877921 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
1877703 TATTCAAAGG
* *
1877713 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGC
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
1877774 ATTC
61 ATTT
1877778 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
1877843 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGTTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
*
1877907 CATGCATCGATGCAC
1 CATGCACCGATGCAC
1877922 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 52 0.41
65 65 0.52
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:1877939 original size:64 final size:65
Alignment explanation
Indices: 1877762--1877924 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
1877752 GAATTAATTG
* * * *
1877762 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
1877827 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGTTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
1877890 A
65 A
1877891 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
1877925 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1885618 original size:17 final size:15
Alignment explanation
Indices: 1885587--1885620 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
1885577 CACCAATATC
1885587 AATCTTTGGTTTTGA
1 AATCTTTGGTTTTGA
1885602 AATCATTTGGATTTTGA
1 AATC-TTTGG-TTTTGA
1885619 AA
1 AA
1885621 ATAAGCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 5 0.29
17 8 0.47
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (15 bp):
AATCTTTGGTTTTGA
Found at i:1885793 original size:14 final size:14
Alignment explanation
Indices: 1885776--1885812 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
1885766 AACCTTAAAG
1885776 AAAAATAAAGAAAA
1 AAAAATAAAGAAAA
*
1885790 AAAAACTAAAGTAAA
1 AAAAA-TAAAGAAAA
1885805 AAAAATAA
1 AAAAATAA
1885813 CTTTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.11
Consensus pattern (14 bp):
AAAAATAAAGAAAA
Found at i:1885799 original size:15 final size:15
Alignment explanation
Indices: 1885771--1885809 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1885761 AAGAAAACCT
*
1885771 TAAAGAAAAATAAAG
1 TAAAAAAAAATAAAG
1885786 -AAAAAAAAACTAAAG
1 TAAAAAAAAA-TAAAG
1885801 TAAAAAAAA
1 TAAAAAAAA
1885810 TAACTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 8 0.38
15 5 0.24
16 8 0.38
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (15 bp):
TAAAAAAAAATAAAG
Found at i:1887403 original size:22 final size:22
Alignment explanation
Indices: 1887378--1887419 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1887368 TTTTATTTTA
1887378 ATTTAG-TCATTATTAATTTCTG
1 ATTTAGCT-ATTATTAATTTCTG
*
1887400 ATTTAGCTATTATTATTTTC
1 ATTTAGCTATTATTAATTTC
1887420 ATTTTTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57
Consensus pattern (22 bp):
ATTTAGCTATTATTAATTTCTG
Found at i:1887729 original size:24 final size:24
Alignment explanation
Indices: 1887702--1887749 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1887692 CTTTTAGAAA
**
1887702 TTAACATTTTCTTTTTTTTTATTT
1 TTAACATTTTCTTCATTTTTATTT
1887726 TTAACATTTTCTTCATTTTTATTT
1 TTAACATTTTCTTCATTTTTATTT
1887750 ATTTATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (24 bp):
TTAACATTTTCTTCATTTTTATTT
Found at i:1887785 original size:33 final size:32
Alignment explanation
Indices: 1887719--1887790 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 32
1887709 TTTCTTTTTT
*
1887719 TTTATTTTTAACATTTTCTTCATTTTTATTTA
1 TTTATTTTTAACATTATCTTCATTTTTATTTA
*
1887751 TTTATCTTTTGACATTAT-TTCACTTTATTA-TTA
1 TTTAT-TTTTAACATTATCTTCA-TTT-TTATTTA
1887784 TTT-TTTT
1 TTTATTTT
1887791 ATCATAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
31 3 0.09
32 10 0.29
33 19 0.54
34 3 0.09
ACGTcount: A:0.21, C:0.10, G:0.01, T:0.68
Consensus pattern (32 bp):
TTTATTTTTAACATTATCTTCATTTTTATTTA
Found at i:1892077 original size:32 final size:32
Alignment explanation
Indices: 1892036--1892105 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
1892026 AAGCAATAGA
* *
1892036 GGGCATCTTTAAAGATTCAATATCAAATGTTG
1 GGGCATCTTTAAAGATTCAACATCAAATATTG
** *
1892068 GGGCATCTTTGGAGATTCAACATCGAATATTG
1 GGGCATCTTTAAAGATTCAACATCAAATATTG
1892100 GGGCAT
1 GGGCAT
1892106 ATTTGGGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (32 bp):
GGGCATCTTTAAAGATTCAACATCAAATATTG
Found at i:1892111 original size:32 final size:32
Alignment explanation
Indices: 1892048--1892123 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
1892038 GCATCTTTAA
* * *
1892048 AGATTCAATATCAAATGTTGGGGCATCTTTGG
1 AGATTCAACATCAAATATTGGGGCATATTTGG
*
1892080 AGATTCAACATCGAATATTGGGGCATATTTGG
1 AGATTCAACATCAAATATTGGGGCATATTTGG
1892112 -GTATTCAACATC
1 AG-ATTCAACATC
1892124 CTTATGTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 1 0.03
32 38 0.97
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGGGGCATATTTGG
Found at i:1892871 original size:120 final size:124
Alignment explanation
Indices: 1892702--1892984 Score: 403
Period size: 120 Copynumber: 2.3 Consensus size: 124
1892692 AAACAACACC
* *
1892702 CTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACGACGAATGGGCCA
1 CTTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
* ** * *
1892767 TCCACGATTTCAACTTCATGACGAAGGATATCGTGTCCACCAGT-A-ATGCA-CAATA-
66 TCCACGATTTCAACTTCACGACGAAGGATATCGTACCCACAAGTAACATCCATCAATAG
* *
1892822 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGTCA
1 CTTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
* **
1892887 TCCACGATTTCAACTTCACGACGAATGATATCGTACCCACAAGTAACATCCATCTTTAG
66 TCCACGATTTCAACTTCACGACGAAGGATATCGTACCCACAAGTAACATCCATCAATAG
* * *
1892946 ATTGGATTTTAACTTCACGAAGAAGGATATCCAACTCAA
1 CTTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAA
1892985 ATAAGGAGTG
Statistics
Matches: 144, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
120 101 0.70
121 1 0.01
122 4 0.03
123 3 0.02
124 35 0.24
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (124 bp):
CTTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
TCCACGATTTCAACTTCACGACGAAGGATATCGTACCCACAAGTAACATCCATCAATAG
Found at i:1893367 original size:84 final size:84
Alignment explanation
Indices: 1893207--1893732 Score: 660
Period size: 84 Copynumber: 6.4 Consensus size: 84
1893197 ATGAGTCATT
* * *
1893207 TGTCAAC-CAAGACCTT-GAGTTCAATTACACTCAGCTCAAAGGCATATCATTTGCAGCATAGCT
1 TGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
*
1893270 CAAGGAAAGAAGGGCTATC
66 CAAGGCAAGAAGGGCTATC
* * *
1893289 TGTTAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATCTGCAGCATAACT
1 TGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
*
1893354 CAAGGCAATAAGGGCTA--
66 CAAGGCAAGAAGGGCTATC
*
1893371 TG-C--C-AAAGACCATCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
1 TGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
*
1893432 CAAAG-AAGAAAGGGCTATC
66 CAAGGCAAG-AAGGGCTATC
* * *
1893451 TGCCAATAAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
1 TGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
* * *
1893516 CAAAGCAAAAAGGGATATC
66 CAAGGCAAGAAGGGCTATC
* * * ** *
1893535 TGTCAAAAAAAGACATTCAAGTTCGATTACACTCAGCTCAAAGAAACATCATTTACAGCATAGCT
1 TGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
* * *
1893600 TAAGGCGAGAAGGGTTATC
66 CAAGGCAAGAAGGGCTATC
* * * *
1893619 TGCCAACAAAAGACCTTCGAGTACGATTACACTCAGCTCAAAGGCACATCATTTGCAGTATAACT
1 TGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
**
1893684 CAAGGTGAGAAGGG-TGATC
66 CAAGGCAAGAAGGGCT-ATC
* *
1893703 TGTCATC-AAAGACCTTTGAGTTCGATTACA
1 TGTCAACAAAAGACCTTCGAGTTCGATTACA
1893733 TTCAACTCGA
Statistics
Matches: 387, Mismatches: 46, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
77 2 0.01
78 66 0.17
79 1 0.00
80 2 0.01
81 1 0.00
82 8 0.02
83 30 0.08
84 275 0.71
85 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (84 bp):
TGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
CAAGGCAAGAAGGGCTATC
Found at i:1894235 original size:132 final size:132
Alignment explanation
Indices: 1893948--1894235 Score: 355
Period size: 132 Copynumber: 2.2 Consensus size: 132
1893938 ACTTAGCGAT
