Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 6 of 20
Found at i:2001126 original size:24 final size:24
Alignment explanation
Indices: 2001036--2001137 Score: 87
Period size: 24 Copynumber: 4.0 Consensus size: 24
2001026 AAAATATTAT
*
2001036 TGTTACACGTCATGTAAAAAAACA
1 TGTTACACGCCATGTAAAAAAACA
*
2001060 TGTTACACGTCATGTTAAAATAAATACTA
1 TGTTACACGCCATG-T-AAA-AAA-AC-A
* * *
2001089 TTGTTATACACCATGTACAAAAACA
1 -TGTTACACGCCATGTAAAAAAACA
**
2001114 TGTTACACGCCATGTTGAAAAACA
1 TGTTACACGCCATGTAAAAAAACA
2001138 AATACTGTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
24 34 0.53
25 2 0.03
26 5 0.08
27 6 0.09
28 4 0.06
29 2 0.03
30 11 0.17
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (24 bp):
TGTTACACGCCATGTAAAAAAACA
Found at i:2001187 original size:29 final size:27
Alignment explanation
Indices: 2001006--2001210 Score: 107
Period size: 30 Copynumber: 7.3 Consensus size: 27
2000996 TATAAAAATA
** *
2001006 TGTTACACATCATGTTAAAAAAAATATTAT
1 TGTTACACGCCATGTT--AAAAAATACT-T
* *
2001036 TGTTACACGTCATG-TAAAAAA-AC-A
1 TGTTACACGCCATGTTAAAAAATACTT
*
2001060 TGTTACACGTCATGTTAAAATAAATACTAT
1 TGTTACACGCCATGTT-AAA-AAATACT-T
* * * *
2001090 TGTTATACACCATG-TACAAAA-AC-A
1 TGTTACACGCCATGTTAAAAAATACTT
2001114 TGTTACACGCCATGTTGAAAAACAAATACTGT
1 TGTTACACGCCATGTT---AAA-AAATACT-T
* * *
2001146 TATAACATGCCATGTTGAAAAAATACTGT
1 TGTTACACGCCATGTT-AAAAAATACT-T
* * *
2001175 TGTTACACACCATGTTCAAAAATATTT
1 TGTTACACGCCATGTTAAAAAATACTT
2001202 TGTTACACG
1 TGTTACACG
2001211 TTAATGCCTA
Statistics
Matches: 137, Mismatches: 24, Indels: 31
0.71 0.12 0.16
Matches are distributed among these distances:
24 26 0.19
25 2 0.01
26 6 0.04
27 21 0.15
28 14 0.10
29 26 0.19
30 29 0.21
32 13 0.09
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (27 bp):
TGTTACACGCCATGTTAAAAAATACTT
Found at i:2001919 original size:23 final size:25
Alignment explanation
Indices: 2001879--2001927 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
2001869 CGATTTCCTC
*
2001879 AAATAAATAAATAATAGAATTAAAA
1 AAATAAATAAATAATAGAAATAAAA
*
2001904 AAAT-AAT-AATAGTAGAAATAAAA
1 AAATAAATAAATAATAGAAATAAAA
2001927 A
1 A
2001928 GAAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
24 3 0.14
25 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.22
Consensus pattern (25 bp):
AAATAAATAAATAATAGAAATAAAA
Found at i:2002048 original size:57 final size:57
Alignment explanation
Indices: 2001957--2002066 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 57
2001947 ACTTTCATCC
* * *
2001957 TTACTTACATAACCTTTGATATTAAGGAATATCACAAAACCTTGAGCTTTAGCTTCT
1 TTACTTACATAACCTTTGATACTAAGGAAAATCACAAAACCTTGAACTTTAGCTTCT
* * * *
2002014 TTACTTAGATAAGCTTTGATGCTAAGGAAAATCACAAAATCTTGAACTTTAGC
1 TTACTTACATAACCTTTGATACTAAGGAAAATCACAAAACCTTGAACTTTAGC
2002067 AATCAACAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (57 bp):
TTACTTACATAACCTTTGATACTAAGGAAAATCACAAAACCTTGAACTTTAGCTTCT
Found at i:2009534 original size:2 final size:2
Alignment explanation
Indices: 2009529--2009558 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2009519 ATATATATAT
*
2009529 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2009559 TTTAGCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2009611 original size:15 final size:16
Alignment explanation
Indices: 2009579--2009614 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2009569 ATTATTATAT
*
2009579 ATATAAAATTTTTAAC
1 ATATAAAATTTATAAC
2009595 ATATAAAA-TTATAAC
1 ATATAAAATTTATAAC
2009610 ATATA
1 ATATA
2009615 TTAATTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAAAATTTATAAC
Found at i:2012248 original size:2 final size:2
Alignment explanation
Indices: 2012241--2012266 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2012231 TGGTTTTAAT
2012241 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
2012267 CACACACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2013571 original size:38 final size:38
Alignment explanation
Indices: 2013523--2013608 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 38
2013513 ATATCATGTG
* * *
2013523 GATAAGGGTACAATCCTAACT-ATCTATGACATAACACA
1 GATAATGGTACAATCCCAA-TAATCTAAGACATAACACA
*
2013561 GATAATGGTACAATCCCCATAATCTAAGACATAACACA
1 GATAATGGTACAATCCCAATAATCTAAGACATAACACA
2013599 GATAATGGTA
1 GATAATGGTA
2013609 TAGTCCACTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 1 0.02
38 42 0.98
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (38 bp):
GATAATGGTACAATCCCAATAATCTAAGACATAACACA
Found at i:2013916 original size:38 final size:38
Alignment explanation
Indices: 2013813--2013921 Score: 164
Period size: 38 Copynumber: 2.9 Consensus size: 38
2013803 CATTACATAG
* * * *
2013813 TCATAAAGGTGAGTATTTATTCATCCAAACATGCATTA
1 TCATAAAGGTGGGTATTCATTCATCCACACTTGCATTA
2013851 TCATAAAGGTGGGTATTCATTCATCCACACTTGCATTA
1 TCATAAAGGTGGGTATTCATTCATCCACACTTGCATTA
* *
2013889 TCATAAAGGTGGGCATTCACTCATCCACACTTG
1 TCATAAAGGTGGGTATTCATTCATCCACACTTG
2013922 TATACCTCCA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (38 bp):
TCATAAAGGTGGGTATTCATTCATCCACACTTGCATTA
Found at i:2017787 original size:36 final size:36
Alignment explanation
Indices: 2017715--2017935 Score: 248
Period size: 36 Copynumber: 6.2 Consensus size: 36
2017705 AAGGAATGTG
* * *
2017715 CTTTTTAATGGGATCAAGC-AAAACCCTCACAATAA
1 CTTTTTAATGGGATTAAGCGATAACCCTTACAATAA
* * * *
2017750 CTTTTTTATGAGATTAAGCGATAACTCTTACACTAA
1 CTTTTTAATGGGATTAAGCGATAACCCTTACAATAA
*
2017786 CTTTTTAATGGGATCAAGCGATAACCCTTACAATAA
1 CTTTTTAATGGGATTAAGCGATAACCCTTACAATAA
* *** * * *
2017822 CTTTTTTACAAGATCAAGCGATAACCCTTACAGTAG
1 CTTTTTAATGGGATTAAGCGATAACCCTTACAATAA
* * * *
2017858 CTCTTTAATGGGATTAAGCGATAACCCTTATACTGA
1 CTTTTTAATGGGATTAAGCGATAACCCTTACAATAA
*
2017894 CTTTTTAATGGGATTAAGTGATAACCCTTACAATAA
1 CTTTTTAATGGGATTAAGCGATAACCCTTACAATAA
2017930 -TTTTTA
1 CTTTTTA
2017936 CAGGGCTCAA
Statistics
Matches: 152, Mismatches: 33, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
35 22 0.14
36 130 0.86
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (36 bp):
CTTTTTAATGGGATTAAGCGATAACCCTTACAATAA
Found at i:2017903 original size:108 final size:106
Alignment explanation
Indices: 2017726--2017934 Score: 292
Period size: 108 Copynumber: 2.0 Consensus size: 106
2017716 TTTTTAATGG
* * *
2017726 GATCAAGCAAAACCCTCACAATAACTTTTTTATGAGATTAAGCGATAACTCTTACACTAACTTTT
1 GATCAAGCAAAACCCTCACAATAACTCTTTAATGAGATTAAGCGATAACCCTTACACTAACTTTT
2017791 TAATGGGATCAAGCGATAACCCTTACAATAACTTTTTTACAA
66 TAATGGGATCAAGCGATAACCCTTACAATAA-TTTTTTACAA
* * * * * * *
2017833 GATCAAGCGATAACCCTTACAGTAGCTCTTTAATGGGATTAAGCGATAACCCTTATACTGACTTT
1 GATCAAGC-AAAACCCTCACAATAACTCTTTAATGAGATTAAGCGATAACCCTTACACTAACTTT
* *
2017898 TTAATGGGATTAAGTGATAACCCTTACAATAATTTTT
65 TTAATGGGATCAAGCGATAACCCTTACAATAATTTTT
2017935 ACAGGGCTCA
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
107 13 0.15
108 76 0.85
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (106 bp):
GATCAAGCAAAACCCTCACAATAACTCTTTAATGAGATTAAGCGATAACCCTTACACTAACTTTT
TAATGGGATCAAGCGATAACCCTTACAATAATTTTTTACAA
Found at i:2019755 original size:73 final size:73
Alignment explanation
Indices: 2019654--2019820 Score: 226
Period size: 73 Copynumber: 2.3 Consensus size: 73
2019644 GATCAAGTGA
* * **
2019654 CATTGTTAGTTGACTAAGAGCTTACTGCCAAAAACTGAGTTCAGAGACAAAAATGACTTAATCGA
1 CATTGTTAGTCGACTAAGAGCCTACTGCCAAAAACTGAGTTCAGAGACAAAAACAACTTAATCGA
2019719 CTAAGAAG
66 CTAAGAAG
* * * * *
2019727 TATTGTTAGTCAACTAAGAGCCTACTGCCAGAAACTGGGTTCAGAGACAAAGACAACTTAATCGA
1 CATTGTTAGTCGACTAAGAGCCTACTGCCAAAAACTGAGTTCAGAGACAAAAACAACTTAATCGA
**
2019792 CTAAGTGG
66 CTAAGAAG
*
2019800 CAATGTTAGTCGACTAAGAGC
1 CATTGTTAGTCGACTAAGAGC
2019821 ATTCTGTCTG
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 80 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (73 bp):
CATTGTTAGTCGACTAAGAGCCTACTGCCAAAAACTGAGTTCAGAGACAAAAACAACTTAATCGA
CTAAGAAG
Found at i:2026018 original size:33 final size:33
Alignment explanation
Indices: 2025981--2026055 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
2025971 ATCATGGCAA
* * * *
2025981 ATTAACATATTATGTCATCATTAATTGTGATAT
1 ATTAACATATCATATCATCATCAATTATGATAT
* *
2026014 ATTAACATCTCATATTATCATCAATTATGATAT
1 ATTAACATATCATATCATCATCAATTATGATAT
*
2026047 TTTAACATA
1 ATTAACATA
2026056 GCACATCAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (33 bp):
ATTAACATATCATATCATCATCAATTATGATAT
Found at i:2026162 original size:30 final size:30
Alignment explanation
Indices: 2026116--2026187 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
2026106 TAATTATTAG
* *
2026116 ATATAATGGTTTATTTGACTCAAAATAAAA
1 ATATAACGGCTTATTTGACTCAAAATAAAA
* * *
2026146 ATGTAACGGCTTATTTGGCTTAAAATAAAA
1 ATATAACGGCTTATTTGACTCAAAATAAAA
*
2026176 ATATAAGGGCTT
1 ATATAACGGCTT
2026188 GATTAAATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (30 bp):
ATATAACGGCTTATTTGACTCAAAATAAAA
Found at i:2032011 original size:40 final size:41
Alignment explanation
Indices: 2031956--2032080 Score: 155
Period size: 40 Copynumber: 3.0 Consensus size: 41
2031946 ATTGTATTTT
