Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 45 of 132
Found at i:12290003 original size:30 final size:31
Alignment explanation
Indices: 12289962--12290025 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
12289952 TGAACTATTT
12289962 AAAAATCATATTTTAACCCCTAAACTTTCCA
1 AAAAATCATATTTTAACCCCTAAACTTTCCA
* *
12289993 AAAAAT-ATATTTTCACCCCTGAACTTTCCA
1 AAAAATCATATTTTAACCCCTAAACTTTCCA
12290023 AAA
1 AAA
12290026 TTTACATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.81
31 6 0.19
ACGTcount: A:0.42, C:0.25, G:0.02, T:0.31
Consensus pattern (31 bp):
AAAAATCATATTTTAACCCCTAAACTTTCCA
Found at i:12290047 original size:30 final size:28
Alignment explanation
Indices: 12289984--12290477 Score: 158
Period size: 29 Copynumber: 16.8 Consensus size: 28
12289974 TTAACCCCTA
* * *
12289984 AACTTTCCAAAAAATATATTTTCACCCCTG
1 AACTTTCCAAAAATTACATTTT-ACCTC-G
*
12290014 AACTTTCCAAAATTTACATTATTACCCTCG
1 AACTTTCCAAAAATTACATT-TTA-CCTCG
*
12290044 AAC-TTCATAAAAATTACCATTTTACCTCG
1 AACTTTC-CAAAAATTA-CATTTTACCTCG
* *
12290073 AA-TTTCCAAAAAGTCCATTTTTGACCTCG
1 AACTTTCCAAAAATTACA-TTTT-ACCTCG
* * *
12290102 AACTTTTCAAAAATTACCATTCTACCCCCG
1 AACTTTCCAAAAATTA-CATTTTA-CCTCG
* * * *
12290132 AA-TGTCAAAAAATTCCAATTTTCACC-CTA
1 AACTTTCCAAAAATTAC-ATTTT-ACCTC-G
* * *
12290161 AAC-TTCCCAAAATTACCATTTTACCCCA
1 AACTTTCCAAAAATTA-CATTTTACCTCG
*
12290189 AGAC-TTCCAAAAAATCTA-TTTTTGAGCC-CG
1 A-ACTTTCC-AAAAAT-TACATTTT-A-CCTCG
* *
12290219 AACTTTCCCAAAATTACCATTTTACCCCTG
1 AACTTTCCAAAAATTA-CATTTTACCTC-G
* * * *
12290249 AA-TGTCTAAAAATTCCATTTTAGACCTCA
1 AACTTTCCAAAAATTACATTTT--ACCTCG
* *
12290278 AACTTTCCCAAAATTAGCATTTTACCCCCG
1 AACTTTCCAAAAATTA-CATTTTA-CCTCG
* * *
12290308 AAC-ATCCAAAAATTTA-TTTTTGACC-CC
1 AACTTTCCAAAAA-TTACATTTT-ACCTCG
* *
12290335 ATACTTTCCCAAAATTACCATTTTACC-CTT
1 A-ACTTTCCAAAAATTA-CATTTTACCTC-G
* * *
12290365 AAATTTCCAAAAATTCCATTTTTAACC-CTA
1 AACTTTCCAAAAATTACA-TTTT-ACCTC-G
*
12290395 AACTTTCCCAAAATTACCATTTTACCCTCG
1 AACTTTCCAAAAATTA-CATTTTA-CCTCG
* * *
12290425 AA-TGTCTAATAATT-CTATTTTTGACCTCG
1 AACTTTCCAAAAATTAC-A-TTTT-ACCTCG
12290454 AAC-TTCCTAAAAATTTACCATTTT
1 AACTTTCC-AAAAA-TTA-CATTTT
12290478 TCCCCTGGCA
Statistics
Matches: 349, Mismatches: 64, Indels: 101
0.68 0.12 0.20
Matches are distributed among these distances:
27 5 0.01
28 41 0.12
29 141 0.40
30 130 0.37
31 30 0.09
32 1 0.00
33 1 0.00
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.34
Consensus pattern (28 bp):
AACTTTCCAAAAATTACATTTTACCTCG
Found at i:12290321 original size:176 final size:176
Alignment explanation
Indices: 12290053--12290475 Score: 516
Period size: 176 Copynumber: 2.4 Consensus size: 176
12290043 GAACTTCATA
* * * * *
12290053 AAAATTACCATTTTACCTC-GAATTTCCAAAAAGTCCATTTTTGACCTCGAACTTTTCAAAAATT
1 AAAATTACCATTTTACCCCTGAATGTCTAAAAATTCCATTTTTGACCTCGAACTTTCCAAAAATT
** *
12290117 ACCATTCTACCCCCGAATGTCAAAAAATTCCAATTTTCACCCTAAAC-TTCCCAAAATTACCATT
66 ACCATTCTACCCCCGAACATCAAAAAATT-CAATTTTCACCCCAAACTTTCCCAAAATTACCATT
* * *
12290181 TTACCC-CAAGACTTCCAAAAAATCTATTTTTGAGCCC-GAACTTTCCC
130 TTACCCTCAA-ACTTCCAAAAAATCCATTTTT-AACCCTAAACTTTCCC
* * *
12290228 AAAATTACCATTTTACCCCTGAATGTCTAAAAATTCCATTTTAGACCTCAAACTTTCCCAAAATT
1 AAAATTACCATTTTACCCCTGAATGTCTAAAAATTCCATTTTTGACCTCGAACTTTCCAAAAATT
* * * * * * *
12290293 AGCATTTTACCCCCGAACATCCAAAAATTTATTTTTGACCCCATACTTTCCCAAAATTACCATTT
66 ACCATTCTACCCCCGAACATCAAAAAATTCAATTTTCACCCCAAACTTTCCCAAAATTACCATTT
* * *
12290358 TACCCTTAAATTTCCAAAAATTCCATTTTTAACCCTAAACTTTCCC
131 TACCCTCAAACTTCCAAAAAATCCATTTTTAACCCTAAACTTTCCC
* *
12290404 AAAATTACCATTTTA-CCCTCGAATGTCTAATAATTCTATTTTTGACCTCGAAC-TTCCTAAAAA
1 AAAATTACCATTTTACCCCT-GAATGTCTAAAAATTCCATTTTTGACCTCGAACTTTCC-AAAAA
12290467 TTTACCATT
64 -TTACCATT
12290476 TTTCCCCTGG
Statistics
Matches: 211, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
175 42 0.20
176 160 0.76
177 9 0.04
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (176 bp):
AAAATTACCATTTTACCCCTGAATGTCTAAAAATTCCATTTTTGACCTCGAACTTTCCAAAAATT
ACCATTCTACCCCCGAACATCAAAAAATTCAATTTTCACCCCAAACTTTCCCAAAATTACCATTT
TACCCTCAAACTTCCAAAAAATCCATTTTTAACCCTAAACTTTCCC
Found at i:12290458 original size:59 final size:58
Alignment explanation
Indices: 12290053--12290477 Score: 414
Period size: 59 Copynumber: 7.2 Consensus size: 58
12290043 GAACTTCATA
* * * * *
12290053 AAAATTACCATTTTA-CCTCGAATTTCCAAAAAGTCCATTTTTGACCTCGAACTTTTCA
1 AAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACC-CAAACTTTCCC
* * * * *
12290111 AAAATTACCATTCTACCCCCGAATGTCAAAAAATTCCAATTTTCACCCTAAAC-TTCCC
1 AAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACCC-AAACTTTCCC
* * * *
12290169 AAAATTACCATTTTACCC-CAAGACT-TCCAAAAAATCTATTTTTGAGCCCGAACTTTCCC
1 AAAATTACCATTTTACCCTC--GAATGTCCAAAAATTCCATTTTTGA-CCCAAACTTTCCC
* *
12290228 AAAATTACCATTTTACCC-CTGAATGTCTAAAAATTCCATTTTAGACCTCAAACTTTCCC
1 AAAATTACCATTTTACCCTC-GAATGTCCAAAAATTCCATTTTTGACC-CAAACTTTCCC
* * ** * *
12290287 AAAATTAGCATTTTACCCCCGAACATCCAAAAATT-TATTTTTGACCCCATACTTTCCC
1 AAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGA-CCCAAACTTTCCC
** * *
12290345 AAAATTACCATTTTACCCTTAAATTTCCAAAAATTCCATTTTTAACCCTAAACTTTCCC
1 AAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACCC-AAACTTTCCC
* * * * *
12290404 AAAATTACCATTTTACCCTCGAATGTCTAATAATTCTATTTTTGACCTCGAAC-TTCCTA
1 AAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACC-CAAACTTTCC-C
12290463 AAAATTTACCATTTT
1 AAAA-TTACCATTTT
12290478 TCCCCTGGCA
Statistics
Matches: 302, Mismatches: 50, Indels: 28
0.79 0.13 0.07
Matches are distributed among these distances:
57 1 0.00
58 111 0.37
59 178 0.59
60 12 0.04
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACCCAAACTTTCCC
Found at i:12290506 original size:117 final size:115
Alignment explanation
Indices: 12290053--12290484 Score: 489
Period size: 117 Copynumber: 3.7 Consensus size: 115
12290043 GAACTTCATA
* * *
12290053 AAAATTACCATTTTA-CCTCGAATTTCCAAAAAGTCCATTTTTGACCTCGAACTTTTCAAAAATT
1 AAAATTACCATTTTACCCTCGAA-TTCCAAAAATTCTATTTTTGACC-CGAACTTTCCAAAAATT
* * *
12290117 ACCATTCTACCCCCGAATGTCAAAAAATTCCAATTTTCACCCTAAAC-TTCCC
64 ACCATTTTACCCCTGAATGTCAAAAAATTCC-ATTTTAACCCTAAACTTTCCC
* * *
12290169 AAAATTACCATTTTACCC-CAAGACTTCCAAAAAATCTATTTTTGAGCCCGAACTTTCCCAAAAT
1 AAAATTACCATTTTACCCTC--GAATTCCAAAAATTCTATTTTTGA-CCCGAACTTTCCAAAAAT
*
12290233 TACCATTTTACCCCTGAATGTCTAAAAATTCCATTTTAGA-CCTCAAACTTTCCC
63 TACCATTTTACCCCTGAATGTCAAAAAATTCCATTTTA-ACCCT-AAACTTTCCC
* * * * *
12290287 AAAATTAGCATTTTACCCCCGAACATCCAAAAATT-TATTTTTGACCCCATACTTTCCCAAAATT
1 AAAATTACCATTTTACCCTCGAA-TTCCAAAAATTCTATTTTTGACCCGA-ACTTTCCAAAAATT
* * * *
12290351 ACCATTTTACCCTTAAATTTCCAAAAATTCCATTTTTAACCCTAAACTTTCCC
64 ACCATTTTACCCCTGAATGTCAAAAAATTCCA-TTTTAACCCTAAACTTTCCC
* *
12290404 AAAATTACCATTTTACCCTCGAATGTCTAATAATTCTATTTTTGACCTCGAAC-TTCCTAAAAAT
1 AAAATTACCATTTTACCCTCGAAT-TCCAAAAATTCTATTTTTGACC-CGAACTTTCC-AAAAA-
*
12290468 TTACCATTTTTCCCCTG
62 TTACCATTTTACCCCTG
12290485 GCAGCAATAA
Statistics
Matches: 271, Mismatches: 28, Indels: 31
0.82 0.08 0.09
Matches are distributed among these distances:
116 28 0.10
117 166 0.61
118 60 0.22
119 17 0.06
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (115 bp):
AAAATTACCATTTTACCCTCGAATTCCAAAAATTCTATTTTTGACCCGAACTTTCCAAAAATTAC
CATTTTACCCCTGAATGTCAAAAAATTCCATTTTAACCCTAAACTTTCCC
Found at i:12294433 original size:23 final size:23
Alignment explanation
Indices: 12294407--12294468 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
12294397 ATTACGTACA
* *
12294407 TGCATTTTTTCACATTGCATATT
1 TGCATATTTTCACATAGCATATT
*
12294430 TGCATATTTTCGCATAGCATATT
1 TGCATATTTTCACATAGCATATT
*
12294453 TGCATATTTTCGCATA
1 TGCATATTTTCACATA
12294469 ATAATTCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (23 bp):
TGCATATTTTCACATAGCATATT
Found at i:12302051 original size:23 final size:25
Alignment explanation
Indices: 12302025--12302070 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12302015 CCAATTAAGG
12302025 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
12302048 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
12302071 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:12303181 original size:20 final size:22
Alignment explanation
Indices: 12303137--12303187 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 22
12303127 TTTTATTATT
*
12303137 TATTTTT-ATTTTATTATTTGC
1 TATTTTTAATTTAATTATTTGC
12303158 -ATTTTTAATTTAATT-TTT-C
1 TATTTTTAATTTAATTATTTGC
12303177 TA-TTTTAATTT
1 TATTTTTAATTT
12303188 TTTTCCCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 10 0.37
20 10 0.37
21 7 0.26
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (22 bp):
TATTTTTAATTTAATTATTTGC
Found at i:12306953 original size:10 final size:10
Alignment explanation
Indices: 12306940--12306978 Score: 60
Period size: 10 Copynumber: 3.7 Consensus size: 10
12306930 AGTCGAAAAG
12306940 AAAAAAATGA
1 AAAAAAATGA
12306950 AAAAAAATGA
1 AAAAAAATGA
12306960 AAAAAAATTGA
1 AAAAAAA-TGA
12306971 GAAAAAAA
1 -AAAAAAA
12306979 GAAGAAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 17 0.63
11 3 0.11
12 7 0.26
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:12306954 original size:11 final size:11
Alignment explanation
Indices: 12306940--12306978 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
12306930 AGTCGAAAAG
12306940 AAAAAAATG-A
1 AAAAAAATGAA
12306950 AAAAAAATGAA
1 AAAAAAATGAA
*
12306961 AAAAAATTGAGA
1 AAAAAAATGA-A
12306973 AAAAAA
1 AAAAAA
12306979 GAAGAAGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 9 0.35
11 10 0.38
12 7 0.27
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:12308029 original size:23 final size:25
Alignment explanation
Indices: 12308003--12308048 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12307993 CCAATTAAGG
12308003 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
12308026 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
12308049 TGAATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:12310522 original size:209 final size:208
Alignment explanation
Indices: 12309873--12310528 Score: 850
Period size: 209 Copynumber: 3.1 Consensus size: 208
12309863 AACATAAAGC
* *
12309873 GGTTACCTTCCTGATGAGATA-TAGAGAAGTAAACCAGATCTGTCTTCCTGATGAGACACAGAGA
1 GGTTACCTTCCTGATAAGATACT-GAGAAGTGAACCAGATCTGTCTTCCTGATGAGACACAGAGA
* * * *
12309937 AGTGGATCAAAACAAGCGATGCGGTCTTCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAT
65 AGTGGATTAAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAATCAAT
* ** * * * *
12310002 AAAATCAGGCTCAAAGTGAGAGAATCTTCGAACCCCAGCTTCCTAATAAGATATTGAGAAGCAGG
130 GAAGCCAAGCTCAAAGTGAGCGAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCA-G
**
12310067 TCGAAGCAATAAAGC
194 TCGAAGCAATAAAAT
* * *
12310082 AGTTACCTTCCTGATAAGATACAT-AGAAGTGAACCAGATCCGTCTTCCTGATAAGACACAGAGA
1 GGTTACCTTCCTGATAAGATAC-TGAGAAGTGAACCAGATCTGTCTTCCTGATGAGACACAGAGA
* * *
12310146 AGTGGA-TCAAACTAAGCGAAGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGGCCAAATCAA
65 AGTGGATTAAAAC-AAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAATCAA
* * * *
12310210 TGAAGCCAAGCTCAAAATGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATATTAAGAAGCAT
129 TGAAGCCAAGCTCAAAGTGAGCGAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCA-
12310275 GTCGAAGCAATAAAAT
193 GTCGAAGCAATAAAAT
* * * * * * * * * *
12310291 GGTTAGCTTCCTAATGAGATACTGAGAAGTGGACCAAATTTGCCTTCTTGATGAGATACTGAGAA
1 GGTTACCTTCCTGATAAGATACTGAGAAGTGAACCAGATCTGTCTTCCTGATGAGACACAGAGAA
** * *
12310356 GCAGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAATCAATG
66 GTGGATTAAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAATCAATG
* *
12310421 AAGCCAAGCTCAAAGTAAGCGAATCTTCGAACCCCAGCTGCCTGATGAGATATTGAGAAGCAGAT
131 AAGCCAAGCTCAAAGTGAGCGAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAG-T
12310486 CGAAGCAATAAAAT
195 CGAAGCAATAAAAT
* *
12310500 GGTTATCTTCCTGATAAGATACTCAGAAG
1 GGTTACCTTCCTGATAAGATACTGAGAAG
12310529 CGGATTGAAA
Statistics
Matches: 386, Mismatches: 55, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
208 6 0.02
209 374 0.97
210 5 0.01
211 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (208 bp):
GGTTACCTTCCTGATAAGATACTGAGAAGTGAACCAGATCTGTCTTCCTGATGAGACACAGAGAA
GTGGATTAAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAATCAATG
AAGCCAAGCTCAAAGTGAGCGAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGTC
GAAGCAATAAAAT
Found at i:12310926 original size:12 final size:12
Alignment explanation
Indices: 12310911--12310978 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
12310901 TATTTTAAGA
*
12310911 TTAAATTTATTT
1 TTAAATTTATGT
*
12310923 TTAAATTTGT-T
1 TTAAATTTATGT
*
12310934 TTAAAATTTAAGT
1 TT-AAATTTATGT
*
12310947 TT-AATTTAAGT
1 TTAAATTTATGT
* *
12310958 TTAAATTCATAT
1 TTAAATTTATGT
12310970 TTAAATTTA
1 TTAAATTTA
12310979 AAAATATTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
11 14 0.30
12 29 0.63
13 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (12 bp):
TTAAATTTATGT
Found at i:12310954 original size:29 final size:29
Alignment explanation
Indices: 12310893--12310960 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
12310883 CTAAACCCAT
* *
12310893 TTTAAATTTATTTTAAGATTAAATTTATT
1 TTTAAATTTATTTTAAAATTAAATTTATA
* *
12310922 TTTAAATTTGTTTTAAAATTTAAGTTTA-A
1 TTTAAATTTATTTTAAAA-TTAAATTTATA
*
12310951 TTTAAGTTTA
1 TTTAAATTTA
12310961 AATTCATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (29 bp):
TTTAAATTTATTTTAAAATTAAATTTATA
Found at i:12310998 original size:16 final size:16
Alignment explanation
Indices: 12310966--12310999 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
12310956 GTTTAAATTC
12310966 ATATTTAAATTTAAAA
1 ATATTTAAATTTAAAA
12310982 ATATTCTAAATTTAAAA
1 ATATT-TAAATTTAAAA
12310999 A
1 A
12311000 AACAAAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATTTAAATTTAAAA
Found at i:12312921 original size:30 final size:30
Alignment explanation
Indices: 12312885--12312951 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
12312875 CCCTAAAATG
*
12312885 TCCAAAAATCATATTTTGACCCCCAAACTT
1 TCCAAAAATCACATTTTGACCCCCAAACTT
* *
12312915 TCCAAAAGTTACATTTTGACCCCCAAACTT
1 TCCAAAAATCACATTTTGACCCCCAAACTT
12312945 TCCAAAA
1 TCCAAAA
12312952 TTTACATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.28
Consensus pattern (30 bp):
TCCAAAAATCACATTTTGACCCCCAAACTT
Found at i:12312957 original size:30 final size:30
Alignment explanation
Indices: 12312897--12312959 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
12312887 CAAAAATCAT
12312897 ATTTTGACCCCCAAACTTTCCAAAAGTTAC
1 ATTTTGACCCCCAAACTTTCCAAAAGTTAC
*
12312927 ATTTTGACCCCCAAACTTTCCAAAATTTAC
1 ATTTTGACCCCCAAACTTTCCAAAAGTTAC
12312957 ATT
1 ATT
12312960 ATCACGAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (30 bp):
ATTTTGACCCCCAAACTTTCCAAAAGTTAC
Found at i:12313031 original size:29 final size:28
Alignment explanation
Indices: 12312999--12313281 Score: 159
Period size: 29 Copynumber: 9.6 Consensus size: 28
12312989 ACCACTAAAT
*
12312999 TTCCAAAAATTCAATTTTTGACCCTGAAC
1 TTCCAAAAATTCCATTTTT-ACCCTGAAC
* * *
12313028 TTCCTAAAAACTACCA-TTTTACCTTGGAC
1 TTCC-AAAAA-TTCCATTTTTACCCTGAAC
* *** * **
12313057 TTCCAAAACTTTTGTCCTAAACCCTGAAC
1 TTCCAAAAATTCCAT-TTTTACCCTGAAC
*
12313086 TTTCCCAAAATTACCA-TTTTACCCCTGAA-
1 -TTCCAAAAATT-CCATTTTTA-CCCTGAAC
**
12313115 TGTCCAAAAATTCCATTTTTTACTTTGAAC
