Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001444.1 Hibiscus syriacus cultivar Beakdansim tig00002793_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: 2564052
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 12
Found at i:2125272 original size:4 final size:4
Alignment explanation
Indices: 2125263--2125321 Score: 56
Period size: 4 Copynumber: 15.5 Consensus size: 4
2125253 ATAATACTAT
*
2125263 AATA AATA AATA AATA TAA-A AA-A AAT- AA-A AATA AATA AA-A AACCA
1 AATA AATA AATA AATA -AATA AATA AATA AATA AATA AATA AATA AA-TA
2125308 AATA AATA AATA AA
1 AATA AATA AATA AA
2125322 AATAAGTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
3 12 0.25
4 31 0.65
5 5 0.10
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (4 bp):
AATA
Found at i:2125288 original size:15 final size:15
Alignment explanation
Indices: 2125260--2125303 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
2125250 CCAATAATAC
2125260 TATAATAAATAAATAAA
1 TATAA-AAA-AAATAAA
2125277 TATAAAAAAAATAAA
1 TATAAAAAAAATAAA
*
2125292 AATAAATAAAAA
1 TATAAA-AAAAA
2125304 ACCAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 12 0.48
16 8 0.32
17 5 0.20
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
TATAAAAAAAATAAA
Found at i:2125312 original size:45 final size:45
Alignment explanation
Indices: 2125263--2125348 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
2125253 ATAATACTAT
*
2125263 AATAAATAAATAAATATAA-AAAAAATAAAAATAAATAAAAAACCA
1 AATAAATAAATAAAAATAAGAAAAAATAAAAA-AAATAAAAAACCA
* * *
2125308 AATAAATAAATAAAAATAAGTAAAGATAAACAAAATAAAAA
1 AATAAATAAATAAAAATAAGAAAAAATAAAAAAAATAAAAA
2125349 TAAAAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
45 27 0.75
46 9 0.25
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.17
Consensus pattern (45 bp):
AATAAATAAATAAAAATAAGAAAAAATAAAAAAAATAAAAAACCA
Found at i:2125314 original size:20 final size:18
Alignment explanation
Indices: 2125266--2125420 Score: 82
Period size: 20 Copynumber: 8.0 Consensus size: 18
2125256 ATACTATAAT
2125266 AAATAAATAAATATAAAAA
1 AAATAAATAAATA-AAAAA
2125285 AAATAAAAATAAATAAAAAA
1 AAAT--AAATAAATAAAAAA
*
2125305 CCAAATAAATAAATAAAAAT
1 --AAATAAATAAATAAAAAA
* *
2125325 AAGTAAAGATAAACAAAATAA
1 AAAT-AA-ATAAATAAAA-AA
*
2125346 AAATAAA-AATATAAAAATT
1 AAATAAATAA-ATAAAAA-A
* * * *
2125365 ACAGAGAATAAAGAAAATA
1 AAATA-AATAAATAAAAAA
*
2125384 AAAGAAATAAA-AGAAAAA
1 AAATAAATAAATA-AAAAA
2125402 ATAA-AAATAGAATAAAAAA
1 A-AATAAATA-AATAAAAAA
2125421 TAAACAAGGT
Statistics
Matches: 107, Mismatches: 14, Indels: 30
0.71 0.09 0.20
Matches are distributed among these distances:
17 1 0.01
18 22 0.21
19 28 0.26
20 37 0.35
21 15 0.14
22 4 0.04
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (18 bp):
AAATAAATAAATAAAAAA
Found at i:2125356 original size:45 final size:45
Alignment explanation
Indices: 2125263--2125424 Score: 118
Period size: 45 Copynumber: 3.4 Consensus size: 45
2125253 ATAATACTAT
* *
2125263 AATAAATAAATAAATATAAAAAAAATAAAAATAAATAAAAAACCA
1 AATAAATAAATAAAAATAAAAAAAATAAAAATAAATAAAAAACAA
* * *
2125308 AATAAATAAATAAAAATAAGTAAAGATAAACA-AAATAAAAATA-AA
1 AATAAATAAATAAAAATAA-AAAAAATAAAAATAAATAAAAA-ACAA
* *
2125353 AATATAA-AAATTACAGAGAATAAAGAAAAT-AAAAGAAATAAAAGAA-AA
1 AATA-AATAAA-TA-A-A-AATAAAAAAAATAAAAATAAATAAAA-AACAA
2125401 AATAAAAATAGAATAAAAAATAAA
1 AAT--AAATA-AAT-AAAAATAAA
2125425 CAAGGTAAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
45 35 0.37
46 14 0.15
47 4 0.04
48 25 0.27
49 9 0.10
50 4 0.04
51 3 0.03
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (45 bp):
AATAAATAAATAAAAATAAAAAAAATAAAAATAAATAAAAAACAA
Found at i:2125459 original size:3 final size:3
Alignment explanation
Indices: 2125444--2125567 Score: 67
Period size: 3 Copynumber: 40.0 Consensus size: 3
2125434 ATATATAAGT
* * * *
2125444 TAA TAA TGA -AA TAA TAA TAA TAA TAA TAA TAA TAG TAA TGA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
2125491 TAA AAA AAA TATG TATA TAA GGTATA TAA AAA TATA TAAA TAA -AA TAA
1 TAA TAA TAA TA-A TA-A TAA --TA-A TAA TAA TA-A T-AA TAA TAA TAA
*
2125539 TAA -AA TAA -AA TACA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
2125568 AGGATTAAAT
Statistics
Matches: 94, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
2 7 0.07
3 70 0.74
4 13 0.14
5 3 0.03
6 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:2125537 original size:13 final size:12
Alignment explanation
Indices: 2125519--2125568 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 12
2125509 AAGGTATATA
2125519 AAAATATATAAAT
1 AAAATA-ATAAAT
2125532 AAAATAATAAAAT
1 AAAATAAT-AAAT
2125545 AAAATACA-AAAT
1 AAAATA-ATAAAT
2125557 AATAATAATAAA
1 AA-AATAATAAA
2125569 GGATTAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 9 0.27
13 23 0.70
14 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:2125550 original size:26 final size:26
Alignment explanation
Indices: 2125519--2125568 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2125509 AAGGTATATA
*
2125519 AAAATATATAAATAA-AATAATAAAAT
1 AAAATACA-AAATAATAATAATAAAAT
2125545 AAAATACAAAATAATAATAATAAA
1 AAAATACAAAATAATAATAATAAA
2125569 GGATTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (26 bp):
AAAATACAAAATAATAATAATAAAAT
Found at i:2130329 original size:21 final size:21
Alignment explanation
Indices: 2130287--2130329 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2130277 TTTTTGGGCT
* * *
2130287 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
2130308 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
2130329 A
1 A
2130330 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:2131156 original size:23 final size:23
Alignment explanation
Indices: 2131112--2131156 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2131102 ATCATTATAT
*
2131112 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
2131135 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2131157 AGCTGTTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:2137976 original size:149 final size:150
Alignment explanation
Indices: 2137787--2138102 Score: 548
Period size: 150 Copynumber: 2.1 Consensus size: 150
2137777 GGGTAGAGGG
* *
2137787 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* *
2137851 TACTTGATC-CTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCAT
66 TACTTGATCTC-TAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATAGACATCAT
2137915 TATATGGCACTACGGTGCAAT
130 TATATGGCACTACGGTGCAAT
*
2137936 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
2138001 TACTTGATCTCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATAGACATCATT
66 TACTTGATCTCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATAGACATCATT
2138066 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
2138086 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
2138103 TGCATTTATA
Statistics
Matches: 159, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
149 52 0.33
150 106 0.67
151 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCTCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATAGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:2138114 original size:23 final size:23
Alignment explanation
Indices: 2138070--2138114 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2138060 ATCATTATAT
*
2138070 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
2138093 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2138115 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:2140745 original size:18 final size:18
Alignment explanation
Indices: 2140719--2140757 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2140709 ACTCCTCGCT
* *
2140719 GTCATCATCATCGTCGTC
1 GTCACCATCATCATCGTC
*
2140737 GTCACCATCGTCATCGTC
1 GTCACCATCATCATCGTC
2140755 GTC
1 GTC
2140758 GTCGTCGTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.36, G:0.18, T:0.31
Consensus pattern (18 bp):
GTCACCATCATCATCGTC
Found at i:2140750 original size:21 final size:21
Alignment explanation
Indices: 2140721--2140760 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2140711 TCCTCGCTGT
2140721 CATCATCATCGTCGTCGTCAC
1 CATCATCATCGTCGTCGTCAC
*
2140742 CATCGTCATCGTCGTCGTC
1 CATCATCATCGTCGTCGTC
2140761 GTCGTCCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.38, G:0.17, T:0.30
Consensus pattern (21 bp):
CATCATCATCGTCGTCGTCAC
Found at i:2142768 original size:111 final size:111
Alignment explanation
Indices: 2142631--2142852 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
2142621 ATTACAAAAA
*
2142631 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATCA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATCA
* *
2142696 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
2142742 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATCA
2142807 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
2142853 ATGATTTCCA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATCA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:2142999 original size:10 final size:11
Alignment explanation
Indices: 2142974--2143015 Score: 54
Period size: 10 Copynumber: 4.0 Consensus size: 11
2142964 TACCTTAAAA
2142974 AGAGAATATTTG
1 AGAGAA-ATTTG
2142986 AGAGAAATTT-
1 AGAGAAATTTG
2142996 AGAG-AATTTG
1 AGAGAAATTTG
2143006 AGAG-AATTTG
1 AGAGAAATTTG
2143016 GTGTGATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.17
10 14 0.48
11 4 0.14
12 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (11 bp):
AGAGAAATTTG
Found at i:2143191 original size:50 final size:50
Alignment explanation
Indices: 2143137--2143234 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 50
2143127 AGATATCCAA
* * * * *
2143137 GTATAGCGCGGATCAGGGGGCGCGCTATACTCACGTGGCGCCAGATCACC
1 GTATAGCGCGGAGCAGGGGGAGCGCTATACCCACGTGACGCCAAATCACC
* * *
2143187 GTATATCGCGGGGCAGGGGGAGCGCTATACCCTCGTGACGCCAAATCA
1 GTATAGCGCGGAGCAGGGGGAGCGCTATACCCACGTGACGCCAAATCA
2143235 GTATATAACG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.21, C:0.29, G:0.34, T:0.16
Consensus pattern (50 bp):
GTATAGCGCGGAGCAGGGGGAGCGCTATACCCACGTGACGCCAAATCACC
Found at i:2150163 original size:117 final size:117
Alignment explanation
Indices: 2149957--2150193 Score: 465
Period size: 117 Copynumber: 2.0 Consensus size: 117
2149947 AGGTCAGCTA
*
2149957 TTGATTACATGGAAAAAGTGCCTAATGTGAAGGCTCCTGTTCGAGAAGCATGGGGTTTTCAGTGC
1 TTGATTACATGGAAAAAGTGCCTAATGTGAAGGCTCCCGTTCGAGAAGCATGGGGTTTTCAGTGC
2150022 CCGAATCTCAGTATCAATAGTTGGATGTGGTTGCCTCTCTATGATGCTGATT
66 CCGAATCTCAGTATCAATAGTTGGATGTGGTTGCCTCTCTATGATGCTGATT
2150074 TTGATTACATGGAAAAAGTGCCTAATGTGAAGGCTCCCGTTCGAGAAGCATGGGGTTTTCAGTGC
1 TTGATTACATGGAAAAAGTGCCTAATGTGAAGGCTCCCGTTCGAGAAGCATGGGGTTTTCAGTGC
2150139 CCGAATCTCAGTATCAATAGTTGGATGTGGTTGCCTCTCTATGATGCTGATT
66 CCGAATCTCAGTATCAATAGTTGGATGTGGTTGCCTCTCTATGATGCTGATT
2150191 TTG
1 TTG
2150194 GATGAGGTCA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 119 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (117 bp):
TTGATTACATGGAAAAAGTGCCTAATGTGAAGGCTCCCGTTCGAGAAGCATGGGGTTTTCAGTGC
CCGAATCTCAGTATCAATAGTTGGATGTGGTTGCCTCTCTATGATGCTGATT
Found at i:2153706 original size:2 final size:2