2031956 GACTTTGTGAAGCTTGAGGGTGAGAGATTATAGGATCGT-A
1 GACTTTGTGAAGCTTGAGGGTGAGAGATTATAGGATCGTCA
2031996 GACTTTGTGAAGCTTGAGGGTGAAGGTGAAAGATTATAGGATCGTCA
1 GACTTTGTGAAGCTTGAGGGTG-A---G--AGATTATAGGATCGTCA
* * *
2032043 -AGTTTATGAAGCTTGAGGGTGAGAGATTAGAGGATCGT
1 GACTTTGTGAAGCTTGAGGGTGAGAGATTATAGGATCGT
2032081 GCTGATAACG
Statistics
Matches: 75, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
40 36 0.48
41 1 0.01
42 1 0.01
44 1 0.01
45 1 0.01
46 34 0.45
47 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.35, T:0.29
Consensus pattern (41 bp):
GACTTTGTGAAGCTTGAGGGTGAGAGATTATAGGATCGTCA
Found at i:2032053 original size:46 final size:46
Alignment explanation
Indices: 2031974--2032064 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
2031964 GAAGCTTGAG
* *
2031974 GGTGAGAGATTATAGGATCGTAGACTTTGTGAAGCTTGAGGGTGAA
1 GGTGAAAGATTATAGGATCGTAGACTTTATGAAGCTTGAGGGTGAA
*
2032020 GGTGAAAGATTATAGGATCGTCA-AGTTTATGAAGCTTGAGGGTGA
1 GGTGAAAGATTATAGGATCGT-AGACTTTATGAAGCTTGAGGGTGA
2032065 GAGATTAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 40 0.98
47 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.35, T:0.29
Consensus pattern (46 bp):
GGTGAAAGATTATAGGATCGTAGACTTTATGAAGCTTGAGGGTGAA
Found at i:2037100 original size:3 final size:3
Alignment explanation
Indices: 2037092--2037135 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
2037082 ATAAAAACAA
* *
2037092 AAT AAT AAT AAT AAT AAT AAT GAC AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2037136 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2040046 original size:20 final size:20
Alignment explanation
Indices: 2040023--2040062 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2040013 TAACCACTTG
2040023 GGTTCTTTTTTCACCAGCAA
1 GGTTCTTTTTTCACCAGCAA
*
2040043 GGTTCTTTTTTCACCGGCAA
1 GGTTCTTTTTTCACCAGCAA
2040063 AAGCGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (20 bp):
GGTTCTTTTTTCACCAGCAA
Found at i:2043792 original size:13 final size:13
Alignment explanation
Indices: 2043774--2043804 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2043764 AAACATTTTG
2043774 ACAGATTTTCTCC
1 ACAGATTTTCTCC
2043787 ACAGATTTTCTCC
1 ACAGATTTTCTCC
2043800 ACAGA
1 ACAGA
2043805 AATATCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (13 bp):
ACAGATTTTCTCC
Found at i:2055358 original size:6 final size:6
Alignment explanation
Indices: 2055347--2055380 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2055337 AATGATGCAC
* *
2055347 AAAATA AAAATA AAATTA AAAACA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
2055381 CCATAATCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:2059161 original size:74 final size:73
Alignment explanation
Indices: 2059082--2059331 Score: 349
Period size: 74 Copynumber: 3.4 Consensus size: 73
2059072 CTTTTAGTTG
* * *
2059082 ACTAACCATGCTTCTTAGTCGATTAAGTCTTCACTATTTTGTAATCAAATTCTCTAGTAGTAAGC
1 ACTAACCATACTTCTTAGTCGATTAAGTCTT-TCTATTTTGTAATCAAATTCTCTAGTAGTGAGC
2059147 TCTTAGCTA
65 TCTTAGCTA
*
2059156 ACTAACCATGCTTCTTAGTCGATTAAGTCTTTTCTATTTTGTAATCAAATTCTCTAGTAGTGAGC
1 ACTAACCATACTTCTTAGTCGATTAAGTC-TTTCTATTTTGTAATCAAATTCTCTAGTAGTGAGC
*
2059221 TCTTATCTA
65 TCTTAGCTA
* * *
2059230 ACTAACCATACTTCTTAGTCAATTAAGTCCTTTCTATTTTGTAATTC-AATTCTCTAGCAGCGAG
1 ACTAACCATACTTCTTAGTCGATTAAGT-CTTTCTATTTTGTAA-TCAAATTCTCTAGTAGTGAG
*
2059294 CTCTTAGCTG
64 CTCTTAGCTA
* * *
2059304 GCTAACTATACTTCTTAGTCCATTAAGT
1 ACTAACCATACTTCTTAGTCGATTAAGT
2059332 GTTCTATGTC
Statistics
Matches: 161, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
74 156 0.97
75 5 0.03
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (73 bp):
ACTAACCATACTTCTTAGTCGATTAAGTCTTTCTATTTTGTAATCAAATTCTCTAGTAGTGAGCT
CTTAGCTA
Found at i:2059403 original size:148 final size:147
Alignment explanation
Indices: 2059071--2059405 Score: 358
Period size: 148 Copynumber: 2.3 Consensus size: 147
2059061 TAGACAATGT
*
2059071 GCTTTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTCTTCACTATTTTGTAATCAAATTCTC
1 GCTTTTAGTTGACTAACCATACTTCTTAGTCGATTAAGTCTTCACTATTTTGTAATCAAATTCTC
* * * * * **
2059136 TAGTAGTAAGCTCTTAGCTAACTAACCATGCTTCTTAGTCGATTAAGTCTTTTCTATTTTGTAAT
66 TAGCAGCAAGCTCTTAGCTAACTAACCATACTTCTTAGTCCATTAAG-CTGTTCTATTTACTAAT
*
2059201 CAAATTCTCTAGTAGTGA
130 CAAATTCTCTAGCAGTGA
* * * *
2059219 GCTCTTA-TCTAACTAACCATACTTCTTAGTCAATTAAGTCCTT-TCTATTTTGTAATTC-AATT
1 GCTTTTAGT-TGACTAACCATACTTCTTAGTCGATTAAGT-CTTCACTATTTTGTAA-TCAAATT
* ** *
2059281 CTCTAGCAGCGAGCTCTTAGCTGGCTAACTATACTTCTTAGTCCATTAAG-TGTTCTATGTCTCA
63 CTCTAGCAGCAAGCTCTTAGCTAACTAACCATACTTCTTAGTCCATTAAGCTGTTCTAT-T-T-A
* * *
2059345 CTAATCAAATT-TTTTGCCGTGA
125 CTAATCAAATTCTCTAGCAGTGA
* *
2059367 GTTTTTAGTTGGCTAACCATACTTCTT-GATCGATTAAGT
1 GCTTTTAGTTGACTAACCATACTTCTTAG-TCGATTAAGT
2059406 TTTCTCTGTC
Statistics
Matches: 154, Mismatches: 25, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
146 7 0.05
147 3 0.02
148 128 0.83
149 16 0.10
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (147 bp):
GCTTTTAGTTGACTAACCATACTTCTTAGTCGATTAAGTCTTCACTATTTTGTAATCAAATTCTC
TAGCAGCAAGCTCTTAGCTAACTAACCATACTTCTTAGTCCATTAAGCTGTTCTATTTACTAATC
AAATTCTCTAGCAGTGA
Found at i:2080531 original size:39 final size:39
Alignment explanation
Indices: 2080444--2080535 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 39
2080434 TTCTTGTTTG
** * *
2080444 TTTGATTTATTCATATGATGGACATTGATTTATGAATAA
1 TTTGATTTATTCATATGACAGAAATTGATTTATCAATAA
*
2080483 TTTGATTTATTCATATGACAGAAATTGATTTA-CAATTGA
1 TTTGATTTATTCATATGACAGAAATTGATTTATCAA-TAA
2080522 TTT-AGTTTATTCAT
1 TTTGA-TTTATTCAT
2080536 GAGATGAAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 3 0.07
39 43 0.93
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (39 bp):
TTTGATTTATTCATATGACAGAAATTGATTTATCAATAA
Found at i:2085651 original size:2 final size:2
Alignment explanation
Indices: 2085644--2085668 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2085634 TTGAATTCTG
2085644 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 A
2085669 ATTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2107461 original size:2 final size:2
Alignment explanation
Indices: 2107454--2107478 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2107444 TTTCTTGAGA
2107454 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 A
2107479 ATAAAAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2108025 original size:22 final size:21
Alignment explanation
Indices: 2108000--2108049 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
2107990 TATGAAAAGA
*
2108000 TTAAAATATTTATT-TTATTAAT
1 TTAAAA-AATTATTATTA-TAAT
*
2108022 TTAAAAAATTATTATTATATT
1 TTAAAAAATTATTATTATAAT
2108043 TTAAAAA
1 TTAAAAA
2108050 TATATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAAAAAATTATTATTATAAT
Found at i:2108853 original size:29 final size:29
Alignment explanation
Indices: 2108821--2108903 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 29
2108811 TAAAGGCCAG
2108821 AATGATATTGTGCATATGTTTGGCAC-CTA
1 AATGATATTGTGCATATGTTTGGCACAC-A
*
2108850 AATGATGATGTTGTGCAAATGTTTGGCACACA
1 AATGAT-A--TTGTGCATATGTTTGGCACACA
* *
2108882 AATGGTATAGTGCATA-GTTTGG
1 AATGATATTGTGCATATGTTTGG
2108904 TAGTTAAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
28 6 0.13
29 13 0.28
30 1 0.02
31 1 0.02
32 24 0.52
33 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (29 bp):
AATGATATTGTGCATATGTTTGGCACACA
Found at i:2111090 original size:21 final size:20
Alignment explanation
Indices: 2111039--2111107 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
2111029 TTGACAATAG
* * * *
2111039 AATTGAATTATAATTTAATT
1 AATTCAATTTTAAATTAACT
2111059 AATT-AA-TTTAAATTAA-T
1 AATTCAATTTTAAATTAACT
2111076 CATATTCAATTTTAAATTAACT
1 -A-ATTCAATTTTAAATTAACT
2111098 AATTCAATTT
1 AATTCAATTT
2111108 CATAAACCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
17 1 0.02
18 9 0.21
19 5 0.12
20 15 0.36
21 11 0.26
22 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (20 bp):
AATTCAATTTTAAATTAACT
Found at i:2121528 original size:36 final size:35
Alignment explanation
Indices: 2121450--2121569 Score: 125
Period size: 35 Copynumber: 3.3 Consensus size: 35
2121440 TAAATTTATA
* * *
2121450 TTTTTTT-TAATAATACATATAACTATTAGAAGTAAT
1 TTTTTTTGTAATAATACCTAGAACTATTA-AACT-AT
* *
2121486 TCTTTTTTGTAATACTGCCTAGAACTATTAAACTAT
1 T-TTTTTTGTAATAATACCTAGAACTATTAAACTAT
* *
2121522 TTTTTTTGTAATAATATCTAGAACTATTAAAACTAA
1 TTTTTTTGTAATAATACCTAGAACTATT-AAACTAT
*
2121558 TTATTTTGTAAT
1 TTTTTTTGTAAT
2121570 CATTACTTGC
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 24 0.34
36 21 0.30
37 9 0.13
38 17 0.24
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (35 bp):
TTTTTTTGTAATAATACCTAGAACTATTAAACTAT
Found at i:2122000 original size:3 final size:3
Alignment explanation
Indices: 2121992--2122040 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
2121982 ATGAAATAAC
2121992 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2122040 A
1 A
2122041 GCCATTGTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2125088 original size:35 final size:35
Alignment explanation
