Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008025.1 Hibiscus syriacus cultivar Beakdansim tig00110500_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2744542
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:317612 original size:11 final size:11
Alignment explanation
Indices: 317541--317603 Score: 60
Period size: 10 Copynumber: 5.7 Consensus size: 11
317531 ATTTTGCTTG
*
317541 AAGAATAAATAA
1 AAGAA-AAAGAA
317553 AAGAAGAAA-AA
1 AAGAA-AAAGAA
*
317564 AAGAAAATTGAA
1 AAGAAAA-AGAA
317576 AA-AAAAAGAA
1 AAGAAAAAGAA
317586 AA-AAAAAGAA
1 AAGAAAAAGAA
317596 AAGAAAAA
1 AAGAAAAA
317604 TAAATGAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
10 17 0.38
11 16 0.36
12 12 0.27
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:319063 original size:82 final size:82
Alignment explanation
Indices: 318931--319193 Score: 348
Period size: 82 Copynumber: 3.2 Consensus size: 82
318921 AGATTTTTCG
* * * * * * *
318931 AGTCTTATTTCCCCTGAATGAATAGTAGAGCATACACATCTCCCAAAATAGATATGTCTACCCGA
1 AGTCTGATTTCCCCTGAATGAATAGTGGAGCAGACACGTCTTCTAAAATAGATCTGTCTACCCGA
318996 AAAAGAGGCACAGATCA
66 AAAAGAGGCACAGATCA
* * * *
319013 AGTCTGATTTCCCCTGAATGAATAGTGGAGCAGATACGTCTTCTAGAATAGATCTGTATACCTGA
1 AGTCTGATTTCCCCTGAATGAATAGTGGAGCAGACACGTCTTCTAAAATAGATCTGTCTACCCGA
*
319078 AAAAGAGGCACGGATCA
66 AAAAGAGGCACAGATCA
* ** * *
319095 AGTCTGATTT-CCCTAAATGAATAGTGGAATAGACATGTCTTCTAAAATAGATCTGTCTACCCAA
1 AGTCTGATTTCCCCTGAATGAATAGTGGAGCAGACACGTCTTCTAAAATAGATCTGTCTACCCGA
*
319159 AAAAGAGGCACATATCA
66 AAAAGAGGCACAGATCA
*
319176 AGTCTGATTTTCCCTGAA
1 AGTCTGATTTCCCCTGAA
319194 AGAAGAATGG
Statistics
Matches: 156, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
81 70 0.45
82 86 0.55
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (82 bp):
AGTCTGATTTCCCCTGAATGAATAGTGGAGCAGACACGTCTTCTAAAATAGATCTGTCTACCCGA
AAAAGAGGCACAGATCA
Found at i:319243 original size:81 final size:81
Alignment explanation
Indices: 318975--319261 Score: 301
Period size: 82 Copynumber: 3.5 Consensus size: 81
318965 CACATCTCCC
* * * * *
318975 AAAATAGATATGTCTACCCGAAAAAGAGGCACAGATCAAGTCTGATTTCCCCTGAATGAATAGTG
1 AAAATAGATCTGTATACCCAAAAAAGAGGCACAGATCAAGTCTGATTTTCCCTGAAAGAATAGTG
*
319040 GAGCAGA-TACGTCTTCT
66 GAG-AGACT-TGTCTTCT
* ** *
319057 AGAATAGATCTGTATACCTGAAAAAGAGGCACGGATCAAGTCTGA-TTTCCCT-AAATGAATAGT
1 AAAATAGATCTGTATACCCAAAAAAGAGGCACAGATCAAGTCTGATTTTCCCTGAAA-GAATAGT
* *
319120 GGAATAGACATGTCTTCT
65 GG-AGAGACTTGTCTTCT
* * * *
319138 AAAATAGATCTGTCTACCCAAAAAAGAGGCACATATCAAGTCTGATTTTCCCTGAAAGAAGAATG
1 AAAATAGATCTGTATACCCAAAAAAGAGGCACAGATCAAGTCTGATTTTCCCTGAAAGAATAGTG
* *
319203 GAGAGGACTTGTTTTCC
66 GAGA-GACTTGTCTTCT
* * * * *
319220 AAAATTGATCTGAATACCCAAAAACGAGGAATAGATCAAGTC
1 AAAATAGATCTGTATACCCAAAAAAGAGGCACAGATCAAGTC
319262 CGACCTACCC
Statistics
Matches: 170, Mismatches: 29, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
80 2 0.01
81 66 0.39
82 99 0.58
83 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (81 bp):
AAAATAGATCTGTATACCCAAAAAAGAGGCACAGATCAAGTCTGATTTTCCCTGAAAGAATAGTG
GAGAGACTTGTCTTCT
Found at i:319644 original size:13 final size:13
Alignment explanation
Indices: 319626--319651 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
319616 ATATATATAT
319626 GAAATCATTATTA
1 GAAATCATTATTA
319639 GAAATCATTATTA
1 GAAATCATTATTA
319652 TATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
GAAATCATTATTA
Found at i:323749 original size:21 final size:21
Alignment explanation
Indices: 323724--323825 Score: 136
Period size: 21 Copynumber: 4.8 Consensus size: 21
323714 TCATACCAAG
**
323724 GACGAGAAGATTATTCATAAA
1 GACGAGAAGACCATTCATAAA
323745 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCATAAA
323766 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCATAAA
*
323787 GAC-ATGAAGACCCTTCATAAA
1 GACGA-GAAGACCATTCATAAA
323808 GAC-ATGAAGACCACTTCA
1 GACGA-GAAGACCA-TTCA
323826 CATTGGATGA
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
20 1 0.01
21 70 0.93
22 4 0.05
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.18