Alignment explanation
Indices: 2153699--2153729 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2153689 ATTCAAAGCA
2153699 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
2153730 ACACTCTTTT
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:2153894 original size:29 final size:30
Alignment explanation
Indices: 2153852--2153919 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
2153842 ATTATTTGCT
2153852 GCAACAACCCAATAGTA-TTTACGAAGAAA
1 GCAACAACCCAATAGTATTTTACGAAGAAA
*
2153881 GCAATAACCCAATAGTATTTTACGAAGAAA
1 GCAACAACCCAATAGTATTTTACGAAGAAA
*
2153911 ACAACAACC
1 GCAACAACC
2153920 TAATTTTATG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 16 0.46
30 19 0.54
ACGTcount: A:0.49, C:0.22, G:0.12, T:0.18
Consensus pattern (30 bp):
GCAACAACCCAATAGTATTTTACGAAGAAA
Found at i:2154071 original size:19 final size:18
Alignment explanation
Indices: 2154043--2154078 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
2154033 ACAGAAACAC
2154043 TAAAAAAATACTTGTGAT
1 TAAAAAAATACTTGTGAT
2154061 TAAAGAAAATACTTGTGA
1 TAAA-AAAATACTTGTGA
2154079 CTGAGACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.31
Consensus pattern (18 bp):
TAAAAAAATACTTGTGAT
Found at i:2157149 original size:26 final size:27
Alignment explanation
Indices: 2157120--2157177 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
2157110 CCGCTTAATT
*
2157120 TAAAATTT-ATAAAATTT-GAGAGAAAA
1 TAAAATTTAAAAAAATTTAGAGA-AAAA
*
2157146 T-AAATTTAAAAAAATTTATAGAAAAA
1 TAAAATTTAAAAAAATTTAGAGAAAAA
2157172 TAAAAT
1 TAAAAT
2157178 AAATTACCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 6 0.22
26 14 0.52
27 7 0.26
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (27 bp):
TAAAATTTAAAAAAATTTAGAGAAAAA
Found at i:2158023 original size:15 final size:15
Alignment explanation
Indices: 2158003--2158031 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2157993 TTAAATCGCT
2158003 CCGTCAAAACCCGCA
1 CCGTCAAAACCCGCA
2158018 CCGTCAAAACCCGC
1 CCGTCAAAACCCGC
2158032 GGGCTAAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.48, G:0.14, T:0.07
Consensus pattern (15 bp):
CCGTCAAAACCCGCA
Found at i:2158975 original size:49 final size:49
Alignment explanation
Indices: 2158917--2159038 Score: 131
Period size: 49 Copynumber: 2.5 Consensus size: 49
2158907 GTAGGAAAGC
* *
2158917 GTGC-CCCCTGCACCGCGCTATATGCTGATTTGGCACCACGTGGGTATA
1 GTGCGCCCCTGCACCGCGCTATACGCTGATCTGGCACCACGTGGGTATA
* * * **
2158965 GTGCGCCCCTGCCCCGCGATATACGGTGATCTGGCGTCACGTGGGTATA
1 GTGCGCCCCTGCACCGCGCTATACGCTGATCTGGCACCACGTGGGTATA
**
2159014 GCACGCCCCCTG-ATCCGCGCTATAC
1 GTGCG-CCCCTGCA-CCGCGCTATAC
2159039 TCCGTATCAA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
48 4 0.07
49 40 0.67
50 16 0.27
ACGTcount: A:0.16, C:0.34, G:0.28, T:0.22
Consensus pattern (49 bp):
GTGCGCCCCTGCACCGCGCTATACGCTGATCTGGCACCACGTGGGTATA
Found at i:2162069 original size:111 final size:111
Alignment explanation
Indices: 2161931--2162152 Score: 372
Period size: 111 Copynumber: 2.0 Consensus size: 111
2161921 ATTACAAAAA
* *
2161931 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* * * * *
2161996 AATTAAAATGTTAAAATGTTATCGTATTAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
*
2162042 TTAATTCTTAGTCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
2162107 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
2162153 ATGATTTCCA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:2162290 original size:12 final size:10
Alignment explanation
Indices: 2162276--2162316 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
2162266 ACCTTAAAAA
*
2162276 GAGAGTATTT
1 GAGAGAATTT
2162286 GAGAGAAATTT
1 GAGAG-AATTT
2162297 -AGAGAATTT
1 GAGAGAATTT
2162306 GAGAGAATTT
1 GAGAGAATTT
2162316 G
1 G
2162317 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:2162492 original size:50 final size:49
Alignment explanation
Indices: 2162438--2162563 Score: 144
Period size: 50 Copynumber: 2.5 Consensus size: 49
2162428 AGATATCCAG
* * * *
2162438 GTATAGCGCGGATCAGGGGGCGCGCTATACCTACGTGGGGCTAGATCACC
1 GTATAGCGCGG-TCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
* * * *
2162488 GTATATCGCGGGGCAGGGGGCGCACTATACCCACGTGGCGCCAAATCAGC
1 GTATAGCGC-GGTCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
*
2162538 ATATAGCGCGGTGCAGGGGGCGCGCT
1 GTATAGCGCGGT-CAGGGGGCGCGCT
2162564 TTCCTGCTAA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
49 2 0.03
50 58 0.94
51 2 0.03
ACGTcount: A:0.20, C:0.27, G:0.37, T:0.16
Consensus pattern (49 bp):
GTATAGCGCGGTCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:2163130 original size:21 final size:21
Alignment explanation
Indices: 2163096--2163135 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2163086 TAAAGCGCCC
*
2163096 AATAATAACATTTTCGGTAGA
1 AATAATAACATTTTAGGTAGA
**
2163117 AATAATAATGTTTTAGGTA
1 AATAATAACATTTTAGGTA
2163136 ATTTTTTACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (21 bp):
AATAATAACATTTTAGGTAGA
Found at i:2167448 original size:40 final size:40
Alignment explanation
Indices: 2167419--2167515 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
2167409 AGTATCATAT
* *
2167419 GAACAATATTGATACTATTCATGAGGTATCAATACTGTAA
1 GAACAATATCGATACTATTCATGAGGTATCAATACTATAA
* * *
2167459 GAACAATATCGGTACTGTTCATGAGGTATCGATACTATAA
1 GAACAATATCGATACTATTCATGAGGTATCAATACTATAA
*
2167499 GAACAATATCGGTACTA
1 GAACAATATCGATACTA
2167516 CTTGTCCAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (40 bp):
GAACAATATCGATACTATTCATGAGGTATCAATACTATAA
Found at i:2178207 original size:23 final size:22
Alignment explanation
Indices: 2178164--2178207 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2178154 CGAAATAATA
* **
2178164 TATTTATTAAAAATATTATTTT
1 TATTTAATAAAAATAGGATTTT
2178186 TATTTAATAAAAATAGGGATTT
1 TATTTAATAAAAATA-GGATTT
2178208 AATGGAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (22 bp):
TATTTAATAAAAATAGGATTTT
Found at i:2180641 original size:15 final size:14
Alignment explanation
Indices: 2180618--2180665 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
2180608 AATTTGAAAG
2180618 TTAGAGTAATTAAA
1 TTAGAGTAATTAAA
2180632 TTAGGAGTAATTTGACAA
1 TTA-GAGTAA-TT-A-AA
2180650 TTA-AGTAATTAAA
1 TTAGAGTAATTAAA
2180663 TTA
1 TTA
2180666 AAAAAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.17
14 4 0.13
15 8 0.27
16 7 0.23
17 1 0.03
18 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.38
Consensus pattern (14 bp):
TTAGAGTAATTAAA
Found at i:2182678 original size:21 final size:22
Alignment explanation
Indices: 2182654--2182731 Score: 97
Period size: 22 Copynumber: 3.5 Consensus size: 22
2182644 CAAAATATAT
2182654 AATATATATATAGTTTTT-AAA
1 AATATATATATAGTTTTTGAAA
2182675 AATATATAATATAGTTTTTGAAA
1 AATATAT-ATATAGTTTTTGAAA
*
2182698 ACATAT-TATATTGTTTTTGAAA
1 A-ATATATATATAGTTTTTGAAA
*
2182720 TATAATATATAT
1 AAT-ATATATAT
2182732 TATATAGTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
21 9 0.18
22 27 0.54
23 10 0.20
24 4 0.08
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.47
Consensus pattern (22 bp):
AATATATATATAGTTTTTGAAA
Found at i:2182689 original size:22 final size:22
Alignment explanation
Indices: 2182654--2182745 Score: 87
Period size: 22 Copynumber: 4.0 Consensus size: 22
2182644 CAAAATATAT
2182654 AATATAT-ATATAGTTTTTAAA
1 AATATATAATATAGTTTTTAAA
*
2182675 AATATATAATATAGTTTTTGAA
1 AATATATAATATAGTTTTTAAA
* * *
2182697 AACATATTATATTGTTTTTGAAATA
1 AATATATAATATAGTTTTT--AA-A
2182722 TAATATATATTATATAGTTTTTAA
1 -AATATATA--ATATAGTTTTTAA
2182746 TATGTCAAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
21 7 0.12
22 29 0.52
24 1 0.02
25 1 0.02
26 8 0.14
28 10 0.18
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (22 bp):
AATATATAATATAGTTTTTAAA
Found at i:2183108 original size:28 final size:28
Alignment explanation
Indices: 2183070--2183136 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
2183060 TTTTTTATAT
*
2183070 TATATAGTATACATTATA-ATTTCAAAAA
1 TATATAATATACA-TATAGATTTCAAAAA
* * *
2183098 TATATAATATATATATAGTTTTTAAAAA
1 TATATAATATACATATAGATTTCAAAAA
2183126 TATATAATATA
1 TATATAATATA
2183137 GTTTTTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 4 0.12
28 30 0.88
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (28 bp):
TATATAATATACATATAGATTTCAAAAA
Found at i:2183127 original size:21 final size:22
Alignment explanation
Indices: 2183103--2183180 Score: 97
Period size: 22 Copynumber: 3.5 Consensus size: 22
2183093 AAAAATATAT
2183103 AATATATATATAGTTTTT-AAA
1 AATATATATATAGTTTTTGAAA
2183124 AATATATAATATAGTTTTTGAAA
1 AATATAT-ATATAGTTTTTGAAA
*
2183147 ACATAT-TATATTGTTTTTGAAA
1 A-ATATATATATAGTTTTTGAAA
*
2183169 TATAATATATAT
1 AAT-ATATATAT
2183181 TATATAGTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
21 9 0.18
22 27 0.54
23 10 0.20
24 4 0.08
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.47
Consensus pattern (22 bp):
AATATATATATAGTTTTTGAAA
Found at i:2183138 original size:22 final size:22
Alignment explanation
Indices: 2183103--2183194 Score: 87
Period size: 22 Copynumber: 4.0 Consensus size: 22
2183093 AAAAATATAT
2183103 AATATAT-ATATAGTTTTTAAA
1 AATATATAATATAGTTTTTAAA
*
2183124 AATATATAATATAGTTTTTGAA
1 AATATATAATATAGTTTTTAAA
* * *
2183146 AACATATTATATTGTTTTTGAAATA
1 AATATATAATATAGTTTTT--AA-A
2183171 TAATATATATTATATAGTTTTTAA
1 -AATATATA--ATATAGTTTTTAA
2183195 TATATCAAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
21 7 0.12
22 29 0.52
24 1 0.02
25 1 0.02
26 8 0.14
28 10 0.18
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (22 bp):
AATATATAATATAGTTTTTAAA
Found at i:2183181 original size:28 final size:29
Alignment explanation
Indices: 2183149--2183214 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
2183139 TTTTGAAAAC
* *
2183149 ATATTATATTGTTTTTGAA-ATAT-AATAT
1 ATATTATATAGTTTTT-AATATATCAAGAT
2183177 ATATTATATAGTTTTTAATATATCAAGAT
1 ATATTATATAGTTTTTAATATATCAAGAT
2183206 -TATTATATA
1 ATATTATATA
2183215 TTGTTATTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 28 0.82
29 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (29 bp):
ATATTATATAGTTTTTAATATATCAAGAT
Found at i:2184488 original size:21 final size:21
Alignment explanation
Indices: 2184423--2184489 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
2184413 CTTTTCAATA
* *
2184423 TTTATATTGTTAATTTAACAT
1 TTTATATTTTTAATTTAACCT
* * **
2184444 TTT-TATTTTTTTACTTATTTCT
1 TTTATA-TTTTTAATTTA-ACCT
2184466 TTTATATTTTTAATTTAACCT
1 TTTATATTTTTAATTTAACCT
2184487 TTT
1 TTT
2184490 TTATCTAACA
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 13 0.39
23 2 0.06
ACGTcount: A:0.24, C:0.07, G:0.01, T:0.67
Consensus pattern (21 bp):
TTTATATTTTTAATTTAACCT
Found at i:2184490 original size:22 final size:22
Alignment explanation
Indices: 2184423--2184490 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
2184413 CTTTTCAATA
*
2184423 TTTATATTGTTAATTTAACATT
1 TTTATATTTTTAATTTAACATT
* * **
2184445 TTTAT-TTTTTTACTT-ATTTCT
1 TTTATATTTTTAATTTAACAT-T
*
2184466 TTTATATTTTTAATTTAACCTT
1 TTTATATTTTTAATTTAACATT
2184488 TTT
1 TTT