Indices: 2125061--2125214 Score: 191
Period size: 35 Copynumber: 4.3 Consensus size: 35
2125051 CTTAACTATT
*
2125061 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
1 TAATTTAATCAATTAAGCCCAATAACTTAATTAAA
* *
2125096 TAATTTAATTAATTAAGCCTAATAACTTAATTAAA
1 TAATTTAATCAATTAAGCCCAATAACTTAATTAAA
* * * *
2125131 AAATTTTAATCAATTAGGCTCAATGACTTAATTAAA
1 TAA-TTTAATCAATTAAGCCCAATAACTTAATTAAA
* * *
2125167 TAGTTTAATTAATTAAGCCAAATAACTTAATTAAA
1 TAATTTAATCAATTAAGCCCAATAACTTAATTAAA
*
2125202 CAATTTTAATCAA
1 TAA-TTTAATCAA
2125215 GTACTTGAGA
Statistics
Matches: 98, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
35 62 0.63
36 36 0.37
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (35 bp):
TAATTTAATCAATTAAGCCCAATAACTTAATTAAA
Found at i:2125160 original size:71 final size:71
Alignment explanation
Indices: 2125064--2125214 Score: 257
Period size: 71 Copynumber: 2.1 Consensus size: 71
2125054 AACTATTTAA
*
2125064 TTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCTAATAACTTAATTA
1 TTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCAAATAACTTAATTA
2125129 AAAAAT
66 AAAAAT
* * *
2125135 TTTAATCAATTAGGCTCAATGACTTAATTAAATAGTTTAATTAATTAAGCCAAATAACTTAATTA
1 TTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCAAATAACTTAATTA
*
2125200 AACAAT
66 AAAAAT
2125206 TTTAATCAA
1 TTTAATCAA
2125215 GTACTTGAGA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.37
Consensus pattern (71 bp):
TTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCAAATAACTTAATTA
AAAAAT
Found at i:2126442 original size:13 final size:13
Alignment explanation
Indices: 2126424--2126449 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2126414 ATGTTTCAAG
2126424 TTTGAATAATTAT
1 TTTGAATAATTAT
2126437 TTTGAATAATTAT
1 TTTGAATAATTAT
2126450 GTTATATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTGAATAATTAT
Found at i:2129388 original size:19 final size:19
Alignment explanation
Indices: 2129333--2129412 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
2129323 CTCCCTTTTC
* *
2129333 TAATTAGTTAGTAAATTTG
1 TAATTAGTTAATAAAATTG
* * *
2129352 GATTTAATTAAATAAAATTG
1 TAATTAGTT-AATAAAATTG
* *
2129372 TAATTAGTTATTAAAATTT
1 TAATTAGTTAATAAAATTG
* *
2129391 TAATTATTTAACAAAATTG
1 TAATTAGTTAATAAAATTG
2129410 TAA
1 TAA
2129413 GTATAAAATT
Statistics
Matches: 46, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
19 32 0.70
20 14 0.30
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (19 bp):
TAATTAGTTAATAAAATTG
Found at i:2134714 original size:20 final size:20
Alignment explanation
Indices: 2134689--2134729 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2134679 CCACAAACGT
*
2134689 TGACAAAATAAAATTAGCTA
1 TGACAAAATAAAATTAACTA
*
2134709 TGACAAAATAGAATTAACTA
1 TGACAAAATAAAATTAACTA
2134729 T
1 T
2134730 TCATAGGCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (20 bp):
TGACAAAATAAAATTAACTA
Found at i:2149272 original size:31 final size:31
Alignment explanation
Indices: 2149234--2149335 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 31
2149224 CTTGTTACCA
*
2149234 CTCCTCCATCGAGGCTCTAAAACTTTTAAAT
1 CTCCTCCATCGAGGCTCTAAAACTTATAAAT
2149265 CTCCTCCA-CTGAGGCTC-AAAA--TATAAA-
1 CTCCTCCATC-GAGGCTCTAAAACTTATAAAT
* * * * * *
2149292 CTCTTCAATCGACGCTTTACAACTTAAAAAT
1 CTCCTCCATCGAGGCTCTAAAACTTATAAAT
2149323 C-CCTCCATCGAGG
1 CTCCTCCATCGAGG
2149336 TTCCAATATC
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
27 11 0.20
28 9 0.16
30 19 0.35
31 16 0.29
ACGTcount: A:0.31, C:0.30, G:0.11, T:0.27
Consensus pattern (31 bp):
CTCCTCCATCGAGGCTCTAAAACTTATAAAT
Found at i:2149349 original size:31 final size:31
Alignment explanation
Indices: 2149314--2149376 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2149304 CGCTTTACAA
*
2149314 CTTAAAAATCCCTCCATCGAGGTTCCAATAT
1 CTTAAAAATCCCTCCATCAAGGTTCCAATAT
* * *
2149345 CTTAAGAATTCCTCCATCAAGGTTCTAATAT
1 CTTAAAAATCCCTCCATCAAGGTTCCAATAT
2149376 C
1 C
2149377 CCTCCACCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.32
Consensus pattern (31 bp):
CTTAAAAATCCCTCCATCAAGGTTCCAATAT
Found at i:2149387 original size:22 final size:22
Alignment explanation
Indices: 2149355--2149396 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2149345 CTTAAGAATT
*
2149355 CCTCCATCAAGGTTCTAATATC
1 CCTCCACCAAGGTTCTAATATC
2149377 CCTCCACCAAGGTTCTAATA
1 CCTCCACCAAGGTTCTAATA
2149397 ACTTAAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (22 bp):
CCTCCACCAAGGTTCTAATATC
Found at i:2149425 original size:53 final size:53
Alignment explanation
Indices: 2149321--2149429 Score: 139
Period size: 53 Copynumber: 2.1 Consensus size: 53
2149311 CAACTTAAAA
* * * *
2149321 ATCCCTCCATCGAGGTTCCAATATCTTAAGAATTCCTCCATCAAGGTTCTAAT
1 ATCCCTCCACCAAGGTTCCAATAACTTAAGAATTCCTCCATCAAGGCTCTAAT
* * *
2149374 ATCCCTCCACCAAGGTTCTAATAACTTAAGAATTCCTCGA-CTGAGGCTCTAAT
1 ATCCCTCCACCAAGGTTCCAATAACTTAAGAATTCCTCCATC-AAGGCTCTAAT
2149427 ATC
1 ATC
2149430 TTAAGAATCC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 1 0.02
53 47 0.98
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.30
Consensus pattern (53 bp):
ATCCCTCCACCAAGGTTCCAATAACTTAAGAATTCCTCCATCAAGGCTCTAAT
Found at i:2149495 original size:31 final size:31
Alignment explanation
Indices: 2149454--2149523 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
2149444 ATCGAGGATC
**
2149454 TAAGAATTCCTCCACCAAGGTTTGAACATCT
1 TAAGAATTCCTCCACCAAGGTTCCAACATCT
* * * *
2149485 TAAGATTTCCTCTATCGAGGTTCCAACATCT
1 TAAGAATTCCTCCACCAAGGTTCCAACATCT
2149516 TAAGAATT
1 TAAGAATT
2149524 TTTTTATTGA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (31 bp):
TAAGAATTCCTCCACCAAGGTTCCAACATCT
Found at i:2149529 original size:85 final size:84
Alignment explanation
Indices: 2149310--2149535 Score: 231
Period size: 85 Copynumber: 2.7 Consensus size: 84
2149300 TCGACGCTTT
* * * ** * * *
2149310 ACAACTTAAAAATCCCTCCATCGAGGTTCCAATATCTTAAGAATTCCTCCATCAAGGTTCTAATA
1 ACAACTTAAGAATTCCTCCATCGAGGTTCCAATATCTTAAGAATTCTTTTATCGAGGATCTAAAA
2149375 TCCCTCCACCAAGGTTCTA
66 TCCCTCCACCAAGGTTCTA
* * * * *
2149394 ATAACTTAAGAATTCCTCGA-CTGAGGCTCTAATATCTTAAGAATCCTTTTATCGAGGATCTAAG
1 ACAACTTAAGAATTCCTCCATC-GAGGTTCCAATATCTTAAGAATTCTTTTATCGAGGATCTAA-
*
2149458 AATTCCTCCACCAAGGTT-TGA
64 AATCCCTCCACCAAGGTTCT-A
* * * * * *
2149479 ACATCTTAAGATTTCCTCTATCGAGGTTCCAACATCTTAAGAATTTTTTTATTGAGG
1 ACAACTTAAGAATTCCTCCATCGAGGTTCCAATATCTTAAGAATTCTTTTATCGAGG
2149536 TTTCAATATC
Statistics
Matches: 114, Mismatches: 24, Indels: 7
0.79 0.17 0.05
Matches are distributed among these distances:
83 1 0.01
84 50 0.44
85 62 0.54
86 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (84 bp):
ACAACTTAAGAATTCCTCCATCGAGGTTCCAATATCTTAAGAATTCTTTTATCGAGGATCTAAAA
TCCCTCCACCAAGGTTCTA
Found at i:2149536 original size:31 final size:32
Alignment explanation
Indices: 2149478--2149585 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 32
2149468 CCAAGGTTTG
2149478 AACATCTTAAG-ATTTCCTCTATCGAGGTTCC
1 AACATCTTAAGAATTTCCTCTATCGAGGTTCC
* * * *
2149509 AACATCTTAAGAATTT-TTTTATTGAGGTTTC
1 AACATCTTAAGAATTTCCTCTATCGAGGTTCC
* * * *
2149540 AATATCTTAAGAA-TCCCTCTATCGAGGATCT
1 AACATCTTAAGAATTTCCTCTATCGAGGTTCC
*
2149571 AATATCTTAAGAATT
1 AACATCTTAAGAATT
2149586 CCTTCACCGA
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
30 1 0.02
31 56 0.90
32 5 0.08
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (32 bp):
AACATCTTAAGAATTTCCTCTATCGAGGTTCC
Found at i:2149598 original size:62 final size:62
Alignment explanation
Indices: 2149454--2149599 Score: 166
Period size: 62 Copynumber: 2.4 Consensus size: 62
2149444 ATCGAGGATC
* * * * * *
2149454 TAAGAATTCCTCCACCAAGGTTTGAACATCTTAAGATTTCCTCTATCGAGGTTCCAACATCT
1 TAAGAATTCCTTCACCGAGGTTTCAACATCTTAAGAATCCCTCTATCGAGGATCCAACATCT
** * ** * * *
2149516 TAAGAATTTTTTTATTGAGGTTTCAATATCTTAAGAATCCCTCTATCGAGGATCTAATATCT
1 TAAGAATTCCTTCACCGAGGTTTCAACATCTTAAGAATCCCTCTATCGAGGATCCAACATCT
2149578 TAAGAATTCCTTCACCGAGGTT
1 TAAGAATTCCTTCACCGAGGTT
2149600 ACAAAAAGAA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (62 bp):
TAAGAATTCCTTCACCGAGGTTTCAACATCTTAAGAATCCCTCTATCGAGGATCCAACATCT
Found at i:2155527 original size:26 final size:27
Alignment explanation
Indices: 2155498--2155553 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
2155488 GTAATTGTAG
*
2155498 GGTTTAG-GTACCCTGCGTCTTAATAA
1 GGTTTAGAGTACCCTACGTCTTAATAA
* * *
2155524 GG-TTCGAGTACCCTACTTGTTAATAA
1 GGTTTAGAGTACCCTACGTCTTAATAA
2155550 GGTT
1 GGTT
2155554 CGAGTTTGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
25 3 0.12
26 20 0.83
27 1 0.04
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (27 bp):
GGTTTAGAGTACCCTACGTCTTAATAA
Found at i:2160385 original size:3 final size:3
Alignment explanation
Indices: 2160377--2160424 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2160367 NNNNNNNNNN
2160377 TAA TAA TAA TAA 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 TAA TAA TAA TAA
2160425 GCCATTGTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2172124 original size:30 final size:29
Alignment explanation