1 T-TCCAAAAATTCCA-TTTTTACCCTGAAC
*
12313145 TTCCCAAAAATTACCA-TTTTACCCTCAAAC
1 TT-CCAAAAATT-CCATTTTTACCCT-GAAC
*
12313175 TTCCAAAAATTCC-TTTTTAACCCCGAAC
1 TTCCAAAAATTCCATTTTT-ACCCTGAAC
* *
12313203 TTTCCCAAAATTATCA-TTTTACCCTCG-AC
1 -TTCCAAAAATT-CCATTTTTACCCT-GAAC
12313232 TGTCCAAAAATTCCATTTTTGA-CCTCGAAC
1 T-TCCAAAAATTCCATTTTT-ACCCT-GAAC
12313262 TTCCTAAAAATTACCATTTT
1 TTCC-AAAAATT-CCATTTT
12313282 CCTCGAGCAT
Statistics
Matches: 193, Mismatches: 35, Indels: 50
0.69 0.13 0.18
Matches are distributed among these distances:
27 1 0.01
28 20 0.10
29 97 0.50
30 62 0.32
31 13 0.07
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (28 bp):
TTCCAAAAATTCCATTTTTACCCTGAAC
Found at i:12313037 original size:59 final size:57
Alignment explanation
Indices: 12312965--12313281 Score: 260
Period size: 59 Copynumber: 5.4 Consensus size: 57
12312955 ACATTATCAC
* * * * *
12312965 GAACTTCAAAAAAATTACCAATTTACCACTAAATTTCCAAAAATTCAATTTTTGACCCT
1 GAACTTC-CAAAAATTACCATTTTACC-CTGAATTTCCAAAAATTCCATTTTTAACCCT
* * * * * *** ** *
12313024 GAACTTCCTAAAAACTACCATTTTACCTTGGACTTCCAAAACTTTTGTCCTAAACCCT
1 GAACTTCC-AAAAATTACCATTTTACCCTGAATTTCCAAAAATTCCATTTTTAACCCT
* * * **
12313082 GAACTTTCCCAAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCATTTTTTACTTT
1 GAAC-TTCCAAAAATTACCATTTTA-CCCTGAATTTCCAAAAATTCCATTTTTAACCCT
* * *
12313141 GAACTTCCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCC-TTTTTAACCCC
1 GAACTT-CCAAAAATTACCATTTTACCCT-GAATTTCCAAAAATTCCATTTTTAACCCT
* * * * *
12313199 GAACTTTCCCAAAATTATCATTTTACCCTCGACTGTCCAAAAATTCCATTTTTGA-CCT
1 GAAC-TTCCAAAAATTACCATTTTACCCT-GAATTTCCAAAAATTCCATTTTTAACCCT
12313257 CGAACTTCCTAAAAATTACCATTTT
1 -GAACTTCC-AAAAATTACCATTTT
12313282 CCTCGAGCAT
Statistics
Matches: 200, Mismatches: 49, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
58 94 0.47
59 106 0.53
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (57 bp):
GAACTTCCAAAAATTACCATTTTACCCTGAATTTCCAAAAATTCCATTTTTAACCCT
Found at i:12313107 original size:117 final size:115
Alignment explanation
Indices: 12312975--12313281 Score: 368
Period size: 117 Copynumber: 2.6 Consensus size: 115
12312965 GAACTTCAAA
* * * * *
12312975 AAAATTACCAATTTACCACTAAATTTCCAAAAATTCAATTTTTGACCCTGAACTTCCTAAAAACT
1 AAAATTACCATTTTACC-CTGAATGTCCAAAAATTCCATTTTTGACCCTGAACTTCCTAAAAATT
*** * *
12313040 ACCATTTTA-CCTTGGACTTCCAAAACTT-TTGTCCTAAACCCTGAACTTTCCC
65 ACCATTTTACCCTCAAACTTCCAAAAATTCTT-T--TAAACCCCGAACTTTCCC
* ** *
12313092 AAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCATTTTTTACTTTGAACTTCCCAAAAATT
1 AAAATTACCATTTTA-CCCTGAATGTCCAAAAATTCCATTTTTGACCCTGAACTTCCTAAAAATT
*
12313157 ACCATTTTACCCTCAAACTTCCAAAAATTCCTTTTTAACCCCGAACTTTCCC
65 ACCATTTTACCCTCAAACTTCCAAAAATT-CTTTTAAACCCCGAACTTTCCC
* *
12313209 AAAATTATCATTTTACCCTCGACTGTCCAAAAATTCCATTTTTGA-CCTCGAACTTCCTAAAAAT
1 AAAATTACCATTTTACCCT-GAATGTCCAAAAATTCCATTTTTGACCCT-GAACTTCCTAAAAAT
12313273 TACCATTTT
64 TACCATTTT
12313282 CCTCGAGCAT
Statistics
Matches: 163, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
116 5 0.03
117 138 0.85
118 17 0.10
119 1 0.01
120 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (115 bp):
AAAATTACCATTTTACCCTGAATGTCCAAAAATTCCATTTTTGACCCTGAACTTCCTAAAAATTA
CCATTTTACCCTCAAACTTCCAAAAATTCTTTTAAACCCCGAACTTTCCC
Found at i:12316514 original size:17 final size:17
Alignment explanation
Indices: 12316473--12316528 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
12316463 AATATGAAAA
* *
12316473 TAAATTTAAATTCAATT
1 TAAATTTAAAATAAATT
*
12316490 TCAAATTTAAAATAAATC
1 T-AAATTTAAAATAAATT
12316508 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
12316525 TAAA
1 TAAA
12316529 AGGGCTCGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 20 0.59
18 14 0.41
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:12327927 original size:23 final size:23
Alignment explanation
Indices: 12327901--12327962 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
12327891 ATTACATACA
* *
12327901 TGCATTTTTTCACATTGCATATT
1 TGCATATTTTCACATAGCATATT
*
12327924 TGCATATTTTCGCATAGCATATT
1 TGCATATTTTCACATAGCATATT
*
12327947 TGCATATTTTCGCATA
1 TGCATATTTTCACATA
12327963 ATAATTCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (23 bp):
TGCATATTTTCACATAGCATATT
Found at i:12335550 original size:23 final size:25
Alignment explanation
Indices: 12335524--12335569 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12335514 CCAATTAAGG
12335524 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
12335547 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
12335570 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:12336666 original size:20 final size:22
Alignment explanation
Indices: 12336622--12336672 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 22
12336612 TTTTATTATT
*
12336622 TATTTTT-ATTTTATTATTTGC
1 TATTTTTAATTTAATTATTTGC
12336643 -ATTTTTAATTTAATT-TTT-C
1 TATTTTTAATTTAATTATTTGC
12336662 TA-TTTTAATTT
1 TATTTTTAATTT
12336673 TTTTCCCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 10 0.37
20 10 0.37
21 7 0.26
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (22 bp):
TATTTTTAATTTAATTATTTGC
Found at i:12339490 original size:10 final size:11
Alignment explanation
Indices: 12339474--12339499 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12339464 TCATTTTTTT
12339474 AAAAAAAATTG
1 AAAAAAAATTG
12339485 AAAAAAAATTG
1 AAAAAAAATTG
12339496 AAAA
1 AAAA
12339500 GTTCAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:12340437 original size:11 final size:11
Alignment explanation
Indices: 12340423--12340462 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
12340413 AGTCGAAAAG
12340423 AAAAAAA-TGA
1 AAAAAAATTGA
12340433 AAAAAAATTGA
1 AAAAAAATTGA
12340444 AAAAAAATTGA
1 AAAAAAATTGA
12340455 GAAAAAAA
1 -AAAAAAA
12340463 GAAGAAGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 7 0.25
11 14 0.50
12 7 0.25
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:12341512 original size:23 final size:25
Alignment explanation
Indices: 12341486--12341531 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12341476 CCAATTAAGA
12341486 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
12341509 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
12341532 TGAATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:12343719 original size:209 final size:207
Alignment explanation
Indices: 12343346--12344001 Score: 821
Period size: 209 Copynumber: 3.1 Consensus size: 207
12343336 TATCCAAAAC
* * * *
12343346 ATAAAGCGGTTAACTTCCTGATGAGATATAGAGAAGTAAACCAGATCTGTCTTCCTGATGAGACA
1 ATAAAACGGTTAACTTCCTGATAAGATACAGAGAAGTGAACCAGATC-GTCTTCCTGATGAGACA
* * * *
12343411 CAGAGTAGTGGATCAAAACAAGC-AATGCGGTCTTCTTCTTGATGAGATACTGAGAAGAAGACCA
65 CAGAGAAGTGGATC-AAACAAGCGAA-GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCA
* ** ** * *
12343475 AATCAATAAAATCGGGCTCAAAGTGAG-AGAATCTTCGAACCCCAGCTTCCTAATAAGATATTGA
128 AATCAATGAAGCCAAGCTCAAAGTGAGCA-AATCTTCGAACCCCAGCTTCCTGATGAGATATTGA
*
12343539 GAAGCAGGTCAAAGCA
192 GAAGCAGGTCGAAGCA
* * * *
12343555 ATAAAGCAGTTACCTTCCTGATAAGATACAGAGAAGTGAACCAGATACGTCTTCCTGATAAGACA
1 ATAAAACGGTTAACTTCCTGATAAGATACAGAGAAGTGAACCAGAT-CGTCTTCCTGATGAGACA
*
12343620 CAGAGAAGTGGATCAAACTAAGCGAAGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGGCCAA
65 CAGAGAAGTGGATCAAAC-AAGCGAAGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAA
* * * *
12343685 ATCAATGAAGCCAAGCTCAAAATGAGCAAATCTTCGAACCCCAACTTCTTGATGAGATATTAAGA
129 ATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGA
*
12343750 AGCATGTCGAAGCA
194 AGCAGGTCGAAGCA
* * * * * * * *
12343764 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGCCTTCCTGATGAGATA
1 ATAAAACGGTTAACTTCCTGATAAGATACAGAGAAGTGAACCAGA-TCGTCTTCCTGATGAGACA
* ** * * *
12343829 CTGAGAAGCAGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAA
65 CAGAGAAGTGGA-TCAAACAAGCGAAGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAA
* * *
12343894 ATCAATGAAGCCAAGCTCAAAGTAAGCGAATCTTCGAACCCCAGCTGCCTGATGAGATATTGAGA
129 ATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGA
12343959 AGCAGGTCGAAGCA
194 AGCAGGTCGAAGCA
* *
12343973 ATAAAATGGTTATCTTCCTGATAAGATAC
1 ATAAAACGGTTAACTTCCTGATAAGATAC
12344002 TCAGAAGCGG
Statistics
Matches: 389, Mismatches: 52, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
208 4 0.01
209 375 0.96
210 10 0.03
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (207 bp):
ATAAAACGGTTAACTTCCTGATAAGATACAGAGAAGTGAACCAGATCGTCTTCCTGATGAGACAC
AGAGAAGTGGATCAAACAAGCGAAGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAAT
CAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAG
CAGGTCGAAGCA
Found at i:12344406 original size:12 final size:12
Alignment explanation
Indices: 12344391--12344458 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
12344381 TATTTTAAGA
*
12344391 TTAAATTTATTT
1 TTAAATTTATGT
*
12344403 TTAAATTTGT-T
1 TTAAATTTATGT
*
12344414 TTAAAATTTAAGT
1 TT-AAATTTATGT
*
12344427 TT-AATTTAAGT
1 TTAAATTTATGT
* *
12344438 TTAAATTCATAT
1 TTAAATTTATGT
12344450 TTAAATTTA
1 TTAAATTTA
12344459 AAAATATTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
11 14 0.30
12 29 0.63
13 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (12 bp):
TTAAATTTATGT
Found at i:12344434 original size:29 final size:29
Alignment explanation
Indices: 12344373--12344440 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
12344363 CTAAACCCAT
* *
12344373 TTTAAATTTATTTTAAGATTAAATTTATT
1 TTTAAATTTATTTTAAAATTAAATTTATA
* *
12344402 TTTAAATTTGTTTTAAAATTTAAGTTTA-A
1 TTTAAATTTATTTTAAAA-TTAAATTTATA
*
12344431 TTTAAGTTTA
1 TTTAAATTTA
12344441 AATTCATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (29 bp):
TTTAAATTTATTTTAAAATTAAATTTATA
Found at i:12344478 original size:16 final size:16
Alignment explanation
Indices: 12344446--12344479 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
12344436 GTTTAAATTC
12344446 ATATTTAAATTTAAAA
1 ATATTTAAATTTAAAA
12344462 ATATTCTAAATTTAAAA
1 ATATT-TAAATTTAAAA
12344479 A
1 A
12344480 AACAAAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATTTAAATTTAAAA
Found at i:12346381 original size:30 final size:30
Alignment explanation
Indices: 12346345--12346411 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
12346335 CACTAAAATG
* *
12346345 TCCAAAAATCATAGTTTGACCCCCAAACTT
1 TCCAAAAATCACAGTTTAACCCCCAAACTT
* * *
12346375 TCCAAAAGTTACATTTTAACCCCCAAACTT
1 TCCAAAAATCACAGTTTAACCCCCAAACTT
12346405 TCCAAAA
1 TCCAAAA
12346412 TTTACATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.30, G:0.04, T:0.27
Consensus pattern (30 bp):
TCCAAAAATCACAGTTTAACCCCCAAACTT
Found at i:12346417 original size:30 final size:30
Alignment explanation
Indices: 12346363--12346419 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
12346353 TCATAGTTTG
12346363 ACCCCCAAACTTTCCAAAAGTTACATTTTA
1 ACCCCCAAACTTTCCAAAAGTTACATTTTA
*
12346393 ACCCCCAAACTTTCCAAAATTTACATT
1 ACCCCCAAACTTTCCAAAAGTTACATT
12346420 ATCATGAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.37, C:0.32, G:0.02, T:0.30
Consensus pattern (30 bp):
ACCCCCAAACTTTCCAAAAGTTACATTTTA
Found at i:12346467 original size:29 final size:28
Alignment explanation
Indices: 12346434--12346849 Score: 158
Period size: 29 Copynumber: 14.5 Consensus size: 28
12346424 TGAACTTCAA
12346434 AAAAATTACCATTTTACCCCTAAATTTCC
1 AAAAATTACCATTTTA-CCCTAAATTTCC
* * *
12346463 AAAAATT-CAATTTTTGACCCTGAACTTCC
1 AAAAATTACCA-TTTT-ACCCTAAATTTCC
* * ** *
12346492 TAAAAACTACCATTTTACCTTGGACTTCC
1 -AAAAATTACCATTTTACCCTAAATTTCC
* ****
12346521 AAAATTTTTGTTTTTAACCCTAAACTTTCC
1 AAAAATTACCATTTT-ACCCTAAA-TTTCC
* ** *
12346551 CAAAATTACCATTTTACCCCCGAATGTCC
1 AAAAATTACCATTTTA-CCCTAAATTTCC
** * *
12346580 AAAAATT-CCATTTTTTACTTTGAACTTCCC
1 AAAAATTACCA--TTTTACCCT-AAATTTCC
*
12346610 AAAAATTACCATTTTACCCCTAAACTTCC
1 AAAAATTACCATTTTA-CCCTAAATTTCC
*
12346639 AAAAATT-CCATTTTTGACCCTGAACTTTCC
1 AAAAATTACCA-TTTT-ACCCT-AAATTTCC
* * **
12346669 CAAAATTACCATTTTACCCCCAAACATCC
1 AAAAATTACCATTTTA-CCCTAAATTTCC
**
12346698 AAAAATT-CCATTTT----T---TACCC
1 AAAAATTACCATTTTACCCTAAATTTCC
* * *
12346718 CAAAATTACCATTTTACCCTCAAACTTCT
1 AAAAATTACCATTTTACCCT-AAATTTCC
* * * *
12346747 TAAAATT-CCTTTTTAACCTTGAACTTTCC
1 AAAAATTACCATTTT-ACCCT-AAATTTCC
* * *
12346776 CAAAATTACCATTTTACCCTCGAATGTCC
1 AAAAATTACCATTTTACCCT-AAATTTCC
* *
12346805 AAAAATT-CCATTTTTGA-CCTCGAACTTCC
1 AAAAATTACCA-TTTT-ACCCT-AAATTTCC
12346834 TAAAAATTACCATTTT
1 -AAAAATTACCATTTT
12346850 CCTTGGGCAT
Statistics
Matches: 283, Mismatches: 72, Indels: 63
0.68 0.17 0.15
Matches are distributed among these distances:
20 9 0.03
21 7 0.02
25 1 0.00
28 33 0.12
29 137 0.48
30 85 0.30
31 11 0.04
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAAATTACCATTTTACCCTAAATTTCC
Found at i:12346497 original size:59 final size:58
Alignment explanation
Indices: 12346424--12346849 Score: 371
Period size: 59 Copynumber: 7.4 Consensus size: 58
12346414 TACATTATCA
* * *
12346424 TGAACTTCAAAAAAATTACCATTTTACCCCTAAATTTCCAAAAATTCAATTTTTGACCC
1 TGAACTTC-CAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCC
* * ** * *** *
12346483 TGAACTTCCTAAAAACTACCATTTTA-CCTTGGACTTCCAAAATTTTTGTTTTTAACCC
1 TGAACTTCC-AAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCC
* * ** * **
12346541 TAAACTTTCCCAAAATTACCATTTTACCCCCGAA-TGTCCAAAAATTCCATTTTTTACTT
1 TGAAC-TTCCAAAAATTACCATTTTACCCCTAAACT-TCCAAAAATTCCATTTTTGACCC
12346600 TGAACTTCCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCC
1 TGAACTT-CCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCC
* * *
12346659 TGAACTTTCCCAAAATTACCATTTTACCCCCAAACATCCAAAAATTCCATTTTT-----
1 TGAAC-TTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCC
* ** * *
12346713 T--AC--CCCAAAATTACCATTTTA-CCCTCAAACTTCTTAAAATTCC-TTTTTAACCT
1 TGAACTTCCAAAAATTACCATTTTACCCCT-AAACTTCCAAAAATTCCATTTTTGACCC
* *
12346766 TGAACTTTCCCAAAATTACCATTTTA-CCCTCGAA-TGTCCAAAAATTCCATTTTTGA-CC
1 TGAAC-TTCCAAAAATTACCATTTTACCCCT-AAACT-TCCAAAAATTCCATTTTTGACCC
12346824 TCGAACTTCCTAAAAATTACCATTTT
1 T-GAACTTCC-AAAAATTACCATTTT
12346850 CCTTGGGCAT
Statistics
Matches: 301, Mismatches: 44, Indels: 44
0.77 0.11 0.11
Matches are distributed among these distances:
48 8 0.03
49 32 0.11
52 2 0.01
53 1 0.00
54 1 0.00
55 2 0.01
57 1 0.00
58 85 0.28
59 166 0.55
60 3 0.01
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (58 bp):
TGAACTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCC
Found at i:12346556 original size:88 final size:87
Alignment explanation
Indices: 12346424--12346854 Score: 280
Period size: 88 Copynumber: 5.0 Consensus size: 87
12346414 TACATTATCA
** *
12346424 TGAACTTCAAAAAAATTACCATTTTACCCCTAAA-TTTCCAAAAATTCAATTTTTGACCCTGAAC
1 TGAACTTCCCAAAAATTACCATTTTACCCCTAAACTTTCCAAAAATTCCATTTTTGACCCTGAAC
12346488 TTCCTAAAAACTACCATTTTACCT
66 TTCC-AAAAA-TACCATTTTACCT
* * **** * * *
12346512 TGGACTT-CCAAAATTTTTGTTTTTAACCCTAAACTTTCCCAAAATTACCA-TTTT-ACCCCCGA
1 TGAACTTCCCAAAAATTACCATTTTACCCCTAAACTTTCCAAAAATT-CCATTTTTGA-CCCTGA
* *
12346574 A-TGTCCAAAAATTCCATTTTTTACTT
64 ACT-TCCAAAAATACCA--TTTTACCT
12346600 TGAACTTCCCAAAAATTACCATTTTACCCCTAAAC-TTCCAAAAATTCCATTTTTGACCCTGAAC
1 TGAACTTCCCAAAAATTACCATTTTACCCCTAAACTTTCCAAAAATTCCATTTTTGACCCTGAAC
* *
12346664 TTTCCCAAAATTACCATTTTACCCC
66 -TT-CCAAAAATACCATTTTA-CCT
** * * * *
12346689 CAAACAT-CCAAAAATT-CCATTTT-----T-TAC---CCCAAAATTACCA-TTTT-ACCCTCAA