2184491 TATCTAACAA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
20 2 0.06
21 13 0.38
22 17 0.50
23 2 0.06
ACGTcount: A:0.24, C:0.07, G:0.01, T:0.68
Consensus pattern (22 bp):
TTTATATTTTTAATTTAACATT
Found at i:2190183 original size:21 final size:21
Alignment explanation
Indices: 2190132--2190184 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
2190122 ATTATGACTA
2190132 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
2190153 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
2190174 TCGCAATGCGA
1 TCGCAATGCGA
2190185 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2190217 original size:21 final size:21
Alignment explanation
Indices: 2190174--2190246 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
2190164 TTTTCCCAAT
** *
2190174 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
2190194 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
2190215 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
2190236 TCGCAACGCGA
1 TCGCAATGCGA
2190247 TAATACAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
20 12 0.25
21 36 0.75
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:2190376 original size:21 final size:21
Alignment explanation
Indices: 2190350--2190392 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2190340 CACTCTCTCA
2190350 CCCATCTCC-GACGAAATCCGT
1 CCCATCTCCTG-CGAAATCCGT
*
2190371 CCCATCTCCTGTGAAATCCGT
1 CCCATCTCCTGCGAAATCCGT
2190392 C
1 C
2190393 TATCTCCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.21, C:0.42, G:0.14, T:0.23
Consensus pattern (21 bp):
CCCATCTCCTGCGAAATCCGT
Found at i:2190703 original size:20 final size:20
Alignment explanation
Indices: 2190654--2190712 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2190644 TTTATTCTCT
* **
2190654 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
2190674 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
2190694 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
2190713 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:2190903 original size:25 final size:24
Alignment explanation
Indices: 2190849--2190903 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2190839 TGTTTATTAT
* *
2190849 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
2190873 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
2190899 TGTTT
1 TGTTT
2190904 ATTGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2192058 original size:18 final size:18
Alignment explanation
Indices: 2192032--2192079 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2192022 TCCACTTCGG
2192032 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
2192050 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2192068 GAGCCATCACCT
1 GAGCCATCACCT
2192080 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2192643 original size:20 final size:20
Alignment explanation
Indices: 2192618--2192663 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2192608 TAGTTTACTT
2192618 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
2192638 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
2192658 TCGCAA
1 TCGCAA
2192664 TGCAAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:2192664 original size:20 final size:20
Alignment explanation
Indices: 2192629--2192666 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2192619 CGCAACACGA
2192629 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
2192649 AAATGGCTATCGCAATGC
1 AAATGACTATCGCAATGC
2192667 AAAATGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:2192679 original size:19 final size:19
Alignment explanation
Indices: 2192637--2192735 Score: 100
Period size: 19 Copynumber: 5.4 Consensus size: 19
2192627 GAAAATGACT
***
2192637 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
*
2192657 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2192676 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
2192690 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2192709 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2192728 ATCGCAAT
1 ATCGCAAT
2192736 ACGATTTGTG
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 2 0.03
17 1 0.02
18 1 0.02
19 40 0.62
20 10 0.15
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2192818 original size:20 final size:20
Alignment explanation
Indices: 2192789--2192851 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
2192779 TTTCGCATTA
*
2192789 CGATAACCATTTCCGCGTTG
1 CGATAGCCATTTCCGCGTTG
*
2192809 TGATAGCCATTTCCGCGTTG
1 CGATAGCCATTTCCGCGTTG
* *
2192829 CGATAGTCATTTTCGCGTTG
1 CGATAGCCATTTCCGCGTTG
2192849 CGA
1 CGA
2192852 AAGTAAGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.33
Consensus pattern (20 bp):
CGATAGCCATTTCCGCGTTG
Found at i:2192862 original size:20 final size:20
Alignment explanation
Indices: 2192822--2192877 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2192812 TAGCCATTTC
* * *
2192822 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
2192842 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
2192862 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
2192878 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:2193271 original size:21 final size:20
Alignment explanation
Indices: 2193219--2193279 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
2193209 GACTCACCTG
2193219 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** *
2193239 CCAATCGTTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGTCCCCT
2193260 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
2193280 CCCCCCCACC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.43, G:0.13, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:2193310 original size:45 final size:42
Alignment explanation
Indices: 2193215--2193310 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 42
2193205 GCCCGACTCA
* *
2193215 CCTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCC
1 CCTGTCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCC
* *
2193257 CCTATCATCCCTCAAGAGTCCCCCCCCCCCACCGTTCAAGAGGCC
1 CCTGTCATCCCTCAAGAGT---CCCCCCCAACCGTTCAAGAGGCC
*
2193302 GCTGTCATC
1 CCTGTCATC
2193311 GTTGAAGAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 18 0.40
45 27 0.60
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.20
Consensus pattern (42 bp):
CCTGTCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCC
Found at i:2195006 original size:20 final size:20
Alignment explanation
Indices: 2194948--2195008 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
2194938 TCGCATTGCG
* *
2194948 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGTC
2194968 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
2194988 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
2195008 A
1 A
2195009 AATGAATGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGTC
Found at i:2195228 original size:20 final size:20
Alignment explanation
Indices: 2195212--2195308 Score: 158
Period size: 20 Copynumber: 4.8 Consensus size: 20
2195202 ATTGCGATTT
*
2195212 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
2195232 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
2195252 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
2195272 TCAGTATCACGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
2195292 TCAGTATCGCGTTGCGA
1 TCAGAATCGCGTTGCGA
2195309 TTTTGTATTA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 73 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:2195432 original size:21 final size:22
Alignment explanation
Indices: 2195380--2195432 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2195370 ATTTACTTAT
2195380 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
** *
2195401 TCGCAACGCGAAATT-GTAAAA
1 TCGCATTGCGAAATTGGGAAAA
2195422 TCGCATTGCGA
1 TCGCATTGCGA
2195433 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:2195887 original size:19 final size:19
Alignment explanation
Indices: 2195863--2195911 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2195853 AAAAACAAAC
*
2195863 ACAAAAACAAACCCATAGA
1 ACAAAATCAAACCCATAGA
2195882 ACAAAATCAAACCCATAGA
1 ACAAAATCAAACCCATAGA
2195901 ACAAAATCAAA
1 ACAAAATCAAA
2195912 ACTTTGCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.63, C:0.24, G:0.04, T:0.08
Consensus pattern (19 bp):
ACAAAATCAAACCCATAGA
Found at i:2196783 original size:20 final size:20
Alignment explanation
Indices: 2196758--2196800 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2196748 TCTAAGAGCC
* *
2196758 CATTTAGGATCATTTAGATG
1 CATTTAGGAGCATATAGATG
*
2196778 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
2196798 CAT
1 CAT
2196801 GAGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:2197063 original size:27 final size:27
Alignment explanation
Indices: 2197025--2197076 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
2197015 CTATTTCATA
2197025 GGATCTCTGATCATGACCGAGAAATTT
1 GGATCTCTGATCATGACCGAGAAATTT
2197052 GGATCTCTGATCATGACCGAGAAAT
1 GGATCTCTGATCATGACCGAGAAAT
2197077 CTGCCTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (27 bp):
GGATCTCTGATCATGACCGAGAAATTT
Found at i:2202064 original size:20 final size:20
Alignment explanation
Indices: 2202023--2202065 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2202013 TCTAAGAGCC
*
2202023 CATTTAGGATCATTTAGATG
1 CATTTAGGATCATATAGATG
*
2202043 CATTTAGGAGT-ATATAGTTG
1 CATTTAGGA-TCATATAGATG
2202063 CAT
1 CAT
2202066 GAGGTGGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (20 bp):
CATTTAGGATCATATAGATG
Found at i:2207348 original size:20 final size:20
Alignment explanation
Indices: 2207323--2207365 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2207313 TCTAAGAGCC
* *
2207323 CATTTAGGATCATTTAGATG
1 CATTTAGGAGCATATAGATG
*
2207343 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
2207363 CAT
1 CAT
2207366 GAGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:2207633 original size:27 final size:27
Alignment explanation
Indices: 2207595--2207649 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2207585 TATTTTCACG
2207595 GGATCTCTGATCATGACCGAGAAATCT
1 GGATCTCTGATCATGACCGAGAAATCT
2207622 GGATCTCTGATCATGACCGAGAAATCT
1 GGATCTCTGATCATGACCGAGAAATCT
2207649 G
1 G
2207650 CCTGGATCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (27 bp):
GGATCTCTGATCATGACCGAGAAATCT
Found at i:2217582 original size:22 final size:22
Alignment explanation
Indices: 2217556--2217634 Score: 99
Period size: 22 Copynumber: 3.7 Consensus size: 22
2217546 CCAGTGTGGA
*
2217556 AGTATCGGTACCATAGTATAAT
1 AGTATCGATACCATAGTATAAT
* *
2217578 AGTATCGGTACCATAGTATAGT
1 AGTATCGATACCATAGTATAAT
*
2217600 AGTATCGATACCAT-GT-TAAG
1 AGTATCGATACCATAGTATAAT
*
2217620 GGTATCGATACCATA
1 AGTATCGATACCATA
2217635 CAACATCAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
20 15 0.29
21 2 0.04
22 34 0.67
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAAT
Found at i:2236233 original size:39 final size:38
Alignment explanation
Indices: 2236189--2236265 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 38
2236179 ACTGAATATT
*