Indices: 2172086--2172147 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
2172076 ATTAGTTTTA
*
2172086 AAATTTTATTTGAGTCAAAATAAAAGTAT
1 AAATTTTATTTAAGTCAAAATAAAAGTAT
* *
2172115 AAATGTTTATTTAATTTAAAATAAAAGTAT
1 AAAT-TTTATTTAAGTCAAAATAAAAGTAT
2172145 AAA
1 AAA
2172148 AAGTTGATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.39
Consensus pattern (29 bp):
AAATTTTATTTAAGTCAAAATAAAAGTAT
Found at i:2178335 original size:16 final size:15
Alignment explanation
Indices: 2178310--2178360 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
2178300 GCTACTTCCT
*
2178310 TTTTCTTTTTATTCAA
1 TTTTCATTTTATTC-A
*
2178326 TTTTCATTTTTTTCA
1 TTTTCATTTTATTCA
2178341 -TTTCACTTTTTATTCA
1 TTTTCA--TTTTATTCA
2178357 TTTT
1 TTTT
2178361 TTGCAAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 5 0.17
15 1 0.03
16 20 0.69
17 3 0.10
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTCATTTTATTCA
Found at i:2188909 original size:22 final size:23
Alignment explanation
Indices: 2188881--2188924 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2188871 TATGAGCCAG
2188881 TCACGCAATA-CCTATCAACTAA
1 TCACGCAATATCCTATCAACTAA
2188903 TCACGCAATATCCTATCAACTA
1 TCACGCAATATCCTATCAACTA
2188925 GTCATGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.39, C:0.32, G:0.05, T:0.25
Consensus pattern (23 bp):
TCACGCAATATCCTATCAACTAA
Found at i:2188973 original size:44 final size:43
Alignment explanation
Indices: 2188920--2189003 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
2188910 ATATCCTATC
* **
2188920 AACTAGTCATGTAATGTCTAAAAATCAATCACACAATGCCTAAA
1 AACTAGTCATGCAATACCT-AAAATCAATCACACAATGCCTAAA
* *
2188964 AACTAGTCATGCAATACCTAAAATTAATCACGCAATGCCT
1 AACTAGTCATGCAATACCTAAAATCAATCACACAATGCCT
2189004 TACAAACCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 19 0.54
44 16 0.46
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.25
Consensus pattern (43 bp):
AACTAGTCATGCAATACCTAAAATCAATCACACAATGCCTAAA
Found at i:2188978 original size:22 final size:22
Alignment explanation
Indices: 2188881--2189003 Score: 79
Period size: 22 Copynumber: 5.6 Consensus size: 22
2188871 TATGAGCCAG
* **
2188881 TCACGCAATACCTATCAACTAA
1 TCACGCAATGCCTAAAAACTAA
* ** *
2188903 TCACGCAATATCCTATCAACTAG
1 TCACGCAAT-GCCTAAAAACTAA
* * *
2188926 TCATGTAATGTCTAAAAA-TCAA
1 TCACGCAATGCCTAAAAACT-AA
* *
2188948 TCACACAATGCCTAAAAACTAG
1 TCACGCAATGCCTAAAAACTAA
* * *
2188970 TCATGCAATACCT-AAAATTAA
1 TCACGCAATGCCTAAAAACTAA
2188991 TCACGCAATGCCT
1 TCACGCAATGCCT
2189004 TACAAACCAA
Statistics
Matches: 77, Mismatches: 21, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
21 18 0.23
22 40 0.52
23 19 0.25
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (22 bp):
TCACGCAATGCCTAAAAACTAA
Found at i:2189104 original size:23 final size:21
Alignment explanation
Indices: 2189053--2189112 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 21
2189043 ATACCTAAGT
*
2189053 TACGTAATACCTAAAAGTCAG
1 TACGTAATGCCTAAAAGTCAG
*
2189074 TACATAATGCCTTACAAAGT-AG
1 TACGTAATGCC-TA-AAAGTCAG
*
2189096 TCACGTAATGACTAAAA
1 T-ACGTAATGCCTAAAA
2189113 ATTAGTCACA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 12 0.38
22 7 0.22
23 13 0.41
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.25
Consensus pattern (21 bp):
TACGTAATGCCTAAAAGTCAG
Found at i:2189119 original size:22 final size:22
Alignment explanation
Indices: 2189093--2189181 Score: 72
Period size: 22 Copynumber: 4.0 Consensus size: 22
2189083 CCTTACAAAG
2189093 TAGTCACGTAATGACTAAAAAT
1 TAGTCACGTAATGACTAAAAAT
** * *
2189115 TAGTCACACAATGCCTATAAAT
1 TAGTCACGTAATGACTAAAAAT
* * ** *
2189137 CAGTCATGTAAT-ACTCTACCAAC
1 TAGTCACGTAATGA--CTAAAAAT
2189160 TAGTCACGTAATGACTAAAAAT
1 TAGTCACGTAATGACTAAAAAT
2189182 CAGTAACACA
Statistics
Matches: 47, Mismatches: 17, Indels: 6
0.67 0.24 0.09
Matches are distributed among these distances:
22 31 0.66
23 15 0.32
24 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (22 bp):
TAGTCACGTAATGACTAAAAAT
Found at i:2189352 original size:81 final size:79
Alignment explanation
Indices: 2189207--2189546 Score: 353
Period size: 81 Copynumber: 4.2 Consensus size: 79
2189197 TAAAAATTGA
* * * * *
2189207 TCACGCAATCCCCTATCAACCAATCATGCAAACCTTAAGTCACGCAATCCCTAAAACCCTTAAAC
1 TCACGC-ATGCCCTATCAACTAGTCATGCAAACC-TAAGTCATGCAATGCCTAAAACCC-TAAAC
*
2189272 CCAATGTCTAAAACAAG
63 CCAATGACTAAAACAAG
* * * *
2189289 TCACGCATACCCTATCAACTAGTCACGCAAACACTAAGTCATGAAATGCCAAAAATCCCTAAACC
1 TCACGCATGCCCTATCAACTAGTCATGCAAAC-CTAAGTCATGCAATGCCTAAAA-CCCTAAACC
*
2189354 CATTGACTAAAACCAA-
64 CAATGACTAAAA-CAAG
* *
2189370 TCACGCATGCCCTATCAACTAGTCATGTAAACCCTAAGTCATGCGATGCCTAAAACCCCTAAACC
1 TCACGCATGCCCTATCAACTAGTCATGCAAA-CCTAAGTCATGCAATGCCTAAAA-CCCTAAACC
* *
2189435 TAAT-ACTTAAAACTAG
64 CAATGAC-TAAAACAAG
* * * *
2189451 TCACACATGCCTTATCAACTAGTCATGCAAATCTTAAGTCATGCAATGCCTAAAACCTTTAAACC
1 TCACGCATGCCCTATCAACTAGTCATGCAAA-CCTAAGTCATGCAATGCCTAAAACC-CTAAACC
* *
2189516 TAAT-ACTTAAAACCAG
64 CAATGAC-TAAAACAAG
*
2189532 TCATGCATGCCCTAT
1 TCACGCATGCCCTAT
2189547 TAATGCTCGA
Statistics
Matches: 220, Mismatches: 31, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
80 6 0.03
81 200 0.91
82 14 0.06
ACGTcount: A:0.38, C:0.30, G:0.09, T:0.23
Consensus pattern (79 bp):
TCACGCATGCCCTATCAACTAGTCATGCAAACCTAAGTCATGCAATGCCTAAAACCCTAAACCCA
ATGACTAAAACAAG
Found at i:2189469 original size:162 final size:162
Alignment explanation
Indices: 2189206--2189546 Score: 393
Period size: 162 Copynumber: 2.1 Consensus size: 162
2189196 TTAAAAATTG
* * *
2189206 ATCACGCAATCCCCTATCAACCAATCATGCAAACCTTAAGTCACGCAATCCCTAAAACCCTTAAA
1 ATCACGC-ATGCCCTATCAACCAATCATGCAAACCCTAAGTCACGCAATCCCTAAAACCCCTAAA
* *
2189271 CCCAATGTCTAAAACAAGTCACGCATACCCTATCAACTAGTCACGCAAA-CACTAAGTCATGAAA
65 CCCAATCTCTAAAACAAGTCACACATACCCTATCAACTAGTCACGCAAATC-CTAAGTCATGAAA
*
2189335 TGCCAAAAATCC-CTAAACCCATTGAC-TAAAACCA
129 TGCCAAAAA-CCTCTAAACCCAAT-ACTTAAAACCA
* * * * * *
2189369 ATCACGCATGCCCTATCAACTAGTCATGTAAACCCTAAGTCATGCGATGCCTAAAACCCCTAAAC
1 ATCACGCATGCCCTATCAACCAATCATGCAAACCCTAAGTCACGCAATCCCTAAAACCCCTAAAC
* * * * * * *
2189434 CTAATACT-TAAAACTAGTCACACATGCCTTATCAACTAGTCATGCAAATCTTAAGTCATGCAAT
66 CCAAT-CTCTAAAACAAGTCACACATACCCTATCAACTAGTCACGCAAATCCTAAGTCATGAAAT
* * *
2189498 GCCTAAAACCTTTAAACCTAATACTTAAAACCA
130 GCCAAAAACCTCTAAACCCAATACTTAAAACCA
* *
2189531 GTCATGCATGCCCTAT
1 ATCACGCATGCCCTAT
2189547 TAATGCTCGA
Statistics
Matches: 150, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
161 4 0.03
162 137 0.91
163 9 0.06
ACGTcount: A:0.38, C:0.30, G:0.09, T:0.23
Consensus pattern (162 bp):
ATCACGCATGCCCTATCAACCAATCATGCAAACCCTAAGTCACGCAATCCCTAAAACCCCTAAAC
CCAATCTCTAAAACAAGTCACACATACCCTATCAACTAGTCACGCAAATCCTAAGTCATGAAATG
CCAAAAACCTCTAAACCCAATACTTAAAACCA
Found at i:2194843 original size:143 final size:143
Alignment explanation
Indices: 2194585--2194871 Score: 459
Period size: 143 Copynumber: 2.0 Consensus size: 143
2194575 GCTTTCAATC
*
2194585 TCTTATGTTGTACGATAGGAGAAAGCCTTGTAACAACATAGCATTAATATGTGCTTCTTCATCTG
1 TCTTATGTTGTACGATAGGAGAAAGCCTTGTAACAACATAGCATTAATATGTGCTTCTTCATCTC
* * *
2194650 GGAAACCATATGAAGTCAAGCACGCTGCTCATTCCCATACAATTACAGAAGTCAAGTACGTGAGC
66 AGAAACCATATGAAGTCAAGCACGCTACTCATTCCCATACAATTAAAGAAGTCAAGTACGTGAGC
2194715 GTTTAAGCTAATT
131 GTTTAAGCTAATT
* *
2194728 TCTTATGTTTTGCGATAGGAGAAAGCCTTGTAACAACATAGCATTAATA-GTTGCTTCTTCATCT
1 TCTTATGTTGTACGATAGGAGAAAGCCTTGTAACAACATAGCATTAATATG-TGCTTCTTCATCT
* * *
2194792 CAGAAACCATATGAAGTCAAGGACGTTACTCATTCCCATACAATTAAAGAAGTCAAGTATGTGAG
65 CAGAAACCATATGAAGTCAAGCACGCTACTCATTCCCATACAATTAAAGAAGTCAAGTACGTGAG
* *
2194857 TGTTTAAGGTAATT
130 CGTTTAAGCTAATT
2194871 T
1 T
2194872 TCATGAAAAT
Statistics
Matches: 132, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
142 1 0.01
143 131 0.99
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (143 bp):
TCTTATGTTGTACGATAGGAGAAAGCCTTGTAACAACATAGCATTAATATGTGCTTCTTCATCTC
AGAAACCATATGAAGTCAAGCACGCTACTCATTCCCATACAATTAAAGAAGTCAAGTACGTGAGC
GTTTAAGCTAATT
Found at i:2203508 original size:15 final size:15
Alignment explanation
Indices: 2203488--2203536 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
2203478 ATCTAATATG
*
2203488 ATATTTTAATAAATT
1 ATATTTTAATAAATA
*
2203503 ATATTTT--TAAGTA
1 ATATTTTAATAAATA
*
2203516 ATATTTTAATTAATA
1 ATATTTTAATAAATA
2203531 ATATTT
1 ATATTT
2203537 AATTATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 11 0.39
15 17 0.61
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
ATATTTTAATAAATA
Found at i:2206666 original size:4 final size:4
Alignment explanation
Indices: 2206659--2206687 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2206649 TATATATATA
2206659 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
2206688 TCCCTTGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:2208258 original size:25 final size:25
Alignment explanation
Indices: 2208224--2208276 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
2208214 TTGAATGTTA
2208224 AGATAGAAGCTATCAATGCAATATG
1 AGATAGAAGCTATCAATGCAATATG
2208249 AGATAGAAGCTATCAATGCAATATG
1 AGATAGAAGCTATCAATGCAATATG