1 TGAACTTCCCAAAAATTACCATTTTACCCCTAAACTTTCCAAAAATT-CCATTTTTGACCCT-GA
** * *
12346741 ACTTCTTAAAATTCCTTTTTAACCT
64 ACTTCCAAAAATACCATTTT-ACCT
* *
12346766 TGAACTTTCCC-AAAATTACCATTTTA-CCCTCGAA-TGTCCAAAAATTCCATTTTTGA-CCTCG
1 TGAAC-TTCCCAAAAATTACCATTTTACCCCT-AAACTTTCCAAAAATTCCATTTTTGACCCT-G
12346827 AACTTCCTAAAAATTACCATTTT-CCT
63 AACTTCC-AAAAA-TACCATTTTACCT
12346853 TG
1 TG
12346855 GGCATCCAAA
Statistics
Matches: 262, Mismatches: 49, Indels: 65
0.70 0.13 0.17
Matches are distributed among these distances:
77 16 0.06
78 15 0.06
79 24 0.09
80 3 0.01
81 2 0.01
82 1 0.00
83 1 0.00
85 1 0.00
86 7 0.03
87 62 0.24
88 82 0.31
89 37 0.14
90 11 0.04
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (87 bp):
TGAACTTCCCAAAAATTACCATTTTACCCCTAAACTTTCCAAAAATTCCATTTTTGACCCTGAAC
TTCCAAAAATACCATTTTACCT
Found at i:12346716 original size:30 final size:30
Alignment explanation
Indices: 12346424--12346718 Score: 165
Period size: 29 Copynumber: 10.0 Consensus size: 30
12346414 TACATTATCA
*
12346424 TGAACTTCAAAAAAATTACCA--TTTTACCCC
1 TGAACTTC-CAAAAATT-CCATTTTTTACCCC
* * * *
12346454 TAAATTTCCAAAAATTCAATTTTTGA-CCC
1 TGAACTTCCAAAAATTCCATTTTTTACCCC
* *
12346483 TGAACTTCCTAAAAACTACCA--TTTTA-CCT
1 TGAACTTCC-AAAAA-TTCCATTTTTTACCCC
* ** *
12346512 TGGACTTCC-AAAATT-TTTGTTTTTAACCC
1 TGAACTTCCAAAAATTCCAT-TTTTTACCCC
* *
12346541 TAAACTTTCCCAAAATTACCA--TTTTACCCC
1 TGAAC-TTCCAAAAATT-CCATTTTTTACCCC
* **
12346571 CGAA-TGTCCAAAAATTCCATTTTTTA-CTT
1 TGAACT-TCCAAAAATTCCATTTTTTACCCC
12346600 TGAACTTCCCAAAAATTACCA--TTTTACCCC
1 TGAACTT-CCAAAAATT-CCATTTTTTACCCC
* *
12346630 TAAACTTCCAAAAATTCCATTTTTGA-CCC
1 TGAACTTCCAAAAATTCCATTTTTTACCCC
*
12346659 TGAACTTTCCCAAAATTACCA--TTTTACCCC
1 TGAAC-TTCCAAAAATT-CCATTTTTTACCCC
** *
12346689 CAAACATCCAAAAATTCCATTTTTTACCCC
1 TGAACTTCCAAAAATTCCATTTTTTACCCC
12346719 AAAATTACCA
Statistics
Matches: 201, Mismatches: 38, Indels: 52
0.69 0.13 0.18
Matches are distributed among these distances:
26 1 0.00
27 4 0.02
28 17 0.08
29 84 0.42
30 80 0.40
31 15 0.07
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (30 bp):
TGAACTTCCAAAAATTCCATTTTTTACCCC
Found at i:12346725 original size:49 final size:48
Alignment explanation
Indices: 12346667--12346760 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 48
12346657 CCTGAACTTT
12346667 CCCAAAATTACCATTTTACCCCCAAACATCCAAAAATTCCATTTTTTAC
1 CCCAAAATTACCATTTTACCCCCAAACATCCAAAAATTCC-TTTTTTAC
* * **
12346716 CCCAAAATTACCATTTTACCCTCAAACTTCTTAAAATTCCTTTTT
1 CCCAAAATTACCATTTTACCCCCAAACATCCAAAAATTCCTTTTT
12346761 AACCTTGAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 5 0.12
49 36 0.88
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.35
Consensus pattern (48 bp):
CCCAAAATTACCATTTTACCCCCAAACATCCAAAAATTCCTTTTTTAC
Found at i:12346806 original size:107 final size:108
Alignment explanation
Indices: 12346611--12346819 Score: 323
Period size: 107 Copynumber: 1.9 Consensus size: 108
12346601 GAACTTCCCA
*
12346611 AAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCTGAACTTTCCCAAAATT
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTCCCAAAATT
12346676 ACCATTTTACCCCCAAACATCCAAAAATTCCATTTTTTACCCC
66 ACCATTTTACCCCCAAACATCCAAAAATTCCATTTTTTACCCC
** *
12346719 AAAATTACCATTTTA-CCCTCAAACTTCTTAAAATTCC-TTTTTAACCTTGAACTTTCCCAAAAT
1 AAAATTACCATTTTACCCCT-AAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTCCCAAAAT
* * **
12346782 TACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTT
65 TACCATTTTACCCCCAAACATCCAAAAATTCCATTTTT
12346820 GACCTCGAAC
Statistics
Matches: 92, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
107 62 0.67
108 30 0.33
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.35
Consensus pattern (108 bp):
AAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTCCCAAAATT
ACCATTTTACCCCCAAACATCCAAAAATTCCATTTTTTACCCC
Found at i:12346842 original size:166 final size:167
Alignment explanation
Indices: 12346549--12346849 Score: 427
Period size: 166 Copynumber: 1.8 Consensus size: 167
12346539 CCTAAACTTT
* * *
12346549 CCCAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTTACTTTGAACTTCCCAAAA
1 CCCAAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTAACCTTGAACTTCCCAAAA
*
12346614 ATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCTGAACTTTCCCAAAATTACC
66 ATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCTGAACTTTCCAAAAATTACC
12346679 ATTTTACCCCCAAACATCCAAAAATTCCATTTTTTAC
131 ATTTTACCCCCAAACATCCAAAAATTCCATTTTTTAC
* **
12346716 CCCAAAATTACCATTTTACCCTCAAACT-TCTTAAAATTCC-TTTTTAACCTTGAACTTTCCC-A
1 CCCAAAATTACCATTTTACCCCCAAA-TGTCCAAAAATTCCATTTTTAACCTTGAAC-TTCCCAA
*
12346778 AAATTACCATTTTA-CCCTCGAA-TGTCCAAAAATTCCATTTTTGA-CCTCGAAC-TTCCTAAAA
64 AAATTACCATTTTACCCCT-AAACT-TCCAAAAATTCCATTTTTGACCCT-GAACTTTCC-AAAA
12346839 ATTACCATTTT
125 ATTACCATTTT
12346850 CCTTGGGCAT
Statistics
Matches: 120, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
165 12 0.10
166 68 0.57
167 39 0.32
168 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (167 bp):
CCCAAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTAACCTTGAACTTCCCAAAA
ATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCTGAACTTTCCAAAAATTACC
ATTTTACCCCCAAACATCCAAAAATTCCATTTTTTAC
Found at i:12351538 original size:30 final size:29
Alignment explanation
Indices: 12351501--12351663 Score: 134
Period size: 29 Copynumber: 5.6 Consensus size: 29
12351491 AGTAAAACAA
*
12351501 TAATTTTTGAAAGTTTCGGGGTCTAAAATG
1 TAATTTTTGGAAGTTTCGGGGT-TAAAATG
*
12351531 -AAGTTTTTGGAAGTTTAGGGG-TAGAAATG
1 TAA-TTTTTGGAAGTTTCGGGGTTA-AAATG
*
12351560 TAATTTTTGGAAGTTTCAGGGTTAAAATG
1 TAATTTTTGGAAGTTTCGGGGTTAAAATG
** * * * *
12351589 GGATTTTTAGATG-TCCGGGGTAAAAATG
1 TAATTTTTGGAAGTTTCGGGGTTAAAATG
* * * * **
12351617 TATTTTTTAGAATTTTAGGGGCAAAAATG
1 TAATTTTTGGAAGTTTCGGGGTTAAAATG
*
12351646 TAATTTTTAGAAGTTTCG
1 TAATTTTTGGAAGTTTCG
12351664 AGGCCAAAAT
Statistics
Matches: 106, Mismatches: 22, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
28 22 0.21
29 64 0.60
30 20 0.19
ACGTcount: A:0.31, C:0.04, G:0.26, T:0.39
Consensus pattern (29 bp):
TAATTTTTGGAAGTTTCGGGGTTAAAATG
Found at i:12351644 original size:57 final size:57
Alignment explanation
Indices: 12351548--12351656 Score: 130
Period size: 57 Copynumber: 1.9 Consensus size: 57
12351538 TGGAAGTTTA
* * ** *
12351548 GGGGTAGAAATGTAATTTTTGGAAGTTTCAGGGTTAAAATGGGATTTTTAGATGTCC
1 GGGGTAAAAATGTAATTTTTAGAAGTTTCAGGGCAAAAATGGAATTTTTAGATGTCC
* * *
12351605 GGGGTAAAAATGTATTTTTTAGAA-TTTTAGGGGCAAAAATGTAATTTTTAGA
1 GGGGTAAAAATGTAATTTTTAGAAGTTTCA-GGGCAAAAATGGAATTTTTAGA
12351657 AGTTTCGAGG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
56 4 0.09
57 39 0.91
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.38
Consensus pattern (57 bp):
GGGGTAAAAATGTAATTTTTAGAAGTTTCAGGGCAAAAATGGAATTTTTAGATGTCC
Found at i:12351672 original size:29 final size:29
Alignment explanation
Indices: 12351525--12351680 Score: 93
Period size: 29 Copynumber: 5.4 Consensus size: 29
12351515 TTCGGGGTCT
* * *
12351525 AAAATG-AAGTTTTTGGAAGTTTAGGGGTA
1 AAAATGTAA-TTTTTAGAAGTTTAGAGGCA
* * **
12351554 GAAATGTAATTTTTGGAAGTTTCAG-GGTT
1 AAAATGTAATTTTTAGAAGTTT-AGAGGCA
** * ** * *
12351583 AAAATGGGATTTTTAGATG-TCCGGGGTA
1 AAAATGTAATTTTTAGAAGTTTAGAGGCA
* * *
12351611 AAAATGTATTTTTTAGAATTTTAGGGGCA
1 AAAATGTAATTTTTAGAAGTTTAGAGGCA
* *
12351640 AAAATGTAATTTTTAGAAGTTTCGAGGCC
1 AAAATGTAATTTTTAGAAGTTTAGAGGCA
*
12351669 AAAATATAATTT
1 AAAATGTAATTT
12351681 CTGAACAGTT
Statistics
Matches: 99, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
27 1 0.01
28 18 0.18
29 76 0.77
30 4 0.04
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTTAGAAGTTTAGAGGCA
Found at i:12368956 original size:33 final size:34
Alignment explanation
Indices: 12368914--12368978 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
12368904 GAGGTTCGAC
*
12368914 GTCGGTCGGAGT-GCTGCACGATGGCGGTGTGAT
1 GTCGATCGGAGTGGCTGCACGATGGCGGTGTGAT
* *
12368947 GTCGATCGGAGTGGGTGCACGATGGTGGTGTG
1 GTCGATCGGAGTGGCTGCACGATGGCGGTGTG
12368979 GCGTCAGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 11 0.39
34 17 0.61
ACGTcount: A:0.12, C:0.15, G:0.48, T:0.25
Consensus pattern (34 bp):
GTCGATCGGAGTGGCTGCACGATGGCGGTGTGAT
Found at i:12378772 original size:145 final size:145
Alignment explanation
Indices: 12378503--12378799 Score: 447
Period size: 145 Copynumber: 2.0 Consensus size: 145
12378493 AACCCAATGC
* * *
12378503 TTCTCTTTATCATGGGACTACAAATCGATTATTTTATTCCTTGTTCGACGTTGTCTTTTTTGGTG
1 TTCTCTTTATCATGAGACTACAAATCGATTATTGTATTCCTTGTTCGACGTTGTCTTTTTTGATG
* * *
12378568 AACGCGTTGTCACTCAACTTTACTAAAGTAAGGATGACAACTTTGAGTGATATAACTAATGGAAC
66 AACGCGTTGTCACTCAACTTCACTAAACTAAGGATGACAACTTTGAGTGAAATAACTAATGGAAC
12378633 TTGTCCAACGACAAA
131 TTGTCCAACGACAAA
* *
12378648 TTCTCTTTATCATGAGACTACAAATTGATTATTGTATT-CTTCGTTTGACGTTGTCTTTTTTGAT
1 TTCTCTTTATCATGAGACTACAAATCGATTATTGTATTCCTT-GTTCGACGTTGTCTTTTTTGAT
*
12378712 GAACGCGTTGTC-CGTC-ACGTTCACTAAACTAAGGATGACAACTTTGAGTGAAATATCTAATGG
65 GAACGCGTTGTCAC-TCAAC-TTCACTAAACTAAGGATGACAACTTTGAGTGAAATAACTAATGG
* *
12378775 AACTTGTCCGACGATAAA
128 AACTTGTCCAACGACAAA
12378793 TTCTCTT
1 TTCTCTT
12378800 ATAGAGTTAA
Statistics
Matches: 138, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
144 6 0.04
145 132 0.96
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (145 bp):
TTCTCTTTATCATGAGACTACAAATCGATTATTGTATTCCTTGTTCGACGTTGTCTTTTTTGATG
AACGCGTTGTCACTCAACTTCACTAAACTAAGGATGACAACTTTGAGTGAAATAACTAATGGAAC
TTGTCCAACGACAAA
Found at i:12384293 original size:29 final size:29
Alignment explanation
Indices: 12384261--12384356 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 29
12384251 AAACGATAAT
* *
12384261 TTTTGAAAGTTTTGGGGTCAAAAATGAAA
1 TTTTGGAAGTTTCGGGGTCAAAAATGAAA
* *
12384290 TTTTGGAAGTTTGGGGGTC-AAAATGTAAT
1 TTTTGGAAGTTTCGGGGTCAAAAATG-AAA
* *
12384319 TTTTGGAAGTTTCAGGGTCAAAAATGGAA
1 TTTTGGAAGTTTCGGGGTCAAAAATGAAA
12384348 TATTTGGAA
1 T-TTTGGAA
12384357 TATTTGGAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.11
29 38 0.67
30 13 0.23
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (29 bp):
TTTTGGAAGTTTCGGGGTCAAAAATGAAA
Found at i:12384357 original size:9 final size:9
Alignment explanation
Indices: 12384343--12384371 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
12384333 GGGTCAAAAA
12384343 TGGAATATT
1 TGGAATATT
12384352 TGGAATATT
1 TGGAATATT
12384361 TGGAAT-TT
1 TGGAATATT
12384369 TGG
1 TGG
12384372 GGGCAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (9 bp):
TGGAATATT
Found at i:12384439 original size:29 final size:30
Alignment explanation
Indices: 12384379--12384457 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
12384369 TGGGGGCAAT
* *
12384379 AATGTAATTTTTGGAAG-TTCGAGGGTACA
1 AATGTAATTTTTAGAAGTTTCGAGGGCACA
12384408 AATGTAATTTTTAGAAGTTTC-AGGGC-CAA
1 AATGTAATTTTTAGAAGTTTCGAGGGCAC-A
* *
12384437 AATATAATTTTTTGACAGTTT
1 AATGTAATTTTTAGA-AGTTT
12384458 AAGGACCCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
28 1 0.02
29 34 0.79
30 8 0.19
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (30 bp):
AATGTAATTTTTAGAAGTTTCGAGGGCACA
Found at i:12386294 original size:27 final size:27
Alignment explanation
Indices: 12386264--12386316 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
12386254 TTAACTTTGA
*
12386264 AAATT-AATTTAAATTCAAATTTAAAAT
1 AAATTAAATTTAAAAT-AAATTTAAAAT
12386291 AAATTAAATTTAAAATAAATTTAAAA
1 AAATTAAATTTAAAATAAATTTAAAA
12386317 GGGCTCGGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATTAAATTTAAAATAAATTTAAAAT
Found at i:12386299 original size:16 final size:17
Alignment explanation
Indices: 12386273--12386311 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
12386263 AAAATTAATT
12386273 TAAATTCAAATTTAAAA
1 TAAATTCAAATTTAAAA
12386290 TAAATT-AAATTTAAAA
1 TAAATTCAAATTTAAAA
12386306 TAAATT
1 TAAATT
12386312 TAAAAGGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTCAAATTTAAAA
Found at i:12386974 original size:207 final size:204
Alignment explanation
Indices: 12386614--12387420 Score: 1100
Period size: 205 Copynumber: 4.0 Consensus size: 204
12386604 TTTCATTCAC
* * * **
12386614 TTGGCCTTCTTCTCTGTATCTCATCAGGAAGATGACCACATCACTTGTTTTGATCCACTTCTCTG
1 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTG
* * * * * *
12386679 TGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCACTTTAT
66 TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* * ** *
12386744 TGCTTAGACCTACTTCTCAGTATCTCATCAAAAAGCTAAGGGTTCGAAGATTTGCTCACATCGAG
131 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-AGGGTTCGAAGATTTGCTCACATTGAG
12386809 CGTTTGTTTGAT
195 CG--TGTTTGAT
*** **
12386821 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATTGTTTGTTTCAATCTGCTTCTCTG
1 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTG
*
12386886 TATCTCATCAGGAAGACGAATGTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
66 TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
*
12386951 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAGATTTGCTCACATTGAGA
131 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATTGAGC
12387015 GTGGGTTTGAT
196 GT--GTTTGAT
* *
12387026 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCACTTCTCTA
1 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTG
*
12387091 TACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
66 TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* * * * *
12387156 TGCTTCGATCTGCTTCTCTGTATCTCATCAGGAAGTTAGGGTTCAAAGATTTGCTCACTTTGAGC
131 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATTGAGC
* *
12387221 ---CTTGAG
196 GTGTTTGAT
* * * * * * * *
12387227 TTGGTATACTTCTCTGTATCTCATCAGGAAGGTGACCGCCTCACTTGTTTCAATTCGCTTCTCTC
1 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTG
12387292 TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
66 TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* * * * * * * *
12387357 TACTTCGCCCTGCCTCTCAGTATGTCATCAGGAAGCTGGGGTTCAAAGATCTGTTCACATTGAG
131 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATTGAG
12387421 TTGGTATACT
Statistics
Matches: 538, Mismatches: 59, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
201 177 0.33
203 1 0.00
205 190 0.35
206 24 0.04
207 146 0.27
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (204 bp):
TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTG
TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATTGAGC
GTGTTTGAT
Found at i:12387388 original size:406 final size:409
Alignment explanation
Indices: 12386614--12387420 Score: 1154
Period size: 406 Copynumber: 2.0 Consensus size: 409
12386604 TTTCATTCAC
* ** *
12386614 TTGGCCTTCTTCTCTGTATCTCATCAGGAAGATGACCACATCACTTGTTTTGATCCACTTCTCTG
1 TTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCACTTCTCTA
*** * * *
12386679 TGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCACTTTAT
66 TACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTTAT
*
12386744 TGCTTAGACCTACTTCTCAGTATCTCATCAAAAAGCTAAGGGTTCGAAGATTTGCTCACATCGAG
131 TGCTTAGACCTACTTCTCAGTATCTCATCAAAAAGCTAAGGGTTCAAAGATTTGCTCACATCGAG
* * * * ***
12386809 CGTTTGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATTGTTTGTTTCAA
196 C---T-CTTGAGTTGGTATACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAA
*
12386874 TCTGCTTCTCTGTATCTCATCAGGAAGACGAATGTGGTCCACTTCTCAGTATCTCATCAGGAAGC