Consensus pattern (21 bp):
GACGAGAAGACCATTCATAAA
Found at i:328267 original size:11 final size:11
Alignment explanation
Indices: 328251--328276 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
328241 AGAGAAAAAG
328251 AAAAAAAGAAA
1 AAAAAAAGAAA
328262 AAAAAAAGAAA
1 AAAAAAAGAAA
328273 AAAA
1 AAAA
328277 TTAAAAATGA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:328282 original size:15 final size:15
Alignment explanation
Indices: 328264--328304 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
328254 AAAAGAAAAA
328264 AAAAAGAAAAAAATT
1 AAAAAGAAAAAAATT
*
328279 AAAAATG-AGAAAATT
1 AAAAA-GAAAAAAATT
328294 AAAAA-AAAAAA
1 AAAAAGAAAAAA
328305 GAATGAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.18
15 17 0.77
16 1 0.05
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (15 bp):
AAAAAGAAAAAAATT
Found at i:330467 original size:36 final size:37
Alignment explanation
Indices: 330405--330510 Score: 119
Period size: 37 Copynumber: 2.9 Consensus size: 37
330395 GGGCAAATCT
* * * *
330405 ATCTTAAGCCTTCA-TTGGAGAATAGTGAAGTAA-TCC
1 ATCTTAAGCCTTCACCT-GAGAGTAGTGAAGCAACTCA
*
330441 ATTTTAAGCCTTCACCTGAGAGTAGTGAAGCAACTCA
1 ATCTTAAGCCTTCACCTGAGAGTAGTGAAGCAACTCA
*
330478 ATCTTAAGCCTTCACC-GAAGAGTAGTAAAGCAA
1 ATCTTAAGCCTTCACCTG-AGAGTAGTGAAGCAA
330511 ATCTATCCAT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
36 28 0.47
37 32 0.53
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCTGAGAGTAGTGAAGCAACTCA
Found at i:330490 original size:37 final size:36
Alignment explanation
Indices: 330400--330510 Score: 118
Period size: 36 Copynumber: 3.1 Consensus size: 36
330390 GATTGGGGCA
* * * *
330400 AATCTATCTTAAGCCTTCA-TTGGAGAATAGTGAAGT
1 AATCAATCTTAAGCCTTCACCT-GAGAGTAGTGAAGC
* *
330436 AATCCATTTTAAGCCTTCACCTGAGAGTAGTGAAGC
1 AATCAATCTTAAGCCTTCACCTGAGAGTAGTGAAGC
*
330472 AACTCAATCTTAAGCCTTCACC-GAAGAGTAGTAAAGC
1 AA-TCAATCTTAAGCCTTCACCTG-AGAGTAGTGAAGC
330509 AA
1 AA
330511 ATCTATCCAT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
36 32 0.50
37 32 0.50
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (36 bp):
AATCAATCTTAAGCCTTCACCTGAGAGTAGTGAAGC
Found at i:330697 original size:42 final size:41
Alignment explanation
Indices: 330630--330731 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 41
330620 TTCACAATTT
* * ** * *
330630 ATAAGTCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCTGTAAGTCTTTAGAGCAAGATG
* *
330671 TTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCTGTAAGTCTTTAGAGCAAGATG
*
330713 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
330732 CATAAGACCT
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCTGTAAGTCTTTAGAGCAAGATG
Found at i:330926 original size:201 final size:201
Alignment explanation
Indices: 330581--330985 Score: 695
Period size: 201 Copynumber: 2.0 Consensus size: 201
330571 GTTTTAAGAA
* *
330581 GATGAAATTTTTGAAAACGAAGAATGCGATTTTCAGAATTTCACAATTTATAAGTCCTTCAGGCC
1 GATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCC
* *
330646 ATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGA
66 ATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
330711 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTATGATGTCTTCAAATGAATTCGAAAATG
131 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTATGATGTCTTCAAATGAATTCGAAAATG
330776 AAAAAT
196 AAAAAT
* *
330782 GATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATGTATAAGTCCTTCGGGCC
1 GATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCC
* *
330847 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
66 ATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
* * * *
330912 TGATAAGTCCTTCGGGCCATCCGTAATACCTTCGGGTAGGATGT-TTCAAATGAATTTGAAAATG
131 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTATGATGTCTTCAAATGAATTCGAAAATG
330976 AAAAAT
196 AAAAAT
330982 GATG
1 GATG
330986 TTTTAAGAAG
Statistics
Matches: 192, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
200 29 0.15
201 163 0.85
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (201 bp):
GATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCC
ATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTATGATGTCTTCAAATGAATTCGAAAATG
AAAAAT
Found at i:331120 original size:42 final size:41
Alignment explanation
Indices: 331043--331222 Score: 180
Period size: 42 Copynumber: 4.3 Consensus size: 41
331033 TTCACAATTT
* ** *
331043 ATAAGTCCTTCGGGTCATCAATAAGTCTTCCGAGCATGATG
1 ATAAATCCTTCGGGTCATCAATAAGTCTTTAGAGCAAGATG
* ** *
331084 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGTCATCAATAAGTCTTTAGAGCAAGATG
* * * * * *
331126 ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGTATGATG
1 ATAAATCCTTCGGGTCATCAATAAGTCTTTAGAGCAAGATG
* **
331167 CTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGTCATCAATAAGTCTTTAGAGCAAGATG
*
331209 ATAAGTCCTTCGGG
1 ATAAATCCTTCGGG
331223 CCATACATAA
Statistics
Matches: 108, Mismatches: 29, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
41 43 0.40
42 65 0.60
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGTCATCAATAAGTCTTTAGAGCAAGATG
Found at i:331191 original size:295 final size:296
Alignment explanation
Indices: 330831--331440 Score: 1024
Period size: 295 Copynumber: 2.1 Consensus size: 296
330821 TTCACAATGT
*
330831 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTA
1 ATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTA
* * * *
330896 AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAATACCTTCGGGTAGGATGTTTCAA
66 AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATACATAAGACCTTCGGGTAGGATGATTCAA
* *
330961 ATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATG-AAATTTTAAAAATGAAGAATGCGATT
131 ATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGAAAATTTTAAAAACGAAGAATGCGAGT
* * * *
331025 TTCGAAATTTCACAATTTATAAGTCCTTCGGGTCATCAATAAGTCTTCCGAGCATGATGCTTAAA
196 TTCAAAATTTCACAATGTATAAGTCATTCGGGCCATCAATAAGTCTTCCGAGCATGATGCTTAAA
331090 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
261 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
* * *
331126 ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGTATGATGCTTAAATCCTTCGGGTCATCTGTA
1 ATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTA
*
331191 AGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATACATAAGACCTTCGGGTAGGATGATTCAA
66 AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATACATAAGACCTTCGGGTAGGATGATTCAA
* * *
331256 ATGAATTTGAAAATGAAAAATGATGTTTTAAGATGATGAAAATTTTTAAAACGAAGAATGTGAGT
131 ATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGAAAATTTTAAAAACGAAGAATGCGAGT
* * *
331321 TTCAAAATTTCACAATGTATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGGTGCTTAAA
196 TTCAAAATTTCACAATGTATAAGTCATTCGGGCCATCAATAAGTCTTCCGAGCATGATGCTTAAA
331386 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
261 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
331422 ATAAGTCCTTCGGGCCATC
1 ATAAGTCCTTCGGGCCATC
331441 CGTAAGACCT
Statistics
Matches: 292, Mismatches: 22, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
295 158 0.54
296 134 0.46
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (296 bp):
ATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTA
AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATACATAAGACCTTCGGGTAGGATGATTCAA
ATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGAAAATTTTAAAAACGAAGAATGCGAGT
TTCAAAATTTCACAATGTATAAGTCATTCGGGCCATCAATAAGTCTTCCGAGCATGATGCTTAAA
TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
Found at i:331233 original size:83 final size:83
Alignment explanation
Indices: 331043--331226 Score: 323
Period size: 83 Copynumber: 2.2 Consensus size: 83
331033 TTCACAATTT
*
331043 ATAAGTCCTTCGGGTCATCAATAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
1 ATAAGTCCTTCGGGCCATCAATAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
331108 AGCCTTTAGAGCAAGATG
66 AGCCTTTAGAGCAAGATG
* * *
331126 ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGTATGATGCTTAAATCCTTCGGGTCATCTGTA
1 ATAAGTCCTTCGGGCCATCAATAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
*
331191 AGTCTTTAGAGCAAGATG
66 AGCCTTTAGAGCAAGATG