2208274 AGA
1 AGA
2208277 GTAAAGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (25 bp):
AGATAGAAGCTATCAATGCAATATG
Found at i:2208408 original size:25 final size:25
Alignment explanation
Indices: 2208379--2208433 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
2208369 ACAATGAGAA
2208379 GATAAAAAAGTGAGAGAGAGAATTT
1 GATAAAAAAGTGAGAGAGAGAATTT
2208404 GATAAAAAAGTGAGAGAGAGAATTT
1 GATAAAAAAGTGAGAGAGAGAATTT
2208429 GATAA
1 GATAA
2208434 TTTTGAGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (25 bp):
GATAAAAAAGTGAGAGAGAGAATTT
Found at i:2210786 original size:16 final size:17
Alignment explanation
Indices: 2210756--2210796 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2210746 TAAATAATCA
*
2210756 AAATC-AAATAATTAATT
1 AAATCTAAA-AATTAACT
2210773 AAA-CTAAAAATTAACT
1 AAATCTAAAAATTAACT
2210789 AAATCTAA
1 AAATCTAA
2210797 TTAACAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATCTAAAAATTAACT
Found at i:2211928 original size:20 final size:20
Alignment explanation
Indices: 2211899--2211966 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
2211889 CAAAAACAAA
* *
2211899 AAAATGAACATAAATAACAT
1 AAAATAAACATTAATAACAT
* *
2211919 AAAACT-AACATTATTAACTT
1 AAAA-TAAACATTAATAACAT
2211939 AAAATAAACATTAA-AACAT
1 AAAATAAACATTAATAACAT
*
2211958 AAATTAAAC
1 AAAATAAAC
2211967 TAAACTAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
19 13 0.32
20 26 0.65
21 1 0.03
ACGTcount: A:0.62, C:0.12, G:0.01, T:0.25
Consensus pattern (20 bp):
AAAATAAACATTAATAACAT
Found at i:2213467 original size:26 final size:25
Alignment explanation
Indices: 2213424--2213479 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 25
2213414 TTAGTTTGCT
2213424 TTTATTAATTTAATTTAATTTTACA
1 TTTATTAATTTAATTTAATTTTACA
*
2213449 TTTATTTATCTTAATTTAATTTT--A
1 TTTATTAAT-TTAATTTAATTTTACA
2213473 TTTATTA
1 TTTATTA
2213480 GTTTTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 7 0.25
25 8 0.29
26 13 0.46
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTATTAATTTAATTTAATTTTACA
Found at i:2219476 original size:21 final size:21
Alignment explanation
Indices: 2219437--2219477 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2219427 TTAAATTAAT
*
2219437 TTAATTTAATATTTGTTTATC
1 TTAATTTAATATTTATTTATC
2219458 TTAATTTAAT-TATTATTTAT
1 TTAATTTAATAT-TTATTTAT
2219478 TAGTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTAATTTAATATTTATTTATC
Found at i:2220208 original size:104 final size:104
Alignment explanation
Indices: 2220028--2220251 Score: 439
Period size: 104 Copynumber: 2.2 Consensus size: 104
2220018 TGGCTAAACT
2220028 TTATATGTTTTTATTTTTTTTTATAATTAGGGGAGGGGGGATTCGAACCTTGCCCTTTAAGCAGA
1 TTATATGTTTTTATTTTTTTTTATAATTAGGGGAGGGGGGATTCGAACCTTGCCCTTTAAGCAGA
2220093 GGGACAATGCACCAACTAATGAGCTAAATGCTCAGGTGC
66 GGGACAATGCACCAACTAATGAGCTAAATGCTCAGGTGC
*
2220132 TTATATGTTTTTATTTTTTTTTATAATTAGGGGAGGGGGGATTCGAACCTTGCTCTTTAAGCAGA
1 TTATATGTTTTTATTTTTTTTTATAATTAGGGGAGGGGGGATTCGAACCTTGCCCTTTAAGCAGA
2220197 GGGACAATGCACCAACTAATGAGCTAAATGCTCAGGTGC
66 GGGACAATGCACCAACTAATGAGCTAAATGCTCAGGTGC
2220236 TTATATGTTTTTATTT
1 TTATATGTTTTTATTT
2220252 ACTTTTGCAA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 119 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (104 bp):
TTATATGTTTTTATTTTTTTTTATAATTAGGGGAGGGGGGATTCGAACCTTGCCCTTTAAGCAGA
GGGACAATGCACCAACTAATGAGCTAAATGCTCAGGTGC
Found at i:2220813 original size:19 final size:19
Alignment explanation
Indices: 2220791--2220831 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2220781 TTAATTAGAT
2220791 TTAATTA-GTTTAGATTTAA
1 TTAATTATGTTTAG-TTTAA
*
2220810 TTAATTATTTTTAGTTTAA
1 TTAATTATGTTTAGTTTAA
2220829 TTA
1 TTA
2220832 GTATTCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (19 bp):
TTAATTATGTTTAGTTTAA
Found at i:2229656 original size:35 final size:36
Alignment explanation
Indices: 2229617--2229705 Score: 108
Period size: 36 Copynumber: 2.5 Consensus size: 36
2229607 GTCTTGATAG
*
2229617 AGGTTACGCTTGATCCT-GCAAAAAGCATGTTGTGA
1 AGGTTACGCTTGATCCTAGCAAAAAGCATGTTGTAA
* * * *
2229652 AGGTTACGCTTAATCTTAGTAAAAGGCATGTTGTAA
1 AGGTTACGCTTGATCCTAGCAAAAAGCATGTTGTAA
* *
2229688 AGGTTATGTTTGATCCTA
1 AGGTTACGCTTGATCCTA
2229706 CTGAAAAGGC
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
35 15 0.34
36 29 0.66
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (36 bp):
AGGTTACGCTTGATCCTAGCAAAAAGCATGTTGTAA
Found at i:2232353 original size:21 final size:21
Alignment explanation
Indices: 2232328--2232367 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2232318 TAGAGAAGGC
2232328 TTAATCGA-TTAAAGCTTGTCA
1 TTAAT-GAGTTAAAGCTTGTCA
*
2232349 TTAATTAGTTAAAGCTTGT
1 TTAATGAGTTAAAGCTTGT
2232368 TTGCACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (21 bp):
TTAATGAGTTAAAGCTTGTCA
Found at i:2237832 original size:2 final size:2
Alignment explanation
Indices: 2237825--2237849 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2237815 TTTCTTCGGT
2237825 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2237850 TTGTGCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2245283 original size:37 final size:38
Alignment explanation
Indices: 2245228--2245302 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 38
2245218 TCAATAATGT
2245228 TACCACTTACTTCTCACAAAACTTAATTGAATTTTTGG
1 TACCACTTACTTCTCACAAAACTTAATTGAATTTTTGG
* *
2245266 TACCACTTGC-TCTCACAAAACTTAGTTGAATTTTTGG
1 TACCACTTACTTCTCACAAAACTTAATTGAATTTTTGG
2245303 ATGTGTGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 26 0.74
38 9 0.26
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (38 bp):
TACCACTTACTTCTCACAAAACTTAATTGAATTTTTGG
Found at i:2248742 original size:16 final size:17
Alignment explanation
Indices: 2248712--2248751 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2248702 CATCTATTTT
*
2248712 TTTTTCTTTTCTCTTGTC
1 TTTTT-TTTTCTCTTGCC
2248730 TTTTTTTTT-TCTTGCC
1 TTTTTTTTTCTCTTGCC
2248746 TTTTTT
1 TTTTTT
2248752 ACATGGCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
17 4 0.19
18 5 0.24
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (17 bp):
TTTTTTTTTCTCTTGCC
Found at i:2251248 original size:20 final size:20
Alignment explanation
Indices: 2251223--2251287 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
2251213 AATTTATTTT
2251223 TTAATATTTTAAGTGAAATA
1 TTAATATTTTAAGTGAAATA
* ** *
2251243 TTAATATTTTTAG-G-TTTT
1 TTAATATTTTAAGTGAAATA
* *
2251261 TTAATATTTTAAATTAAATA
1 TTAATATTTTAAGTGAAATA
2251281 TTAATAT
1 TTAATAT
2251288 CCATCAAAAG
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
18 12 0.36
19 1 0.03
20 20 0.61
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (20 bp):
TTAATATTTTAAGTGAAATA
Found at i:2253687 original size:16 final size:16
Alignment explanation
Indices: 2253666--2253705 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2253656 TTTTTATAAA
*
2253666 CATATATACATGTATG
1 CATATATACATATATG
*
2253682 CATATATATATATATG
1 CATATATACATATATG
*
2253698 TATATATA
1 CATATATA
2253706 ACTTCACCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (16 bp):
CATATATACATATATG
Found at i:2257547 original size:17 final size:17
Alignment explanation
Indices: 2257516--2257548 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2257506 TTCTTGATAA
2257516 AATAAAACTTCTTATTG
1 AATAAAACTTCTTATTG
2257533 AATAATAACTT-TTATT
1 AATAA-AACTTCTTATT
2257549 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (17 bp):
AATAAAACTTCTTATTG
Found at i:2257790 original size:58 final size:58
Alignment explanation
Indices: 2257690--2257856 Score: 153
Period size: 59 Copynumber: 2.9 Consensus size: 58
2257680 TTAAGACAAC
* * * * * *
2257690 TCTTGTCTTTAATTAAG-ATAAAAATATTTTATTTTATCTAAATTGAGACAA-GTATGTTT
1 TCTTGTC-TAAATTAAGAACAAAAATATTTT-TCTTGTCTAAATTAAGACAACATAT-TTT
* *
2257749 TCTTGTCTAGATTAA-AACAAAAATATTTTTCTTGTCTTAAATTAAGGAAAACATATTTT
1 TCTTGTCTAAATTAAGAACAAAAATATTTTTCTTGTC-TAAATTAA-GACAACATATTTT
* * * *
2257808 TTTTGTCTAAATTAAGACCAAACAT-GTTTTCTTGTCTAAATTAAGACAA
1 TCTTGTCTAAATTAAGAACAAAAATATTTTTCTTGTCTAAATTAAGACAA
2257857 ACATGTTAAA
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
57 9 0.10
58 33 0.37
59 37 0.42
60 10 0.11
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (58 bp):
TCTTGTCTAAATTAAGAACAAAAATATTTTTCTTGTCTAAATTAAGACAACATATTTT
Found at i:2257805 original size:30 final size:29
Alignment explanation
Indices: 2257690--2257860 Score: 152
Period size: 29 Copynumber: 5.8 Consensus size: 29
2257680 TTAAGACAAC
* * *
2257690 TCTTGTCTTTAATTAAGATAAAAATATTTT
1 TCTTGTC-TAAATTAAGACAAACATATTTT
* * * *
2257720 ATTTTATCTAAATTGAGAC-AA-GTATGTTT
1 -TCTTGTCTAAATTAAGACAAACATAT-TTT
* * *
2257749 TCTTGTCTAGATTAAAACAAAAATATTTT
1 TCTTGTCTAAATTAAGACAAACATATTTT
2257778 TCTTGTCTTAAATTAAGGA-AAACATATTTT
1 TCTTGTC-TAAATTAA-GACAAACATATTTT
* *
2257808 TTTTGTCTAAATTAAGACCAAACAT-GTTT
1 TCTTGTCTAAATTAAGA-CAAACATATTTT
2257837 TCTTGTCTAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGACAAACAT
2257861 GTTAAAGCTG
Statistics
Matches: 115, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
28 25 0.22
29 44 0.38