257 TCTGCTTCTCTCTATCTCATCAGGAAGACGAATGTGGTCCACTTCTCAGTATCTCATCAGGAAGC
* * * *
12386939 TAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAGATTTG
322 TAACCATTTTATTACTTCGACCTGCCTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATCTG
12387003 CTCACATTGAGAGTGGGTTTGAT
387 CTCACATTGAGAGTGGGTTTGAT
* * *
12387026 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCACTTCTCTA
1 TTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCACTTCTCTA
*
12387091 TACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
66 TACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTTAT
* * * * ** * * *
12387156 TGCTTCGATCTGCTTCTCTGTATCTCATCAGGAAG-TTAGGGTTCAAAGATTTGCTCACTTTGAG
131 TGCTTAGACCTACTTCTCAGTATCTCATCAAAAAGCTAAGGGTTCAAAGATTTGCTCACATCGAG
* * *
12387220 C-CTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGGTGACCGCCTCACTTGTTTCAAT-TC
196 CTCTTGAGTTGGTATACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCT-
*
12387283 GCTTCTCTCTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAA
260 GCTTCTCTCTATCTCATCAGGAAGACGAATGTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAA
* * *
12387348 CCATTTTATTACTTCGCCCTGCCTCTCAGTATGTCATCAGGAAGCTGGGGTTCAAAGATCTGTTC
325 CCATTTTATTACTTCGACCTGCCTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATCTGCTC
12387413 ACATTGAG
390 ACATTGAG
12387421 TTGGTATACT
Statistics
Matches: 350, Mismatches: 43, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
405 1 0.00
406 155 0.44
407 23 0.07
411 26 0.07
412 145 0.41
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (409 bp):
TTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCACTTCTCTA
TACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTTAT
TGCTTAGACCTACTTCTCAGTATCTCATCAAAAAGCTAAGGGTTCAAAGATTTGCTCACATCGAG
CTCTTGAGTTGGTATACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCTG
CTTCTCTCTATCTCATCAGGAAGACGAATGTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
CATTTTATTACTTCGACCTGCCTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATCTGCTCA
CATTGAGAGTGGGTTTGAT
Found at i:12387873 original size:49 final size:49
Alignment explanation
Indices: 12387807--12388013 Score: 186
Period size: 49 Copynumber: 4.2 Consensus size: 49
12387797 CGACTTAAAC
** * *
12387807 CTTTCCCTTCAAATCTTCGTGGTACTGGATCTGCTGTCACAGCTTAGAT
1 CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCTGTCACGGCTTAGAT
* * * * * *
12387856 CTTTCTCTTCCTGTCTTCGTAGTACTGGGTCCG-TCATCGCGGCTTAGAT
1 CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCT-GTCACGGCTTAGAT
* *
12387905 CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTACGGCTTTAGAT
1 CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCTGTCACGGC-TTAGAT
* * * * *
12387955 CTTTCCCTT-TTGTATCTTTGCGGTACTGGATCCGCCGTTGCA-GTCTTAGAT
1 CTTTCCCTTCATG--TCTTCGTGGTACTGGATCCGCTG-T-CACGGCTTAGAT
12388006 CTTTCCCT
1 CTTTCCCT
12388014 GTCAAATCTG
Statistics
Matches: 128, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
48 1 0.01
49 73 0.57
50 15 0.12
51 35 0.27
52 3 0.02
53 1 0.01
ACGTcount: A:0.13, C:0.28, G:0.20, T:0.39
Consensus pattern (49 bp):
CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCTGTCACGGCTTAGAT
Found at i:12394109 original size:59 final size:59
Alignment explanation
Indices: 12394006--12394185 Score: 186
Period size: 58 Copynumber: 3.1 Consensus size: 59
12393996 AAAAATGACA
* * ** *
12394006 TTTTAGACATTCGAGGGTAAAATGGTAATTTTTGGAAA-AATCGGGATCAAAAATGGATT
1 TTTTGGACATTCGAGGGTAAAAAGGTAATTTTT-GAAAGTTTCGGGGTCAAAAATGGATT
* * * * * *
12394065 TTTTGGACATCCGAGAGTAAAACGGTAATTTTTGAAAGTTTCGGGGTCCAAAATAGA-A
1 TTTTGGACATTCGAGGGTAAAAAGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGATT
* * *
12394123 TTTTGGA-AGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATT
1 TTTTGGACA-TTCGAGGGTAAAAAGGTAATTTTTGAAAGTTTCGGGGTCAAAAAT-GGATT
12394183 TTT
1 TTT
12394186 AGATTTTTGG
Statistics
Matches: 98, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
57 1 0.01
58 49 0.50
59 45 0.46
60 3 0.03
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.34
Consensus pattern (59 bp):
TTTTGGACATTCGAGGGTAAAAAGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGATT
Found at i:12394126 original size:29 final size:30
Alignment explanation
Indices: 12394089--12394253 Score: 144
Period size: 29 Copynumber: 5.6 Consensus size: 30
12394079 GAGTAAAACG
* *
12394089 GTAATTTTTGAAAGTTTCGGGGTCCAAAAT
1 GTAATTTTTGGAAGTTTCGGGGTCAAAAAT
12394119 AG-AA-TTTTGGAAG-TTCGAGGGT-AAAAAT
1 -GTAATTTTTGGAAGTTTCG-GGGTCAAAAAT
*
12394147 GTAATTTTTGGAAGTTTTGGGGTCAAAAAT
1 GTAATTTTTGGAAGTTTCGGGGTCAAAAAT
** * ** *
12394177 GGGATTTTTAGATTTTTGGGGGT-AAAAAT
1 GTAATTTTTGGAAGTTTCGGGGTCAAAAAT
* **
12394206 GTAATTTTTGGAATTTTAAGGGT-AAAAAT
1 GTAATTTTTGGAAGTTTCGGGGTCAAAAAT
* *
12394235 GTAAATTTTAGAAGTTTCG
1 GTAATTTTTGGAAGTTTCG
12394254 ATGCCAAAAT
Statistics
Matches: 109, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
27 1 0.01
28 11 0.10
29 68 0.62
30 28 0.26
31 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (30 bp):
GTAATTTTTGGAAGTTTCGGGGTCAAAAAT
Found at i:12394154 original size:58 final size:57
Alignment explanation
Indices: 12394014--12394215 Score: 183
Period size: 59 Copynumber: 3.5 Consensus size: 57
12394004 CATTTTAGAC
** *
12394014 ATTCGAGGGT-AAAATGGTAATTTTTGGAAA-AATCGGGATCAAAAATGGATTTTTTGGA
1 ATTCGAGGGTAAAAAT-GTAATTTTT-GAAAGTTTCGGGGTCAAAAATGGA-TTTTTGGA
* * ** * * *
12394072 CATCCGAGAGTAAAACGGTAATTTTTGAAAGTTTCGGGGTCCAAAATAGAATTTTGGA
1 -ATTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGATTTTTGGA
* * *
12394130 AGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTAGA
1 A-TTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTCAAAAAT-GGATTTTTGGA
* * *
12394189 TTTTTGGGGGTAAAAATGTAATTTTTG
1 -ATTCGAGGGTAAAAATGTAATTTTTG
12394216 GAATTTTAAG
Statistics
Matches: 115, Mismatches: 23, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
57 1 0.01
58 49 0.43
59 62 0.54
60 3 0.03
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.35
Consensus pattern (57 bp):
ATTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGATTTTTGGA
Found at i:12394668 original size:5 final size:5
Alignment explanation
Indices: 12394658--12394690 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
12394648 GGATCCTAGA
*
12394658 TCGGG TCGGG TCGGG TCGGG TCGGA T-GGG TCGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGG
12394691 TCATGGGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.03, C:0.18, G:0.58, T:0.21
Consensus pattern (5 bp):
TCGGG
Found at i:12396139 original size:6 final size:6
Alignment explanation
Indices: 12396114--12396183 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
12396104 GTTTTTTTTT
* * *
12396114 TTTAAA TTTGAAA -ATAAA TTTAAA TTTAAA TTCAAA TTTAAA -ATAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
12396161 TCTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
12396184 AGGGCCCGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
5 11 0.22
6 37 0.73
7 3 0.06
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:12396167 original size:17 final size:17
Alignment explanation
Indices: 12396116--12396183 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
12396106 TTTTTTTTTT
*
12396116 TAAATTTGAAAATAAATT
1 TAAATTT-AAAATAAATC
12396134 TAAATTT-AAAT---TC
1 TAAATTTAAAATAAATC
12396147 -AAATTTAAAATAAATC
1 TAAATTTAAAATAAATC
*
12396163 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATC
12396180 TAAA
1 TAAA
12396184 AGGGCCCGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
12 6 0.14
13 5 0.12
16 6 0.14
17 19 0.44
18 7 0.16
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAAATAAATC
Found at i:12400011 original size:30 final size:29
Alignment explanation
Indices: 12399968--12400372 Score: 225
Period size: 30 Copynumber: 13.7 Consensus size: 29
12399958 TGAACTGTTT
* * * *
12399968 AAAAATCATATTTTGACCCCTCAACTTTTC
1 AAAAATTACATTTTGA-CCCTGAACTTTCC
12399998 AAAAATTACATTTTGACCCTTGAACTTTCC
1 AAAAATTACATTTTGACCC-TGAACTTTCC
* *
12400028 AAAATTTACATTATTG-CCCTCGAGC-TTCAC
1 AAAAATTACATT-TTGACCCT-GAACTTTC-C
*
12400058 AAAAATTACCATTTT-ACCTTGAA-TTTCC
1 AAAAATTA-CATTTTGACCCTGAACTTTCC
*
12400086 AAAAATTCCATTTTTGACCC-GAACTTTCC
1 AAAAATTACA-TTTTGACCCTGAACTTTCC
* *
12400115 CAAAATTACCATTTT-ACCCCTAAACTTT-C
1 AAAAATTA-CATTTTGA-CCCTGAACTTTCC
12400144 AAAAATT-CTATTTTTGA-CCTCGAACTTTCC
1 AAAAATTAC-A-TTTTGACCCT-GAACTTTCC
* * *
12400174 CAAAATAAGCATTTT-ACCCTCGAAC-ATCC
1 AAAAATTA-CATTTTGACCCT-GAACTTTCC
** *
12400203 AAAAATTTTATTTTTGACCC-CATACTTTCC
1 AAAAATTACA-TTTTGACCCTGA-ACTTTCC
* * *
12400233 CAAAATTACCATTTT-ACCCTTAAAC-TACC
1 AAAAATTA-CATTTTGACCC-TGAACTTTCC
* * *
12400262 AAAAATTCCATTTTTAACCCTAAACTTTCC
1 AAAAATTACA-TTTTGACCCTGAACTTTCC
* *
12400292 CAAAATTACCATTTT-ACCCTCGAA-TGTCC
1 AAAAATTA-CATTTTGACCCT-GAACTTTCC
*
12400321 AAAAATTCCATTTTTGA-CCTCGAAC-TTCC
1 AAAAATTACA-TTTTGACCCT-GAACTTTCC
*
12400350 TAAAAATTACCATTTTGCCCCTG
1 -AAAAATTA-CATTTTGACCCTG
12400373 GCATCGAAAA
Statistics
Matches: 294, Mismatches: 42, Indels: 78
0.71 0.10 0.19
Matches are distributed among these distances:
27 3 0.01
28 26 0.09
29 116 0.39
30 131 0.45
31 17 0.06
32 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCTGAACTTTCC
Found at i:12400048 original size:59 final size:59
Alignment explanation
Indices: 12399985--12400365 Score: 361
Period size: 59 Copynumber: 6.5 Consensus size: 59
12399975 ATATTTTGAC
* * * * *
12399985 CCCTCAACTTTTCAAAAATTA-CATTTTGACCCTTGAACTTTCCAAAATTTACATTATTG
1 CCCTCAACTTTCCCAAAATTACCATTTT-ACCCTTGAACTTTCCAAAAATTCCATTTTTG
* *
12400044 CCCTCGAGC-TTCACAAAAATTACCATTTTA-CCTTGAA-TTTCCAAAAATTCCATTTTTG
1 CCCTC-AACTTTC-CCAAAATTACCATTTTACCCTTGAACTTTCCAAAAATTCCATTTTTG
* * * *
12400102 ACCC-GAACTTTCCCAAAATTACCATTTTACCCCTAAACTTT-CAAAAATTCTATTTTTG
1 -CCCTCAACTTTCCCAAAATTACCATTTTACCCTTGAACTTTCCAAAAATTCCATTTTTG
* * * * * **
12400160 ACCTCGAACTTTCCCAAAATAAGCATTTTACCCTCGAAC-ATCCAAAAATTTTATTTTTG
1 CCCTC-AACTTTCCCAAAATTACCATTTTACCCTTGAACTTTCCAAAAATTCCATTTTTG
* * *
12400219 ACCC-CATACTTTCCCAAAATTACCATTTTACCCTTAAAC-TACCAAAAATTCCATTTTTAA
1 -CCCTCA-ACTTTCCCAAAATTACCATTTTACCCTTGAACTTTCCAAAAATTCCATTTTT-G
* * *
12400279 CCCTAAACTTTCCCAAAATTACCATTTTACCCTCGAA-TGTCCAAAAATTCCATTTTTG
1 CCCTCAACTTTCCCAAAATTACCATTTTACCCTTGAACTTTCCAAAAATTCCATTTTTG
* *
12400337 ACCTCGAAC-TTCCTAAAAATTACCATTTT
1 CCCTC-AACTTTCC-CAAAATTACCATTTT
12400366 GCCCCTGGCA
Statistics
Matches: 266, Mismatches: 39, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
57 20 0.08
58 51 0.19
59 174 0.65
60 15 0.06
61 6 0.02
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
CCCTCAACTTTCCCAAAATTACCATTTTACCCTTGAACTTTCCAAAAATTCCATTTTTG
Found at i:12400119 original size:118 final size:117
Alignment explanation
Indices: 12399990--12400365 Score: 424
Period size: 118 Copynumber: 3.2 Consensus size: 117
12399980 TTGACCCCTC
* * * * * *
12399990 AACTTTTCAAAAATTA-CATTTTGACCCTTGAACTTTCCAAAATTTACATTATTGCCCTCGAGC-
1 AACTTTCCCAAAATTACCATTTT-ACCCTTAAACTTTCCAAAAATT-CATTTTTGCCCTCGAACT
* * *
12400053 TTCACAAAAATTACCATTTTA-CCTTGAATTTCCAAAAATTCCATTTTTGACCCG
64 TTC-CCAAAATTACCATTTTACCCTCGAATATCCAAAAATTCCATTTTTGACCCG
* *
12400107 AACTTTCCCAAAATTACCATTTTACCCCTAAACTTT-CAAAAATTCTATTTTTGACCTCGAACTT
1 AACTTTCCCAAAATTACCATTTTACCCTTAAACTTTCCAAAAATTC-ATTTTTGCCCTCGAACTT
* * * ** *
12400171 TCCCAAAATAAGCATTTTACCCTCGAACATCCAAAAATTTTATTTTTGACCCC
65 TCCCAAAATTACCATTTTACCCTCGAATATCCAAAAATTCCATTTTTGACCCG
* * *
12400224 ATACTTTCCCAAAATTACCATTTTACCCTTAAAC-TACCAAAAATTCCATTTTTAACCCT-AAAC
1 A-ACTTTCCCAAAATTACCATTTTACCCTTAAACTTTCCAAAAATT-CATTTTT-GCCCTCGAAC
*
12400287 TTTCCCAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACCTCG
63 TTTCCCAAAATTACCATTTTACCCTCGAATATCCAAAAATTCCATTTTTGACC-CG
*
12400343 AAC-TTCCTAAAAATTACCATTTT
1 AACTTTCC-CAAAATTACCATTTT
12400366 GCCCCTGGCA
Statistics
Matches: 219, Mismatches: 30, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
115 1 0.00
116 34 0.16
117 61 0.28
118 117 0.53
119 6 0.03
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.36
Consensus pattern (117 bp):
AACTTTCCCAAAATTACCATTTTACCCTTAAACTTTCCAAAAATTCATTTTTGCCCTCGAACTTT
CCCAAAATTACCATTTTACCCTCGAATATCCAAAAATTCCATTTTTGACCCG
Found at i:12404316 original size:23 final size:23
Alignment explanation
Indices: 12404290--12404385 Score: 72
Period size: 23 Copynumber: 4.2 Consensus size: 23
12404280 GCCTTTTCTT
12404290 GCATTACATACATGCAT-TTTTCC
1 GCATTACATACATGCATATTTT-C
* **
12404313 GCATTGCATATTTGCATATTTTC
1 GCATTACATACATGCATATTTTC
**
12404336 GCA-TAGCATATTTGCATATTTTC
1 GCATTA-CATACATGCATATTTTC
* **
12404359 TCA-TAGCATATTTGCATATTTTC
1 GCATTA-CATACATGCATATTTTC
12404382 GCAT
1 GCAT
12404386 AATAATTCTA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
22 1 0.02
23 59 0.92
24 4 0.06
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (23 bp):
GCATTACATACATGCATATTTTC
Found at i:12404386 original size:23 final size:23
Alignment explanation
Indices: 12404302--12404386 Score: 136
Period size: 23 Copynumber: 3.7 Consensus size: 23
12404292 ATTACATACA
*
12404302 TGCAT-TTTTCCGCATTGCATATT
1 TGCATATTTT-CGCATAGCATATT
12404325 TGCATATTTTCGCATAGCATATT
1 TGCATATTTTCGCATAGCATATT
*
12404348 TGCATATTTTCTCATAGCATATT
1 TGCATATTTTCGCATAGCATATT
12404371 TGCATATTTTCGCATA
1 TGCATATTTTCGCATA
12404387 ATAATTCTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 54 0.93
24 4 0.07
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.46
Consensus pattern (23 bp):
TGCATATTTTCGCATAGCATATT
Found at i:12419001 original size:20 final size:19
Alignment explanation
Indices: 12418969--12419025 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
12418959 TAATTTAGTC
**
12418969 AAAAAGAAAATAACAACTTAT
1 AAAAA-AAAATAACAA-AAAT
*
12418990 AAAAAAATATAAACAAAAAT
1 AAAAAAAAAT-AACAAAAAT
12419010 AAAAAAAAATAACAAA
1 AAAAAAAAATAACAAA
12419026 TTGACTAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 6 0.19
20 15 0.48
21 10 0.32
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAAAAAAATAACAAAAAT
Found at i:12419009 original size:12 final size:10
Alignment explanation
Indices: 12418988--12419021 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
12418978 ATAACAACTT
*
12418988 ATAAAAAAAT
1 ATAAAAAAAA
*
12418998 ATAAACAAAA
1 ATAAAAAAAA
12419008 ATAAAAAAAA
1 ATAAAAAAAA
12419018 ATAA
1 ATAA
12419022 CAAATTGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (10 bp):
ATAAAAAAAA
Found at i:12428168 original size:269 final size:270
Alignment explanation
Indices: 12427672--12428201 Score: 882
Period size: 269 Copynumber: 2.0 Consensus size: 270
12427662 TGATGGGTGT
** *
12427672 CGAATCCAACAAATATAAATATTCCTATGACAAATAATACAAAACAGTAGTATAAGGCAGTAAGG
1 CGAATCCAACAAATATAAATATTCCTACAAAAAATAATACAAAACAGTAGTATAAGGCAGTAAGG
* *
12427737 TCGATTCCACAGGGACTGGCTACTATAATCTACTATTGTGTCTTCCTCTTTAACGTCGTGTCAAA
66 TCGATTCCACAGGGACTGGCTACTATAATCTACTATCGTGTCTTCCTCTTTAACGTCATGTCAAA
* *
12427802 GGGAGTGCTCACGACACGTGACTGTCTCCTAAATAAAAATAAAAGAGTGGGGGATTAGAGAAACA
131 GGGAGTGCCCACGACACGTGACTGTCTCCTAAATAAAAATAAAAGAGTGAGGGATTAGAGAAACA
12427867 TTAAATTAAGATAAAATAAAAATAAAATAAAAACAACAAATAAATCTTGACAAAAAATAATCAAT
196 TTAAATTAAGATAAAATAAAAATAAAATAAAAACAACAAATAAATCTTGACAAAAAATAATCAAT
12427932 CAAAATTTGA
261 CAAAATTTGA
* *
12427942 CGAATCTAACAAATAT-AATATTCCTACAAAAAATAATACAAAACAGTAGTATAAGGCAGTAGGG
1 CGAATCCAACAAATATAAATATTCCTACAAAAAATAATACAAAACAGTAGTATAAGGCAGTAAGG