* * * *
1893948 TCCATCAAAGAAGGAGTTAAATCAGCGTCAACTTTTAGCTTGATTCTATCAAAGAAATAGGTAGA
1 TCCATCACAGAAGGAGTTAGATCAGCGTCAACTTTTAGCTTGATTCTAACAAAGAAAGAGGTAGA
* * * * * *
1894013 TCAACACCAACATCTCGTTCGATTCCATCATAGAATGAGGTGGATTGACATTTTTATTTCGCTCA
66 TCAACACCAACATCTCGTTCAATTCCATCACAGAAGGAGGGGGATCGACATTTTCATTTCGCTCA
1894078 AA
131 AA
* * *
1894080 TCCATCACAGAAGGAGTTGGATCAGTGTCAACTTTTTA-CTCT-ATTCTAACACAGAAAGAGGTA
1 TCCATCACAGAAGGAGTTAGATCAGCGTCAAC-TTTTAGCT-TGATTCTAACAAAGAAAGAGGTA
* * * * * *
1894143 GATTAGCACCGACATCTTGTTTAATTCCATCACAGAAGGAGGGGGATCGACATTTTCATTTTGCT
64 GATCAACACCAACATCTCGTTCAATTCCATCACAGAAGGAGGGGGATCGACATTTTCATTTCGCT
1894208 CAAA
129 CAAA
* *
1894212 TCTATCACAGAAGGAGGTAGATCA
1 TCCATCACAGAAGGAGTTAGATCA
1894236 ACACCGACAT
Statistics
Matches: 132, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
132 126 0.95
133 6 0.05
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (132 bp):
TCCATCACAGAAGGAGTTAGATCAGCGTCAACTTTTAGCTTGATTCTAACAAAGAAAGAGGTAGA
TCAACACCAACATCTCGTTCAATTCCATCACAGAAGGAGGGGGATCGACATTTTCATTTCGCTCA
AA
Found at i:1896498 original size:19 final size:20
Alignment explanation
Indices: 1896474--1896513 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1896464 ATACCTAAAC
1896474 CATAAATAT-AAAGAAAAAT
1 CATAAATATGAAAGAAAAAT
1896493 CATAAATATGAAAGAAAAAT
1 CATAAATATGAAAGAAAAAT
1896513 C
1 C
1896514 CAATTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.20
Consensus pattern (20 bp):
CATAAATATGAAAGAAAAAT
Found at i:1896564 original size:23 final size:23
Alignment explanation
Indices: 1896531--1896581 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1896521 TTTTCTATCA
1896531 AAAAACCCAATCACTTTTT-TGTC
1 AAAAACCCAATCA-TTTTTATGTC
* *
1896554 GAAAACTCAATCATTTTTATGTC
1 AAAAACCCAATCATTTTTATGTC
1896577 AAAAA
1 AAAAA
1896582 TCTAGGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (23 bp):
AAAAACCCAATCATTTTTATGTC
Found at i:1908756 original size:6 final size:6
Alignment explanation
Indices: 1908740--1908772 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1908730 TTAATTATTT
1908740 ATTTG- ATTTGA ATTTGA ATTTGA ATTTGA ATTT
1 ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTT
1908773 TTTTCTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (6 bp):
ATTTGA
Found at i:1908856 original size:16 final size:16
Alignment explanation
Indices: 1908826--1908879 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
1908816 TAAATATATA
* *
1908826 ATAATTAAATAAATCT
1 ATAATTAATTTAATCT
1908842 A-AATTTAATTTAATCT
1 ATAA-TTAATTTAATCT
1908858 ATAATTAA-TTAAT-T
1 ATAATTAATTTAATCT
1908872 AATAATTA
1 -ATAATTA
1908880 TAATAAAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 1 0.03
15 14 0.42
16 16 0.48
17 2 0.06
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTAATTTAATCT
Found at i:1912392 original size:21 final size:21
Alignment explanation
Indices: 1912365--1912425 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1912355 GACCGTTATA
1912365 ATATTGACGTGATAGTTCACG
1 ATATTGACGTGATAGTTCACG
* * * *
1912386 GTATTGACGTGGTAATCCACG
1 ATATTGACGTGATAGTTCACG
* *
1912407 ATATTAACGTGACAGTTCA
1 ATATTGACGTGATAGTTCA
1912426 TCTGCCATAC
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (21 bp):
ATATTGACGTGATAGTTCACG
Found at i:1918094 original size:56 final size:56
Alignment explanation
Indices: 1918008--1918183 Score: 289
Period size: 56 Copynumber: 3.1 Consensus size: 56
1917998 CAGGGCCCCA
* *
1918008 AAAAATAGGGTCCCCGAAATCGAATATATCTTTCAGTTGTTGCCATTAATAAGCAT
1 AAAAATAGGGTCCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAATAAACAT
* * *
1918064 AAAAATAGGGGCCCCAAAATCGAATATATCTATCAGTTGTTGCCATTAATAATCAT
1 AAAAATAGGGTCCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAATAAACAT
* *
1918120 AAAAATAGGGTCCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAACAT
1 AAAAATAGGGTCCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAATAAACAT
1918176 AAAAATAG
1 AAAAATAG
1918184 AATCTCAGAA
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
56 111 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (56 bp):
AAAAATAGGGTCCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAATAAACAT
Found at i:1918195 original size:56 final size:56
Alignment explanation
Indices: 1918008--1918207 Score: 267
Period size: 56 Copynumber: 3.6 Consensus size: 56
1917998 CAGGGCCCCA
* * *
1918008 AAAAATAGGGTCCCCGAAATCGAATATATCTTTCAGTTGTTGCCATTAATAAGCAT
1 AAAAATAGGGTCCCAGAAATCGAATATATCTATCAGTTGTTGCCATTAATAAACAT
* *
1918064 AAAAATAGGGGCCCCA-AAATCGAATATATCTATCAGTTGTTGCCATTAATAATCAT
1 AAAAATA-GGGTCCCAGAAATCGAATATATCTATCAGTTGTTGCCATTAATAAACAT
* * *
1918120 AAAAATAGGGTCCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAACAT
1 AAAAATAGGGTCCCAGAAATCGAATATATCTATCAGTTGTTGCCATTAATAAACAT
** * * *
1918176 AAAAATAGAATCTCAGAAATCAAATCTATCTA
1 AAAAATAGGGTCCCAGAAATCGAATATATCTA
1918208 GAAAATAGGG
Statistics
Matches: 126, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
55 6 0.05
56 114 0.90
57 6 0.05
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Consensus pattern (56 bp):
AAAAATAGGGTCCCAGAAATCGAATATATCTATCAGTTGTTGCCATTAATAAACAT
Found at i:1921124 original size:2 final size:2
Alignment explanation
Indices: 1921117--1921145 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1921107 ACTTATATGC
1921117 AT AT AT AT 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 A
1921146 ATTTCATATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1921776 original size:53 final size:53
Alignment explanation
Indices: 1921711--1921986 Score: 390
Period size: 53 Copynumber: 5.1 Consensus size: 53
1921701 GAACTCGAAT
* * * *
1921711 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACA
1 ATCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACA
* * *
1921764 ATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACG
1 ATCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACA
* * * *
1921819 ATCTTCAACGATTGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACA
1 ATCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACA
1921872 ATCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACA
1 ATCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACA
* * *
1921925 ATCTTCATCAATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACA
1 ATCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACA
1921980 ATCTTCA
1 ATCTTCA
1921987 ATAATTGTTG
Statistics
Matches: 200, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
53 142 0.71
54 3 0.01
55 55 0.28
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.30
Consensus pattern (53 bp):
ATCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACA
Found at i:1921993 original size:108 final size:108
Alignment explanation
Indices: 1921703--1921986 Score: 421
Period size: 108 Copynumber: 2.6 Consensus size: 108
1921693 GGTGAATAGA
* *
1921703 ACTCGAA-TATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAACAATTGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
*
1921767 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
1921810 ACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAACAATTGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
1921875 TTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * *
1921918 AC-C-CACAATCTTCATCAATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAA
1 ACTCGAACAATCTTCAACAATTGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAA
1921981 TCTTCA
64 TCTTCA
1921987 ATAATTGTTG
Statistics
Matches: 159, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
106 44 0.28
107 9 0.06
108 106 0.67
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.30
Consensus pattern (108 bp):
ACTCGAACAATCTTCAACAATTGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
TTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:1922931 original size:9 final size:8
Alignment explanation
Indices: 1922917--1922971 Score: 50
Period size: 8 Copynumber: 7.5 Consensus size: 8
1922907 GAACCCTTCT
1922917 TTTTTTCCA
1 TTTTTT-CA
1922926 TTTTTTCA
1 TTTTTTCA
1922934 TTTTTT-A
1 TTTTTTCA