2236189 TGTCCCGAAGGACCACTATATCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACTATAT-CCGAAGAACCACTGATA
* *
2236228 TGTCCCGAAGGACCACTATGTCCGAATAACCACTGATA
1 TGTCCCGAAGGACCACTATATCCGAAGAACCACTGATA
2236266 ATCCCTCGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 15 0.43
39 20 0.57
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.19
Consensus pattern (38 bp):
TGTCCCGAAGGACCACTATATCCGAAGAACCACTGATA
Found at i:2236235 original size:21 final size:20
Alignment explanation
Indices: 2236189--2236246 Score: 93
Period size: 18 Copynumber: 3.0 Consensus size: 20
2236179 ACTGAATATT
2236189 TGTCCCGAAGGACCACTATA
1 TGTCCCGAAGGACCACTATA
2236209 --TCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACT-ATA
2236228 TGTCCCGAAGGACCACTAT
1 TGTCCCGAAGGACCACTAT
2236247 GTCCGAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 15 0.43
19 3 0.09
20 2 0.06
21 15 0.43
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (20 bp):
TGTCCCGAAGGACCACTATA
Found at i:2243056 original size:18 final size:21
Alignment explanation
Indices: 2243021--2243086 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 21
2243011 TCCCATAGGG
2243021 CACTAATATTTGTCCCGAAGGAC
1 CACTAATA--TGTCCCGAAGGAC
*
2243044 CACT-AT-T-TCCCGAAAGAC
1 CACTAATATGTCCCGAAGGAC
2243062 CA-TAGATATGTCCCGAAGGAC
1 CACTA-ATATGTCCCGAAGGAC
2243083 CACT
1 CACT
2243087 GATAATCCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
17 1 0.03
18 12 0.33
19 3 0.08
20 1 0.03
21 12 0.33
22 3 0.08
23 4 0.11
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.23
Consensus pattern (21 bp):
CACTAATATGTCCCGAAGGAC
Found at i:2243090 original size:21 final size:21
Alignment explanation
Indices: 2243031--2243090 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
2243021 CACTAATATT
2243031 TGTCCCGAAGGACCACT-AT-
1 TGTCCCGAAGGACCACTGATA
*
2243050 T-TCCCGAAAGACCA-TAGATA
1 TGTCCCGAAGGACCACT-GATA
2243070 TGTCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACTGATA
2243091 ATCCCTCGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
17 1 0.03
18 12 0.35
19 3 0.09
20 1 0.03
21 16 0.47
22 1 0.03
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTGATA
Found at i:2248764 original size:87 final size:88
Alignment explanation
Indices: 2248611--2248780 Score: 245
Period size: 87 Copynumber: 1.9 Consensus size: 88
2248601 ACACACCCTT
*
2248611 TTATAGCCAAGTTACCCTAATCATATTAAGATTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAA-CATATTAAGATTTTATTATTTCAAATTAATTAAATCTATAATTA
* *
2248676 ATTAATTGGAATTTAATAATCCTC
65 ATTAATTGAAATTAAATAATCCTC
* **
2248700 TTATATCCAAGTTACCCTAA-ATATTGGGGA-TTTATTATTTCAAATTAATTAAATCTATAATTA
1 TTATAGCCAAGTTACCCTAACATATT-AAGATTTTATTATTTCAAATTAATTAAATCTATAATTA
*
2248763 ATTGATTGAAATTAAATA
65 ATTAATTGAAATTAAATA
2248781 TTCAGGATTA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
87 52 0.71
88 2 0.03
89 19 0.26
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (88 bp):
TTATAGCCAAGTTACCCTAACATATTAAGATTTTATTATTTCAAATTAATTAAATCTATAATTAA
TTAATTGAAATTAAATAATCCTC
Found at i:2255187 original size:23 final size:21
Alignment explanation
Indices: 2255138--2255188 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
2255128 ATATATTCTT
*
2255138 TATTTA-AATATTAATTAAAC
1 TATTTATAATAATAATTAAAC
*
2255158 -ATGTATAATAATATATTAAAAC
1 TATTTATAATAATA-ATT-AAAC
2255180 TATTTATAA
1 TATTTATAA
2255189 AAAAACTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.17
20 6 0.25
21 3 0.12
22 4 0.17
23 7 0.29
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (21 bp):
TATTTATAATAATAATTAAAC
Found at i:2255606 original size:15 final size:15
Alignment explanation
Indices: 2255586--2255690 Score: 176
Period size: 15 Copynumber: 7.0 Consensus size: 15
2255576 TAATAAGGTT
*
2255586 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
2255601 ATTTATTATAAAATA
1 ATTTATTATAAAATA
2255616 ATTTATTATAAAATA
1 ATTTATTATAAAATA
2255631 ATTTATTATAAAATA
1 ATTTATTATAAAATA
2255646 ATTTATTATAAAATA
1 ATTTATTATAAAATA
2255661 ATTTACTT-TAAAATA
1 ATTTA-TTATAAAATA
*
2255676 AATTATTATAAAATA
1 ATTTATTATAAAATA
2255691 TGTATTGATT
Statistics
Matches: 86, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
14 2 0.02
15 82 0.95
16 2 0.02
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTATTATAAAATA
Found at i:2255738 original size:22 final size:22
Alignment explanation
Indices: 2255722--2255764 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2255712 AATTTATTAG
2255722 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
2255744 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
2255765 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:2255782 original size:32 final size:32
Alignment explanation
Indices: 2255744--2255850 Score: 135
Period size: 32 Copynumber: 3.7 Consensus size: 32
2255734 TATTTTAAAA
2255744 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
2255776 TATGGATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
2255798 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
2255830 TATGAATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2255851 ATATGGATTG
Statistics
Matches: 64, Mismatches: 1, Indels: 20
0.75 0.01 0.24
Matches are distributed among these distances:
22 14 0.22
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 34 0.53
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:2255790 original size:54 final size:54
Alignment explanation
Indices: 2255678--2256720 Score: 530
Period size: 54 Copynumber: 19.8 Consensus size: 54
2255668 TTAAAATAAA
* * *
2255678 TTATTATAAAATATGTATTGATTTATTTTAAAATAATTTATTAGTATGAATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTT-AAATAATTTATTAGTATGGATTGAT
2255733 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
*
2255787 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* *
2255841 TTATTTTAAAATATGGATTGATTTA--TT--GT-A---GTT-GTATGGA-TGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* * * *
2255885 TTATTTTAAATAATTTATTAGTGGATTGATTTATTTTAAAATGGATTGATT--TAT---TTTAA
1 TTATTTT--A-AA---A-TA-TGGATTGATTTATTTT-AAAT-AATTTATTAGTATGGATTGAT
* * * * * * *
2255944 ATAATTTATTAGTATGGATTGATTTAATTTAAA-AAATTATTTGTATGGATTGAT
1 TTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* * * *
2255998 TTATTTTAAAACATAGATTGA--TATATT--AT--TGTAGTT-GTATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGAT
** * ** * * *
2256046 TTATTTT-AAATAATTTATTAGTATTGA-TTTATTTATTTTA-AAATATGGATTG-T
1 TTATTTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGAT
* * ** * * ** *
2256099 TTATTTT-AAATA---ATTTA-TTAGTATGGATTGATTTATTTTAAAATTGAATTGAT
1 TTATTTTAAAATATGGATTGATTTA-TTTTAAATAATTTA--TTAGTA-TGGATTGAT
2256152 TTATTTT-AAATATGGA-TGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* * ** * * *
2256204 TTATTTT-AAATA---ATTTATTTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTA-TTTTAAATAATTTA--TT--AGTATGGATTGAT
*** *
2256259 TTATTATTGTAGTTGTATGGATTAATTTA-TTTAAA-AA--TATTAGTATGGATTGAT
1 TTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
*
2256313 TTA-TTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
*
2256366 TT-TTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGAT
** ** * * **
2256413 TTATTTT-AAATA---ATT-A-TTAGATGGATTGATTTATTTAAAATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGAT
** ** * ** * * *
2256462 TTATTTT-AAATAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGAT
1 TTATTTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGAT
* * * *
2256516 TTATTTAAATAATTATTAGTATGAATTGATTTATTTT--A-AA---A-TAGGATTGATTTA-
1 TTATTT---TAA--A--A-TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* ***
2256570 TTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
2256625 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
2256679 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
2256721 TTGTAGTTGT
Statistics
Matches: 763, Mismatches: 123, Indels: 205
0.70 0.11 0.19
Matches are distributed among these distances:
42 3 0.00
43 1 0.00
44 15 0.02
45 6 0.01
46 6 0.01
47 44 0.06
48 44 0.06
49 51 0.07
50 20 0.03
51 34 0.04
52 57 0.07
53 86 0.11
54 255 0.33
55 72 0.09
56 16 0.02
57 8 0.01
58 5 0.01
59 8 0.01
60 7 0.01
61 8 0.01
62 8 0.01
63 9 0.01
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
Found at i:2255801 original size:22 final size:22
Alignment explanation
Indices: 2255776--2255818 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2255766 AATTTATTAG
2255776 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2255798 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2255819 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2255929 original size:20 final size:20
Alignment explanation
Indices: 2255906--2255944 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2255896 AATTTATTAG
2255906 TGGATTGATTTATTTTAAAA
1 TGGATTGATTTATTTTAAAA
2255926 TGGATTGATTTATTTTAAA
1 TGGATTGATTTATTTTAAA
2255945 TAATTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (20 bp):
TGGATTGATTTATTTTAAAA
Found at i:2255954 original size:126 final size:127
Alignment explanation
Indices: 2255744--2255977 Score: 400
Period size: 126 Copynumber: 1.8 Consensus size: 127
2255734 TATTTTAAAA
2255744 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGA-TGATTTATTTTAAATAATTTATTAG-ATGGATTGATTTATTTT-AAATATGGATTGAT
*
2255809 TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTGTAGTT
63 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTGTA-TT
2255874 G
127 G
2255875 TATGGATGATTTATTTTAAATAATTTATTAG-TGGATTGATTTATTTTAAA-ATGGATTGATTTA
1 TATGGATGATTTATTTTAAATAATTTATTAGATGGATTGATTTATTTTAAATATGGATTGATTTA
*
2255938 TTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAAA
66 TTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
2255978 AATTATTTGT
Statistics
Matches: 101, Mismatches: 2, Indels: 5
0.94 0.02 0.05
Matches are distributed among these distances:
126 51 0.50
127 3 0.03
128 16 0.16
130 25 0.25
131 6 0.06
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (127 bp):
TATGGATGATTTATTTTAAATAATTTATTAGATGGATTGATTTATTTTAAATATGGATTGATTTA
TTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTGTATTG
Found at i:2255990 original size:31 final size:31
Alignment explanation
Indices: 2255925--2256008 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 31
2255915 TTATTTTAAA
*
2255925 ATGGATTGATTTATTTTAAATAATTTATTAGT
1 ATGGATTGATTTATTTTAAA-AAATTATTAGT
* *
2255957 ATGGATTGATTTAATTTAAAAAATTATTTGT
1 ATGGATTGATTTATTTTAAAAAATTATTAGT
2255988 ATGGATTGATTTATTTTAAAA
1 ATGGATTGATTTATTTTAAAA
2256009 CATAGATTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
31 29 0.60
32 19 0.40
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (31 bp):
ATGGATTGATTTATTTTAAAAAATTATTAGT
Found at i:2256061 original size:237 final size:238
Alignment explanation
Indices: 2255798--2256451 Score: 804
Period size: 237 Copynumber: 2.7 Consensus size: 238
2255788 TATTTTAAAA
2255798 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAAATATGGATTGAT
* * ** *
2255863 TTATTGT-AGT-TGTA-T-GGAT-GATTTATTTTAAATAATTTATTAGTGGATTGATTTATTTTA
65 TTATTGTAAATATGTATTAGGATGGATTGA-TTT--AT--TTTAAAAGTGAATTGATTTATTTTA