* * * * *
12428006 TCGATTCCACAGGGATTGGTTACTATAATCTACTCTCGTTTCTTCCTCTTTAATGTCATGTCAAA
66 TCGATTCCACAGGGACTGGCTACTATAATCTACTATCGTGTCTTCCTCTTTAACGTCATGTCAAA
* *
12428071 GGGCGTGCCCACGACACGTGACTGTCTCCTAAATAAAAATAAAAGAGTGAGGGATTAGAGAAACG
131 GGGAGTGCCCACGACACGTGACTGTCTCCTAAATAAAAATAAAAGAGTGAGGGATTAGAGAAACA
** *
12428136 TTAAATTAAGATAAAATAAAAATAAAATAAAAACAGTAAATAAATCTTGACGAAAAATAATCAAT
196 TTAAATTAAGATAAAATAAAAATAAAATAAAAACAACAAATAAATCTTGACAAAAAATAATCAAT
12428201 C
261 C
12428202 GAGAATAAAA
Statistics
Matches: 241, Mismatches: 19, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
269 226 0.94
270 15 0.06
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (270 bp):
CGAATCCAACAAATATAAATATTCCTACAAAAAATAATACAAAACAGTAGTATAAGGCAGTAAGG
TCGATTCCACAGGGACTGGCTACTATAATCTACTATCGTGTCTTCCTCTTTAACGTCATGTCAAA
GGGAGTGCCCACGACACGTGACTGTCTCCTAAATAAAAATAAAAGAGTGAGGGATTAGAGAAACA
TTAAATTAAGATAAAATAAAAATAAAATAAAAACAACAAATAAATCTTGACAAAAAATAATCAAT
CAAAATTTGA
Found at i:12445449 original size:30 final size:29
Alignment explanation
Indices: 12445356--12445451 Score: 122
Period size: 29 Copynumber: 3.3 Consensus size: 29
12445346 AAACGGTAAT
* *
12445356 TTTTGAAAGTTTTGGGGTCAAAAATGAAA
1 TTTTGGAAGTTTCGGGGTCAAAAATGAAA
* *
12445385 TTTTGGAAGTTTGGGGGTC-AAAATGTAAT
1 TTTTGGAAGTTTCGGGGTCAAAAATG-AAA
*
12445414 TTTTGGAAGTTTCGGGGTCAAAAATGGAA
1 TTTTGGAAGTTTCGGGGTCAAAAATGAAA
12445443 TGTTTGGAA
1 T-TTTGGAA
12445452 TATTTGGAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 6 0.10
29 39 0.67
30 13 0.22
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.35
Consensus pattern (29 bp):
TTTTGGAAGTTTCGGGGTCAAAAATGAAA
Found at i:12445489 original size:38 final size:39
Alignment explanation
Indices: 12445415--12445489 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
12445405 AAATGTAATT
*
12445415 TTTGGAAGTTTCGGGGTCAAAAATGGAATGTTTGGAATA
1 TTTGGAAGTTTCGGGGGCAAAAATGGAATGTTTGGAATA
* * * *
12445454 TTTGGAA-TTTTGGGGGCAATAATGTAATTTTTGGAA
1 TTTGGAAGTTTCGGGGGCAAAAATGGAATGTTTGGAA
12445490 GTTCGAGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 24 0.77
39 7 0.23
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.37
Consensus pattern (39 bp):
TTTGGAAGTTTCGGGGGCAAAAATGGAATGTTTGGAATA
Found at i:12447389 original size:17 final size:18
Alignment explanation
Indices: 12447369--12447412 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
12447359 AAAATTAATT
12447369 TAAATTC-AAATTTAAAA
1 TAAATTCTAAATTTAAAA
12447386 TAAA-TCTAAATTTAAAA
1 TAAATTCTAAATTTAAAA
12447403 TAAATT-TAAA
1 TAAATTCTAAA
12447413 AGGGCTCGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.08
17 22 0.88
18 1 0.04
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATTCTAAATTTAAAA
Found at i:12448276 original size:204 final size:205
Alignment explanation
Indices: 12447712--12448722 Score: 1489
Period size: 204 Copynumber: 4.9 Consensus size: 205
12447702 TCTGGTTTCA
* * * * * ** *
12447712 TTGACTTGGCCTTCTTCTCTGTATCTCATCAGGAAGATGACCACATCACTT-TTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAAT-CGCTT
* * * * * *
12447776 CTCTGTGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCAC
65 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * **
12447841 TTTATTGCTTAGACCTGCTTCTCAATATCTCATCAAAAAGCTAAGGGTTCGAAGATTTGCTCACA
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-AGGGTTCGAAGATTTGCTCACA
*
12447906 TCGAGCGTTGGT
194 TCGAGCGTGGGT
*
12447918 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCTGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATC-GCTT
12447983 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
65 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
12448048 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAGATTTGCTCACAT
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
12448112 CGAGCGTGGGT
195 CGAGCGTGGGT
12448123 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCGCTTC
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCGCTTC
* * *
12448188 TCTGTACCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATT
66 TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
*
12448253 TTATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCT-GGGTTCGAAGATTTGCTCACATC
131 TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATC
12448317 GAGCGTGGGT
196 GAGCGTGGGT
12448327 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAAT-CGCTT
* *
12448392 CTCTATACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
65 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * *
12448457 TTTATTGCTTCGATCTGCTTCTCTGTATCTCATCAGGAAGTTAGGGTTCGAAGATTTGCTCACTT
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
* *
12448522 TGAGC-----C
195 CGAGCGTGGGT
* * * * * * *
12448528 TTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGGTGACCGCCTCACTTGTTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAA-TCGCTT
*
12448593 CTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
65 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * * * * * *
12448658 TTTATTACTTCGCCCTGCCTCTCAGTATGTCATCAGGAAGCTGGGGTTCAAAGATCTGTTCACAT
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
12448723 TGAGTTGGTA
Statistics
Matches: 743, Mismatches: 57, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
201 171 0.23
202 1 0.00
204 199 0.27
205 196 0.26
206 71 0.10
207 105 0.14
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (205 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCGCTTC
TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATC
GAGCGTGGGT
Found at i:12448487 original size:409 final size:406
Alignment explanation
Indices: 12447712--12448722 Score: 1506
Period size: 409 Copynumber: 2.5 Consensus size: 406
12447702 TCTGGTTTCA
* * ** *
12447712 TTGACTTGGCCTTCTTCTCTGTATCTCATCAGGAAGATGACCACATCACTT-TTTTGATCCACTT
1 TTGACTTGGTCTTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAAT-CGCTT
* * * * * *
12447776 CTCTGTGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCAC
65 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * **
12447841 TTTATTGCTTAGACCTGCTTCTCAATATCTCATCAAAAAGCTAAGGGTTCGAAGATTTGCTCACA
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-AGGGTTCGAAGATTTGCTCACA
* *
12447906 TCGAGCGTTGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGT
194 TCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGT
* * *
12447971 TTCAATCTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAG
259 TTCAATCCGCTTCTCTATACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAG
12448036 GAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAG
324 GAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAG
*
12448100 ATTTGCTCACATCGAGCGTGGGT
389 ATTTGCTCACATCGAGC-----C
* * *
12448123 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCGCTTC
1 TTGACTTGGTCTTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCGCTTC
* * *
12448188 TCTGTACCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATT
66 TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
*
12448253 TTATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCT-GGGTTCGAAGATTTGCTCACATC
131 TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATC
12448317 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
196 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
12448382 CAATCCGCTTCTCTATACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGA
261 CAATCCGCTTCTCTATACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGA
* * *
12448447 AGCTAACCATTTTATTGCTTCGATCTGCTTCTCTGTATCTCATCAGGAAGTTAGGGTTCGAAGAT
326 AGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGAT
* *
12448512 TTGCTCACTTTGAGCC
391 TTGCTCACATCGAGCC
* * * * *
12448528 TTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGGTGACCGCCTCACTTGTTTCAATTCGCTT
1 TTGACTTGGTCTTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAA-TCGCTT
*
12448593 CTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
65 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * * * * * *
12448658 TTTATTACTTCGCCCTGCCTCTCAGTATGTCATCAGGAAGCTGGGGTTCAAAGATCTGTTCACAT
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
12448723 TGAGTTGGTA
Statistics
Matches: 544, Mismatches: 52, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
405 51 0.09
406 104 0.19
407 19 0.03
409 197 0.36
410 25 0.05
411 143 0.26
412 5 0.01
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (406 bp):
TTGACTTGGTCTTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCGCTTC
TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATC
GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
CAATCCGCTTCTCTATACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGA
AGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGAT
TTGCTCACATCGAGCC
Found at i:12449179 original size:49 final size:49
Alignment explanation
Indices: 12449113--12449319 Score: 157
Period size: 49 Copynumber: 4.2 Consensus size: 49
12449103 CGACTTAAAC
** * *
12449113 CTTTCCCTTCAAATCTTCGTGGTACTGGATCTG-CTGTCGCAGCTTAGAT
1 CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGTC-ATCGCAGCTTAGAT
* * * * *
12449162 CTTTCTCTTCCTGTCTTCGTAGTACTGGGTCCGTCATCGCGGCTTAGAT
1 CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGTCATCGCAGCTTAGAT
* * * ** *
12449211 CTTTCCCTTCATGTCTTCGTGATACTGGATCCGCCGTTACGGCTTTAGAT
1 CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGTCATCGCAGC-TTAGAT
* * * * * * *
12449261 CTTTCCCTT-TTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGAT
1 CTTTCCCTTCATG--TCTTCGTGGTACTGGATCCGTCATCGCAG-CTTAGAT
12449312 CTTTCCCT
1 CTTTCCCT
12449320 GTCAAATCTG
Statistics
Matches: 130, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
49 74 0.57
50 16 0.12
51 39 0.30
52 1 0.01
ACGTcount: A:0.12, C:0.28, G:0.21, T:0.39
Consensus pattern (49 bp):
CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGTCATCGCAGCTTAGAT
Found at i:12455337 original size:59 final size:59
Alignment explanation
Indices: 12455274--12455500 Score: 198
Period size: 59 Copynumber: 3.9 Consensus size: 59
12455264 GACTCTCGGA
* *
12455274 GGTAAAATGGTAA-TTTTGGAAAAATTTTGGGGTTAAAAATGACATTTTAGACATTCGAG
1 GGTAAAATGGTAATTTTTGG-AAAATTTTGGGGTCAAAAATGAAATTTTAGACATTCGAG
* * * ** * *
12455333 GGTAAAATGGTAATTTTTGGAAAA-ATCGGGATCAAAAATGGATTTTTTGGACATCCGAG
1 GGTAAAATGGTAATTTTTGGAAAATTTTGGGGTCAAAAAT-GAAATTTTAGACATTCGAG
* * * * * ** *
12455392 AGTAAAACGGTAATTTTT-GAAAGTTTTGGGGTCAAAAATGGGATTTTTAGATTTTCGGG
1 GGTAAAATGGTAATTTTTGGAAAATTTTGGGGTCAAAAAT-GAAATTTTAGACATTCGAG
12455451 GGTAAAAAT-GTAATTTTTGG--AATTTTAGGGGT-AAAAATGTAAATTTTAGA
1 GGT-AAAATGGTAATTTTTGGAAAATTTT-GGGGTCAAAAATG-AAATTTTAGA
12455501 AGTTTCGATG
Statistics
Matches: 135, Mismatches: 26, Indels: 15
0.77 0.15 0.09
Matches are distributed among these distances:
57 1 0.01
58 34 0.25
59 89 0.66
60 11 0.08
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.35
Consensus pattern (59 bp):
GGTAAAATGGTAATTTTTGGAAAATTTTGGGGTCAAAAATGAAATTTTAGACATTCGAG
Found at i:12455438 original size:30 final size:29
Alignment explanation
Indices: 12455403--12455489 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
12455393 GTAAAACGGT
12455403 AATTTTTGAAAGTTTT-GGGGTCAAAAATGG
1 AATTTTTGAAA-TTTTAGGGGT-AAAAATGG
* * * *
12455433 GATTTTT-AGATTTTCGGGGGTAAAAATGT
1 AATTTTTGAAATTTT-AGGGGTAAAAATGG
*
12455462 AATTTTTGGAATTTTAGGGGTAAAAATG
1 AATTTTTGAAATTTTAGGGGTAAAAATG
12455490 TAAATTTTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
28 4 0.09
29 27 0.57
30 16 0.34
ACGTcount: A:0.32, C:0.02, G:0.26, T:0.39
Consensus pattern (29 bp):
AATTTTTGAAATTTTAGGGGTAAAAATGG
Found at i:12455451 original size:29 final size:28
Alignment explanation
Indices: 12455415--12455501 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 28
12455405 TTTTTGAAAG
*
12455415 TTTTGGGGTCAAAAATGGGATTTTTAG-A
1 TTTTGGGGT-AAAAATGGAATTTTTAGAA
* *
12455443 TTTTCGGGGGTAAAAATGTAATTTTTGGAA
1 TTTT--GGGGTAAAAATGGAATTTTTAGAA
* *
12455473 TTTTAGGGGTAAAAATGTAAATTTTAGAA
1 TTTT-GGGGTAAAAATGGAATTTTTAGAA
12455502 GTTTCGATGC
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
28 4 0.08
29 36 0.72
30 10 0.20
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.39
Consensus pattern (28 bp):
TTTTGGGGTAAAAATGGAATTTTTAGAA
Found at i:12457387 original size:6 final size:6
Alignment explanation
Indices: 12457362--12457431 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
12457352 TGTTTTTTTT
* * *
12457362 TTTAAA TTTGAAA -ATAAA TTTAAA TTTAAA TTCAAA TTTAAA -ATAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
12457409 TCTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
12457432 AGGGCCCGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
5 11 0.22
6 37 0.73
7 3 0.06
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:12457415 original size:17 final size:17
Alignment explanation
Indices: 12457364--12457431 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
12457354 TTTTTTTTTT
*
12457364 TAAATTTGAAAATAAATT
1 TAAATTT-AAAATAAATC
12457382 TAAATTT-AAAT---TC
1 TAAATTTAAAATAAATC
12457395 -AAATTTAAAATAAATC
1 TAAATTTAAAATAAATC
*
12457411 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATC
12457428 TAAA
1 TAAA
12457432 AGGGCCCGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
12 6 0.14
13 5 0.12
16 6 0.14
17 19 0.44
18 7 0.16
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAAATAAATC
Found at i:12461242 original size:30 final size:29
Alignment explanation
Indices: 12461199--12461660 Score: 226
Period size: 30 Copynumber: 15.7 Consensus size: 29
12461189 TGAACTGTTT
* * * *
12461199 AAAAATCATATTTTGACCCCTCAACTTTTC
1 AAAAATTACATTTT-ACCCCTGAACTTTCC
*
12461229 AAAAATTACATTTTGACCCTTGAACTTTCC
1 AAAAATTACATTTT-ACCCCTGAACTTTCC
* * *
12461259 AAAATTTACATTATT-GCCCTCGAGC-TTCAC
1 AAAAATTACATT-TTACCCCT-GAACTTTC-C
*
12461289 AAAAATTACCATTTTA-CCTTGAA-TTTCC
1 AAAAATTA-CATTTTACCCCTGAACTTTCC
*
12461317 AAAAATTCCATTTTTGA-CCC-GAACTTTCC
1 AAAAATTACA-TTTT-ACCCCTGAACTTTCC
* *
12461346 CAAAATTACCATTTTACCCC-GAA-TGTCC
1 AAAAATTA-CATTTTACCCCTGAACTTTCC
* * *
12461374 AAAAATTCCATTTTTCACCCTGAACTTCCC
1 AAAAATTACATTTTAC-CCCTGAACTTTCC
* **
12461404 AAAAAATACCATTTTACCCCCAAACTTT-C
1 AAAAATTA-CATTTTACCCCTGAACTTTCC
*
12461433 AAAAATT-CTATTTTTGACCTC-GAACTTTCC
1 AAAAATTAC-A-TTTT-ACCCCTGAACTTTCC
* *
12461463 CAAAATTAGCATTTTACCCC-GAAC-ATCC
1 AAAAATTA-CATTTTACCCCTGAACTTTCC
**
12461491 AAAAATTTTATTTTTGACCCC--ATACTTTCC
1 AAAAATTACA-TTTT-ACCCCTGA-ACTTTCC
* * * *
12461521 CAAAATTACCATTTTACCCTTAAAC-TACC
1 AAAAATTA-CATTTTACCCCTGAACTTTCC
* * *
12461550 AAAAATTCCATTTTTAACCCTAAACTTTCC
1 AAAAATTACA-TTTTACCCCTGAACTTTCC
* * *
12461580 CAAAATTACCATTTTA-CCCTCGAA-TGTCT
1 AAAAATTA-CATTTTACCCCT-GAACTTTCC
* *
12461609 AAAAATTCCATTTTTGACCTC-GAAC-TTCC
1 AAAAATTACA-TTTT-ACCCCTGAACTTTCC
*
12461638 TAAAAATTACCATTTTGCCCCTG
1 -AAAAATTA-CATTTTACCCCTG
12461661 GCATCGAAAA
Statistics
Matches: 332, Mismatches: 61, Indels: 78
0.70 0.13 0.17
Matches are distributed among these distances:
27 11 0.03
28 48 0.14
29 120 0.36
30 130 0.39
31 22 0.07
32 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAAATTACATTTTACCCCTGAACTTTCC
Found at i:12461350 original size:58 final size:58
Alignment explanation
Indices: 12461221--12461653 Score: 423
Period size: 59 Copynumber: 7.4 Consensus size: 58
12461211 TTGACCCCTC
* * * * * * *
12461221 AACTTTTCAAAAATTA-CATTTTGACCCTTGAACTTTCCAAAATTTACATTATTGCCCTCG