1922941 --TTTT--
1 TTTTTTCA
1922945 TTTTTT-A
1 TTTTTTCA
*
1922952 TTTTTTTA
1 TTTTTTCA
1922960 TTTTTTCA
1 TTTTTTCA
1922968 TTTT
1 TTTT
1922972 CACTCATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
5 4 0.10
6 4 0.10
7 7 0.17
8 20 0.49
9 6 0.15
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTCA
Found at i:1922935 original size:8 final size:7
Alignment explanation
Indices: 1922925--1922971 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
1922915 CTTTTTTTCC
1922925 ATTTTTT
1 ATTTTTT
1922932 CATTTTTT
1 -ATTTTTT
1922940 ATTTTTT
1 ATTTTTT
*
1922947 -TTTTAT
1 ATTTTTT
1922953 -TTTTTT
1 ATTTTTT
1922959 ATTTTTT
1 ATTTTTT
1922966 CATTTT
1 -ATTTT
1922972 CACTCATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 10 0.29
7 13 0.37
8 12 0.34
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (7 bp):
ATTTTTT
Found at i:1922948 original size:11 final size:11
Alignment explanation
Indices: 1922934--1922958 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1922924 CATTTTTTCA
1922934 TTTTTTATTTT
1 TTTTTTATTTT
1922945 TTTTTTATTTT
1 TTTTTTATTTT
1922956 TTT
1 TTT
1922959 ATTTTTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:1922954 original size:26 final size:27
Alignment explanation
Indices: 1922916--1922971 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1922906 TGAACCCTTC
1922916 TTTTTTTCCATTTTTTCATTTTTT-AT
1 TTTTTTTCCATTTTTTCATTTTTTCAT
** *
1922942 TTTTTTTTTATTTTTTTATTTTTTCAT
1 TTTTTTTCCATTTTTTCATTTTTTCAT
1922969 TTT
1 TTT
1922972 CACTCATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (27 bp):
TTTTTTTCCATTTTTTCATTTTTTCAT
Found at i:1936252 original size:2 final size:2
Alignment explanation
Indices: 1936245--1936286 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1936235 ATAACATACT
1936245 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1936287 ATTTCATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1940586 original size:20 final size:19
Alignment explanation
Indices: 1940539--1940586 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1940529 AATGAAAGAG
*
1940539 TTTTATAATTTTTATTTTA
1 TTTTATAAATTTTATTTTA
*
1940558 TCATT-TAAATTTTATTTTTA
1 T-TTTATAAATTTTA-TTTTA
1940578 TTTTATAAA
1 TTTTATAAA
1940587 ATTATGAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTATAAATTTTATTTTA
Found at i:1955592 original size:2 final size:2
Alignment explanation
Indices: 1955585--1955615 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1955575 TTAATAAGCA
1955585 AT AT AT AT AT 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
1955616 AAGAGGATGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1957472 original size:21 final size:19
Alignment explanation
Indices: 1957435--1958006 Score: 361
Period size: 23 Copynumber: 27.3 Consensus size: 19
1957425 TGCAATTTAT
*
1957435 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
1957454 TCCAAGTTCGTAATGCGATAG
1 TCCAAGTTCGT--TGCGATAG
*
1957475 TCTAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* * *
1957494 TCGAAATTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
* *
1957517 TTCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
1957536 TCCAAGTTCGCGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
1957557 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
1957576 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
1957599 TCCAAGTTCACGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
1957622 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
** * *
1957641 TTGAAATTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
1957664 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
1957687 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
1957706 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
* *
1957729 TCCAAATTCGTTACGATAG
1 TCCAAGTTCGTTGCGATAG
* *
1957748 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
1957771 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
1957794 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
1957813 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
1957836 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
1957855 TCCAAGTTCGTTGTGATAG
1 TCCAAGTTCGTTGCGATAG
* *
1957874 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
1957897 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
1957916 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
* *
1957939 TCTAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
1957962 TCCAAGTTCGCGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
*
1957983 TCGAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
1958002 TCCAA
1 TCCAA
1958007 AATCGCAACG
Statistics
Matches: 462, Mismatches: 55, Indels: 72
0.78 0.09 0.12
Matches are distributed among these distances:
19 133 0.29
21 163 0.35
23 166 0.36
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:1957535 original size:42 final size:42
Alignment explanation
Indices: 1957404--1958006 Score: 560
Period size: 42 Copynumber: 14.3 Consensus size: 42
1957394 ACTATCGCAA
* * * *
1957404 TGCGATAGTCGAAGTTTGCGTTGCAATTTATTCCAAATTCGT
1 TGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
*** * *
1957446 TGCGATAGTCCAAGTTCGTAATGCGA--TAGTCTAAGTTCGT
1 TGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
* * * *
1957486 TGCGATAGTCGAAATTCGCGTTGCGATTTATTTCAAATTCGT
1 TGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
*
1957528 TGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCCAAGTTCGT
1 TGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
*
1957568 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCACGT
1 TGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT--CGT
* * *
1957612 TGCGATTTATTCCAAGTT--CGTTGCGA--TAGTT-GAAATTCGCGT
1 TGCGA--TAGTCCAAGTTCGCGTTGCGATTTA-TTCCAAGTT--CGT
*
1957654 TGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
1 TGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
* *
1957698 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
1 TGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
* *
1957740 TACGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT--CGT
* * *
1957784 TGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGT
1 TGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT--CGT
* * *
1957826 TGCGATTTATTCCAAATT--CGTTGCGA--TAGTCCAAGTTCGT
1 TGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
* * *
1957866 TGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
1 TGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
*
1957908 TGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT--CGT
* * *
1957952 TGCGATTTATTCCAAGTTCGCGTTGCGA--TAGTCGAAGTTCGT
1 TGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
1957994 TGCGATAGTCCAA
1 TGCGATAGTCCAA
1958007 AATCGCAACG
Statistics
Matches: 477, Mismatches: 58, Indels: 54
0.81 0.10 0.09
Matches are distributed among these distances:
38 8 0.02
40 90 0.19
42 267 0.56
43 2 0.00
44 64 0.13
45 2 0.00
46 44 0.09
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
TGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
Found at i:1957639 original size:65 final size:63
Alignment explanation
Indices: 1957536--1958006 Score: 368
Period size: 65 Copynumber: 7.4 Consensus size: 63
1957526 GTTGCGATAG
1957536 TCCAAGTTCGCGTTGCGA-TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTC-CGTTGCGATTAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* * *
1957599 TCCAAGTTCACGTTGCGATTTATTCCAAGTTCGTTGCGATAGTTGAAATTCGCGTTGCGATTTAT
1 TCCAAGTTC-CGTTGCGA-TTAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
1957664 TCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTC-CGTTGCGA-TTAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* * * * *
1957729 TCCAAATT-CGTTACGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGCGTTGCGATTT
1 TCCAAGTTCCGTTGCGATTAGTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTT
1957792 AT
62 AT
* * * *
1957794 TCCAAGTT-CGTTGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGA--T
1 TCCAAGTTCCGTTGCGATTAGTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTT
*
1957853 AG
62 AT
* * * * *
1957855 TCCAAGTT-CGTTGTGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGA--T
1 TCCAAGTTCCGTTGCGATTAGTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTT
*
1957914 AG
62 AT
* * * *
1957916 TCCAAGTTCGCGTTGCGATTTATTCTAAGTTCGCGTTGCGATTTATTCCAAGTTCGCGTTGCGA-
1 TCCAAGTTC-CGTTGCGA-TTAGTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTGCGAT
*
1957980 -TAG
60 TTAT
*
1957983 TCGAAGTT-CGTTGCGA-TAGTCCAA
1 TCCAAGTTCCGTTGCGATTAGTCCAA
1958007 AATCGCAACG
Statistics
Matches: 371, Mismatches: 25, Indels: 24
0.88 0.06 0.06
Matches are distributed among these distances:
61 79 0.21
63 53 0.14
65 221 0.60
67 18 0.05
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (63 bp):
TCCAAGTTCCGTTGCGATTAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:1957727 original size:107 final size:105
Alignment explanation
Indices: 1957443--1957999 Score: 684
Period size: 107 Copynumber: 5.3 Consensus size: 105
1957433 ATTCCAAATT
*** * * *
1957443 CGTTGCGATAGTCCAAGTTCGTAATGCGA--TAGTCTAAGTTCGTTGCGATAGTCGAAATTCGCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
*
1957506 TTGCGATTTATTTCAAATTCGTTGCGATAGTCCAAGTTCG
66 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
* * * *
1957546 CGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCGAAGTT
* * ** *
1957607 CACGTTGCGATTTATTCCAAGTTCGTTGCGATAGTTGAAATTCG
62 CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
*
1957651 CGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
* *
1957716 CGTTGCGATTTATTCCAAATTCGTTACGATAGTCGAAGTTCG
64 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
*
1957758 CGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1957823 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT--
64 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
* * * *
1957863 CGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
* * *
1957928 TTGCGATTTATTCTAAGTTCGCGTTGCGATTTATTCCAAGTTCG
66 TTGCGATTTATTCCAAATT--CGTTGCGA--TAGTCCAAGTTCG
*
1957972 CGTTGCGATAGTCGAAGTT--CGTTGCGAT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGAT
1958000 AGTCCAAAAT
Statistics
Matches: 404, Mismatches: 34, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
101 15 0.04
103 97 0.24
105 69 0.17
107 180 0.45
109 34 0.08
111 9 0.02
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (105 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
Found at i:1958893 original size:19 final size:19
Alignment explanation
Indices: 1958832--1959003 Score: 113
Period size: 21 Copynumber: 8.7 Consensus size: 19
1958822 CGTCGTGATT
1958832 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
1958851 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
1958874 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
1958893 TTGGACTATCG---C--A-
1 TTGGACTATCGCAACGAAC
*
1958906 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
* *
1958929 TTGGACCATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
**
1958948 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAAC
* *
1958969 TTCGACTATCGAAACGCGAAC
1 TTGGACTATCGCAA--CGAAC
1958990 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1959004 TGCGAATATG
Statistics
Matches: 120, Mismatches: 17, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
13 6 0.05
14 1 0.01
15 4 0.03
16 1 0.01
19 37 0.31
20 1 0.01
21 54 0.45
22 1 0.01
23 15 0.12
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:1958959 original size:55 final size:55
Alignment explanation
Indices: 1958851--1958960 Score: 166
Period size: 55 Copynumber: 2.0 Consensus size: 55
1958841 CGCAACGAAC
* * **
1958851 TTGGAATAAATCGCAATGCGAACTTCGACTATCGCAACGAACTTGGACTATCGCA
1 TTGGAATAAATCGCAACGCGAACTTCGACCATCGCAACGAACTTGGAAAATCGCA
* *
1958906 TTGGAATAAATCGCAACGCGAACTTGGACCATCGCAACGAATTTGGAAAATCGCA
1 TTGGAATAAATCGCAACGCGAACTTCGACCATCGCAACGAACTTGGAAAATCGCA
1958961 ACGCGAACTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (55 bp):
TTGGAATAAATCGCAACGCGAACTTCGACCATCGCAACGAACTTGGAAAATCGCA
Found at i:1959048 original size:21 final size:21
Alignment explanation
Indices: 1959024--1959070 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1959014 TAAATCGCAA
1959024 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
1959045 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
1959066 TGCGA
1 TGCGA
1959071 ATCTGGAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:1959231 original size:21 final size:21
Alignment explanation
Indices: 1959207--1959247 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1959197 ATTCGAATTG
1959207 CGATAGTCCAAGTTCGCGTTT
1 CGATAGTCCAAGTTCGCGTTT
**
1959228 CGATAGTTGAAGTTCGCGTT
1 CGATAGTCCAAGTTCGCGTT
1959248 GCGAATCTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (21 bp):
CGATAGTCCAAGTTCGCGTTT
Found at i:1959328 original size:181 final size:181
Alignment explanation
Indices: 1959024--1959373 Score: 664
Period size: 181 Copynumber: 1.9 Consensus size: 181
1959014 TAAATCGCAA
*
1959024 TGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGAATCTGGAAACTGATTTGC
1 TGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGAATCTGGAAACTGATTTGC
1959089 GATACTAGAGATCGCGTTGCGAATTATCGATCGCATTGCGATTTAATTGGTCATTTTGACAAATC
66 GATACTAGAGATCGCGTTGCGAATTATCGATCGCATTGCGATTTAATTGGTCATTTTGACAAATC
1959154 CAAAAAAAGTTGATTAAAATCGTATATTATAAGACATTTACATATTCGAAT
131 CAAAAAAAGTTGATTAAAATCGTATATTATAAGACATTTACATATTCGAAT
* *
1959205 TGCGATAGTCCAAGTTCGCGTTTCGATAGTTGAAGTTCGCGTTGCGAATCTGGAAACTGATTTGC
1 TGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGAATCTGGAAACTGATTTGC
*
1959270 GATACTGGAGATCGCGTTGCGAATTATCGATCGCATTGCGATTTAATTGGTCATTTTGACAAATC
66 GATACTAGAGATCGCGTTGCGAATTATCGATCGCATTGCGATTTAATTGGTCATTTTGACAAATC
1959335 CAAAAAAAGTTGATTAAAATCGTATATTATAAGACATTT
131 CAAAAAAAGTTGATTAAAATCGTATATTATAAGACATTT
1959374 TTTATCACTG
Statistics
Matches: 165, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
181 165 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (181 bp):
TGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGAATCTGGAAACTGATTTGC
GATACTAGAGATCGCGTTGCGAATTATCGATCGCATTGCGATTTAATTGGTCATTTTGACAAATC
CAAAAAAAGTTGATTAAAATCGTATATTATAAGACATTTACATATTCGAAT
Found at i:1962063 original size:171 final size:171
Alignment explanation
Indices: 1961772--1962119 Score: 581
Period size: 171 Copynumber: 2.0 Consensus size: 171
1961762 ACAAAGATGC
* * *
1961772 AAATTCATGTGATACGTATGTCCATATTATGTATGTTTTATTGATCAATGGTCATGAATGGTCAA
1 AAATTTATGTGATACGTATGTCCATATTATGCATGTTTTATTGATCAATGGTCAGGAATGGTCAA
*
1961837 GCATGCAATCTGCATTCTCTTCTTGATTTGGCCATCTTCATTTCTTCACATAAGAATGAACCCTT
66 GCAAGCAATCTGCATTCTCTTCTTGATTTGGCCATCTTCATTTCTTCACATAAGAATGAACCCTT
* *
1961902 GTAATTCTAGGATGGTGACAATTTGTTCTTCTTGCCTTAAT
131 GTAATTCTAGGATGATGACAATTCGTTCTTCTTGCCTTAAT
*
1961943 AAATTTATGTGATACGTATGTCCATATTATGCATGTTTTCTTGATCAATGGTCAGGAATGGTCAC
1 AAATTTATGTGATACGTATGTCCATATTATGCATGTTTTATTGATCAATGGTCAGGAATGGTCA-
* * *
1962008 A-CAAGCAATCTTCATTCTCTTTTTGATTTGGTCATCTTCATTTCTTCACATAAGAATGAACCCT
65 AGCAAGCAATCTGCATTCTCTTCTTGATTTGGCCATCTTCATTTCTTCACATAAGAATGAACCCT
*
1962072 TGTAATTCTTGGATGATGACAATTCGTTCTTCTTGCCTTAAT
130 TGTAATTCTAGGATGATGACAATTCGTTCTTCTTGCCTTAAT
1962114 AAATTT
1 AAATTT
1962120 TTCTCCAAAA
Statistics
Matches: 165, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
171 164 0.99
172 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.41
Consensus pattern (171 bp):
AAATTTATGTGATACGTATGTCCATATTATGCATGTTTTATTGATCAATGGTCAGGAATGGTCAA
GCAAGCAATCTGCATTCTCTTCTTGATTTGGCCATCTTCATTTCTTCACATAAGAATGAACCCTT
GTAATTCTAGGATGATGACAATTCGTTCTTCTTGCCTTAAT
Found at i:1963965 original size:16 final size:16
Alignment explanation
Indices: 1963946--1963998 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1963936 CCATAACCCC
1963946 TATCACACATATATCA
1 TATCACACATATATCA
* * *
1963962 TATCATACACACATCA
1 TATCACACATATATCA
1963978 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
1963996 TAT
1 TAT
1963999 ATCACATACA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 21 0.72
17 3 0.10
18 5 0.17