2255923 AA-ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAA-AAATTATTT
125 AATATGGA-TGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAATAAATTATTT
2255986 -GTATGGATTGATTTATTTTAAAACATAGATTGATATATTATTGTAGTTG
189 AGTATGGATTGATTTATTTTAAAACATAGATTGATATATTATTGTAGTTG
*
2256035 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTTATTTATTTTAAAATATGGATTG-T
1 TATGGATTGATTTATTTTAAATAATTTATTAGTA-TGATTGATTTATTTTAAAATATGGATTGAT
* * * *
2256099 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATTGAATTGATTTATTTTAAATA
65 TTATTGTAAAT-ATGTATTAGGATGGATTGATTTATTTTAAAAGTGAATTGATTTATTTTAAATA
* *
2256164 TGGATGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTAGTAT
129 TGGATGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAATAAATTATTTAGTAT
* * *
2256229 GGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
194 GGATTGATTTATTTTAAAACATAGATTGATATATTATTGTAGTTG
*
2256274 TATGGATTAATTTA-TTTAAA-AA--TATTAGTATGGATTGATTTA-TTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATGGATTGAT
* * * * * *
2256334 TTATTTTAAATAATTTATTAGTATGAATTGATTT-TTTTAAAATATGGATTGATTTATTATTGTA
65 TTATTGTAAAT-ATGTATTAGGATGGATTGATTTATTTTAAAA-GTGAATTGATTTA-T-TT-TA
**
2256398 GTTGTATGGATTGATTTATTTTAAATAA-TTATTAG-ATGGATTGATTT-ATTTAAA
125 --AATATGGA-TGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAA
2256452 ATGGATTGAT
Statistics
Matches: 375, Mismatches: 23, Indels: 37
0.86 0.05 0.09
Matches are distributed among these distances:
234 25 0.07
235 62 0.17
236 8 0.02
237 133 0.35
238 29 0.08
239 76 0.20
240 14 0.04
241 23 0.06
242 5 0.01
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (238 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAATATGGATTGATT
TATTGTAAATATGTATTAGGATGGATTGATTTATTTTAAAAGTGAATTGATTTATTTTAAATATG
GATGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAATAAATTATTTAGTATGG
ATTGATTTATTTTAAAACATAGATTGATATATTATTGTAGTTG
Found at i:2256108 original size:53 final size:54
Alignment explanation
Indices: 2255875--2256571 Score: 451
Period size: 53 Copynumber: 13.3 Consensus size: 54
2255865 ATTGTAGTTG
*
2255875 TATGGA-TGATTTATTTTAAATAATTTATTAG--TGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
* *
2255925 -ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAAAAATTA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTT-ATTT--TAAA--A
* * ***
2255983 TTTGTATGGATTGATTTATTTT-AA-AA--CA-TAG-ATTGA-T-ATATTATTGTAGTTG
1 ----TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGAT-TTATTTTA-AAA
*
2256035 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTTATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
*
2256089 TATGGATTG-TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
* ** * * ** * * *
2256142 T-TGAATTGATTTATTTTAAAT-ATGGA-T-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGA-TTGATTTATTTTA-AAA
*
2256193 TATGGATTGATTTATTTTAAATAATTTATTTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATTGATTGATTTATTTTAAAA
* * * *
2256248 TATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTAATTTATTTAAAAATATTA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATTGATTGATTTATTT--TAA-A--A
* ** * * ** * * *
2256301 GTATGGATTGATTTATTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 -TATGGATTGATTTATTTTAAATAATTTATTAGTATTGA-TTGATTTATTTTA-AAA
* * * * ***
2256355 TATGAATTGATTT-TTTT-AA-AA--TA-T-GGATTGATTTA-TTATTGTAGTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTA-AAA
*
2256402 TATGGATTGATTTATTTTAAATAA-TTATTAG-ATGGATTGATTTA-TTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
*
2256452 -ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
2256505 TATGGATTGATTTA-TTTAAATAA-TTATTAGTA-TGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTG-ATTGATTTATTTTAAAA
2256557 TA-GGATTGATTTATT
1 TATGGATTGATTTATT
2256572 ATTGTAGTTG
Statistics
Matches: 516, Mismatches: 69, Indels: 122
0.73 0.10 0.17
Matches are distributed among these distances:
47 19 0.04
48 45 0.09
49 45 0.09
50 48 0.09
51 36 0.07
52 85 0.16
53 97 0.19
54 41 0.08
55 29 0.06
56 20 0.04
57 10 0.02
58 16 0.03
59 4 0.01
61 2 0.00
62 2 0.00
63 17 0.03
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
Found at i:2256165 original size:73 final size:73
Alignment explanation
Indices: 2256068--2256213 Score: 251
Period size: 73 Copynumber: 2.0 Consensus size: 73
2256058 ATTTATTAGT
*
2256068 ATTGATTTATTTATTTTAAAATATGGATTG-TTTATTTTAAATAATTTATTAGTATGGATTGATT
1 ATTGATTGATTTATTTTAAAATATGGA-TGATTTATTTTAAATAATTTATTAGTATGGATTGATT
2256132 TATTTTAAA
65 TATTTTAAA
2256141 ATTGAATTGATTTATTTT-AAATATGGATGATTTATTTTAAATAATTTATTAGTATGGATTGATT
1 ATTG-ATTGATTTATTTTAAAATATGGATGATTTATTTTAAATAATTTATTAGTATGGATTGATT
2256205 TATTTTAAA
65 TATTTTAAA
2256214 TAATTTATTT
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
72 2 0.03
73 56 0.80
74 12 0.17
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (73 bp):
ATTGATTGATTTATTTTAAAATATGGATGATTTATTTTAAATAATTTATTAGTATGGATTGATTT
ATTTTAAA
Found at i:2256171 original size:20 final size:21
Alignment explanation
Indices: 2256120--2256183 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
2256110 AATTTATTAG
2256120 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
*
2256141 -ATTGAATTGATTTATTTTAAA
1 TA-TGGATTGATTTATTTTAAA
2256162 TATGGA-TGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2256182 TA
1 TA
2256184 ATTTATTAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
20 17 0.44
21 21 0.54
22 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (21 bp):
TATGGATTGATTTATTTTAAA
Found at i:2256254 original size:22 final size:22
Alignment explanation
Indices: 2256226--2256343 Score: 94
Period size: 22 Copynumber: 5.0 Consensus size: 22
2256216 ATTTATTTAG
2256226 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
***
2256248 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTA-T-TT-TA-AAA
* *
2256274 TATGGATTAATTTATTTAAAAATATTA
1 TATGGATTGATTTATTT--TAA-A--A
2256301 GTATGGATTGATTTA-TTTAAAA
1 -TATGGATTGATTTATTTTAAAA
2256323 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2256344 TAATTTATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
21 14 0.19
22 21 0.28
23 1 0.01
24 5 0.07
25 6 0.08
26 13 0.17
27 2 0.03
28 13 0.17
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2256327 original size:21 final size:21
Alignment explanation
Indices: 2256302--2256345 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2256292 AAAATATTAG
2256302 TATGGATTGATTTATTTAAAA
1 TATGGATTGATTTATTTAAAA
*
2256323 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTAAAA
2256344 TA
1 TA
2256346 ATTTATTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (21 bp):
TATGGATTGATTTATTTAAAA
Found at i:2256350 original size:31 final size:31
Alignment explanation
Indices: 2256315--2256374 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
2256305 GGATTGATTT
*
2256315 ATTTA-AAATATGGATTGATTTATTTTAAATA
1 ATTTATAAATATGAATTGATTT-TTTTAAATA
* *
2256346 ATTTATTAGTATGAATTGATTTTTTTAAA
1 ATTTATAAATATGAATTGATTTTTTTAAA
2256375 ATATGGATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (31 bp):
ATTTATAAATATGAATTGATTTTTTTAAATA
Found at i:2256372 original size:128 final size:128
Alignment explanation
Indices: 2255744--2256651 Score: 772
Period size: 128 Copynumber: 6.9 Consensus size: 128
2255734 TATTTTAAAA
2255744 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTA-TTTAAA-AA--TATTAG-ATGGATTGATTTA-TTTAAAATATGGATTGAT
*
2255809 TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA--T-TTATTGTA
60 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
2255871 GTTG
125 GTTG
*
2255875 TATGGA-TGATTTATTTTAAATAATTTATTAG-TGGATTGATTTATTTTAAA-ATGGATTGATTT
1 TATGGATTGATTTA-TTTAAA-AA--TATTAGATGGATTGATTTATTTAAAATATGGATTGATTT
* * * *
2255937 ATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAAAAATTATTTGTATGGATTGATTTAT
62 ATTTTAAATAATTTATTAGTATGGATTGATTT-ATTT-TAAAA-TA--TGGATTGATTTA-TTAT
* ***
2256002 TTTA-AAA
121 TGTAGTTG
* * * *** * **
2256009 CATAGATTGATATA-TT-ATTGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATT
1 TATGGATTGATTTATTTAAAAATA-TTAG-ATGGATTGATTTATTTAAAAT-ATGGATT-G-ATT
* ** * * * ** **
2256071 GA-TTTATTTATTTTA-AAATATGGATTG-TTTATTTT-AAATAATTTATTAGTATGGATTGATT
61 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G-ATTTATT-ATT
*
2256132 -TA-TTT
122 GTAGTTG
* * * * * *
2256137 TAAAATTGAATTGATTTATTT-TAAATA-TGGAT-GATTTATTTTAAATAATTTATTAGTATGGA
1 T---A-TGGATTGATTTATTTAAAAATATTAGATGGATTGA--TT---T-ATTTA-AAATATGGA
2256199 TTGATTTATTTTAAATAATTTATTTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
55 TTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
2256264 ATTGTAGTTG
119 ATTGTAGTTG
*
2256274 TATGGATTAATTTATTTAAAAATATTAGTATGGATTGATTTATTTAAAATATGGATTGATTTATT
1 TATGGATTGATTTATTTAAAAATATTAG-ATGGATTGATTTATTTAAAATATGGATTGATTTATT
*
2256339 TTAAATAATTTATTAGTATGAATTGATTT-TTTTAAAATATGGATTGATTTATTATTGTAGTTG
65 TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
2256402 TATGGATTGATTTATTTTAAATAATTATTAGATGGATTGATTTATTT-AAA-ATGGATTGATTTA
1 TATGGATTGATTTA-TTTAAA-AA-TATTAGATGGATTGATTTATTTAAAATATGGATTGATTTA
2256465 TTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTAAATAAT-
63 TTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA-TT--AT--TG
2256529 TA-TTAG
123 TAGTT-G
* * * * * ***
2256535 TATGAATTGATTTATTTTAAAATA--GGATTGATTTA-TTATTGTAGTTGTATGGATTGATTTAT
1 TATGGATTGATTTATTTAAAAATATTAGATGGATTGATTTATT-TA-AAATATGGATTGATTTAT
2256597 TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
64 TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
2256652 TTAAATAATT
Statistics
Matches: 644, Mismatches: 74, Indels: 119
0.77 0.09 0.14
Matches are distributed among these distances:
126 43 0.07
127 19 0.03
128 121 0.19
129 63 0.10
130 85 0.13
131 119 0.18
132 26 0.04
133 50 0.08
134 26 0.04
135 36 0.06
136 18 0.03
137 21 0.03
138 13 0.02
139 4 0.01
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (128 bp):
TATGGATTGATTTATTTAAAAATATTAGATGGATTGATTTATTTAAAATATGGATTGATTTATTT
TAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
Found at i:2256417 original size:79 final size:75
Alignment explanation
Indices: 2256323--2256466 Score: 234
Period size: 79 Copynumber: 1.9 Consensus size: 75
2256313 TTATTTAAAA
*
2256323 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTTTTTAAAATATGGATTGATT
1 TATGGATTGATTTATTTTAAATAA-TTATTAG-ATGAATTGATTTATTT-AAA-ATGGATTGATT
2256388 TATTATTGTAGTTG
62 TATTATTGTAGTTG
*
2256402 TATGGATTGATTTATTTTAAATAATTATTAGATGGATTGATTTATTTAAAATGGATTGATTTATT
1 TATGGATTGATTTATTTTAAATAATTATTAGATGAATTGATTTATTTAAAATGGATTGATTTATT
2256467 TTAAATAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
75 15 0.24
76 3 0.05
77 14 0.22
78 7 0.11
79 24 0.38
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (75 bp):
TATGGATTGATTTATTTTAAATAATTATTAGATGAATTGATTTATTTAAAATGGATTGATTTATT
ATTGTAGTTG
Found at i:2256439 original size:239 final size:240
Alignment explanation
Indices: 2255925--2256688 Score: 885
Period size: 235 Copynumber: 3.1 Consensus size: 240
2255915 TTATTTTAAA
* *
2255925 ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAA-AAATTATTT-GT