1 AACTTTCCCAAAATTACCATTTT-ACCCTCGAA-TTTCCAAAAATTCCATTTTTGACC-CG
* * *
12461281 AGC-TTCACAAAAATTACCATTTTA-CCTTGAATTTCCAAAAATTCCATTTTTGACCCG
1 AACTTTC-CCAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACCCG
* *
12461338 AACTTTCCCAAAATTACCATTTTACCC-CGAATGTCCAAAAATTCCATTTTTCACCCTG
1 AACTTTCCCAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACCC-G
* * * *
12461396 AAC-TTCCCAAAAAATACCATTTTACCCCCAAACTTT-CAAAAATTCTATTTTTGACCTCG
1 AACTTTCCC-AAAATTACCATTTTACCCTCGAA-TTTCCAAAAATTCCATTTTTGACC-CG
* ** ** *
12461455 AACTTTCCCAAAATTAGCATTTTACCC-CGAACATCCAAAAATTTTATTTTTGACCCC
1 AACTTTCCCAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACCCG
** * * * *
12461512 ATACTTTCCCAAAATTACCATTTTACCCTTAAACTACCAAAAATTCCATTTTTAACCCTA
1 A-ACTTTCCCAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACCC-G
* *
12461572 AACTTTCCCAAAATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTTGACCTCG
1 AACTTTCCCAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACC-CG
*
12461631 AAC-TTCCTAAAAATTACCATTTT
1 AACTTTCC-CAAAATTACCATTTT
12461654 GCCCCTGGCA
Statistics
Matches: 316, Mismatches: 41, Indels: 33
0.81 0.11 0.08
Matches are distributed among these distances:
57 54 0.17
58 97 0.31
59 137 0.43
60 22 0.07
61 6 0.02
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (58 bp):
AACTTTCCCAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACCCG
Found at i:12461484 original size:117 final size:116
Alignment explanation
Indices: 12461221--12461658 Score: 456
Period size: 117 Copynumber: 3.7 Consensus size: 116
12461211 TTGACCCCTC
* * * * * * * *
12461221 AACTTTTCAAAAATTA-CATTTTGACCCTTGAACTTTCCAAAATTTACATTATTG-CCCTCGAGC
1 AACTTTCCCAAAATTACCATTTT-ACCC-CGAA-TGTCCAAAAATTCCATTTTTGACCCT-GAAC
* *** * *
12461284 TTCACAAAAATTACCATTTTA-CCTTGAATTTCCAAAAATTCCATTTTTGACCCG
62 TTCCCAAAAATTACCATTTTACCCCCAAACTACCAAAAATTCCATTTTTGACCCG
*
12461338 AACTTTCCCAAAATTACCATTTTACCCCGAATGTCCAAAAATTCCATTTTTCACCCTGAACTTCC
1 AACTTTCCCAAAATTACCATTTTACCCCGAATGTCCAAAAATTCCATTTTTGACCCTGAACTTCC
* ** *
12461403 CAAAAAATACCATTTTACCCCCAAACTTTCAAAAATTCTATTTTTGACCTCG
66 CAAAAATTACCATTTTACCCCCAAACTACCAAAAATTCCATTTTTGACC-CG
* ** ** *
12461455 AACTTTCCCAAAATTAGCATTTTACCCCGAACATCCAAAAATTTTATTTTTGACCC-CATACTTT
1 AACTTTCCCAAAATTACCATTTTACCCCGAATGTCCAAAAATTCCATTTTTGACCCTGA-AC-TT
** * *
12461519 CCC-AAAATTACCATTTTACCCTTAAACTACCAAAAATTCCATTTTTAACCCTA
64 CCCAAAAATTACCATTTTACCCCCAAACTACCAAAAATTCCATTTTTGACCC-G
*
12461572 AACTTTCCCAAAATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTTGA-CCTCGAACTT
1 AACTTTCCCAAAATTACCATTTTACCC-CGAATGTCCAAAAATTCCATTTTTGACCCT-GAACTT
* *
12461636 CCTAAAAATTACCATTTTGCCCC
64 CCCAAAAATTACCATTTTACCCC
12461659 TGGCATCGAA
Statistics
Matches: 268, Mismatches: 42, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
115 38 0.14
116 34 0.13
117 144 0.54
118 51 0.19
119 1 0.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (116 bp):
AACTTTCCCAAAATTACCATTTTACCCCGAATGTCCAAAAATTCCATTTTTGACCCTGAACTTCC
CAAAAATTACCATTTTACCCCCAAACTACCAAAAATTCCATTTTTGACCCG
Found at i:12465597 original size:23 final size:23
Alignment explanation
Indices: 12465578--12465650 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
12465568 GCCTTTTCTT
12465578 GCATTACATACATGCATTTTTTC
1 GCATTACATACATGCATTTTTTC
* ** *
12465601 GCATTGCATATTTGCATATTTTC
1 GCATTACATACATGCATTTTTTC
** *
12465624 GCA-TAGCATATTTGCATATTTTC
1 GCATTA-CATACATGCATTTTTTC
12465647 GCAT
1 GCAT
12465651 AATAATTCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 1 0.02
23 42 0.98
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (23 bp):
GCATTACATACATGCATTTTTTC
Found at i:12465651 original size:23 final size:23
Alignment explanation
Indices: 12465590--12465651 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
12465580 ATTACATACA
* *
12465590 TGCATTTTTTCGCATTGCATATT
1 TGCATATTTTCGCATAGCATATT
12465613 TGCATATTTTCGCATAGCATATT
1 TGCATATTTTCGCATAGCATATT
12465636 TGCATATTTTCGCATA
1 TGCATATTTTCGCATA
12465652 ATAATTCTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.47
Consensus pattern (23 bp):
TGCATATTTTCGCATAGCATATT
Found at i:12476830 original size:6 final size:6
Alignment explanation
Indices: 12476793--12476862 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
12476783 CTAAATCCAT
* * *
12476793 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTATA TTTAAA
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
12476839 TTTAAA ATT--A TTCTAAA TTTAAA T
1 TTTAAA TTTAAA TT-TAAA TTTAAA T
12476863 AAACAAAGTC
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
4 2 0.04
5 10 0.20
6 34 0.69
7 3 0.06
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:12476834 original size:13 final size:12
Alignment explanation
Indices: 12476811--12476842 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
12476801 TATTTTAAGA
12476811 TTAAATTTAT-T
1 TTAAATTTATAT
12476822 TTAAATTTATAT
1 TTAAATTTATAT
12476834 TTAAATTTA
1 TTAAATTTA
12476843 AAATTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAAATTTATAT
Found at i:12476835 original size:17 final size:18
Alignment explanation
Indices: 12476793--12476836 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
12476783 CTAAATCCAT
12476793 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
12476811 -TTAAATTTATTTTAA-A
1 TTTAAATTTATTTTAAGA
*
12476827 TTTATATTTA
1 TTTAAATTTA
12476837 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:12476844 original size:18 final size:17
Alignment explanation
Indices: 12476793--12476862 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
12476783 CTAAATCCAT
*
12476793 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTCTAA-A
*
12476811 -TTAAATTTATTTTAAA
1 TTTAAATTTATTCTAAA
12476827 TTT--A--TATT-TAAA
1 TTTAAATTTATTCTAAA
*
12476839 TTTAAAATTATTCTAAA
1 TTTAAATTTATTCTAAA
12476856 TTTAAAT
1 TTTAAAT
12476863 AAACAAAGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
12 7 0.16
13 4 0.09
14 1 0.02
15 1 0.02
16 5 0.11
17 27 0.60
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTCTAAA
Found at i:12476849 original size:29 final size:28
Alignment explanation
Indices: 12476791--12476859 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 28
12476781 AACTAAATCC
*
12476791 ATTTTAAATTTATTTTAAGATTAAATTT
1 ATTTTAAATTTATTTTAAGATTAAAATT
12476819 ATTTTAAATTTATATTTAA-ATTTAAAATT
1 ATTTTAAATTTAT-TTTAAGA-TTAAAATT
*
12476848 ATTCTAAATTTA
1 ATTTTAAATTTA
12476860 AATAAACAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 14 0.38
29 23 0.62
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
ATTTTAAATTTATTTTAAGATTAAAATT
Found at i:12476985 original size:3 final size:3
Alignment explanation
Indices: 12476977--12477054 Score: 77
Period size: 3 Copynumber: 25.7 Consensus size: 3
12476967 AAATAGTATC
* * ** *
12476977 AAT AAT AAT CAAT AAT AAT AAT ACT ATT CTT AAT AGT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
12477023 AAT AAT GAT -AT AAT AAAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA
12477055 GGCAGTCGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 2 0.03
3 56 0.88
4 6 0.09
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:12477023 original size:30 final size:30
Alignment explanation
Indices: 12476977--12477054 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
12476967 AAATAGTATC
** *
12476977 AATAATAATCAATAATAATAAT-ACTATTCTT
1 AATAATAAT-AATAATAATAATGA-TATAATA
*
12477008 AATAGTAATAATAATAATAATGATATAATA
1 AATAATAATAATAATAATAATGATATAATA
12477038 AATAATAATAATAATAA
1 AATAATAATAATAATAA
12477055 GGCAGTCGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 32 0.78
31 9 0.22
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (30 bp):
AATAATAATAATAATAATAATGATATAATA
Found at i:12478217 original size:30 final size:30
Alignment explanation
Indices: 12478181--12478243 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
12478171 TAAAAATCAT
12478181 ATTTTGACCCTTAAACTTTCCAAGAA-TTAC
1 ATTTTGACCCTTAAACTTTCCAA-AATTTAC
*
12478211 ATTTTGACCCTTGAACTTTCCAAAATTTAC
1 ATTTTGACCCTTAAACTTTCCAAAATTTAC
12478241 ATT
1 ATT
12478244 ATTGCACTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (30 bp):
ATTTTGACCCTTAAACTTTCCAAAATTTAC
Found at i:12478257 original size:30 final size:27
Alignment explanation
Indices: 12478194--12478328 Score: 87
Period size: 30 Copynumber: 4.6 Consensus size: 27
12478184 TTGACCCTTA
*
12478194 AACTTTCCAAGAATTACATTTTGACCCTTG
1 AACTTTCCAA-AATTACATTTTG--CCTCG
12478224 AACTTTCCAAAATTTACATTATTGCACTCG
1 AACTTTCCAAAA-TTACATT-TTGC-CTCG
*
12478254 AAC-TTCACAAAAATTACCATTTTACCTCG
1 AACTTTC-C-AAAATTA-CATTTTGCCTCG
*
12478283 AA-TTTCCAAAAATT-CTATTTTTGACCCCG
1 AACTTTCC-AAAATTAC-A-TTTTG-CCTCG
*
12478312 AACTTTTCCATAATTAC
1 AAC-TTTCCAAAATTAC
12478329 CATTCTACCC
Statistics
Matches: 87, Mismatches: 5, Indels: 25
0.74 0.04 0.21
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 12 0.14
29 21 0.24
30 35 0.40
31 17 0.20
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36
Consensus pattern (27 bp):
AACTTTCCAAAATTACATTTTGCCTCG
Found at i:12478363 original size:59 final size:58
Alignment explanation
Indices: 12478263--12478747 Score: 471
Period size: 59 Copynumber: 8.3 Consensus size: 58
12478253 GAACTTCACA
* * * * * *
12478263 AAAATTACCATTTTACCTCGAATTTCCAAAAATTCTATTTTTGACCCCGAACTTTTCC
1 AAAATTACCATTTTACCCCCAAATTCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
* * * * * *
12478321 ATAATTACCATTCTACCCCCAAATGTCCAAAAATTCCATTTTTCACCCTAAACTTGCCA
1 AAAATTACCATTTTACCCCCAAAT-TCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
* *
12478380 AAAATTACCATTTTACGCCCAAACTTCCAAAAATTCTATTTTTGACCCCAAACTTTCCC
1 AAAATTACCATTTTACCCCCAAA-TTCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
* * * *
12478439 AAAATTACCATTTCACCCCCGAATGTCTAAAAATTCCATTTTTGACTCCAAAC-TTCCC
1 AAAATTACCATTTTACCCCCAAAT-TCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
** * * *
12478497 AAATATTACCATTTTACCCTTAGACTTCCAAAAATTCCATTTTTGACCTCGAACTTTCCC
1 AAA-ATTACCATTTTACCCCCA-AATTCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
* * * ** * * *
12478557 AAAATTAACATTTTACCCTCAAACATCCAAAAATTTTATTTTTGACCTCATACTTTCCT
1 AAAATTACCATTTTACCCCCAAA-TTCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
** *
12478616 AAAATTACCATTTTACCCTTAAACTTCCAAAAATTCCA--TTT---CCTAAACTTTCCC
1 AAAATTACCATTTTACCCCCAAA-TTCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
* * * * * *
12478670 AAAATTACCATTTTAACCCCGAATGTCCAAAAATTCCATTTTTAACCTCGAAC-TTCCTA
1 AAAATTACCATTTTACCCCCAAAT-TCCAAAAATTCCATTTTTGACCCCAAACTTTCC-C
*
12478729 AAAATTACCATTTTTCCCC
1 AAAATTACCATTTTACCCC
12478748 TGGCATCGAA
Statistics
Matches: 350, Mismatches: 63, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
53 1 0.00
54 41 0.12
56 3 0.01
57 3 0.01
58 33 0.09
59 258 0.74
60 11 0.03
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAATTCCAAAAATTCCATTTTTGACCCCAAACTTTCCC
Found at i:12478408 original size:118 final size:118
Alignment explanation
Indices: 12478254--12478742 Score: 559
Period size: 118 Copynumber: 4.2 Consensus size: 118
12478244 ATTGCACTCG
* * * *
12478254 AACTTCACAAAAATTACCATTTTA-CCTCGAATTTCCAAAAATTCTATTTTTGACCCCGAACTTT
1 AACTTC-CAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAACTTT
* * * *
12478318 TCCATAATTACCATTCTACCCCCAAATGTCCAAAAATTCCATTTTTCACCCT-A
65 CCCAAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCTCA
*
12478371 AACTTGCCAAAAATTACCATTTTACGCC-CAAACTTCCAAAAATTCTATTTTTGACCCCAAACTT
1 AACTT-CCAAAAATTACCATTTTAC-CCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAACTT
* * * *
12478435 TCCCAAAATTACCATTTCACCCCCGAATGTCTAAAAATTCCATTTTTGACTC-CA
64 TCCCAAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCTCA
* * * * *
12478489 AACTTCCCAAATATTACCATTTTACCCTTAGACTTCCAAAAATTCCATTTTTGACCTCGAACTTT
1 AACTT-CCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAACTTT
* * ** **
12478554 CCCAAAATTAACATTTTACCCTCAAACATCCAAAAATTTTATTTTTGA-CCTCA
65 CCCAAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCTCA
* * * *
12478607 TACTTTCCTAAAATTACCATTTTACCCTTAAACTTCCAAAAATTCCA--TTT---CCTAAACTTT
1 AAC-TTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAACTTT
* * * *
12478667 CCCAAAATTACCATTTTAACCCCGAATGTCCAAAAATTCCATTTTT-AACCTCG
65 CCCAAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCTCA
12478720 AACTTCCTAAAAATTACCATTTT
1 AACTTCC-AAAAATTACCATTTT
12478743 TCCCCTGGCA
Statistics
Matches: 317, Mismatches: 46, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
112 5 0.02
113 65 0.21
116 3 0.01
117 25 0.08
118 215 0.68
119 4 0.01
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (118 bp):
AACTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAACTTTC
CCAAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCTCA
Found at i:12478507 original size:177 final size:173
Alignment explanation
Indices: 12478263--12478742 Score: 546
Period size: 177 Copynumber: 2.7 Consensus size: 173
12478253 GAACTTCACA
* * * *
12478263 AAAATTACCATTTTA-CCTCGAATTTCCAAAAATTCTATTTTTGACCCCGAACTTTTCCATAATT
1 AAAATTACCATTTTACCCTCGAA-TTCCAAAAATTCCATTTTTGA-CCCAAACTTTCCCAAAATT
* *
12478327 ACCATTCTACCCCCAAATGTCCAAAAATTCCATTTTTCACC-CTAAACTTGCCAAAAATTACCAT
64 ACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTT-ACCTC-GAACTT-CCAAAAATTACCAT
*
12478391 TTTACGCC-CAAACTTCCAAAAATTCTATTTTTGACCCCAAACTTTCCC
126 TTTAC-CCTCAAACATCCAAAAATTCTATTTTTGACCCCAAACTTTCCC
* * *
12478439 AAAATTACCATTTCACCCCCGAATGTCTAAAAATTCCATTTTTGACTCCAAAC-TTCCCAAATAT
1 AAAATTACCATTTTACCCTCGAAT-TCCAAAAATTCCATTTTTGAC-CCAAACTTTCCCAAA-AT
** * * *
12478503 TACCATTTTACCCTTAGACT-TCCAAAAATTCCATTTTTGACCTCGAACTTTCCCAAAATTAACA
63 TACCATTTTACCCCCA-AATGTCCAAAAATTCCATTTTT-ACCTCGAAC-TTCCAAAAATTACCA
* * * *
12478567 TTTTACCCTCAAACATCCAAAAATTTTATTTTTGACCTCATACTTTCCT
125 TTTTACCCTCAAACATCCAAAAATTCTATTTTTGACCCCAAACTTTCCC
** *
12478616 AAAATTACCATTTTACCCTTAAACTTCCAAAAATTCCA--TTT--CCTAAACTTTCCCAAAATTA
1 AAAATTACCATTTTACCCTCGAA-TTCCAAAAATTCCATTTTTGACCCAAACTTTCCCAAAATTA
* *
12478677 CCATTTTAACCCCGAATGTCCAAAAATTCCATTTTTAACCTCGAACTTCCTAAAAATTACCATTT
65 CCATTTTACCCCCAAATGTCCAAAAATTCCATTTTT-ACCTCGAACTTCC-AAAAATTACCATTT
12478742 T
128 T
12478743 TCCCCTGGCA
Statistics
Matches: 258, Mismatches: 34, Indels: 28
0.81 0.11 0.09
Matches are distributed among these distances:
171 6 0.02
172 59 0.23
173 9 0.03
175 3 0.01
176 24 0.09
177 151 0.59
178 6 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (173 bp):
AAAATTACCATTTTACCCTCGAATTCCAAAAATTCCATTTTTGACCCAAACTTTCCCAAAATTAC
CATTTTACCCCCAAATGTCCAAAAATTCCATTTTTACCTCGAACTTCCAAAAATTACCATTTTAC
CCTCAAACATCCAAAAATTCTATTTTTGACCCCAAACTTTCCC
Found at i:12478734 original size:30 final size:29
Alignment explanation
Indices: 12478254--12478742 Score: 244
Period size: 29 Copynumber: 16.8 Consensus size: 29
12478244 ATTGCACTCG
*
12478254 AACTTCACAAAAATTACCATTTT-ACCTCG
1 AACTTC-CAAAAATTACCATTTTAACCTCA
* * * * *
12478283 AATTTCCAAAAATT-CTATTTTTGACCCCG
1 AACTTCCAAAAATTACCA-TTTTAACCTCA
* * * *
12478312 AACTTTTCC-ATAATTACCATTCTACCCCCA
1 AAC--TTCCAAAAATTACCATTTTAACCTCA
*
12478342 AA-TGTCCAAAAATT-CCATTTTTCACC-CTA
1 AACT-TCCAAAAATTACCA-TTTTAACCTC-A
*
12478371 AACTTGCCAAAAATTACCATTTT-ACGCCCA
1 AACTT-CCAAAAATTACCATTTTAAC-CTCA
* * *
12478401 AACTTCCAAAAATT-CTATTTTTGACCCCA
1 AACTTCCAAAAATTACCA-TTTTAACCTCA
* * * * *
12478430 AACTTTCCCAAAATTACCATTTCACCCCCG
1 AAC-TTCCAAAAATTACCATTTTAACCTCA