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:1963984 original size:12 final size:12
Alignment explanation
Indices: 1963946--1963992 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
1963936 CCATAACCCC
1963946 TATCACACAT-A
1 TATCACACATCA
*
1963957 TAT--CATATCA
1 TATCACACATCA
1963967 TA-CACACATCA
1 TATCACACATCA
1963978 TATCACACATCA
1 TATCACACATCA
1963990 TAT
1 TAT
1963993 ACATATATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
9 4 0.13
10 3 0.10
11 11 0.37
12 12 0.40
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.30
Consensus pattern (12 bp):
TATCACACATCA
Found at i:1964359 original size:23 final size:23
Alignment explanation
Indices: 1964328--1964396 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
1964318 CACCACAGCT
*
1964328 CGTATAATTGCACCAGAGTGCCA
1 CGTAGAATTGCACCAGAGTGCCA
* *
1964351 CGTAGAATTGCACTAGAGTGCCG
1 CGTAGAATTGCACCAGAGTGCCA
1964374 CGTAGAATTGCACC-GTAGTGCCA
1 CGTAGAATTGCACCAG-AGTGCCA
1964397 TATAATAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCAGAGTGCCA
Found at i:1964583 original size:103 final size:103
Alignment explanation
Indices: 1964412--1964732 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 103
1964402 TAATGTCCAT
* * * *
1964412 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
1964477 GACTTCACACATGCTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1964515 AAGGACCACATATCATTCCTTAATAATCATTTACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1964580 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1964618 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
1964683 GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1964721 AAGGACCACATA
1 AAGGACCACATA
1964733 GACCCTCGAC
Statistics
Matches: 209, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 209 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1965867 original size:21 final size:21
Alignment explanation
Indices: 1965842--1965887 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1965832 TTCAGGTTCG
* * *
1965842 CTTGAGGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
1965863 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
1965884 CTTG
1 CTTG
1965888 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:1968394 original size:16 final size:16
Alignment explanation
Indices: 1968375--1968427 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1968365 CCATAACCCC
1968375 TATCACACATATATCA
1 TATCACACATATATCA
* * *
1968391 TATCATACACACATCA
1 TATCACACATATATCA
1968407 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
1968425 TAT
1 TAT
1968428 ATCACATACA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 21 0.72
17 3 0.10
18 5 0.17
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:1968413 original size:12 final size:12
Alignment explanation
Indices: 1968375--1968421 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
1968365 CCATAACCCC
1968375 TATCACACAT-A
1 TATCACACATCA
*
1968386 TAT--CATATCA
1 TATCACACATCA
1968396 TA-CACACATCA
1 TATCACACATCA
1968407 TATCACACATCA
1 TATCACACATCA
1968419 TAT
1 TAT
1968422 ACATATATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
9 4 0.13
10 3 0.10
11 11 0.37
12 12 0.40
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.30
Consensus pattern (12 bp):
TATCACACATCA
Found at i:1968782 original size:23 final size:23
Alignment explanation
Indices: 1968756--1968824 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
1968746 CACCACAGCT
*
1968756 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1968779 CGTAGAATTGCACC-AGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
1968802 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1968825 TATAATAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1969011 original size:103 final size:103
Alignment explanation
Indices: 1968840--1969160 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
1968830 TAATGTCCAT
* * * *
1968840 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1968905 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1968943 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1969008 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1969046 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAATTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
1969111 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1969149 AAGGACCACATA
1 AAGGACCACATA
1969161 GACCCTCGAC
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1973143 original size:23 final size:23
Alignment explanation
Indices: 1973113--1973176 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
1973103 ACATCTTATA
*
1973113 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCAACG
*
1973136 TGGCACTTAGGTGCCA-TTCAACG
1 TGGCACTTCGGTG-CATTTCAACG
1973159 TGGCACTTCGGTGCATTT
1 TGGCACTTCGGTGCATTT
1973177 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 2 0.06
23 32 0.89
24 2 0.06
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCAACG
Found at i:1977667 original size:23 final size:24
Alignment explanation
Indices: 1977609--1977669 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
1977599 ACATCTTATA
1977609 TGGCACTTCGGTG-AATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* * *
1977632 CGGCAGTTAGGTGCAA-TTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
1977655 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
1977670 TTTATATGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 29 0.94
24 2 0.06
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:1979742 original size:26 final size:27
Alignment explanation
Indices: 1979683--1979748 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 27
1979673 CTTCTCATTT
*
1979683 ATTCTCTTTCTTTTTTCGATTTTGTGG
1 ATTCTCTTTCTTTTTTCGATTTTGTGA
* *
1979710 ATT-TCTTTTTTTTCTTC-CTTTTG-GA
1 ATTCTCTTTCTTTT-TTCGATTTTGTGA
*
1979735 ATTCTCTTGCTTTT
1 ATTCTCTTTCTTTT
1979749 ATCATATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 4 0.12
26 22 0.69
27 6 0.19
ACGTcount: A:0.08, C:0.17, G:0.11, T:0.65
Consensus pattern (27 bp):
ATTCTCTTTCTTTTTTCGATTTTGTGA
Found at i:1984161 original size:20 final size:20
Alignment explanation
Indices: 1984133--1984170 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1984123 CGTTAGGCCT
* *
1984133 TATGGTATTGGTACTACTCA
1 TATGATATTGATACTACTCA
1984153 TATGATATTGATACTACT
1 TATGATATTGATACTACT
1984171 ATGTAAAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (20 bp):
TATGATATTGATACTACTCA
Found at i:1984497 original size:3 final size:3
Alignment explanation
Indices: 1984489--1984543 Score: 94
Period size: 3 Copynumber: 18.3 Consensus size: 3
1984479 TAGTTCAAAT
1984489 ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
1984534 ATA ATA ATA A
1 ATA ATA ATA A
1984544 AAAAACTCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1985163 original size:21 final size:22
Alignment explanation
Indices: 1985117--1985164 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1985107 GATCTGATAT
1985117 TATTTTTTAATATTGTAAATCA
1 TATTTTTTAATATTGTAAATCA
*
1985139 -ATTTTTT-ATATT-TAGAATTA
1 TATTTTTTAATATTGTA-AATCA
1985159 TATTTT
1 TATTTT
1985165 ATAACTGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.09
20 9 0.39
21 12 0.52
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
TATTTTTTAATATTGTAAATCA
Found at i:1986035 original size:22 final size:21
Alignment explanation
Indices: 1985993--1986035 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1985983 GGCGACATCC
*
1985993 GTCCCCATCTCGACGAAATCA
1 GTCCCCATCCCGACGAAATCA
*
1986014 GTCCCCATCGCCGACGATATCA
1 GTCCCCATC-CCGACGAAATCA
1986036 ATTTCCATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.26, C:0.40, G:0.16, T:0.19
Consensus pattern (21 bp):
GTCCCCATCCCGACGAAATCA
Found at i:1986448 original size:20 final size:20
Alignment explanation
Indices: 1986423--1986469 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1986413 GATTCTTGCA
1986423 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
** *
1986443 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCGCG
1986463 TTGCGAT
1 TTGCGAT
1986470 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:1986475 original size:20 final size:20
Alignment explanation
Indices: 1986437--1986491 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1986427 GATAGTCAAA
* **
1986437 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
1986457 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
1986477 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
1986492 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1986499 original size:20 final size:20
Alignment explanation
Indices: 1986456--1986499 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1986446 CGATAGTCAT
** *
1986456 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
1986476 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
1986496 TTTC
1 TTTC
1986500 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:1986825 original size:35 final size:35
Alignment explanation
Indices: 1986786--1986862 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
1986776 ATATTACCTT
* *
1986786 AAATTGAAGTATTTTAGAATTTAGAGTTTAGAATA
1 AAATTGAAGTACTTTAGAAATTAGAGTTTAGAATA
* * * * *
1986821 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAAGTACTTTAGAAATTAGAGTTTAGAATA
1986856 AAATTGA
1 AAATTGA
1986863 TGACTGTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.01, G:0.21, T:0.38
Consensus pattern (35 bp):
AAATTGAAGTACTTTAGAAATTAGAGTTTAGAATA
Found at i:1987034 original size:29 final size:29
Alignment explanation
Indices: 1986993--1987054 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
1986983 GCAAACGGAA
* *
1986993 TAAATGTTAGGGGA-CTGTATTGCAAGTTT
1 TAAATGTTAGGGGACCT-AAATGCAAGTTT
1987022 TAAATGTTAGGGGACCTAAATGCAAGTTT
1 TAAATGTTAGGGGACCTAAATGCAAGTTT
1987051 TAAA
1 TAAA
1987055 AATGTTCAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 28 0.93
30 2 0.07
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (29 bp):
TAAATGTTAGGGGACCTAAATGCAAGTTT
Found at i:1987941 original size:22 final size:22
Alignment explanation
Indices: 1987916--1987981 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
1987906 GGCGACATCC
1987916 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
1987938 GTCCCCATCGCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* ** *
1987960 ATTTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1987982 TTCACGGTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1988374 original size:20 final size:20
Alignment explanation
Indices: 1988349--1988398 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1988339 TGCGATTCTT
1988349 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
1988369 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
1988389 GTGTTGCGAT
1 GCGTTGCGAT
1988399 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:1988404 original size:20 final size:20
Alignment explanation
Indices: 1988366--1988420 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1988356 GATAGTCAAA
* **
1988366 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
1988386 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
1988406 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
1988421 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1988428 original size:20 final size:20
Alignment explanation
Indices: 1988385--1988428 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1988375 CGATAGTCAT
** *
1988385 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
1988405 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
1988425 TTTC
1 TTTC
1988429 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:1990318 original size:20 final size:20
Alignment explanation
Indices: 1990293--1990431 Score: 108
Period size: 20 Copynumber: 7.6 Consensus size: 20
1990283 AGAATAGTTT
*
1990293 ACTATCGCAATACGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
1990313 ACTATCGCAACGCAAAAATG
1 ACTATCGCAATGCGAAAATG
*
1990333 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
1990349 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
1990366 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
1990382 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1990400 ACTATCTCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1990420 ACTATCGCAATG
1 ACTATCGCAATG
1990432 AAAGAATCGC
Statistics
Matches: 97, Mismatches: 8, Indels: 28
0.73 0.06 0.21
Matches are distributed among these distances:
14 14 0.14
16 10 0.10
17 8 0.08
18 4 0.04
19 7 0.07
20 54 0.56
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1990479 original size:20 final size:20
Alignment explanation
Indices: 1990450--1990497 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1990440 GCAATGCGAA
*
1990450 ATTGCAATAGTCAAATTCGC
1 ATTGCGATAGTCAAATTCGC
**
1990470 ATTGCGATAGTCATTTTCGC
1 ATTGCGATAGTCAAATTCGC
*
1990490 GTTGCGAT
1 ATTGCGAT
1990498 TTTCTTGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (20 bp):
ATTGCGATAGTCAAATTCGC
Found at i:1990501 original size:14 final size:14
Alignment explanation
Indices: 1990482--1990515 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1990472 TGCGATAGTC
1990482 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
**
1990496 ATTTTCTTGTTGCG
1 ATTTTCGCGTTGCG
1990510 ATTTTC
1 ATTTTC
1990516 ATTTCGCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.18, G:0.21, T:0.53
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1990528 original size:33 final size:34
Alignment explanation
Indices: 1990471--1990564 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 34
1990461 CAAATTCGCA
* *
1990471 TTGCGATAGTCATTTTCGCGTTGCGATTTTCTTG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
** *
1990505 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
1990538 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCGTTGCGAT
1990565 AGTCATTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.55
34 23 0.45
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
Found at i:1990561 original size:20 final size:20
Alignment explanation
Indices: 1990536--1990584 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1990526 GCGATTCTCT
1990536 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1990556 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1990576 CGTTGCGAT
1 CGTTGCGAT
1990585 TTTAAGTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1990594 original size:20 final size:20
Alignment explanation
Indices: 1990536--1990594 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1990526 GCGATTCTCT
* *
1990536 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
* *
1990556 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
1990576 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATAGTAAGTTTC
1990595 AGATTCTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:1991165 original size:42 final size:42
Alignment explanation
Indices: 1991065--1991175 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
1991055 CCCGACTCAC
* * * *
1991065 CTGTCATCGTTTAAGAGGCCTC-CCCTATCGTTCAACAGGCCC
1 CTGTCATCGTTCAAGAGTCCTCTCCC-ACCGTTCAACAGGCCA
* ** *
1991107 CTATCATCCCTCAAGAGTCCTCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCTCTCCCACCGTTCAACAGGCCA
*
1991149 CTGTCATCGTTGAAGAGGTCC-CTCCCA
1 CTGTCATCGTTCAAGA-GTCCTCTCCCA
1991176 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
42 48 0.87
43 7 0.13
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCTCTCCCACCGTTCAACAGGCCA
Found at i:1992658 original size:34 final size:34
Alignment explanation
Indices: 1992615--1992701 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 34
1992605 TTGATTTGTT
1992615 GATTTTCATTTTCGCATTGCAATTCACTCGTTGC
1 GATTTTCATTTTCGCATTGCAATTCACTCGTTGC
* *
1992649 GATTTTCATTTT-GCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTTCGCATTGCAATTCACTCGTTGC
** *
1992682 GATAGTCATTTCCGCATTGC
1 GATTTTCATTTTCGCATTGC
1992702 GATAGTCAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 28 0.60
34 19 0.40
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.44
Consensus pattern (34 bp):
GATTTTCATTTTCGCATTGCAATTCACTCGTTGC