1 ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTAGT
* * *
2255988 ATGGATTGATTTATTTTAAAACATAGATTGATATATTATTGTAGTTGTATGGATTGATTTATTTT
66 ATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTA-TTT
2256053 AAATAATTTATTAGTATTGATTTATTTATTTTAAAATATGGATTG-TTTATTTTAAATAATTTAT
130 AAA-AA--TATTAGTATTGATTTATTTA-TTTAAAATATGGATTGATTTATTTTAAATAATTTAT
* **
2256117 TAGTATGGATTGATTTATTTTAAAAT-TGAATTGATTTA-T-TTTA-AAT
191 TAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTTATTGT
2256163 ATGGA-TGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTAGT
1 ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTAGT
*
2256227 ATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTAATTTATTTA
66 ATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTA
* *
2256292 AAAATATTAGTATGGATTGATTTATTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTA
131 AAAATATTAGTATTGATTTATTTATTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTA
*
2256357 TGAATTGATTT-TTTTAAAATATGGATTGATTTATTATTGTAGTTGT
196 TGGATTGATTTATTTTAAAATATGGATTGATTTATTATT-TA-TTGT
*
2256403 ATGGATTGATTTATTTTAAATAATTATTAGATGGATTGATTTATTTAAAATGGATTGATTTATTT
1 ATGGATTGATTTA-TTT---TAA--A-TA-AT---TT-A-TTA-GT---ATGGATTGATTTATTT
2256468 TAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTAAATAAT-TA
49 TAAATAATTTATTTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA-TT--AT--TGTA
* * * ***
2256531 -TTAGTATGAATTGATTTATTT-TAAA-A-TAGGATTGATTTA-TTATTGTAGTTGTATGGATTG
109 GTT-GTATGGATTGATTTATTTAAAAATATTAGTATTGATTTATTTATT-TA-AAATATGGATTG
2256591 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
171 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA---T--
2256656 ATAATTTATTAGT
231 -T-ATTTATT-GT
2256669 ATGGATTGATTTATTTTAAA
1 ATGGATTGATTTATTTTAAA
2256689 ATATGGATTG
Statistics
Matches: 459, Mismatches: 23, Indels: 66
0.84 0.04 0.12
Matches are distributed among these distances:
234 25 0.05
235 63 0.14
236 1 0.00
237 49 0.11
238 21 0.05
239 59 0.13
240 6 0.01
241 7 0.02
242 3 0.01
245 3 0.01
247 1 0.00
248 2 0.00
249 2 0.00
252 2 0.00
253 1 0.00
254 3 0.01
255 1 0.00
257 45 0.10
258 41 0.09
259 45 0.10
260 30 0.07
261 18 0.04
262 4 0.01
263 1 0.00
265 5 0.01
266 18 0.04
267 3 0.01
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.52
Consensus pattern (240 bp):
ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTAGT
ATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTA
AAAATATTAGTATTGATTTATTTATTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTA
TGGATTGATTTATTTTAAAATATGGATTGATTTATTATTTATTGT
Found at i:2256622 original size:32 final size:32
Alignment explanation
Indices: 2256581--2256688 Score: 146
Period size: 32 Copynumber: 3.7 Consensus size: 32
2256571 TATTGTAGTT
2256581 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2256613 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2256636 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2256667 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
2256689 ATATGGATTG
Statistics
Matches: 66, Mismatches: 0, Indels: 20
0.77 0.00 0.23
Matches are distributed among these distances:
22 14 0.21
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 36 0.55
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:2256639 original size:22 final size:22
Alignment explanation
Indices: 2256614--2256656 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2256604 AATTTATTAG
2256614 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2256636 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2256657 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2256693 original size:22 final size:22
Alignment explanation
Indices: 2256668--2256710 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2256658 AATTTATTAG
2256668 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2256690 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2256711 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2256770 original size:31 final size:31
Alignment explanation
Indices: 2256735--2256793 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2256725 AGTTGTATAG
*
2256735 ATTATTTAAAT-TTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTT-AGTATTGCAAAACTAAA
2256766 ATTATTTAAATCTTAGTATTGCAAAACT
1 ATTATTTAAATCTTAGTATTGCAAAACT
2256794 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTTAGTATTGCAAAACTAAA
Found at i:2258062 original size:22 final size:22
Alignment explanation
Indices: 2258037--2258272 Score: 332
Period size: 22 Copynumber: 10.7 Consensus size: 22
2258027 CCTATTTTAA
2258037 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2258059 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
2258081 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
2258103 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
**
2258125 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
*
2258146 ATTTTATTTTAAAATATAGATTG
1 A-TTTATTTTAAAATATGGATTG
*
2258169 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
* **
2258191 GTTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
2258212 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
2258235 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2258257 ATTTATTTTAAAATAT
1 ATTTATTTTAAAATAT
2258273 TTATTATTGT
Statistics
Matches: 188, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
21 1 0.01
22 185 0.98
23 2 0.01
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:2258350 original size:31 final size:31
Alignment explanation
Indices: 2258293--2258351 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2258283 AGTTGTATGG
* *
2258293 ATTATTTAAATTTTAGTATTATAAAACTAAA
1 ATTATTTAAATTTAAGTATTACAAAACTAAA
*
2258324 ATTATTTAAATTTAAGTATTGCAAAACT
1 ATTATTTAAATTTAAGTATTACAAAACT
2258352 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTAAGTATTACAAAACTAAA
Found at i:2260022 original size:37 final size:35
Alignment explanation
Indices: 2259982--2260237 Score: 238
Period size: 36 Copynumber: 7.2 Consensus size: 35
2259972 TAAAATTACG
2259982 TATATAATATATAGTTTCTAAAAATATTTTGAAAAT
1 TATATAATATATAGTTT-TAAAAATATTTTGAAAAT
* * *
2260018 GTATATAATATATAGTTTTTAAAACACTTTTGAAAAC
1 -TATATAATATATAGTTTTAAAAATA-TTTTGAAAAT
* * *
2260055 TATATAATATATAGTTTTAAAAAAATTTAGAAAAAA
1 TATATAATATATAGTTTTAAAAATATTTTG-AAAAT
2260091 TATATAATATATAGCTTTT-AAAATCATTTTGAAAACT
1 TATATAATATATAG-TTTTAAAAAT-ATTTTGAAAA-T
* * *
2260128 TATATAATATATAGTTTTTGAAAACT-TTTTTAAACT
1 TATATAATATATAG-TTTT-AAAAATATTTTGAAAAT
* *
2260164 TATACAATATATAGTTTTTGAAAACGT-TTTTGAAAAT
1 TATATAATATATAG-TTTT-AAAA-ATATTTTGAAAAT
* *
2260201 TATATAGT-T-T--TTTAAAAAATATTTTGAAAAT
1 TATATAATATATAGTTTTAAAAATATTTTGAAAAT
2260232 TATATA
1 TATATA
2260238 GTTTTTTTAA
Statistics
Matches: 188, Mismatches: 22, Indels: 24
0.80 0.09 0.10
Matches are distributed among these distances:
30 1 0.01
31 20 0.11
32 3 0.02
35 5 0.03
36 80 0.43
37 75 0.40
39 4 0.02
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (35 bp):
TATATAATATATAGTTTTAAAAATATTTTGAAAAT
Found at i:2260069 original size:73 final size:70
Alignment explanation
Indices: 2259982--2260237 Score: 279
Period size: 73 Copynumber: 3.6 Consensus size: 70
2259972 TAAAATTACG
2259982 TATATAATATATAGTTTCTAAAAATATTTTGAAAATGTATATAATATATAGTTTTTAAAACACTT
1 TATATAATATATAGTTT-TAAAAATATTTTGAAAAT-TATATAATATATAGTTTTTAAAACA-TT
2260047 TTGAAAAC
63 TTGAAAAC
* * * *
2260055 TATATAATATATAGTTTTAAAAAAATTTAGAAAAAATATATAATATATAGCTTTTAAAATCATTT
1 TATATAATATATAGTTTTAAAAATATTTTG-AAAATTATATAATATATAGTTTTTAAAA-CATTT
2260120 TGAAAAC
64 TGAAAAC
* * * * *
2260127 TTATATAATATATAGTTTTTGAAAACT-TTTTTAAACTTATACAATATATAGTTTTTGAAAACGT
1 -TATATAATATATAG-TTTT-AAAAATATTTTGAAAATTATATAATATATAGTTTTT-AAAAC-A
*
2260191 TTTTGAAAAT
61 TTTTGAAAAC
* *
2260201 TATATAGT-T-T--TTTAAAAAATATTTTGAAAATTATATA
1 TATATAATATATAGTTTTAAAAATATTTTGAAAATTATATA
2260238 GTTTTTTTAA
Statistics
Matches: 155, Mismatches: 20, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
67 5 0.03
68 16 0.10
71 1 0.01
72 44 0.28
73 65 0.42
74 20 0.13
75 4 0.03
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (70 bp):
TATATAATATATAGTTTTAAAAATATTTTGAAAATTATATAATATATAGTTTTTAAAACATTTTG
AAAAC
Found at i:2260113 original size:109 final size:109
Alignment explanation
Indices: 2259982--2260181 Score: 300
Period size: 109 Copynumber: 1.8 Consensus size: 109
2259972 TAAAATTACG
2259982 TATATAATATATAGTTTCTAAAAAT-ATTTTGAAAA-TGTATATAATATATAGTTTTTAAAACAC
1 TATATAATATATAGTTTCT-AAAATCATTTTGAAAACT-TATATAATATATAGTTTTTAAAA-AC
*
2260045 TTTTGAAAAC-TATATAATATATAGTTTTAAAAAAATTTAGAAAAAA
63 TTTTGAAAACTTATACAATATATAGTTTTAAAAAAATTTAGAAAAAA
*
2260091 TATATAATATATAGCTTT-TAAAATCATTTTGAAAACTTATATAATATATAGTTTTTGAAAACTT
1 TATATAATATATAG-TTTCTAAAATCATTTTGAAAACTTATATAATATATAGTTTTTAAAAACTT
**
2260155 TTTTAAACTTATACAATATATAGTTTT
65 TTGAAAACTTATACAATATATAGTTTT
2260182 TGAAAACGTT
Statistics
Matches: 83, Mismatches: 4, Indels: 8
0.87 0.04 0.08
Matches are distributed among these distances:
108 15 0.18
109 64 0.77
110 4 0.05
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (109 bp):
TATATAATATATAGTTTCTAAAATCATTTTGAAAACTTATATAATATATAGTTTTTAAAAACTTT
TGAAAACTTATACAATATATAGTTTTAAAAAAATTTAGAAAAAA
Found at i:2260207 original size:30 final size:31
Alignment explanation
Indices: 2260171--2260243 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
2260161 ACTTATACAA
**
2260171 TATATAGTTTTTGAAAACGT-TTTTGAAAAT
1 TATATAGTTTTTGAAAAAATATTTTGAAAAT
*
2260201 TATATAGTTTTTTAAAAAATATTTTGAAAAT
1 TATATAGTTTTTGAAAAAATATTTTGAAAAT
2260232 TATATAGTTTTT
1 TATATAGTTTTT
2260244 TTAAAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 17 0.44
31 22 0.56
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.51
Consensus pattern (31 bp):
TATATAGTTTTTGAAAAAATATTTTGAAAAT
Found at i:2260226 original size:31 final size:30
Alignment explanation
Indices: 2260171--2260251 Score: 117
Period size: 30 Copynumber: 2.6 Consensus size: 30
2260161 ACTTATACAA
* **
2260171 TATATAGTTTTTGAAAACGTTTTTGAAAAT
1 TATATAGTTTTTTAAAAAATTTTTGAAAAT
2260201 TATATAGTTTTTTAAAAAATATTTTGAAAAT
1 TATATAGTTTTTTAAAAAAT-TTTTGAAAAT
2260232 TATATAGTTTTTTTAAAAAA
1 TATATAG-TTTTTTAAAAAA
2260252 AACATTTTCG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 17 0.37
31 17 0.37
32 12 0.26
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (30 bp):
TATATAGTTTTTTAAAAAATTTTTGAAAAT
Found at i:2260298 original size:41 final size:38
Alignment explanation
Indices: 2260230--2260339 Score: 123
Period size: 41 Copynumber: 2.7 Consensus size: 38
2260220 TATTTTGAAA
*
2260230 ATTATATAGTTTTTTTAAAAAAAACATTTTCGAAAATTTAT
1 ATTATATAG--TTTTT-AAAAAAACATTTTCAAAAATTTAT
*
2260271 A-TATAATATGTAGTTTTAAAAAAACATTTTTAAAAATTTAT
1 ATTAT-ATA-GT--TTTTAAAAAAACATTTTCAAAAATTTAT
2260312 ATTATATAGTTTTTAAAAGAAACATTTT
1 ATTATATAGTTTTTAAAA-AAACATTTT
2260340 TTATATTATT
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
38 8 0.13
39 9 0.15
40 6 0.10
41 30 0.49
42 8 0.13
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTATATAGTTTTTAAAAAAACATTTTCAAAAATTTAT
Found at i:2260313 original size:39 final size:39