* *
12478460 AA-TGTCTAAAAATT-CCATTTTTGA-CTCCA
1 AACT-TCCAAAAATTACCA-TTTTAACCT-CA
* * *
12478489 AACTTCCCAAATATTACCATTTTACCCTTA
1 AACTT-CCAAAAATTACCATTTTAACCTCA
* * *
12478519 GACTTCCAAAAATT-CCATTTTTGACCTCG
1 AACTTCCAAAAATTACCA-TTTTAACCTCA
* * *
12478548 AACTTTCCCAAAATTAACATTTTACCCTCA
1 AAC-TTCCAAAAATTACCATTTTAACCTCA
* ** *
12478578 AACATCCAAAAATT-TTATTTTTGACCTCA
1 AACTTCCAAAAATTACCA-TTTTAACCTCA
* * * *
12478607 TACTTTCCTAAAATTACCATTTTACCCTTA
1 AAC-TTCCAAAAATTACCATTTTAACCTCA
12478637 AACTTCCAAAAATT-CCA-TTT--CCT-A
1 AACTTCCAAAAATTACCATTTTAACCTCA
* * *
12478661 AACTTTCCCAAAATTACCATTTTAACCCCG
1 AAC-TTCCAAAAATTACCATTTTAACCTCA
*
12478691 AA-TGTCCAAAAATT-CCATTTTTAACCTCG
1 AACT-TCCAAAAATTACCA-TTTTAACCTCA
12478720 AACTTCCTAAAAATTACCATTTT
1 AACTTCC-AAAAATTACCATTTT
12478743 TCCCCTGGCA
Statistics
Matches: 352, Mismatches: 66, Indels: 83
0.70 0.13 0.17
Matches are distributed among these distances:
24 4 0.01
25 13 0.04
26 3 0.01
27 9 0.03
28 37 0.11
29 136 0.39
30 127 0.36
31 23 0.07
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTACCATTTTAACCTCA
Found at i:12482502 original size:23 final size:23
Alignment explanation
Indices: 12482483--12482532 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
12482473 GCCTTTTCTT
12482483 GCATTACATACATGCATTTTTTC
1 GCATTACATACATGCATTTTTTC
* ** *
12482506 GCATTGCATATTTGCATATTTTC
1 GCATTACATACATGCATTTTTTC
12482529 GCAT
1 GCAT
12482533 AGCATATTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (23 bp):
GCATTACATACATGCATTTTTTC
Found at i:12482537 original size:23 final size:23
Alignment explanation
Indices: 12482495--12482553 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
12482485 ATTACATACA
* *
12482495 TGCATTTTTTCGCATTGCATATT
1 TGCATATTTTCGCATAGCATATT
12482518 TGCATATTTTCGCATAGCATATT
1 TGCATATTTTCGCATAGCATATT
12482541 TGCATATTTTCGC
1 TGCATATTTTCGC
12482554 GTAATAATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (23 bp):
TGCATATTTTCGCATAGCATATT
Found at i:12491062 original size:209 final size:209
Alignment explanation
Indices: 12490689--12491351 Score: 898
Period size: 209 Copynumber: 3.2 Consensus size: 209
12490679 TATCCAAAAT
* * * * *
12490689 ATAAAGCAGTTACCTTCCTGATGAGATATAGAGAAGTGAAGCAGATCTGTCTTCCTGATGAGACA
1 ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTGATGAGACA
* * *
12490754 CAGAGAAGTGGATTAAAACAAGCGATTCAGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAA
66 CAGAGAAGTGGATTAAAACAAGCGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAA
* ** * *
12490819 ATCAATAAAATCAGGCTCAAAGTGAG-AGAATCTTCGAACCCCAGCTTCCTAATGAGATATTGAG
131 ATCAATGAAGCCAAGCTCAAAGTGAGCA-AATCTTCGAACCCCAGCTTCCTGATGAGATATTGAG
12490883 AAGCAGGTCGAAGCA
195 AAGCAGGTCGAAGCA
* *
12490898 ATAAAGCAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTAATGAGACA
1 ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTGATGAGACA
* * * * *
12490963 CAGAGAAGTGGA-TCAAACTAAGCGAAGCGGTCATCTTCCTGATAAGATACTAAGAAGAAGGCCA
66 CAGAGAAGTGGATTAAAAC-AAGCGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCA
* * *
12491027 AATCAATGAAGCCAAGCTCAAAATGAGCAAATCTTCGAACCCCAACTTCTTGATGAGATATTGAG
130 AATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAG
12491092 AAGCAGGTCGAAGCA
195 AAGCAGGTCGAAGCA
* * * * * * * * *
12491107 ATAAAACGGTTAGCTTCCAGATGAGATACTGAGAAGTGGACCAAATTCGCCTTTCTGATGAGATA
1 ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTGATGAGACA
* ** * * *
12491172 CGGAGAAGCAGATTGAAACAAGTGATGCTGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAA
66 CAGAGAAGTGGATTAAAACAAGCGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAA
* *
12491237 ATCAATGAAGCCAAGCTCAAAGTAAGCGAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGA
131 ATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGA
12491302 AGCAGGTCGAAGCA
196 AGCAGGTCGAAGCA
** * *
12491316 ATAAAATGGTTATCTTCCTGATGAGATACTGAGAAG
1 ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAG
12491352 CGGATTGAAA
Statistics
Matches: 402, Mismatches: 49, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
208 5 0.01
209 391 0.97
210 6 0.01
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.22
Consensus pattern (209 bp):
ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTGATGAGACA
CAGAGAAGTGGATTAAAACAAGCGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAA
ATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGA
AGCAGGTCGAAGCA
Found at i:12491753 original size:35 final size:34
Alignment explanation
Indices: 12491714--12491821 Score: 141
Period size: 34 Copynumber: 3.2 Consensus size: 34
12491704 CTAAACCCAT
12491714 TTTAAATTTATTTTTAAATTTAAATATGTTTT-AAA
1 TTTAAATTTATTTTTAAATTTAAAT-T-TTTTAAAA
*
12491749 TTTAAATTTATTTTAAAATTTAAATTTTTTAAAA
1 TTTAAATTTATTTTTAAATTTAAATTTTTTAAAA
** *
12491783 TTTAAATTTAAATTTAAATTTAAA-TTTCT-AAA
1 TTTAAATTTATTTTTAAATTTAAATTTTTTAAAA
12491815 TTTAAAT
1 TTTAAAT
12491822 AAACAAAAGT
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
32 10 0.15
33 8 0.12
34 25 0.37
35 24 0.36
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTTAAATTTAAATTTTTTAAAA
Found at i:12491772 original size:7 final size:6
Alignment explanation
Indices: 12491714--12491821 Score: 91
Period size: 6 Copynumber: 18.2 Consensus size: 6
12491704 CTAAACCCAT
** * ** *
12491714 TTTAAA TTTATT TTTAAA TTTAAA TAT-GT TTTAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12491760 TTTAAAA TTTAAA TTT--- TTTAAAA TTTAAA TTTAAA TTTAAA TTTAAA
1 TTT-AAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
12491807 TTTCTAAA TTTAAA T
1 -TT-TAAA TTTAAA T
12491822 AAACAAAAGT
Statistics
Matches: 81, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
3 3 0.04
5 6 0.07
6 57 0.70
7 11 0.14
8 4 0.05
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:12493813 original size:30 final size:30
Alignment explanation
Indices: 12493735--12494214 Score: 165
Period size: 30 Copynumber: 16.5 Consensus size: 30
12493725 AAAGGTCCCT
* * * *
12493735 AAACTATCCAAAAATCATATTTTGACCCCC
1 AAACTTTCCAAAAATTACATTTTAACCCCC
*
12493765 AAACTTTCCAAAAGTTACATTTTAACCCCC
1 AAACTTTCCAAAAATTACATTTTAACCCCC
* * *
12493795 AAACTTTCCAAAATTTACA--TT-A-TCAC
1 AAACTTTCCAAAAATTACATTTTAACCCCC
* *
12493821 GAAC-TTCACAAAAATTACCATTTT-ACCCCT
1 AAACTTTC-CAAAAATTA-CATTTTAACCCCC
* * *
12493851 AAA-TTTCCAAAAATTCCATTTTTGA-CCCT
1 AAACTTTCCAAAAATTACA-TTTTAACCCCC
* **
12493880 AAAC-TTCCTAAAAACTACCATTTT-A-CCTT
1 AAACTTTCC-AAAAATTA-CATTTTAACCCCC
* * *
12493909 AGAC-TTCAAAAAATTCCATTTTTAA-CCCC
1 AAACTTTCCAAAAATTACA-TTTTAACCCCC
* * *
12493938 AAACTTTCCCAAAATTACCA-TTTCACCCTC
1 AAACTTTCCAAAAATTA-CATTTTAACCCCC
* * * * * *
12493968 GAA-TGTCCAAAAATTCCATTTTTGA-CTCT
1 AAACTTTCCAAAAATTACA-TTTTAACCCCC
* **
12493997 AAACTTCCCAAAAATTACCATTTT-ACCCTT
1 AAACTTTCCAAAAATTA-CATTTTAACCCCC
* * **
12494027 AAAC-TTCAAAAAATT-C-CTTTAA-CCTT
1 AAACTTTCCAAAAATTACATTTTAACCCCC
* * *
12494053 GAACTTTCCCAAAATCACTATTTT-ACCCCC
1 AAACTTTCCAAAAATTAC-ATTTTAACCCCC
* * * *
12494083 AAAC-ATCCAAAAATTCCATTTTTA-TCCC
1 AAACTTTCCAAAAATTACATTTTAACCCCC
* * *
12494111 AAATTTTCCTAAAATTACCATTTT-ACCCTC
1 AAACTTTCCAAAAATTA-CATTTTAACCCCC
* *
12494141 AGAC-TTCCAAAAATT-CTATTTTTAA-CCTC
1 AAACTTTCCAAAAATTAC-A-TTTTAACCCCC
* *
12494170 GAACTTTCCCAAAATTACCATTTT-ACCCCC
1 AAACTTTCCAAAAATTA-CATTTTAACCCCC
* *
12494200 GAA-TGTCCAAAAATT
1 AAACTTTCCAAAAATT
12494215 CAATTTTTGA
Statistics
Matches: 337, Mismatches: 75, Indels: 77
0.69 0.15 0.16
Matches are distributed among these distances:
25 3 0.01
26 23 0.07
27 16 0.05
28 29 0.09
29 121 0.36
30 137 0.41
31 7 0.02
32 1 0.00
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTAACCCCC
Found at i:12493863 original size:29 final size:29
Alignment explanation
Indices: 12493731--12494214 Score: 200
Period size: 29 Copynumber: 16.7 Consensus size: 29
12493721 CCCAAAAGGT
* * *
12493731 CCCTAAACTATCCAAAAATCA-TATTTTGAC
1 CCCTAAA-TTTCCAAAAATTACCATTTT-AC
* *
12493761 CCCCAAACTTTCCAAAAGTTA-CATTTTAAC
1 CCCTAAA-TTTCCAAAAATTACCATTTT-AC
* * *
12493791 CCCCAAACTTTCCAAAATTTA-CA--TTAT
1 CCCTAAA-TTTCCAAAAATTACCATTTTAC
* * *
12493818 CAC-GAACTTCACAAAAATTACCATTTTAC
1 CCCTAAATTTC-CAAAAATTACCATTTTAC
12493847 CCCTAAATTTCCAAAAATT-CCATTTTTGA-
1 CCCTAAATTTCCAAAAATTACCA-TTTT-AC
* *
12493876 CCCTAAACTTCCTAAAAACTACCATTTTA-
1 CCCTAAATTTCC-AAAAATTACCATTTTAC
* * * *
12493905 CCTTAGACTTCAAAAAATT-CCATTTTTAAC
1 CCCTAAATTTCCAAAAATTACCA-TTTT-AC
* *
12493935 CCC-AAACTTTCCCAAAATTACCATTTCA-
1 CCCTAAA-TTTCCAAAAATTACCATTTTAC
* *
12493963 CCCTCGAATGTCCAAAAATT-CCATTTTTGA-
1 CCCT-AAATTTCCAAAAATTACCA-TTTT-AC
* *
12493993 CTCTAAACTTCCCAAAAATTACCATTTTAC
1 CCCTAAA-TTTCCAAAAATTACCATTTTAC
* * * *
12494023 CCTTAAACTTCAAAAAATT-CC--TTTAA
1 CCCTAAATTTCCAAAAATTACCATTTTAC
* * * * *
12494049 CCTTGAACTTTCCCAAAATCACTATTTTAC
1 CCCT-AAATTTCCAAAAATTACCATTTTAC
* ** *
12494079 CCCCAAACATCCAAAAATT-CCATTTTTAT
1 CCCTAAATTTCCAAAAATTACCA-TTTTAC
*
12494108 CCC-AAATTTTCCTAAAATTACCATTTTA-
1 CCCTAAA-TTTCCAAAAATTACCATTTTAC
* * *
12494136 CCCTCAGACTTCCAAAAATT-CTATTTTTAAC
1 CCCT-AAATTTCCAAAAATTACCA-TTTT-AC
* * * *
12494167 CTCGAACTTTCCCAAAATTACCATTTTAC
1 CCCTAAATTTCCAAAAATTACCATTTTAC
** *
12494196 CCCCGAATGTCCAAAAATT
1 CCCTAAATTTCCAAAAATT
12494215 CAATTTTTGA
Statistics
Matches: 342, Mismatches: 78, Indels: 69
0.70 0.16 0.14
Matches are distributed among these distances:
25 3 0.01
26 18 0.05
27 18 0.05
28 34 0.10
29 128 0.37
30 128 0.37
31 13 0.04
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCTAAATTTCCAAAAATTACCATTTTAC
Found at i:12493957 original size:58 final size:59
Alignment explanation
Indices: 12493731--12494252 Score: 375
Period size: 59 Copynumber: 9.0 Consensus size: 59
12493721 CCCAAAAGGT
*
12493731 CCCTAAACTATCCAAAAA-T-CATATTTTGACCCCCAAACTTT-CCAAAAGTTA-CATTTTAAC
1 CCCTAAACT-TCCAAAAATTCCAT-TTTT-AACCCCAAACTTTCCCAAAA-TTACCATTTT-AC
* * * * * * *
12493791 CCCCAAACTTTCCAAAATTTACA---TT-ATCACGAAC-TTCACAAAAATTACCATTTTAC
1 CCCTAAAC-TTCCAAAAATTCCATTTTTAACCCCAAACTTTC-CCAAAATTACCATTTTAC
* * * * *
12493847 CCCTAAATTTCCAAAAATTCCATTTTTGACCCTAAAC-TTCCTAAAAACTACCATTTTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAACCCCAAACTTTCC-CAAAATTACCATTTTAC
* * * *
12493905 CCTTAGACTTCAAAAAATTCCATTTTTAACCCCAAACTTTCCCAAAATTACCATTTCA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAACCCCAAACTTTCCCAAAATTACCATTTTAC
* * * *
12493963 CCCTCGAA-TGTCCAAAAATTCCATTTTTGACTCTAAAC-TTCCCAAAAATTACCATTTTAC
1 CCCT-AAACT-TCCAAAAATTCCATTTTTAACCCCAAACTTTCCC-AAAATTACCATTTTAC
* * *** * *
12494023 CCTTAAACTTCAAAAAATTCC---TTTAACCTTGAACTTTCCCAAAATCACTATTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAACCCCAAACTTTCCCAAAATTACCATTTTAC
* * * * *
12494079 CCCCAAACATCCAAAAATTCCATTTTT-ATCCCAAATTTTCCTAAAATTACCATTTTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAACCCCAAACTTTCCCAAAATTACCATTTTAC
* * * *
12494136 CCCTCAGACTTCCAAAAATTCTATTTTTAACCTCGAACTTTCCCAAAATTACCATTTTAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAACCCCAAACTTTCCCAAAATTACCATTTTAC
** * * * * *
12494196 CCCCGAA-TGTCCAAAAATTCAATTTTTGACCTCGAAC-TTCCTAAAGATTACCATTTT
1 CCCTAAACT-TCCAAAAATTCCATTTTTAACCCCAAACTTTCCCAAA-ATTACCATTTT
12494253 TCCTTGGGCA
Statistics
Matches: 367, Mismatches: 69, Indels: 53
0.75 0.14 0.11
Matches are distributed among these distances:
55 14 0.04
56 56 0.15
57 19 0.05
58 108 0.29
59 145 0.40
60 21 0.06
61 2 0.01
62 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (59 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAACCCCAAACTTTCCCAAAATTACCATTTTAC
Found at i:12494147 original size:232 final size:232
Alignment explanation
Indices: 12493831--12494252 Score: 618
Period size: 232 Copynumber: 1.8 Consensus size: 232
12493821 GAACTTCACA
* * **
12493831 AAAATTACCATTTTACCCCTAAATTTCCAAAAATTCCATTTTTGACCCTAAACTTCCTAAAAACT
1 AAAATCACCATTTTACCCCCAAACATCCAAAAATTCCATTTTTGACCCTAAACTTCCTAAAAACT
*
12493896 ACCATTTTACCTTAGACTTCAAAAAATTCCATTTTTAACCCCAAACTTTCCCAAAATTACCATTT
66 ACCATTTTACCTCAGACTTCAAAAAATTCCATTTTTAACCCCAAACTTTCCCAAAATTACCATTT
* *
12493961 CACCCTCGAATGTCCAAAAATTCCATTTTTGA-CTCTAAACTTCCCAAAAATTACCATTTTACCC
131 CACCCCCGAATGTCCAAAAATTCAATTTTTGACCTC-AAACTTCCCAAAAATTACCATTTTACCC
12494025 TTAAACTTCAAAAAATTCCTTTAACCTTGAACTTTCCC
195 TTAAACTTCAAAAAATTCCTTTAACCTTGAACTTTCCC
* *
12494063 AAAATCACTATTTTACCCCCAAACATCCAAAAATTCCATTTTT-ATCCC-AAATTTTCCT-AAAA
1 AAAATCACCATTTTACCCCCAAACATCCAAAAATTCCATTTTTGA-CCCTAAA-CTTCCTAAAAA
* * * * *
12494125 TTACCATTTTACCCTCAGACTTCCAAAAATTCTATTTTTAACCTCGAACTTTCCCAAAATTACCA
64 CTACCATTTTA-CCTCAGACTTCAAAAAATTCCATTTTTAACCCCAAACTTTCCCAAAATTACCA
* * * *
12494190 TTTTACCCCCGAATGTCCAAAAATTCAATTTTTGACCTCGAACTTCCTAAAGATTACCATTTT
128 TTTCACCCCCGAATGTCCAAAAATTCAATTTTTGACCTCAAACTTCCCAAAAATTACCATTTT
12494253 TCCTTGGGCA
Statistics
Matches: 168, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
231 18 0.11
232 147 0.88
233 3 0.02
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (232 bp):
AAAATCACCATTTTACCCCCAAACATCCAAAAATTCCATTTTTGACCCTAAACTTCCTAAAAACT
ACCATTTTACCTCAGACTTCAAAAAATTCCATTTTTAACCCCAAACTTTCCCAAAATTACCATTT
CACCCCCGAATGTCCAAAAATTCAATTTTTGACCTCAAACTTCCCAAAAATTACCATTTTACCCT
TAAACTTCAAAAAATTCCTTTAACCTTGAACTTTCCC
Found at i:12494231 original size:29 final size:29
Alignment explanation
Indices: 12494146--12494233 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
12494136 CCCTCAGACT
* *
12494146 TCCAAAAATTCTATTTTTAACCTCGAACTT
1 TCCAAAAATTCAATTTTT-ACCTCGAACTG
* * *
12494176 TCCCAAAATTACCA-TTTTACCCCCGAA-TG
1 TCCAAAAATT-CAATTTTTA-CCTCGAACTG
12494205 TCCAAAAATTCAATTTTTGACCTCGAACT
1 TCCAAAAATTCAATTTTT-ACCTCGAACT
12494234 TCCTAAAGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
28 2 0.04
29 21 0.46
30 21 0.46
31 2 0.04
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTCAATTTTTACCTCGAACTG
Found at i:12494272 original size:117 final size:117
Alignment explanation
Indices: 12493831--12494252 Score: 534
Period size: 117 Copynumber: 3.6 Consensus size: 117
12493821 GAACTTCACA
* * *
12493831 AAAATTACCATTTTACCCCTAAATTTCCAAAAATTCCATTTTTGACCCTAAACTTCCTAAAAACT
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCTAAACTTCCTAAAAATT
* *
12493896 ACCATTTTA-CCTTAGACTTCAAAAAATTCCATTTTTAACCCCAAACTTTCCC
66 ACCATTTTACCCTTAGACTTCAAAAAATT-CATTTTTAACCTCGAACTTTCCC
* * * * *
12493948 AAAATTACCATTTCACCCTCGAATGTCCAAAAATTCCATTTTTGACTCTAAACTTCCCAAAAATT
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCTAAACTTCCTAAAAATT
* * *
12494013 ACCATTTTACCCTTAAACTTCAAAAAATTC--CTTTAACCTTGAACTTTCCC
66 ACCATTTTACCCTTAGACTTCAAAAAATTCATTTTTAACCTCGAACTTTCCC
* * ** *
12494063 AAAATCACTATTTTACCCCCAAACATCCAAAAATTCCATTTTT-ATCCC-AAATTTTCCT-AAAA
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGA-CCCTAAA-CTTCCTAAAAA
* *
12494125 TTACCATTTTACCCTCAGACTTCCAAAAATTCTATTTTTAACCTCGAACTTTCCC
64 TTACCATTTTACCCTTAGACTTCAAAAAATTC-ATTTTTAACCTCGAACTTTCCC
* * * *
12494180 AAAATTACCATTTTACCCCCGAATGTCCAAAAATTCAATTTTTGA-CCTCGAACTTCCTAAAGAT
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCT-AAACTTCCTAAAAAT
12494244 TACCATTTT
65 TACCATTTT
12494253 TCCTTGGGCA
Statistics
Matches: 258, Mismatches: 37, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
114 37 0.14
115 58 0.22
116 2 0.01
117 127 0.49
118 34 0.13
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (117 bp):
AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCTAAACTTCCTAAAAATT
ACCATTTTACCCTTAGACTTCAAAAAATTCATTTTTAACCTCGAACTTTCCC