Found at i:1992703 original size:20 final size:20
Alignment explanation
Indices: 1992676--1992764 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
1992666 GCGATTCTCT
1992676 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
1992696 CATTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
1992716 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1992736 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
1992756 CGTTGCGAT
1 CGTTGCGAT
1992765 TTCCGCGTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 60 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1995233 original size:24 final size:24
Alignment explanation
Indices: 1995206--1995252 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1995196 CAAAATCCGA
1995206 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
1995230 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
1995253 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:1995261 original size:24 final size:24
Alignment explanation
Indices: 1995210--1995261 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1995200 ATCCGAGTAT
** *
1995210 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
1995234 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
1995258 TGAC
1 TGAC
1995262 TAGTACTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:1996150 original size:21 final size:20
Alignment explanation
Indices: 1996099--1996152 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
1996089 CGATAGTCAT
* **
1996099 AATCTCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACCA
* *
1996119 AATCGCATTGCGATTTTCCA
1 AATCGCGTTGCGATTTACCA
1996139 AATTCGCGTTGCGA
1 AA-TCGCGTTGCGA
1996153 ATTAGGAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.35
Consensus pattern (20 bp):
AATCGCGTTGCGATTTACCA
Found at i:1996194 original size:21 final size:21
Alignment explanation
Indices: 1996148--1996194 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1996138 AAATTCGCGT
1996148 TGCGAATTAGGAAAATCGCAA
1 TGCGAATTAGGAAAATCGCAA
* * *
1996169 CGCGAATTTGGAAAATCGTAA
1 TGCGAATTAGGAAAATCGCAA
1996190 TGCGA
1 TGCGA
1996195 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (21 bp):
TGCGAATTAGGAAAATCGCAA
Found at i:2000991 original size:20 final size:20
Alignment explanation
Indices: 2000966--2001037 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
2000956 TTTTCCGACT
2000966 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
2000986 ATCGCAATGTGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
2001006 ATCGCAATGCGAATATATAA
1 ATCGCAATGCGAATATGTAA
2001026 ATCGCAATGCGA
1 ATCGCAATGCGA
2001038 TTCTGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:2001049 original size:20 final size:20
Alignment explanation
Indices: 2001026--2001113 Score: 140
Period size: 20 Copynumber: 4.4 Consensus size: 20
2001016 GAATATATAA
* *
2001026 ATCGCAATGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
2001046 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
2001066 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
2001086 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
2001106 GTCGCAAC
1 ATCGCAAC
2001114 ACTGAATTTC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:2001050 original size:40 final size:40
Alignment explanation
Indices: 2000904--2001052 Score: 140
Period size: 40 Copynumber: 3.6 Consensus size: 40
2000894 GTTTCCAGAT
* * * * *
2000904 TCGCAACGCGATTCTGACTATCGCATTGCGATTTTTTAAA
1 TCGCAATGCGATTCTGACTATCGCAATGCGAATATATAAA
* *
2000944 TTCGC-ATAGCGATTTTCCGACTATCGCAATGCGAATATGTAAA
1 -TCGCAAT-GCGA--TTCTGACTATCGCAATGCGAATATATAAA
* * * *
2000987 TCGCAATGTGAATATGTA-AATCGCAATGCGAATATATAAA
1 TCGCAATGCGATTCTG-ACTATCGCAATGCGAATATATAAA
2001027 TCGCAATGCGATTCTGACTATCGCAA
1 TCGCAATGCGATTCTGACTATCGCAA
2001053 CGAGATTCTG
Statistics
Matches: 86, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
39 1 0.01
40 43 0.50
41 9 0.10
42 7 0.08
43 26 0.30
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (40 bp):
TCGCAATGCGATTCTGACTATCGCAATGCGAATATATAAA
Found at i:2001966 original size:24 final size:24
Alignment explanation
Indices: 2001934--2001987 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2001924 GTATTCGAAA
2001934 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2001958 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2001982 TTTGAT
1 TTTGAT
2001988 GATTTTCAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2004255 original size:18 final size:18
Alignment explanation
Indices: 2004232--2004266 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2004222 AGAAAAAGGC
*
2004232 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
2004250 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
2004267 CAACCGGCTT
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:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:2004451 original size:20 final size:20
Alignment explanation
Indices: 2004426--2004753 Score: 276
Period size: 20 Copynumber: 17.6 Consensus size: 20
2004416 TTACACATTC
*
2004426 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2004446 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
2004465 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2004480 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
2004500 ATATGACTATCGCAA--CGA
1 ATTTGACTATCGCAACGCGA
**
2004518 A----AAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
2004534 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
2004554 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * *
2004574 ATTTGATTATCGTAACGGGT
1 ATTTGACTATCGCAACGCGA
*
2004594 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
2004614 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
2004628 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
2004648 ATTTGACTATCGAAACACGA
1 ATTTGACTATCGCAACGCGA
* *
2004668 ATTTGA-TCATCGCAACGGGT
1 ATTTGACT-ATCGCAACGCGA
*
2004688 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
2004708 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
2004722 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2004742 A-TTGACTTTCGC
1 ATTTGACTATCGC
2004754 GTTGCGATTT
Statistics
Matches: 247, Mismatches: 35, Indels: 53
0.74 0.10 0.16
Matches are distributed among these distances:
14 39 0.16
15 3 0.01
16 6 0.02
18 6 0.02
19 13 0.05
20 179 0.72
21 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:2004508 original size:54 final size:54
Alignment explanation
Indices: 2004426--2004570 Score: 245
Period size: 54 Copynumber: 2.7 Consensus size: 54
2004416 TTACACATTC
* **
2004426 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACTCAAAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCGA
* *
2004480 ATTTGACTATCGCAACACGAATATGACTATCGCAACGAAAAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCGA
2004534 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
2004571 CGAATTTGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (54 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCGA
Found at i:2004601 original size:94 final size:93
Alignment explanation
Indices: 2004434--2004753 Score: 443
Period size: 94 Copynumber: 3.5 Consensus size: 93
2004424 TCATTTGAAT
* * *
2004434 ATCGCAACGCGAATTTGACTATCGCAACTC-AA---A-AATCGCAACGCGAATTTGACTATCGCA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTGACTATCGCAACGCGAATTTGATTATCGCA
** * * *
2004494 ACACGAATATGACTATCGCAACGAAAAA
66 ACGGGTATTTGACTATCGCAACGAGAAA
*
2004522 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAA-TTGACTATCGCAACGCGAATTTGATTATCGC
2004587 AACGGGTATTTGACTATCGCAACGAGAAA
65 AACGGGTATTTGACTATCGCAACGAGAAA
* * *
2004616 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGAAACACGAATTTGATCATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAA-TTGACTATCGCAACGCGAATTTGATTATCGC
2004681 AACGGGTATTTGACTATCGCAACGAGAAA
65 AACGGGTATTTGACTATCGCAACGAGAAA
* * * *
2004710 ATCGCAAAGCGTATTAGACTATCGCAACGCGAATTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTGACTATCGC
2004754 GTTGCGATTT
Statistics