30 40 0.35
31 6 0.05
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAACATATTTT
Found at i:2257839 original size:88 final size:88
Alignment explanation
Indices: 2257690--2257857 Score: 232
Period size: 88 Copynumber: 1.9 Consensus size: 88
2257680 TTAAGACAAC
* * **
2257690 TCTTGTCTTTAATTAAGATAAAAATATTTTATTTTATCTAAATTGAGACAAGTATGTTTTCTTGT
1 TCTTGTCTTAAATTAAGATAAAAATATTTTATTTTATCTAAATTAAGACAAACATGTTTTCTTGT
*
2257755 CTAGATTAAAACAAAAATATTTT
66 CTAAATTAAAACAAAAATATTTT
* *
2257778 TCTTGTCTTAAATTAAGGA-AAACATATTTT-TTTTGTCTAAATTAAGACCAAACATGTTTTCTT
1 TCTTGTCTTAAATTAA-GATAAAAATATTTTATTTTATCTAAATTAAGA-CAAACATGTTTTCTT
*
2257841 GTCTAAATTAAGACAAA
64 GTCTAAATTAAAACAAA
2257858 CATGTTAAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
87 15 0.21
88 53 0.76
89 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (88 bp):
TCTTGTCTTAAATTAAGATAAAAATATTTTATTTTATCTAAATTAAGACAAACATGTTTTCTTGT
CTAAATTAAAACAAAAATATTTT
Found at i:2265492 original size:17 final size:17
Alignment explanation
Indices: 2265472--2265504 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2265462 TTCTTGATAA
2265472 AATAA-AACTCCTTATTG
1 AATAATAACT-CTTATTG
2265489 AATAATAACTCTTATT
1 AATAATAACTCTTATT
2265505 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAATAACTCTTATTG
Found at i:2268209 original size:21 final size:22
Alignment explanation
Indices: 2268180--2268223 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2268170 AAGTGATTAA
2268180 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
2268201 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
2268223 T
1 T
2268224 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:2268896 original size:11 final size:12
Alignment explanation
Indices: 2268868--2268902 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
2268858 AAAGATTTTT
*
2268868 GAGGCATCAAGA
1 GAGGCAGCAAGA
2268880 GAGGCAGCAAG-
1 GAGGCAGCAAGA
2268891 GAGGCAGCAAGA
1 GAGGCAGCAAGA
2268903 AACTATTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.40, C:0.17, G:0.40, T:0.03
Consensus pattern (12 bp):
GAGGCAGCAAGA
Found at i:2270502 original size:29 final size:28
Alignment explanation
Indices: 2270469--2270538 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
2270459 TTTTGGACAA
*
2270469 AAAAACATATTTCGACTTAATTTAGATAAG
1 AAAAA-ATATTTC-ACTTAATTTAAATAAG
*
2270499 AAAAAATATTTTCTCTTAATTTAAATAAG
1 AAAAAATA-TTTCACTTAATTTAAATAAG
*
2270528 AAAATATATTT
1 AAAAAATATTT
2270539 TTTTAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 3 0.08
29 24 0.67
30 9 0.25
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.39
Consensus pattern (28 bp):
AAAAAATATTTCACTTAATTTAAATAAG
Found at i:2270539 original size:29 final size:28
Alignment explanation
Indices: 2270484--2270657 Score: 133
Period size: 29 Copynumber: 6.2 Consensus size: 28
2270474 CATATTTCGA
* *
2270484 CTTAATTTAGATAAGAAAAAATATTTTCT
1 CTTAATTTAAATAAGAAAATATATTTT-T
2270513 CTTAATTTAAATAAGAAAATATATTTTT
1 CTTAATTTAAATAAGAAAATATATTTTT
*
2270541 -TTAATTTAGAT-A-AAAAT-TAGTTTTAT
1 CTTAATTTAAATAAGAAAATATA-TTTT-T
* * *
2270567 CTTAATTTAAAGAAGAAAACATGTTTTT
1 CTTAATTTAAATAAGAAAATATATTTTT
* ** *
2270595 CTTAGTTTAAGGCAAG-AAATAATATTTAGT
1 CTTAATTTAA-ATAAGAAAAT-ATATTT-TT
* * * *
2270625 CTTAATCTAGACAAGAAAATATATTTGT
1 CTTAATTTAAATAAGAAAATATATTTTT
2270653 CTTAA
1 CTTAA
2270658 CCTAGACAAG
Statistics
Matches: 118, Mismatches: 17, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
24 2 0.02
25 9 0.08
26 2 0.02
27 19 0.16
28 22 0.19
29 51 0.43
30 13 0.11
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.41
Consensus pattern (28 bp):
CTTAATTTAAATAAGAAAATATATTTTT
Found at i:2270583 original size:54 final size:55
Alignment explanation
Indices: 2270470--2270657 Score: 148
Period size: 58 Copynumber: 3.3 Consensus size: 55
2270460 TTTGGACAAA
** * *
2270470 AAAACATATTTCGACTTAATTTAGATAAGAAAAAATATTTTCTCTTAATTTAAATAAG
1 AAAACATATTT-TTCTTAATTTAGAT-A-AAAAAATATTTTATCTTAATTTAAAGAAG
* *
2270528 AAAATATATTTTT-TTAATTTAGAT-AAAAATTAGTTTTATCTTAATTTAAAGAAG
1 AAAACATATTTTTCTTAATTTAGATAAAAAAATA-TTTTATCTTAATTTAAAGAAG
* * ** * * *
2270582 AAAACATGTTTTTCTTAGTTTAAGGCAAGAAATAATA-TTTAGTCTTAATCTAGACAAG
1 AAAACATATTTTTCTTAATTT-AGATAA-AAA-AATATTTTA-TCTTAATTTAAAGAAG
* *
2270640 AAAATATATTTGTCTTAA
1 AAAACATATTTTTCTTAA
2270658 CCTAGACAAG
Statistics
Matches: 104, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
53 7 0.07
54 30 0.29
55 6 0.06
56 13 0.12
57 5 0.05
58 40 0.38
59 3 0.03
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (55 bp):
AAAACATATTTTTCTTAATTTAGATAAAAAAATATTTTATCTTAATTTAAAGAAG
Found at i:2270662 original size:28 final size:28
Alignment explanation
Indices: 2270607--2270685 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
2270597 TAGTTTAAGG
*
2270607 CAAG-AAATAATATTTAGTCTTAATCTAGA
1 CAAGAAAAT-ATATTT-GTCTTAACCTAGA
2270636 CAAGAAAATATATTTGTCTTAACCTAGA
1 CAAGAAAATATATTTGTCTTAACCTAGA
* *
2270664 CAAGATAATATTTTTGTCTTAA
1 CAAGAAAATATATTTGTCTTAA
2270686 TTAAAGGTGC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 32 0.70
29 10 0.22
30 4 0.09
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (28 bp):
CAAGAAAATATATTTGTCTTAACCTAGA
Found at i:2275783 original size:14 final size:14
Alignment explanation
Indices: 2275766--2275811 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
2275756 TTTAAATTAT
2275766 TTTAAGTTAGTTAA
1 TTTAAGTTAGTTAA
* *
2275780 TTTAAGTGAGTCAA
1 TTTAAGTTAGTTAA
*
2275794 TTTAATTTTAGTTAA
1 TTTAA-GTTAGTTAA
2275809 TTT
1 TTT
2275812 TATGATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (14 bp):
TTTAAGTTAGTTAA
Found at i:2283241 original size:32 final size:33
Alignment explanation
Indices: 2283199--2283263 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
2283189 TTGTATCATA
* *
2283199 TTATATAATAATTATTTTATTTTATT-TTATTT
1 TTATAAAATAATTATATTATTTTATTATTATTT
2283231 TTATAAAATAATTATATTATTTTATTATTATTT
1 TTATAAAATAATTATATTATTTTATTATTATTT
2283264 ACTCCGTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 24 0.80
33 6 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (33 bp):
TTATAAAATAATTATATTATTTTATTATTATTT
Found at i:2283954 original size:16 final size:16
Alignment explanation
Indices: 2283920--2283955 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2283910 TATACATTCA
*
2283920 ATATGTATATATATTT
1 ATATGTATATATATGT
*
2283936 ATATGTATATATGTGT
1 ATATGTATATATATGT
2283952 ATAT
1 ATAT
2283956 ACACGTAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (16 bp):
ATATGTATATATATGT
Found at i:2286184 original size:29 final size:30
Alignment explanation
Indices: 2286150--2286207 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
2286140 TAATAAAGAT
2286150 TTATTT-GACTCAAAATAAAAATA-AAAAAC
1 TTATTTAG-CTCAAAATAAAAATATAAAAAC
2286179 TTATTTAGCTCAAAATAAAAATATAAAAA
1 TTATTTAGCTCAAAATAAAAATATAAAAA
2286208 ATTGATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (30 bp):
TTATTTAGCTCAAAATAAAAATATAAAAAC
Found at i:2286675 original size:51 final size:51
Alignment explanation
Indices: 2286615--2286723 Score: 175
Period size: 51 Copynumber: 2.1 Consensus size: 51
2286605 CTTATATTTA
* *
2286615 AATTATTAATAAA-ATTTTATGTTATAATTTAATTTTATTTCAAAAGTGATT
1 AATTTTTAATAAATA-TTTATATTATAATTTAATTTTATTTCAAAAGTGATT
2286666 AATTTTTAATAAATATTTATATTATAATTTAATTTTATTTCAAAAGTGATT
1 AATTTTTAATAAATATTTATATTATAATTTAATTTTATTTCAAAAGTGATT
*
2286717 CATTTTT
1 AATTTTT
2286724 TATTCCAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 53 0.98
52 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (51 bp):
AATTTTTAATAAATATTTATATTATAATTTAATTTTATTTCAAAAGTGATT
Found at i:2290516 original size:2 final size:2
Alignment explanation
Indices: 2290506--2290541 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2290496 TATATATTAT
* *
2290506 CA CA TA CA CA CA CG CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2290542 ATATATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.47, G:0.03, T:0.03
Consensus pattern (2 bp):
CA
Found at i:2291704 original size:18 final size:17
Alignment explanation
Indices: 2291672--2291706 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2291662 TTGTTAGGTC
*
2291672 AATTAAAATATTTTAAA
1 AATTAAAATACTTTAAA
2291689 AATTATAAATACTTTAAA
1 AATTA-AAATACTTTAAA
2291707 TACTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTAAAATACTTTAAA
Found at i:2293849 original size:7 final size:7
Alignment explanation
Indices: 2293832--2293865 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 7
2293822 AAGGGGAAAG
2293832 CTAAAATA
1 CTAAAA-A
2293840 CTAAAAA
1 CTAAAAA
2293847 CTAAAAA
1 CTAAAAA
2293854 CCTAAAAA
1 -CTAAAAA
2293862 CTAA
1 CTAA
2293866 GAAAACTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 12 0.48
8 13 0.52
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAAAAA
Found at i:2294527 original size:76 final size:76
Alignment explanation
Indices: 2294414--2294555 Score: 275
Period size: 76 Copynumber: 1.9 Consensus size: 76
2294404 AAACTAAATG
*
2294414 CTTATATTGAATCCATAGTCTAATGCTTGTTTCATTCTTATAGATGATGAACTGATATGTCATAT