Found at i:12497680 original size:591 final size:592
Alignment explanation
Indices: 12496587--12497685 Score: 1968
Period size: 591 Copynumber: 1.9 Consensus size: 592
12496577 CCAAAAATTC
* *
12496587 TAGTACTCGATTTGAGATGGTTATCAAGTTCCAATGCTATAAAATTAAAAATAATGGCCTTATAA
1 TAGTACTCGATTTGAGATGGTTATCAAGTTCCAATGCAATAAAATTAAAAATAAGGGCCTTATAA
12496652 AATCATAGTGTATTAAGTAATGGCTTCTCTAGAACCATTTAATTTTCGTACAACTAAAATTAATT
66 AATCATAGTGTATTAAGTAATGGCTTCTCTAGAACCATTTAATTTTCGTACAACTAAAATTAATT
* ** *
12496717 TAACTCGACTTAAATTTAACGACAGACAATAATGAAGCTTCCGGAACAATGTTGAAAATAAAGAC
131 TAACTCGACTTAAATTTAACGACACACAATAATGAAGCTTAAGGAACAATATTGAAAATAAAGAC
* * *
12496782 AAAAGAACAATATTGAGCACATCACGTCTTGTAACCTGTTGTTAGTTGAAGCAATCTTATATCAT
196 AAAAGAACAATATTGAGCACATCACGTCCTGTAACCTATTGTTAGTTGAAGCAATCCTATATCAT
*
12496847 TAAGCAGACGGAGACGGTAAATCGATCAATGCCATGCAGTTGTTCCATGTTTCGATGCTCTTTGC
261 TAAGCAGACGGAGACGGTAAATCGATCAATGCCATGCAGTTGTTCCATGTTTCGATGCTCTTCGC
* *
12496912 TATAATTTTAGTTGGGTTTATTTCTTTGAATAGAGGATTCTCGAGAGTCCTCTTTCTTAATGCTG
326 TATAATTGTAGTTGGGTTTAGTTCTTTGAATAGAGGATTCTCGAGAGTCCTCTTTCTTAATGCTG
12496977 CGTGGCAAACTTTTCCCAACGTAACAAGTTCGCTGCAACACTTGTTAGAAATACTACCTGTCTCG
391 CGTGGCAAACTTTTCCCAACGTAACAAGTTCGCTGCAACACTTGTTAGAAATACTACCTGTCTCG
12497042 AAAATACTCGTGAAAGTTTCTTGAAGACAGGGCCAACCAACTTTAGTTTCACATGTTCCATGTTC
456 AAAATACTCGTGAAAGTTTCTTGAAGACAGGGCCAACCAACTTTAGTTTCACATGTTCCATGTTC
12497107 CACATTATTGCAATGAACATAACGTTTATAACATTGCAATTTTTTTCAATTTAAACAATGTGAAA
521 CACATTATTGCAATGAACATAACGTTTATAACATTGCAATTTTTTTCAATTTAAACAATGTGAAA
12497172 CAATATA
586 CAATATA
* *
12497179 TAGTACTCGTTTTGAGATGGTTATCAAGTTCTAATGCAATAAAATTACAAAA-AAGGGCCTTATA
1 TAGTACTCGATTTGAGATGGTTATCAAGTTCCAATGCAATAAAATTA-AAAATAAGGGCCTTATA
*
12497243 AAATCATAGTGTATTACGTAATGGCTTCTCTAGAACCATTTAATTTTCGTACAACTAAAA-TAAT
65 AAATCATAGTGTATTAAGTAATGGCTTCTCTAGAACCATTTAATTTTCGTACAACTAAAATTAAT
*
12497307 TTAACTCGACTTAAATTTAACGACACACAATAATGACGCTTAAGGAACAATATTGAAAATAAAGA
130 TTAACTCGACTTAAATTTAACGACACACAATAATGAAGCTTAAGGAACAATATTGAAAATAAAGA
* * *
12497372 CAAAAGAACAATTTTGAGCACATCACGTCCTGTAACTTATTGTTAGTTGAAGCAATCCTATATCG
195 CAAAAGAACAATATTGAGCACATCACGTCCTGTAACCTATTGTTAGTTGAAGCAATCCTATATCA
* * *
12497437 TTAAGCAGACGGATATGGTGAATCGATCAATGCCATGCAGTTGTTCCATGTTTCGATGCTCTTCG
260 TTAAGCAGACGGAGACGGTAAATCGATCAATGCCATGCAGTTGTTCCATGTTTCGATGCTCTTCG
12497502 CTATAATTGTAGTTGGGTTTAGTTCTTTGAATAGAGGATTCTCGAGAGTCCTCTTTCTTAATGCT
325 CTATAATTGTAGTTGGGTTTAGTTCTTTGAATAGAGGATTCTCGAGAGTCCTCTTTCTTAATGCT
12497567 GCGTGGCAAACTTTTCCCAACGTAACAAGTTCGCTGCAACACTTGTTAGAAATACTACCTGTCTC
390 GCGTGGCAAACTTTTCCCAACGTAACAAGTTCGCTGCAACACTTGTTAGAAATACTACCTGTCTC
*
12497632 GAAAATACTCGTGAAAGTTTCTTGAAGACAGGGCCAACCCACTTTAGTTTCACA
455 GAAAATACTCGTGAAAGTTTCTTGAAGACAGGGCCAACCAACTTTAGTTTCACA
12497686 ATTATTTTCC
Statistics
Matches: 483, Mismatches: 23, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
591 365 0.76
592 114 0.24
593 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (592 bp):
TAGTACTCGATTTGAGATGGTTATCAAGTTCCAATGCAATAAAATTAAAAATAAGGGCCTTATAA
AATCATAGTGTATTAAGTAATGGCTTCTCTAGAACCATTTAATTTTCGTACAACTAAAATTAATT
TAACTCGACTTAAATTTAACGACACACAATAATGAAGCTTAAGGAACAATATTGAAAATAAAGAC
AAAAGAACAATATTGAGCACATCACGTCCTGTAACCTATTGTTAGTTGAAGCAATCCTATATCAT
TAAGCAGACGGAGACGGTAAATCGATCAATGCCATGCAGTTGTTCCATGTTTCGATGCTCTTCGC
TATAATTGTAGTTGGGTTTAGTTCTTTGAATAGAGGATTCTCGAGAGTCCTCTTTCTTAATGCTG
CGTGGCAAACTTTTCCCAACGTAACAAGTTCGCTGCAACACTTGTTAGAAATACTACCTGTCTCG
AAAATACTCGTGAAAGTTTCTTGAAGACAGGGCCAACCAACTTTAGTTTCACATGTTCCATGTTC
CACATTATTGCAATGAACATAACGTTTATAACATTGCAATTTTTTTCAATTTAAACAATGTGAAA
CAATATA
Found at i:12504801 original size:11 final size:11
Alignment explanation
Indices: 12504787--12504811 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12504777 TTAAATTGAG
12504787 ATAAAATAAAA
1 ATAAAATAAAA
12504798 ATAAAATAAAA
1 ATAAAATAAAA
12504809 ATA
1 ATA
12504812 GTAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:12518291 original size:24 final size:24
Alignment explanation
Indices: 12518258--12518320 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
12518248 AGAAATAATC
*
12518258 TTTCAGTTAAACTCTGTGTATTTG
1 TTTCAATTAAACTCTGTGTATTTG
* *
12518282 TTTCAATTAAACTCCGTTTATTTG
1 TTTCAATTAAACTCTGTGTATTTG
* *
12518306 TTTGAATCAAACTCT
1 TTTCAATTAAACTCT
12518321 TATTACTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTGTATTTG
Found at i:12546260 original size:29 final size:28
Alignment explanation
Indices: 12546228--12546292 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
12546218 AAAATGAGAC
12546228 TTTTTGGA-TACCCGAGGACAAAATGGTAA
1 TTTTTGGACT-CCCG-GGACAAAATGGTAA
* * **
12546257 TTTTGGGACTCTCGGGGTAAAATGGTAA
1 TTTTTGGACTCCCGGGACAAAATGGTAA
12546285 TTTTTGGA
1 TTTTTGGA
12546293 AAAATTCGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 19 0.63
29 10 0.33
30 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.34
Consensus pattern (28 bp):
TTTTTGGACTCCCGGGACAAAATGGTAA
Found at i:12546367 original size:29 final size:28
Alignment explanation
Indices: 12546335--12546520 Score: 144
Period size: 29 Copynumber: 6.4 Consensus size: 28
12546325 ATCCAGGAGT
12546335 AAAATGGTAATTTTGAAAGTTTCGGGGTC
1 AAAAT-GTAATTTTGAAAGTTTCGGGGTC
* * * *
12546364 AAAAATGGAATTTTGGAAGTTTGGGGGTA
1 -AAAATGTAATTTTGAAAGTTTCGGGGTC
* *
12546393 AAAATGTAATTTTTGGAAGTTTCAGGGTC
1 AAAATGTAA-TTTTGAAAGTTTCGGGGTC
* * *
12546422 AAAAATGGAATATTTGAAA-TTTTGGGGGC
1 -AAAATGTAAT-TTTGAAAGTTTCGGGGTC
*
12546451 AAAATGTAATTTTTGGAAG-TTCGAGGGT-
1 AAAATGTAA-TTTTGAAAGTTTCG-GGGTC
* * *
12546479 ACAAATGTAATTTTTAGAAGTTTCAGGGCC
1 A-AAATGTAATTTTGA-AAGTTTCGGGGTC
*
12546509 AAAATATAATTT
1 AAAATGTAATTT
12546521 CTTGACAGTT
Statistics
Matches: 124, Mismatches: 22, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
28 30 0.24
29 71 0.57
30 23 0.19
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTGAAAGTTTCGGGGTC
Found at i:12546397 original size:58 final size:56
Alignment explanation
Indices: 12546247--12546492 Score: 201
Period size: 58 Copynumber: 4.2 Consensus size: 56
12546237 ACCCGAGGAC
* * ** *
12546247 AAAATGGTAATTTTGGGACTCTCGGGGTAAAATGGTAATTTTTGGAAAAATTCGGGATCA
1 AAAATGG-AATTTT-GGAATCTGGGGGTAAAAT-GTAATTTTT-GAAAGTTTCGGGGTCA
* ** *
12546307 AAAATGAAATTTTTGGACATCCAGGAGTAAAATGGTAA-TTTTGAAAGTTTCGGGGTCA
1 AAAATGGAA-TTTTGGA-ATCTGGGGGTAAAAT-GTAATTTTTGAAAGTTTCGGGGTCA
* * *
12546365 AAAATGGAATTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAGTTTCAGGGTCA
1 AAAATGGAATTTTGGAA-TCTGGGGGT-AAAATGTAATTTTTGAAAGTTTCGGGGTCA
* * * *
12546423 AAAATGGAATATTTGAAATTTTGGGGGCAAAATGTAATTTTTGGAAG-TTCGAGGGT-A
1 AAAATGGAAT-TTTGGAA-TCTGGGGGTAAAATGTAATTTTTGAAAGTTTCG-GGGTCA
* *
12546480 CAAATGTAATTTT
1 AAAATGGAATTTT
12546493 TAGAAGTTTC
Statistics
Matches: 158, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
56 4 0.03
57 28 0.18
58 77 0.49
59 23 0.15
60 26 0.16
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (56 bp):
AAAATGGAATTTTGGAATCTGGGGGTAAAATGTAATTTTTGAAAGTTTCGGGGTCA
Found at i:12546485 original size:87 final size:88
Alignment explanation
Indices: 12546335--12546512 Score: 245
Period size: 87 Copynumber: 2.0 Consensus size: 88
12546325 ATCCAGGAGT
* * *
12546335 AAAATGGTAATTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTGGAAGTTTGGGGGTAAAAATGT
1 AAAATGGTAATTTTGAAAGTTTCGGGGGCAAAAATGGAATTTTGGAAGTTCGAGGGTAAAAATGT
* *
12546400 AATTTTTGGAAGTTTCAGGGTCA
66 AATTTTTAGAAGTTTCAGGGCCA
* * *
12546423 AAAATGG-AATATTTGAAA-TTTTGGGGGC-AAAATGTAATTTTTGGAAGTTCGAGGGTACAAAT
1 AAAATGGTAAT-TTTGAAAGTTTCGGGGGCAAAAATGGAA-TTTTGGAAGTTCGAGGGTAAAAAT
12546485 GTAATTTTTAGAAGTTTCAGGGCCA
64 GTAATTTTTAGAAGTTTCAGGGCCA
12546510 AAA
1 AAA
12546513 TATAATTTCT
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
86 8 0.10
87 58 0.73
88 14 0.17
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (88 bp):
AAAATGGTAATTTTGAAAGTTTCGGGGGCAAAAATGGAATTTTGGAAGTTCGAGGGTAAAAATGT
AATTTTTAGAAGTTTCAGGGCCA
Found at i:12546512 original size:58 final size:58
Alignment explanation
Indices: 12546335--12546520 Score: 173
Period size: 58 Copynumber: 3.2 Consensus size: 58
12546325 ATCCAGGAGT
* * * ** **
12546335 AAAATGGTAA-TTTTGAAAGTTTCGGGGTCAAAAATGGAAT-TTTGGAAGTTTGGGGGTA
1 AAAAT-GTAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATATTT-GAAATTTCAGGGCC
** *
12546393 AAAATGTAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATATTTGAAATTTTGGGGGC
1 AAAATGTAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATATTTGAAATTTCAGGGCC
* * * *
12546451 AAAATGTAATTTTTGGAAG-TTCGAGGGT-ACAAATGTAATTTTTAGAAGTTTCAGGGCC
1 AAAATGTAATTTTTGGAAGTTTC-AGGGTCAAAAATGGAATATTT-GAAATTTCAGGGCC
*
12546509 AAAATATAATTT
1 AAAATGTAATTT
12546521 CTTGACAGTT
Statistics
Matches: 110, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
57 19 0.17
58 88 0.80
59 3 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.34
Consensus pattern (58 bp):
AAAATGTAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATATTTGAAATTTCAGGGCC
Found at i:12548223 original size:17 final size:17
Alignment explanation
Indices: 12548203--12548239 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
12548193 TTTAAAATTC
12548203 AAATTTAAAATAAATCT
1 AAATTTAAAATAAATCT
*
12548220 AAATTTAAAATAAATTT
1 AAATTTAAAATAAATCT
12548237 AAA
1 AAA
12548240 AGGGCTCGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTTAAAATAAATCT
Found at i:12549110 original size:204 final size:205
Alignment explanation
Indices: 12548538--12549549 Score: 1448
Period size: 204 Copynumber: 4.9 Consensus size: 205
12548528 TCTGGTTTCA
* * * ** *
12548538 TTGACTTGGCCTTCTTCTCT-GTATCTCATCAGGAAGATGACCACATCACTTGTTTTGATCCACT
1 TTGATTTGGTCTTCTTCT-TAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAAT-CGCT
* * * * *
12548602 TCTCTGTGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCA
64 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * **
12548667 CTTTATTGCTTAGACCTGCTTCTCAGTATCTCATCAAAAAGCTAGGGGTTCGAAGATTTGCTCAC
129 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTA-GGGTTCGAAGATTTGCTCAC
*
12548732 ATCGAGCGTCGGT
193 ATCGAGCGTGGGT
* *
12548745 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCATTTGTTTCAATCTGCTT
1 TTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATC-GCTT
12548810 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
65 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
12548875 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAGATTTGCTCACAT
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
*
12548939 GGAGCGTGGGT
195 CGAGCGTGGGT
*
12548950 TTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCGCTTC
1 TTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCGCTTC
* * * *
12549015 TTTGTACCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATT
66 TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
*
12549080 TTATTGCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCT-GGGTTCGAAGATTTGCTCACATC
131 TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATC
12549144 GAGCGTGGGT
196 GAGCGTGGGT
* *
12549154 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAAT-CGCTT
* * *
12549219 CTCTATACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATATCATCAGGAAGCTAACCAT
65 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
12549284 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTAGGGTTCGAAGATTTGCTCACTT
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
* *
12549349 TGAGC-----C
195 CGAGCGTGGGT
* * * * * *
12549355 TTGAGTTGGTATACTTCTCT-GTATCTCATCAGGATGGTGACCGCCTCACTTGTTTCAATTCGCT
1 TTGATTTGGTCTTCTTCT-TAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAA-TCGCT
* *
12549419 TCTCTATATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
64 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * * * * * *
12549484 TTTTATTACTTCGCCCTGCCTCTTAGTATGTCATCAGGAAGCTAGGGTTCAAAGATCTGTTCACA
129 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACA
12549549 T
194 T
12549550 TGAGTTGGTA
Statistics
Matches: 739, Mismatches: 60, Indels: 18
0.90 0.07 0.02
Matches are distributed among these distances:
201 171 0.23
202 1 0.00
204 196 0.27
205 193 0.26
206 26 0.04
207 152 0.21
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (205 bp):
TTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCGCTTC
TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATC
GAGCGTGGGT
Found at i:12550081 original size:49 final size:49
Alignment explanation
Indices: 12549940--12550087 Score: 145
Period size: 49 Copynumber: 3.0 Consensus size: 49
12549930 CGACTTAAAC
* * * * * *
12549940 CTTTCCCTTCAAATCTTCGTGGTACTGGATCTACTGTCGCAGCTTAGAT
1 CTTTCCCTTCATATCTTCGTGATACTGGATCCACCGTTGCGGCTTAGAT
* * * * ** *
12549989 CTTTCTCTTCCTGTCTTCGT-AGTACTGGGTCCGTCATTGCGGCTTAGAT
1 CTTTCCCTTCATATCTTCGTGA-TACTGGATCCACCGTTGCGGCTTAGAT
*
12550038 CTTTCCCTTCATATCTTCGTGATACTGGATCCACCGTTACGGCTTTAGAT
1 CTTTCCCTTCATATCTTCGTGATACTGGATCCACCGTTGCGGC-TTAGAT
12550088 GACTAATGCT
Statistics
Matches: 75, Mismatches: 21, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
49 68 0.91
50 7 0.09
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.39
Consensus pattern (49 bp):
CTTTCCCTTCATATCTTCGTGATACTGGATCCACCGTTGCGGCTTAGAT
Found at i:12551658 original size:29 final size:28
Alignment explanation
Indices: 12551626--12551690 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
12551616 AAAATGAGAC
*
12551626 TTTTTGGA-TACTCGAGGGCAAAATGGTAA
1 TTTTTGGACT-CTCGA-GGCAAAATGGAAA
* *
12551655 TTTTGGGACTCTCGAGGTAAAATGGAAA
1 TTTTTGGACTCTCGAGGCAAAATGGAAA
12551683 TTTTTGGA
1 TTTTTGGA
12551691 AATCGGGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 18 0.58
29 12 0.39
30 1 0.03
ACGTcount: A:0.29, C:0.09, G:0.28, T:0.34
Consensus pattern (28 bp):
TTTTTGGACTCTCGAGGCAAAATGGAAA
Found at i:12554741 original size:29 final size:28
Alignment explanation
Indices: 12554692--12555079 Score: 158
Period size: 29 Copynumber: 13.6 Consensus size: 28
12554682 ACGAACTTCA
12554692 CAAAAATTACCA-TTTTACCCTAAATTTC
1 CAAAAATT-CCATTTTTACCCTAAATTTC
*
12554720 CAAAAATTCCATTTTTGACCCTAAACTTC
1 CAAAAATTCCATTTTT-ACCCTAAATTTC
* * * *
12554749 CTAAAAACTACCA-TTTTACCTTAGACTTC
1 C-AAAAA-TTCCATTTTTACCCTAAATTTC
* *
12554778 AAAAAATTCCATTTTTAACCCCAAACTTTC
1 CAAAAATTCCATTTTT-ACCCTAAA-TTTC
* * * *
12554808 CCAAAATTACCA-TTTCA-CCTCGAATGTC
1 CAAAAATT-CCATTTTTACCCT-AAATTTC
* *
12554836 CAAAAATTCCATTTTTGACTCTAAACTTCC
1 CAAAAATTCCATTTTT-ACCCTAAA-TTTC
*
12554866 CAAAAATTACCA--TTTACCCTTAAACTT-
1 CAAAAATT-CCATTTTTACCC-TAAATTTC
* * *
12554893 CAAAAATTCC---TTAACCTTGAACTTTC
1 CAAAAATTCCATTTTTACCCT-AAATTTC
* * **
12554919 CCAAAA-T-CACTATTTTACCCCCAAACATC
1 CAAAAATTCCA-T-TTTTA-CCCTAAATTTC
*
12554948 CAAAAATTCCATTTTTATCCCAAAATTTTC
1 CAAAAATTCCATTTTTA-CCCTAAA-TTTC
* * *
12554978 CTAAAATTACCA-TTTTACCCTCAGACTTC
1 CAAAAATT-CCATTTTTACCCT-AAATTTC
* * *
12555007 CAAAAATT-CGTTTTTAACCTCGAACTTTC
1 CAAAAATTCCATTTTT-ACC-CTAAATTTC
* *** *
12555036 CCAAAATTACCA-TTTTACCCCCGATGTC
1 CAAAAATT-CCATTTTTACCCTAAATTTC
*
12555064 CAAAAATTCAATTTTT
1 CAAAAATTCCATTTTT
12555080 GACCTCGAAC
Statistics
Matches: 266, Mismatches: 60, Indels: 68
0.68 0.15 0.17
Matches are distributed among these distances:
24 2 0.01
25 10 0.04
26 7 0.03
27 21 0.08
28 59 0.22
29 93 0.35
30 58 0.22
31 16 0.06
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (28 bp):
CAAAAATTCCATTTTTACCCTAAATTTC
Done.