Matches: 208, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
88 29 0.14
89 2 0.01
93 10 0.05
94 167 0.80
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (93 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTGACTATCGCAACGCGAATTTGATTATCGCA
ACGGGTATTTGACTATCGCAACGAGAAA
Found at i:2004684 original size:74 final size:74
Alignment explanation
Indices: 2004426--2004684 Score: 265
Period size: 74 Copynumber: 3.5 Consensus size: 74
2004416 TTACACATTC
* * *
2004426 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACTCA-AAAATCGCAACGCGAATTTGACTAT
1 ATTTGACTATCGCAACACGAATTTGACTATCGCAAC-GAGAAAATCGCAACGCGAATTTGACTAT
*
2004490 CGCAACACGA
65 CGCAACGCGA
* ** * * * *** **
2004500 ATATGACTATCGCAACGAAAAAATCG-C-AACGCGAATTTGACTATCGCAACGCGAATTTGACTA
1 ATTTGACTATCGCAAC-ACGAATTTGACTATCGC-AACGAGAAAATCGCAACGCGAATTTGACTA
2004563 TCGCAACGCGA
64 TCGCAACGCGA
* * ** *
2004574 ATTTGATTATCGTAACGGGTATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACTATC
1 ATTTGACTATCGCAACACGAATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACTATC
2004639 GCAACGCGA
66 GCAACGCGA
*
2004648 ATTTGACTATCGAAACACGAATTTGA-TCATCGCAACG
1 ATTTGACTATCGCAACACGAATTTGACT-ATCGCAACG
2004685 GGTATTTGAC
Statistics
Matches: 145, Mismatches: 34, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
73 8 0.06
74 129 0.89
75 8 0.06
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (74 bp):
ATTTGACTATCGCAACACGAATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACTATC
GCAACGCGA
Found at i:2004772 original size:20 final size:20
Alignment explanation
Indices: 2004743--2004800 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
2004733 GCAACGCGAA
2004743 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
2004763 TTGTCTTTCGCATTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
2004783 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
2004801 AAGTGTACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:2004959 original size:14 final size:14
Alignment explanation
Indices: 2004899--2004960 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
2004889 CACAAATAAG
*
2004899 AATTATTTACACATC
1 AATT-TTTACAAATC
**
2004914 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
2004929 AACTTTTACAAATC
1 AATTTTTACAAATC
*
2004943 AATTTTTATAAATC
1 AATTTTTACAAATC
2004957 AATT
1 AATT
2004961 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:2008047 original size:20 final size:18
Alignment explanation
Indices: 2008009--2008055 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
2007999 GAAACTTAAA
*
2008009 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
2008027 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
2008047 ATCGCAACG
1 ATCGCAACG
2008056 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
20 14 0.54
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:2008340 original size:20 final size:20
Alignment explanation
Indices: 2008315--2008401 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
2008305 TAGTTTACTT
*
2008315 TCGCAACGCAAAATGGACTA
1 TCGCAACGCAAAATTGACTA
2008335 TCGCAACGCGAAAA-TGACTA
1 TCGCAACGC-AAAATTGACTA
* *
2008355 TCGCAACGCGAATTTGACTA
1 TCGCAACGCAAAATTGACTA
* *
2008375 TCGCAACGCTAATTTGACTA
1 TCGCAACGCAAAATTGACTA
2008395 TCGCAAC
1 TCGCAAC
2008402 CAGAGAATCG
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.03
20 55 0.90
21 4 0.07
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (20 bp):
TCGCAACGCAAAATTGACTA
Found at i:2008470 original size:20 final size:20
Alignment explanation
Indices: 2008445--2008492 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2008435 GCGATTCTTT
2008445 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
2008465 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
2008485 CGTTGCGA
1 CGTTGCGA
2008493 AAGTAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2008667 original size:18 final size:18
Alignment explanation
Indices: 2008640--2008689 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
2008630 TTTACTAAGC
2008640 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
*
2008658 AATTTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
2008676 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
2008690 TACGAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:2010475 original size:20 final size:20
Alignment explanation
Indices: 2010420--2010526 Score: 101
Period size: 20 Copynumber: 5.5 Consensus size: 20
2010410 TCTGAAACTT
**
2010420 AAAATCGCAACAAGAAAATG
1 AAAATCGCAACGCGAAAATG
* *
2010440 AAAATCGTAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
2010460 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
2010480 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
2010499 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
2010518 AAAATCGCA
1 AAAATCGCA
2010527 TTGTGATTAT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
19 24 0.33
20 49 0.67
ACGTcount: A:0.47, C:0.21, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:2010937 original size:22 final size:22
Alignment explanation
Indices: 2010908--2010964 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
2010898 GATGTAGATA
2010908 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
2010930 GACTGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2010952 GACGGATGTCGCC
1 GACGGATTTCGCC
2010965 TTAGAGAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.19, G:0.42, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2011159 original size:20 final size:20
Alignment explanation
Indices: 2011136--2011222 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
2011126 GAAAATCGTA
*
2011136 TTGCGATAGTCAGCATCGCG
1 TTGCGATAGTCAGCATCTCG
2011156 TTGCGATAGTCAGCATCTCG
1 TTGCGATAGTCAGCATCTCG
*
2011176 TTGCGATAGTCAGTATCTCG
1 TTGCGATAGTCAGCATCTCG
* *
2011196 TTGCGATAGTCAGAATCACG
1 TTGCGATAGTCAGCATCTCG
2011216 TTGCGAT
1 TTGCGAT
2011223 TTACATATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGCATCTCG
Found at i:2011239 original size:20 final size:20
Alignment explanation
Indices: 2011216--2011262 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
2011206 CAGAATCACG
2011216 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
2011236 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
2011256 TTGCGAT
1 TTGCGAT
2011263 AGTCGGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACATATTCGCA
Found at i:2011283 original size:22 final size:22
Alignment explanation
Indices: 2011258--2011310 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
2011248 TATTCGCATT
**
2011258 GCGATAGTCGGAAAATCGCAAC
1 GCGATAGTCAAAAAATCGCAAC
* * *
2011280 GCGA-ATTTAAAAAATCGCAAT
1 GCGATAGTCAAAAAATCGCAAC
2011301 GCGATAGTCA
1 GCGATAGTCA
2011311 TAATCGCGTT
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.19
Consensus pattern (22 bp):
GCGATAGTCAAAAAATCGCAAC
Found at i:2011948 original size:20 final size:20
Alignment explanation
Indices: 2011889--2011951 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
2011879 AAAAAAATAT
2011889 ATATTTA-AATTATAA-TTAA
1 ATATTTATAATTA-AATTTAA
2011908 ATAATTTCATAA-T--ATTATAA
1 AT-ATTT-ATAATTAAATT-TAA
2011928 ATATTTATAATTAAATTTAA
1 ATATTTATAATTAAATTTAA
2011948 ATAT
1 ATAT
2011952 AAACTTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
18 5 0.14
19 8 0.22
20 16 0.44
21 5 0.14
22 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATTTATAATTAAATTTAA
Found at i:2012664 original size:62 final size:62
Alignment explanation
Indices: 2012549--2012666 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 62
2012539 AAATATAGGG
* * *
2012549 TATTGCTTTATTAAGTTCATCGACTATTAAAAGTTACACAATGATCCTTTGACTATAGAGTA
1 TATTGCTTTATTAAGTCCATCGACTATTAAAAGTTACAAAATGATCCTCTGACTATAGAGTA
* * * *
2012611 TATTGCTTTGTTGAGTCCCTCGACTATTAAAAGTTACAAAATGGTCAC-CTGACTAT
1 TATTGCTTTATTAAGTCCATCGACTATTAAAAGTTACAAAATGATC-CTCTGACTAT
2012667 TCATTATGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 47 0.98
63 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (62 bp):
TATTGCTTTATTAAGTCCATCGACTATTAAAAGTTACAAAATGATCCTCTGACTATAGAGTA
Done.