1 CTTATATTGAATCCATAGGCTAATGCTTGTTTCATTCTTATAGATGATGAACTGATATGTCATAT
2294479 TAAACTACACA
66 TAAACTACACA
2294490 CTTATATTGAATCCATAGGCTAATGCTTGTTTCATTCTTATAGATGATGAACTGATATGTCATAT
1 CTTATATTGAATCCATAGGCTAATGCTTGTTTCATTCTTATAGATGATGAACTGATATGTCATAT
2294555 T
66 T
2294556 TCTATGTGTG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 65 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (76 bp):
CTTATATTGAATCCATAGGCTAATGCTTGTTTCATTCTTATAGATGATGAACTGATATGTCATAT
TAAACTACACA
Found at i:2308973 original size:36 final size:36
Alignment explanation
Indices: 2308907--2309049 Score: 133
Period size: 36 Copynumber: 4.0 Consensus size: 36
2308897 AACAAGTTGG
* **
2308907 TGTAAGGGTTATTTCTTGATCTCATTAAAAAGTAAA
1 TGTAAAGGTTATCACTTGATCTCATTAAAAAGTAAA
* * * * *
2308943 TGTAAAGGTTATCACTTGATCTCGTAAAAAAATCAT
1 TGTAAAGGTTATCACTTGATCTCATTAAAAAGTAAA
* * * * * **
2308979 TATAAAGGTTATCGCTTGATCTCGTTCAAATGGCAA
1 TGTAAAGGTTATCACTTGATCTCATTAAAAAGTAAA
* *
2309015 TGTAAAGGTTATCATTTGATCCCATTAAAAAGTAA
1 TGTAAAGGTTATCACTTGATCTCATTAAAAAGTAA
2309050 TAATCTTTTA
Statistics
Matches: 82, Mismatches: 25, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
36 82 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (36 bp):
TGTAAAGGTTATCACTTGATCTCATTAAAAAGTAAA
Found at i:2310703 original size:23 final size:23
Alignment explanation
Indices: 2310677--2310725 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
2310667 TGATTATTTT
2310677 CTTCTAAG-AATCCAAATACTCTG
1 CTTCT-AGCAATCCAAATACTCTG
*
2310700 CTTCTTGTCAATCCAAATACTCTG
1 CTTCTAG-CAATCCAAATACTCTG
2310724 CT
1 CT
2310726 ACTTGTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 1 0.04
23 5 0.22
24 17 0.74
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.35
Consensus pattern (23 bp):
CTTCTAGCAATCCAAATACTCTG
Found at i:2310713 original size:24 final size:24
Alignment explanation
Indices: 2310685--2310735 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
2310675 TTCTTCTAAG
*
2310685 AATCCAAATACTCTGCTTCTTGTC
1 AATCCAAATACTCTGCTACTTGTC
2310709 AATCCAAATACTCTGCTACTTGTC
1 AATCCAAATACTCTGCTACTTGTC
2310733 AAT
1 AAT
2310736 GCAACTTGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.35
Consensus pattern (24 bp):
AATCCAAATACTCTGCTACTTGTC
Found at i:2312076 original size:2 final size:2
Alignment explanation
Indices: 2312071--2312102 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
2312061 TATGTAGGTA
2312071 AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
2312103 ACTATTGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2318833 original size:18 final size:19
Alignment explanation
Indices: 2318794--2318840 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
2318784 TTAATAATTT
*
2318794 AATAATATTTTAATTATAA
1 AATATTATTTTAATTATAA
*
2318813 AATATTATTTT-ATTTTAA
1 AATATTATTTTAATTATAA
2318831 AATATT-TTTT
1 AATATTATTTT
2318841 TTTACCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 4 0.15
18 12 0.46
19 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATATTATTTTAATTATAA
Found at i:2319517 original size:16 final size:15
Alignment explanation
Indices: 2319494--2319532 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
2319484 AGTAACCACT
2319494 AGAGAAAGAAAGTGAAA
1 AGAGAAAG-AA-TGAAA
2319511 A-AGAAAGAATGAAA
1 AGAGAAAGAATGAAA
2319525 AGAGAAAG
1 AGAGAAAG
2319533 GGAAATTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.29
15 8 0.38
16 6 0.29
17 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (15 bp):
AGAGAAAGAATGAAA
Found at i:2324617 original size:20 final size:20
Alignment explanation
Indices: 2324589--2324627 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2324579 AAATCACTCG
* *
2324589 TCATACATTTAATCATCCTA
1 TCATACATTCAAACATCCTA
*
2324609 TCATGCATTCAAACATCCT
1 TCATACATTCAAACATCCT
2324628 TCAATTTTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (20 bp):
TCATACATTCAAACATCCTA
Found at i:2329487 original size:61 final size:61
Alignment explanation
Indices: 2329408--2329754 Score: 398
Period size: 61 Copynumber: 5.7 Consensus size: 61
2329398 ATTTAACCGA
* *
2329408 CATCTAAGATGTATAAGTCTAGTTATGTTGGCACAACAAGAGTTTAACTCCAATTAAGTGG
1 CATCCAAGATGTATAAGTCTAGTTATGTTGGCACAAAAAGAGTTTAACTCCAATTAAGTGG
* * * *
2329469 CATCCAAGATGTAAAAGTCTAGTTATGTTGGCACAAAAAGAGGTTAAGC-CCAATTAACTGA
1 CATCCAAGATGTATAAGTCTAGTTATGTTGGCACAAAAAGAGTTTAA-CTCCAATTAAGTGG
* ** * * * * *
2329530 CATCCAAGATGTATAGGT-TCAGTTACATTGACACCAAAAGAGTTTAAGC-CTAATTTAACTAG
1 CATCCAAGATGTATAAGTCT-AGTTATGTTGGCACAAAAAGAGTTTAA-CTCCAA-TTAAGTGG
* * * *
2329592 CATCCAAGATGCATAAGTCCAGTTATGTTGGCACAAAAAGAGTTTAAGTCCAGTT-AGCTGG
1 CATCCAAGATGTATAAGTCTAGTTATGTTGGCACAAAAAGAGTTTAACTCCAATTAAG-TGG
* * * *
2329653 CATCCAAGACGTATAAGTCCAGTTATGTTGGCACAAAAGGAGTTTAAGTCCAATT-AGCTGG
1 CATCCAAGATGTATAAGTCTAGTTATGTTGGCACAAAAAGAGTTTAACTCCAATTAAG-TGG
*
2329714 CATCCAAGATGTACAAGTCTAGTTATGTTGGCACAAAAAGA
1 CATCCAAGATGTATAAGTCTAGTTATGTTGGCACAAAAAGA
2329755 TGTATAAGTC
Statistics
Matches: 244, Mismatches: 36, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
60 2 0.01
61 194 0.80
62 48 0.20
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (61 bp):
CATCCAAGATGTATAAGTCTAGTTATGTTGGCACAAAAAGAGTTTAACTCCAATTAAGTGG
Found at i:2329501 original size:31 final size:31
Alignment explanation
Indices: 2329408--2329774 Score: 111
Period size: 31 Copynumber: 11.9 Consensus size: 31
2329398 ATTTAACCGA
*
2329408 CATCTAAGATGTATAAGTCTAGTTATGTTGG
1 CATCCAAGATGTATAAGTCTAGTTATGTTGG
* * * * *
2329439 CA-CAACAAGA-GTTTAACTCCAATTAAG-TGG
1 CATC--CAAGATGTATAAGTCTAGTTATGTTGG
*
2329469 CATCCAAGATGTAAAAGTCTAGTTATGTTGG
1 CATCCAAGATGTATAAGTCTAGTTATGTTGG
* * * * * ** *
2329500 CA-CAAAAAGAGGT-TAAGCCCAATTA-ACTGA
1 CATC--CAAGATGTATAAGTCTAGTTATGTTGG
* ** *
2329530 CATCCAAGATGTATAGGT-TCAGTTACATTGA
1 CATCCAAGATGTATAAGTCT-AGTTATGTTGG
* * * ** *
2329561 CA-CCAAAAGA-GTTTAAGCCTAATTTAACTAG-
1 CATCC--AAGATGTATAAGTCT-AGTTATGTTGG
* *
2329592 CATCCAAGATGCATAAGTCCAGTTATGTTGG
1 CATCCAAGATGTATAAGTCTAGTTATGTTGG
* * * *
2329623 CA-CAAAAAGA-GTTTAAGTCCAGTTA-GCTGG
1 CATC--CAAGATGTATAAGTCTAGTTATGTTGG
* *
2329653 CATCCAAGACGTATAAGTCCAGTTATGTTGG
1 CATCCAAGATGTATAAGTCTAGTTATGTTGG
* * * * *
2329684 CA-CAAAAGGA-GTTTAAGTCCAATTA-GCTGG
1 CATC-CAA-GATGTATAAGTCTAGTTATGTTGG
*
2329714 CATCCAAGATGTACAAGTCTAGTTATGTTGG
1 CATCCAAGATGTATAAGTCTAGTTATGTTGG
* * *
2329745 CA-CAAAAAGATGTATAAGTCCAGTTTTGTT
1 CATC--CAAGATGTATAAGTCTAGTTATGTT
2329775 AGCACAAAAA
Statistics
Matches: 242, Mismatches: 65, Indels: 57
0.66 0.18 0.16
Matches are distributed among these distances:
29 17 0.07
30 83 0.34
31 92 0.38
32 50 0.21
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (31 bp):
CATCCAAGATGTATAAGTCTAGTTATGTTGG
Found at i:2329618 original size:123 final size:120
Alignment explanation
Indices: 2329389--2329754 Score: 455
Period size: 123 Copynumber: 3.0 Consensus size: 120
2329379 ACGAGAAGAT
* *
2329389 TTAAGCCCAATTTAACCGACATCTAAGATGTATAAG-TCTAGTTATGTTGGCACAACAAGAGTTT
1 TTAAGCCCAA-TTAACTGACATCCAAGATGTATAAGTTC-AGTTATGTTGGCACAA-AAGAGTTT
* *
2329453 AACTCCAATTAAGTGGCATCCAAGATGTAAAAGTCTAGTTATGTTGGCACAAAAAGAGG
63 AA-GCCAATTAACTGGCATCCAAGATGTAAAAGTCTAGTTATGTTGGCACAAAAAGAGG
* ** *
2329512 TTAAGCCCAATTAACTGACATCCAAGATGTATAGGTTCAGTTACATTGACACCAAAAGAGTTTAA
1 TTAAGCCCAATTAACTGACATCCAAGATGTATAAGTTCAGTTATGTTGGCA-CAAAAGAGTTTAA
* * * * *
2329577 GCCTAATTTAACTAGCATCCAAGATGCATAAGTCCAGTTATGTTGGCACAAAAAGAGT
65 GCC-AA-TTAACTGGCATCCAAGATGTAAAAGTCTAGTTATGTTGGCACAAAAAGAGG
* * * * * *
2329635 TTAAGTCCAGTTAGCTGGCATCCAAGACGTATAAGTCCAGTTATGTTGGCACAAAAGGAGTTTAA
1 TTAAGCCCAATTAACTGACATCCAAGATGTATAAGTTCAGTTATGTTGGCACAAAA-GAGTTTAA
* *
2329700 GTCCAATTAGCTGGCATCCAAGATGTACAAGTCTAGTTATGTTGGCACAAAAAGA
65 G-CCAATTAACTGGCATCCAAGATGTAAAAGTCTAGTTATGTTGGCACAAAAAGA
2329755 TGTATAAGTC
Statistics
Matches: 209, Mismatches: 28, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
121 2 0.01
122 93 0.44
123 112 0.54
124 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (120 bp):
TTAAGCCCAATTAACTGACATCCAAGATGTATAAGTTCAGTTATGTTGGCACAAAAGAGTTTAAG
CCAATTAACTGGCATCCAAGATGTAAAAGTCTAGTTATGTTGGCACAAAAAGAGG
Found at i:2329708 original size:184 final size:183
Alignment explanation
Indices: 2329384--2329726 Score: 501
Period size: 184 Copynumber: 1.9 Consensus size: 183
2329374 TAAACACGAG
* * * * *
2329384 AAGATTTAAGCCCAATTTAACCGACATCTAAGATGTATAAGTCTAGTTATGTTGGCACAACAAGA
1 AAGATTTAAGCCCAATTTAACAGACATCCAAGATGCATAAGTCCAGTTATGTTGGCACAAAAAGA
* *
2329449 GTTTAACTCCAATTAAGTGGCATCCAAGATGTAAAAGTCTAGTTATGTTGGCACAAAAAGAGGTT
66 GTTTAACTCCAATTAAGTGGCATCCAAGACGTAAAAGTCCAGTTATGTTGGCACAAAAAGAGGTT
2329514 AAGCCCAATTAACTGACATCCAAGATGTATAGGTTCAGTTACATTGACACCAA
131 AAGCCCAATTAACTGACATCCAAGATGTATAGGTTCAGTTACATTGACACCAA
*
2329567 AAGAGTTTAAGCCTAATTTAACTAG-CATCCAAGATGCATAAGTCCAGTTATGTTGGCACAAAAA
1 AAGA-TTTAAGCCCAATTTAAC-AGACATCCAAGATGCATAAGTCCAGTTATGTTGGCACAAAAA
* * * *
2329631 GAGTTTAAGTCCAGTT-AGCTGGCATCCAAGACGTATAAGTCCAGTTATGTTGGCACAAAAGGAG
64 GAGTTTAACTCCAATTAAG-TGGCATCCAAGACGTAAAAGTCCAGTTATGTTGGCACAAAAAGAG
* * * *
2329695 TTTAAGTCCAATTAGCTGGCATCCAAGATGTA