Alignment explanation
Indices: 2260230--2260340 Score: 118
Period size: 39 Copynumber: 2.7 Consensus size: 39
2260220 TATTTTGAAA
* *
2260230 ATTATATAGTTTTTTTAAAAAAAACATTTTCGAAAATTTATAT
1 ATTATATAG--TTTTT-AAAAAAACATTTT-TAAAAATTATAT
*
2260273 ATAATAT-GTAGTTTTAAAAAAACATTTTTAAAAATT-TAT
1 ATTATATAGT--TTTTAAAAAAACATTTTTAAAAATTATAT
2260312 ATTATATAGTTTTTAAAAGAAACATTTTT
1 ATTATATAGTTTTTAAAA-AAACATTTTT
2260341 TATATTATTA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
38 8 0.13
39 19 0.32
40 9 0.15
41 13 0.22
42 5 0.08
43 6 0.10
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (39 bp):
ATTATATAGTTTTTAAAAAAACATTTTTAAAAATTATAT
Found at i:2260383 original size:5 final size:5
Alignment explanation
Indices: 2260351--2260401 Score: 59
Period size: 5 Copynumber: 9.6 Consensus size: 5
2260341 TATATTATTA
2260351 TTTA- TTTAT TATTAT TACTTATT TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT T-TTAT T--TTA-T TTTAT TTTAT TTTAT TTTAT TTTAT
2260399 TTT
1 TTT
2260402 TCGTTTCAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
4 4 0.10
5 25 0.60
6 8 0.19
7 3 0.07
8 2 0.05
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:2261361 original size:4 final size:4
Alignment explanation
Indices: 2261352--2261398 Score: 51
Period size: 4 Copynumber: 11.2 Consensus size: 4
2261342 TTAGTCTCTT
*
2261352 TTTA TTTA TTTA TTTG TTTA TTTTA TTTA -TTA TTTTA TTTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA -TTTA -TTTA TTTA T
2261399 CTAACCGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 3 0.08
4 23 0.61
5 12 0.32
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2261378 original size:17 final size:17
Alignment explanation
Indices: 2261351--2261398 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
2261341 ATTAGTCTCT
2261351 TTTTA-TTTATTTATT-
1 TTTTATTTTATTTATTA
2261366 TGTTTATTTTATTTATTA
1 T-TTTATTTTATTTATTA
2261384 TTTTATTTTATTTAT
1 TTTTATTTTATTTAT
2261399 CTAACCGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.03
16 4 0.13
17 24 0.80
18 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTATTTTATTTATTA
Found at i:2261503 original size:22 final size:22
Alignment explanation
Indices: 2261478--2261521 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2261468 TATTATCACG
2261478 ATATTTATTTA-TTTTATATTTT
1 ATATTTATTTACTTTTAT-TTTT
*
2261500 ATATTTTTTTACTTTTATTTTT
1 ATATTTATTTACTTTTATTTTT
2261522 GTATCTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (22 bp):
ATATTTATTTACTTTTATTTTT
Found at i:2261532 original size:23 final size:22
Alignment explanation
Indices: 2261485--2261544 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
2261475 ACGATATTTA
*
2261485 TTTA-TTTTATATTTTATATTTT
1 TTTACTTTTAT-TTTTATATTCT
*
2261507 TTTACTTTTATTTTTGTATCTCT
1 TTTACTTTTATTTTTATAT-TCT
2261530 TTTAACTTTTTATTT
1 TTT-AC-TTTTATTT
2261545 AGTTATCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 11 0.34
23 11 0.34
24 2 0.06
25 8 0.25
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTACTTTTATTTTTATATTCT
Found at i:2261537 original size:24 final size:23
Alignment explanation
Indices: 2261489--2261544 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
2261479 TATTTATTTA
*
2261489 TTTTATATTTTATATTTTTTTAC-
1 TTTTAT-TTTTATATTTTTTAACT
*
2261512 TTTTATTTTTGTATCTCTTTTAACT
1 TTTTATTTTTATAT-T-TTTTAACT
2261537 TTTTATTT
1 TTTTATTT
2261545 AGTTATCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 7 0.25
23 7 0.25
24 6 0.21
25 8 0.29
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTATTTTTATATTTTTTAACT
Found at i:2266594 original size:110 final size:110
Alignment explanation
Indices: 2266398--2266834 Score: 648
Period size: 110 Copynumber: 4.0 Consensus size: 110
2266388 TGATGGTGGT
*
2266398 AGCTCAACTTCACAGCGAAGGGGCGGTTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* *
2266463 CAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACA
* * *
2266508 AGCTCAACTTCACAGTGAAGGGGCGGCTGAATGTCAACAAACAACTTTTCAGTTTCATTCAGAGC
1 AGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
*
2266573 CAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACA
*
2266618 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * *
2266683 CAATTTCAACTTCACAGTGAATGATATTGGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACA
* ** * * * * *
2266728 AGCTCAACTTCACAGTGAAGGGATGGTTGGCTATCAACAAATAACTTTCCAG--T--TTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * *
2266789 CAATTTCAACTTCACAGCGAATGATATTGGCCTCAAAACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACA
2266834 A
1 A
2266835 ATATTTGGAT
Statistics
Matches: 299, Mismatches: 28, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
106 50 0.17
108 1 0.00
110 248 0.83
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (110 bp):
AGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACA
Found at i:2267083 original size:80 final size:80
Alignment explanation
Indices: 2266949--2267994 Score: 1029
Period size: 80 Copynumber: 12.8 Consensus size: 80
2266939 CCACCAAAAT
* * *
2266949 ACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCACAGCTTAATTCAAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAG
*
2267014 GGCTATCTGCCAAAG
66 GGTTATCTGCCAAAG
* * * **
2267029 GCCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTTGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAG
*
2267094 GGCTATCTGCCAAAG
66 GGTTATCTGCCAAAG
* * * * * * * * *
2267109 ACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTTAAGTCGAGAA
1 ACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAA
2267174 GGGTTATCTGTCACCAAAAG
65 GGGTTATCTG---CC-AAAG
* * * * *
2267194 ACCTTTGAGTTCGACTATGCTCAGCTCCAAGGTACATCATTTGCAACGTAGCTTAAGTCGAA-AA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC-AAGAA
*
2267258 GGGCTATCTGCCAAAG
65 GGGTTATCTGCCAAAG
* * * ** *
2267274 ACCTTCGAGTTCGACTACGCTCAACTCTAAGGCACATCATTTACAATATAGCTTAAGTCGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAG
**
2267339 GACTATCTGCCAAAG
66 GGTTATCTGCCAAAG
* * * * * * * *
2267354 ACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT-AGATA
1 ACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCA-AGA
*
2267418 AGGGTTATCTCTCACCAAAAG
64 AGGGTTA--TCT-GCC-AAAG
* *
2267439 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAACTTAAGTCGAA-AA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC-AAGAA
2267503 GGGTTATCTGCCAAAG
65 GGGTTATCTGCCAAAG
* * * * *
2267519 ACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATATTATTTGCAACATAGCTTAAGTCGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAG
*
2267584 GGCTATCTGCCAAAG
66 GGTTATCTGCCAAAG
* * * ** * * * * *
2267599 ACCCTCAAGTTCGATTACATTCAACTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
1 ACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAA
* *
2267664 TGGTTATCTATCACCAAAAG
65 GGGTTATC--T-GCC-AAAG
* * *
2267684 ACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAG
2267749 GGTTATCTGCCAAAG
66 GGTTATCTGCCAAAG
* * * * * * * *
2267764 ACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGGCTAGAA
1 ACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAA
2267829 GGGTTATCTGCCAACAAAG
65 GGGTTATCTG-C--CAAAG
* * * * * * * * * * *
2267848 ATCTTTGAGTTCGATTACGCTCAGCT-AAACGGTACATCATTTACGGTATAGCTCAAGGCTAGAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCAAGAA
2267912 GGGTTATCTGCCAAAG
65 GGGTTATCTGCCAAAG
* * * ** * * *
2267928 ACCTTCGAGTTCAACTATGCTCAGCTCCAACGCACATCATTCACAACATAGCTCAAGGCAAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAG
2267993 GG
66 GG
2267995 CTATATGTCA
Statistics
Matches: 806, Mismatches: 133, Indels: 54
0.81 0.13 0.05
Matches are distributed among these distances:
79 2 0.00
80 359 0.45
81 168 0.21
82 7 0.01
83 44 0.05
84 153 0.19
85 72 0.09
86 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (80 bp):
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAG
GGTTATCTGCCAAAG
Found at i:2267248 original size:165 final size:161
Alignment explanation
Indices: 2266949--2267939 Score: 1072
Period size: 165 Copynumber: 6.1 Consensus size: 161
2266939 CCACCAAAAT
* * * * * * * * *
2266949 ACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCACAGCTTAATTCAAGAA
1 ACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
* * *
2267013 GGGCTATCTGCCAAAGGCCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACAT
66 GGGTTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACAT
*
2267078 AGCTTAAGTTGAGAAGGGCTATCTGCCAAAG
131 AGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
* * *
2267109 ACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTTAAGTCGAGAA
1 ACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
* * *
2267174 GGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTATGCTCAGCTCCAAGGTACATCATTTGCA
66 GGGTTATCTG---CC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCA
* *
2267239 ACGTAGCTTAAGTCGAAAAGGGCTATCTGCCAAAG
127 ACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
* * * * * * ** *
2267274 ACCTTCGAGTTCGACTACGCTCAAC-TCTAAGGCACATCATTTACAATATAGCTTAAGTCGAGAA
1 ACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
** * * * * * * *
2267338 GGACTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCA
66 GGGTTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAACA
* * * * *
2267403 TAACTTAAGTAGATAAGGGTTATCTCTCACCAAAAG
130 TAGCTTAAGTCGAGAAGGGCTA--TCT-GCC-AAAG
* * * * * *
2267439 ACCTTCGAGTTCGACTACGCTCAGC-TCCAAGACACATCATTTGCAGCATAACTTAAGTCGAAAA
1 ACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
* * *
2267503 GGGTTATCTGCCAAAGACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATATTATTTGCAACAT
66 GGGTTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACAT
2267568 AGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
131 AGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
* * * *
2267599 ACCCTCAAGTTCGATTACATTCAACTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
1 ACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
* * * *
2267664 TGGTTATCTATCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTGCA
66 GGGTTATC--T-GCC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCA
* * * *
2267729 GCATAACTTAAGTCAAGAAGGGTTATCTGCCAAAG
127 ACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
* * *
2267764 ACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGGCTAGAA
1 ACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
* * * * * * *
2267829 GGGTTATCTGCCAACAAAGATCTTTGAGTTCGATTACGCTCAGCT-AAACGGTACATCATTTACG
66 GGGTTATCTG-C--CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCA
** * * * *
2267893 GTATAGCTCAAGGCTAGAAGGGTTATCTGCCAAAG
127 ACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
2267928 ACCTTCGAGTTC
1 ACCTTCGAGTTC
2267940 AACTATGCTC
Statistics
Matches: 696, Mismatches: 116, Indels: 34
0.82 0.14 0.04
Matches are distributed among these distances:
160 66 0.09
161 123 0.18
162 3 0.00
163 8 0.01
164 163 0.23
165 333 0.48
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (161 bp):
ACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
GGGTTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACAT
AGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
Found at i:2267370 original size:245 final size:245
Alignment explanation
Indices: 2266940--2267998 Score: 1376
Period size: 245 Copynumber: 4.3 Consensus size: 245
2266930 GAATCGTGCC
* * * *
2266940 CACCAAAATACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCACAGCTTAA
1 CACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
* * *
2267005 TTCAAGAAGGGCTATCTGCCAAAGGCCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
66 GTCAAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
2267070 TGCAACATAGCTTAAGTTGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCT
131 TGCAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCT
* *
2267135 TCGAGGGCACATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGT
196 TCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTAT
* * * * * *
2267185 CACCAAAAGACCTTTGAGTTCGACTATGCTCAGCTCCAAGGTACATCATTTGCAACGTAGCTTAA
1 CACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
* *
2267250 GTCGAA-AAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAACTCTAAGGCACATCAT
66 GTC-AAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* * *
2267314 TTACAATATAGCTTAAGTCGAGAAGGACTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGC
130 TTGCAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGC
* * *
2267379 TTCGAGGGCACATCATTTGCAGCATAACTTAAGTAGATAAGGGTTATCTCT
195 TTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTAT
*
2267430 CACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAACTTAA
1 CACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
* * * *
2267495 GTCGAA-AAGGGTTATCTGCCAAAGACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATATTAT
66 GTC-AAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* *
2267559 TTGCAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACATTCAAC
130 TTGCAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGC
*
2267624 TTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAATGGTTATCTAT
195 TTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTAT
* *
2267675 CACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAA
1 CACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
* * * * *
2267740 GTCAAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
66 GTCAAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
* * * * * * * * ** *
2267805 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGATCTTTGAGTTCGATTACGCTC
130 TTGCAACATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCTCAAGTTCGATTACACTC
** * * * * * * * * *
2267870 AGC-TAAACGGTACATCATTTACGGTATAGCTCAAGGCTAGAAGGGTTATC--T
192 AGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTAT
* * * * ** * * *
2267921 -GCC-AAAGACCTTCGAGTTCAACTATGCTCAGCTCCAACGCACATCATTCACAACATAGCTCAA
1 CACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
*
2267984 GGCAAGAAGGGCTAT
66 GTCAAGAAGGGCTAT
2267999 ATGTCAATAA
Statistics
Matches: 719, Mismatches: 89, Indels: 13
0.88 0.11 0.02
Matches are distributed among these distances:
244 67 0.09
245 551 0.77
246 42 0.06
247 1 0.00
248 35 0.05
249 23 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (245 bp):
CACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
GTCAAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCT
TCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTAT
Found at i:2268636 original size:37 final size:35
Alignment explanation
Indices: 2268555--2268821 Score: 257
Period size: 37 Copynumber: 7.2 Consensus size: 35
2268545 CGTATATATA
* * *
2268555 TATATATATATTATAGTTTGTAAACGATTTTTAAAAAT
1 TATATA-ATA-TATAGTTTTTAAA-AATTTTTGAAAAT
* *
2268593 ACGTATATAATATATAGTTTCTAAAAATATTTTTAAAAT
1 ---TATATAATATATAGTTTTTAAAAAT-TTTTGAAAAT
* *
2268632 GTATATAATATATAGTTTTTAAAACACTTTTGAAAAC
1 -TATATAATATATAGTTTTTAAAA-ATTTTTGAAAAT
* *
2268669 TATATAATATATAGTTTTTAAAACATTTTAGAAAAAA
1 TATATAATATATAGTTTTTAAAA-ATTTTTG-AAAAT
2268706 TATATAATATATAGTTTTT-AAAATCATTTTGAAAACT
1 TATATAATATATAGTTTTTAAAAAT--TTTTGAAAA-T
* * *
2268743 TATATAATATATAGTTTTTGAAAACTTTTTTAAACT
1 TATATAATATATAGTTTTT-AAAAATTTTTGAAAAT
*
2268779 TATATAATATATAGTTTTTGAAAACGTTTTTGAAAAT
1 TATATAATATATAGTTTTT-AAAA-ATTTTTGAAAAT
2268816 TATATA
1 TATATA
2268822 GTTTTTTTAA
Statistics
Matches: 199, Mismatches: 18, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
35 2 0.01
36 61 0.31
37 99 0.50
38 3 0.02
39 25 0.13
40 3 0.02
41 6 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (35 bp):
TATATAATATATAGTTTTTAAAAATTTTTGAAAAT
Found at i:2268682 original size:73 final size:70
Alignment explanation
Indices: 2268596--2268821 Score: 290
Period size: 73 Copynumber: 3.1 Consensus size: 70
2268586 TAAAAATACG
*
2268596 TATATAATATATAGTTTCTAAAAATATTTTTAAAATGTATATAATATATAGTTTTTAAAACACTT
1 TATATAATATATAGTTTTTAAAAAT-TTTTTAAAAT-TATATAATATATAGTTTTTAAAACA-TT
2268661 TTGAAAAC
63 TTGAAAAC
** *
2268669 TATATAATATATAGTTTTTAAAACATTTTAGAAAAAATATATAATATATAGTTTTTAAAATCATT
1 TATATAATATATAGTTTTTAAAA-ATTTT-TTAAAATTATATAATATATAGTTTTTAAAA-CATT
2268734 TTGAAAAC
63 TTGAAAAC
* * *
2268742 TTATATAATATATAGTTTTTGAAAACTTTTTTAAACTTATATAATATATAGTTTTTGAAAACGTT
1 -TATATAATATATAGTTTTT-AAAAATTTTTTAAAATTATATAATATATAGTTTTT-AAAAC-AT
*
2268807 TTTGAAAAT
62 TTTGAAAAC
2268816 TATATA
1 TATATA
2268822 GTTTTTTTAA
Statistics
Matches: 135, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
73 87 0.64
74 44 0.33
75 4 0.03
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (70 bp):
TATATAATATATAGTTTTTAAAAATTTTTTAAAATTATATAATATATAGTTTTTAAAACATTTTG
AAAAC
Found at i:2268821 original size:110 final size:110
Alignment explanation
Indices: 2268596--2268814 Score: 318
Period size: 110 Copynumber: 2.0 Consensus size: 110
2268586 TAAAAATACG
*
2268596 TATATAATATATAGTTTCTAAAAATATTTTTAAAATGTATATAATATATAGTTTTTAAAACACTT
1 TATATAATATATAGTTTCTAAAAATATTTTGAAAATGTATATAATATATAGTTTTTAAAACACTT
2268661 TTGAAAACTATATAATATATAGTTTTTAAAACATTTTAGAAAAAA
66 TTGAAAACTATATAATATATAGTTTTTAAAACATTTTAGAAAAAA
* *
2268706 TATATAATATATAGTTT-TTAAAATCATTTTGAAAACT-TATATAATATATAGTTTTTGAAA-AC
1 TATATAATATATAGTTTCTAAAAAT-ATTTTGAAAA-TGTATATAATATATAGTTTTTAAAACAC
** * *
2268768 TTTTTTAAACTTATATAATATATAGTTTTTGAAAACGTTTTTGAAAA
64 TTTTGAAAAC-TATATAATATATAGTTTTT-AAAACATTTTAGAAAA
2268815 TTATATAGTT
Statistics
Matches: 98, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
109 16 0.16
110 67 0.68
111 15 0.15
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (110 bp):
TATATAATATATAGTTTCTAAAAATATTTTGAAAATGTATATAATATATAGTTTTTAAAACACTT
TTGAAAACTATATAATATATAGTTTTTAAAACATTTTAGAAAAAA
Found at i:2268848 original size:34 final size:34
Alignment explanation
Indices: 2268805--2268890 Score: 129
Period size: 34 Copynumber: 2.5 Consensus size: 34
2268795 TTTGAAAACG
*
2268805 TTTTTGAAAATTATATAGTTTTTTTAAAAACCAT-
1 TTTTTGAAAATTATATAGTTTTTTTAAAAA-AATA
2268839 TTTTTGAAAATTATATAGTTTTTTTAAAAAAATA
1 TTTTTGAAAATTATATAGTTTTTTTAAAAAAATA
*
2268873 TTTTCGAAAATTTATATA
1 TTTTTGAAAA-TTATATA
2268891 TAATATGTAG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
33 2 0.04
34 39 0.81
35 7 0.15
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (34 bp):
TTTTTGAAAATTATATAGTTTTTTTAAAAAAATA
Found at i:2268946 original size:41 final size:42
Alignment explanation
Indices: 2268848--2268961 Score: 119
Period size: 40 Copynumber: 2.8 Consensus size: 42
2268838 TTTTTTGAAA
* **
2268848 ATTATATAGTTTTTTTAAAAAA-ATATTTTCGAAAATTTATAT
1 ATTATATAGTTTTTTAAAAAAACAT-TTTTTTAAAATTTATAT
* **
2268890 ATAATAT-G-TAGTTAAAAAAACATTTTTTTAAAATTT-TAT
1 ATTATATAGTTTTTTAAAAAAACATTTTTTTAAAATTTATAT
*
2268929 ATTATATAGTTTTTTAAAAGAAACACTTTTTTA
1 ATTATATAGTTTTTTAAAA-AAACATTTTTTTA
2268962 TATTAATATT
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
39 9 0.16
40 21 0.36
41 10 0.17
42 18 0.31
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (42 bp):
ATTATATAGTTTTTTAAAAAAACATTTTTTTAAAATTTATAT
Found at i:2269007 original size:16 final size:16
Alignment explanation
Indices: 2268956--2269011 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
2268946 AAGAAACACT
*
2268956 TTTTTATATTAATATTTA
1 TTTTTAT-TTTAT-TTTA
*
2268974 TTTATTATTATTA-CTTA
1 TTT-TTATT-TTATTTTA
2268991 TTTTTATTTTATTTTA
1 TTTTTATTTTATTTTA
2269007 TTTTT
1 TTTTT
2269012 CGTTTTAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 3 0.09
16 13 0.41
17 6 0.19
18 4 0.12
19 6 0.19
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTATTTTATTTTA
Found at i:2270068 original size:17 final size:17
Alignment explanation
Indices: 2270046--2270087 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
2270036 ATTAGTCCCT
2270046 TTTTATTTATTTGTTTA
1 TTTTATTTATTTGTTTA
2270063 TTTTATTTATTTGTTTA
1 TTTTATTTATTTGTTTA
2270080 TTTTATTT
1 TTTTATTT
2270088 TAATTATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTATTTATTTGTTTA
Found at i:2271849 original size:31 final size:31
Alignment explanation
Indices: 2271813--2271881 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
2271803 AAGATTTGAA
2271813 AGCTTAGGTACTAAAACGGACTAAAATTAAT
1 AGCTTAGGTACTAAAACGGACTAAAATTAAT
2271844 AGCTTAGGTACTAAAACGGACTAAAATTAAT
1 AGCTTAGGTACTAAAACGGACTAAAATTAAT
*
2271875 AGTTTAG
1 AGCTTAG
2271882 ATATTAAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (31 bp):
AGCTTAGGTACTAAAACGGACTAAAATTAAT
Found at i:2272343 original size:33 final size:34
Alignment explanation
Indices: 2272276--2272344 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 34
2272266 TTGACGTTTG
* * *
2272276 GGATTTAGAGTTTAATATTTAGGGTTTAGGATTT
1 GGATTTAGAGTTTAAGATTTAGAGTTTAGAATTT
* *
2272310 GGATTTAGA-TTTAAGATTTATAGTTTATAATTT
1 GGATTTAGAGTTTAAGATTTAGAGTTTAGAATTT
2272343 GG
1 GG
2272345 GGTTCGAGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 21 0.70
34 9 0.30
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (34 bp):
GGATTTAGAGTTTAAGATTTAGAGTTTAGAATTT
Found at i:2281249 original size:32 final size:32
Alignment explanation
Indices: 2281213--2281323 Score: 186
Period size: 32 Copynumber: 3.5 Consensus size: 32
2281203 TTGGGCATAT
* *
2281213 GAGCCAACCTAAGGGAGTACCTTGGGGCCTTA
1 GAGCCTACCCAAGGGAGTACCTTGGGGCCTTA
2281245 GAGCCTACCCAAGGGAGTACCTTGGGGCCTTA
1 GAGCCTACCCAAGGGAGTACCTTGGGGCCTTA
*
2281277 GAGCCTACCCAAGGGAGTACCTTGGGGCCTAA
1 GAGCCTACCCAAGGGAGTACCTTGGGGCCTTA
*
2281309 GAGCCTACCTAAGGG
1 GAGCCTACCCAAGGG
2281324 TTACCTTTGG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 75 1.00
ACGTcount: A:0.24, C:0.27, G:0.32, T:0.17
Consensus pattern (32 bp):
GAGCCTACCCAAGGGAGTACCTTGGGGCCTTA
Found at i:2282228 original size:12 final size:12
Alignment explanation
Indices: 2282213--2282273 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
2282203 CAGAGATATA
2282213 AGAAATCAAAAC
1 AGAAATCAAAAC
* *
2282225 AGAATTCAAATC
1 AGAAATCAAAAC
* *
2282237 AGATATCAGAAC
1 AGAAATCAAAAC
*
2282249 AG-AATCCAAATC
1 AGAAAT-CAAAAC
*
2282261 AGAAATCAGAAC
1 AGAAATCAAAAC
2282273 A
1 A
2282274 TAATTCAGGT
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
11 2 0.06
12 31 0.86
13 3 0.08
ACGTcount: A:0.56, C:0.18, G:0.11, T:0.15
Consensus pattern (12 bp):
AGAAATCAAAAC
Done.