128 GTTAAGCCCAATTAACTGACATCCAAGATGTA
2329727 CAAGTCTAGT
Statistics
Matches: 141, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
183 6 0.04
184 134 0.95
185 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (183 bp):
AAGATTTAAGCCCAATTTAACAGACATCCAAGATGCATAAGTCCAGTTATGTTGGCACAAAAAGA
GTTTAACTCCAATTAAGTGGCATCCAAGACGTAAAAGTCCAGTTATGTTGGCACAAAAAGAGGTT
AAGCCCAATTAACTGACATCCAAGATGTATAGGTTCAGTTACATTGACACCAA
Found at i:2329780 original size:93 final size:94
Alignment explanation
Indices: 2329658--2329848 Score: 258
Period size: 94 Copynumber: 2.0 Consensus size: 94
2329648 GCTGGCATCC
* * * *
2329658 AAGACGTATAAGTCCAGTTATGTTGGCACAAAAGGAGTTT-AAGTCCAATTAGCTGGCATCCAAG
1 AAGACGTATAAGTCCAGTTATGTTAGCACAAAAAGAGTTTAAAATCCAATTAGCTGGCATCAAAG
* *
2329722 ATGTACAAGTCTAGTTATGTTGGCACAAA
66 ATGTACAACTCTAGTTACGTTGGCACAAA
* * * *
2329751 AAGATGTATAAGTCCAGTTTTGTTAGCACAAAAAGAGTTTAAAATCTAATTAGCTGGCATCAAAT
1 AAGACGTATAAGTCCAGTTATGTTAGCACAAAAAGAGTTTAAAATCCAATTAGCTGGCATCAAAG
* * *
2329816 ATGTATAACTTTAGTTACGTTGGCACAGA
66 ATGTACAACTCTAGTTACGTTGGCACAAA
2329845 AAGA
1 AAGA
2329849 ATTTAGGCCT
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
93 36 0.43
94 48 0.57
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (94 bp):
AAGACGTATAAGTCCAGTTATGTTAGCACAAAAAGAGTTTAAAATCCAATTAGCTGGCATCAAAG
ATGTACAACTCTAGTTACGTTGGCACAAA
Found at i:2345536 original size:18 final size:18
Alignment explanation
Indices: 2345513--2345547 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2345503 CTAAAAGATA
2345513 TTTA-TTAATAAAATTTTT
1 TTTATTTAAT-AAATTTTT
2345531 TTTATTTAATAAATTTT
1 TTTATTTAATAAATTTT
2345548 AAATTGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATTTAATAAATTTTT
Found at i:2346033 original size:90 final size:88
Alignment explanation
Indices: 2345860--2346023 Score: 301
Period size: 90 Copynumber: 1.8 Consensus size: 88
2345850 TTCTCTTCTT
2345860 TAAATATAAAAAAAAACAATATTTGACTCTCTCACATCATGCATGGTAGAATTATAATATAATAC
1 TAAATATAAAAAAAAACAATATTTGACTCTCTCACATCATGCATGGTAGAATTATAATATAATAC
2345925 TATTTAAATTAAAAGATTCATCC
66 TATTTAAATTAAAAGATTCATCC
*
2345948 TAAATATATTAAAAAAAACAATATTTGACTCTCTCACATCATGTATGGTAGAATTATAATATAAT
1 TAAATATA--AAAAAAAACAATATTTGACTCTCTCACATCATGCATGGTAGAATTATAATATAAT
2346013 ACTATTTAAAT
64 ACTATTTAAAT
2346024 GTAAGGATTC
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
88 8 0.11
90 65 0.89
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (88 bp):
TAAATATAAAAAAAAACAATATTTGACTCTCTCACATCATGCATGGTAGAATTATAATATAATAC
TATTTAAATTAAAAGATTCATCC
Found at i:2351328 original size:18 final size:18
Alignment explanation
Indices: 2351307--2351350 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2351297 CACGGCCTTC
*
2351307 TTTCTTCCTCTATTTCTT
1 TTTCTTCCTCTATCTCTT
**
2351325 TTTCTTTTTCTATCTCTT
1 TTTCTTCCTCTATCTCTT
2351343 TCTTCTTC
1 T-TTCTTC
2351351 TTTCTTCCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTCTTCCTCTATCTCTT
Found at i:2351329 original size:22 final size:22
Alignment explanation
Indices: 2351303--2351360 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
2351293 TCTTCACGGC
2351303 CTTCTTTCTTCCTCTATTTCTT
1 CTTCTTTCTTCCTCTATTTCTT
* * *
2351325 TTTCTTT-TTCTATCTCTTTCTT
1 CTTCTTTCTTC-CTCTATTTCTT
2351347 CTTCTTTCTTCCTC
1 CTTCTTTCTTCCTC
2351361 GCCAGCATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 3 0.10
22 23 0.79
23 3 0.10
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (22 bp):
CTTCTTTCTTCCTCTATTTCTT
Found at i:2351463 original size:21 final size:19
Alignment explanation
Indices: 2351429--2351469 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
2351419 TCTCTCTTCC
*
2351429 CCTTTCTTTTTCAAATTTT
1 CCTTTCTTTTTCAAACTTT
2351448 CCTTTCTTTTTCTCAAACTTT
1 CCTTTC-TTTT-TCAAACTTT
2351469 C
1 C
2351470 AGCCTTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
21 9 0.47
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.59
Consensus pattern (19 bp):
CCTTTCTTTTTCAAACTTT
Found at i:2381730 original size:2 final size:2
Alignment explanation
Indices: 2381713--2381747 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2381703 TAATTTGATG
* *
2381713 AT AT AT AC AT AC 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 AT A
2381748 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2382570 original size:12 final size:12
Alignment explanation
Indices: 2382540--2382575 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2382530 ATTTAGTGAA
* *
2382540 CTCTCTATCTCT
1 CTCTCTTTCTGT
2382552 CTCTCTTTCTGT
1 CTCTCTTTCTGT
2382564 CTCTCTTTCTGT
1 CTCTCTTTCTGT
2382576 TTACATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.03, C:0.36, G:0.06, T:0.56
Consensus pattern (12 bp):
CTCTCTTTCTGT
Found at i:2409320 original size:48 final size:48
Alignment explanation
Indices: 2409249--2409344 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
2409239 CAAAATGGAA
* *
2409249 CTTAGAAGAAGAAACAGAATCGTAACATCCATTTTCTGGTA-AATTGAG
1 CTTAGAAGAAGAAACAGAATCGTAACAACCATATTCTGG-AGAATTGAG
*
2409297 CTTAGAAGAAGGAACAGAATCGTAACAACCATATTCTGGAGAATTGAG
1 CTTAGAAGAAGAAACAGAATCGTAACAACCATATTCTGGAGAATTGAG
2409345 ACTTTCAGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 1 0.02
48 43 0.98
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.24
Consensus pattern (48 bp):
CTTAGAAGAAGAAACAGAATCGTAACAACCATATTCTGGAGAATTGAG
Found at i:2414481 original size:36 final size:35
Alignment explanation
Indices: 2414426--2414545 Score: 98
Period size: 36 Copynumber: 3.3 Consensus size: 35
2414416 CTTACATCTA
** *
2414426 GGCCTTATTTGTGGGGTATTATTTCCCCTATATTTG
1 GGCCTTATTCATGTGGTATTATTTCCCC-ATATTTG
* * * * *
2414462 GGCCTTATTCATGTTGTATTCTTACCCCCACATCTG
1 GGCCTTATTCATGTGGTATTATT-TCCCCATATTTG
*
2414498 AG-CTTCATTCATGTGGTATTATTTTCCCCATATTTG
1 GGCCTT-ATTCATGTGGTATTA-TTTCCCCATATTTG
* *
2414534 GGCTTTAATCAT
1 GGCCTTATTCAT
2414546 CGTATAAAAT
Statistics
Matches: 63, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
35 3 0.05
36 52 0.83
37 8 0.13
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (35 bp):
GGCCTTATTCATGTGGTATTATTTCCCCATATTTG
Found at i:2419168 original size:17 final size:18
Alignment explanation
Indices: 2419148--2419189 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2419138 ATGAATATGT
*
2419148 TAATATTTTAATCAT-AA
1 TAATATTTGAATCATAAA
*
2419165 TAATATTTGAATTATAAA
1 TAATATTTGAATCATAAA
2419183 TAATATT
1 TAATATT
2419190 AATATTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TAATATTTGAATCATAAA
Found at i:2419616 original size:26 final size:26
Alignment explanation
Indices: 2419587--2419640 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
2419577 ATTAACATTT
*
2419587 TAAAATATTAATGGCTAAATTATAAA
1 TAAAATATTAATAGCTAAATTATAAA
* * *
2419613 TAAAGTATTAATAGTTAAATTATTAA
1 TAAAATATTAATAGCTAAATTATAAA
2419639 TA
1 TA
2419641 GTTAAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (26 bp):
TAAAATATTAATAGCTAAATTATAAA
Found at i:2419636 original size:15 final size:15
Alignment explanation
Indices: 2419613--2419646 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2419603 AAATTATAAA
2419613 TAAAGTATTAATAGT
1 TAAAGTATTAATAGT
*
2419628 TAAATTATTAATAGT
1 TAAAGTATTAATAGT
2419643 TAAA
1 TAAA
2419647 AAATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (15 bp):
TAAAGTATTAATAGT
Found at i:2419822 original size:27 final size:27
Alignment explanation
Indices: 2419787--2419840 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2419777 ATTATTTTAA
2419787 ATCACATAATAATTATTTTATTCTATT
1 ATCACATAATAATTATTTTATTCTATT
*
2419814 ATCATATAATAATTATTTTATTCTATT
1 ATCACATAATAATTATTTTATTCTATT
2419841 TCTACCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (27 bp):
ATCACATAATAATTATTTTATTCTATT
Found at i:2430259 original size:22 final size:20
Alignment explanation
Indices: 2430207--2430244 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2430197 TGAGGTTTAA
2430207 TATTTAAGA-AATTTTAAAAT
1 TATTTAA-ATAATTTTAAAAT
2430227 TATTTAAATAATTTTAAA
1 TATTTAAATAATTTTAAA
2430245 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TATTTAAATAATTTTAAAAT
Found at i:2430950 original size:21 final size:21
Alignment explanation
Indices: 2430920--2430992 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
2430910 TTTATTTCAC
*
2430920 TAAATCAAATATTATTTTTAT
1 TAAATTAAATATTATTTTTAT
*
2430941 TAAATTAAATAAT-TTTTTAT
1 TAAATTAAATATTATTTTTAT
* * *
2430961 GAATAATAATTGATTTATTTTTAT
1 TAA-ATTAAAT-A-TTATTTTTAT
2430985 T-AATTAAA
1 TAAATTAAA
2430993 ATATCATATG
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
20 9 0.23
21 16 0.41
22 5 0.13
23 2 0.05
24 7 0.18
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (21 bp):
TAAATTAAATATTATTTTTAT
Found at i:2431047 original size:21 final size:22
Alignment explanation
Indices: 2431013--2431054 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
2431003 ATATTAATGT
*
2431013 ATTATAATGAATGATTATATACC
1 ATTATAAT-AATGATCATATACC
2431036 ATTATAAT-ATGATCATATA
1 ATTATAATAATGATCATATA
2431055 ATATTTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (22 bp):
ATTATAATAATGATCATATACC
Done.