331209 ATAAGTCCTTCGGGCCAT
1 ATAAGTCCTTCGGGCCAT
331227 ACATAAGACC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 95 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (83 bp):
ATAAGTCCTTCGGGCCATCAATAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
AGCCTTTAGAGCAAGATG
Found at i:331446 original size:41 final size:42
Alignment explanation
Indices: 331339--331451 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
331329 TTCACAATGT
* * * * *
331339 ATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGGTGC
1 ATAAGTCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGC
* * * *
331381 TTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-
1 ATAAGTCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGC
*
331422 ATAAGTCCTTCGGGCCATCCGTAAGACCTT
1 ATAAGTCCTTCGGGCCATCAGTAAG-CCTT
331452 CGGGTAGGAC
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 21 0.37
42 36 0.63
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (42 bp):
ATAAGTCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGC
Found at i:331499 original size:213 final size:213
Alignment explanation
Indices: 331126--331549 Score: 715
Period size: 213 Copynumber: 2.0 Consensus size: 213
331116 GAGCAAGATG
*
331126 ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGTATGATGCTTAAATCCTTCGGGTCATCTGTA
1 ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
* *
331191 AGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATACATAAGACCTTCGGGTAGGATGATTCAA
66 AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATACATAAGACCTTCGGGTAGGACGATTCAA
* * *
331256 ATGAATTTGAAAATGAAAAATGATGTTTTAAGATGATGAAAATTTTT-AAAACGAAGAATGTGAG
131 ATGAATTTGAAAATGAAAAATGAAGTTTTAAGAAGATG-AAATTTTTGAAAACGAAGAATGCGAG
331320 TTTCAAAATTTCACAATGT
195 TTTCAAAATTTCACAATGT
* *
331339 ATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGGTGCTTAAATCCTTCGGGTCATCTGTA
1 ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
* * * *
331404 AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGACGTTTTAA
66 AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATACATAAGACCTTCGGGTAGGACGATTCAA
*
331469 ATGAATTTGAAAATGGAAAATGAAGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGAGT
131 ATGAATTTGAAAATGAAAAATGAAGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGAGT
331534 TTCAAAATTTCACAAT
196 TTCAAAATTTCACAAT
331550 TTTTAAAATC
Statistics
Matches: 197, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
212 8 0.04
213 189 0.96
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (213 bp):
ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATACATAAGACCTTCGGGTAGGACGATTCAA
ATGAATTTGAAAATGAAAAATGAAGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGAGT
TTCAAAATTTCACAATGT
Found at i:337788 original size:8 final size:8
Alignment explanation
Indices: 337775--337803 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
337765 TTTGACTTTC
337775 TTTTTTTA
1 TTTTTTTA
337783 TTTTTTTA
1 TTTTTTTA
337791 TTTTTTTA
1 TTTTTTTA
337799 TTTTT
1 TTTTT
337804 CTTTTACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:340005 original size:31 final size:31
Alignment explanation
Indices: 339963--340066 Score: 190
Period size: 31 Copynumber: 3.4 Consensus size: 31
339953 ATAACTTTTA
* *
339963 ATAGTCAAGAGACACAACAAAGCAACTCTTT
1 ATAGTCGAGAGACACAACAAAGCAACTCTCT
339994 ATAGTCGAGAGACACAACAAAGCAACTCTCT
1 ATAGTCGAGAGACACAACAAAGCAACTCTCT
340025 ATAGTCGAGAGACACAACAAAGCAACTCTCT
1 ATAGTCGAGAGACACAACAAAGCAACTCTCT
340056 ATAGTCGAGAG
1 ATAGTCGAGAG
340067 GTCATTTCGT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (31 bp):
ATAGTCGAGAGACACAACAAAGCAACTCTCT
Found at i:345318 original size:194 final size:193
Alignment explanation
Indices: 345118--345486 Score: 465
Period size: 194 Copynumber: 1.9 Consensus size: 193
345108 AAATGTCTCG
* * * * * *
345118 AAAGTATCGATACCTTACATACATGTATCGATACATAATAATATAACATGTTGAAGTTTGACAAA
1 AAAGTATCGATACCTTACACAAATGTATCGATACATAACAATATAACAGGTTAAAATTTGACAAA
* * * * * * *
345183 ATCAGTTTCAGTTTGACAAAACATGTAGAGATA-CC-AGAT-TGTTGAAATTTGTATCGATATTT
66 ATCAGTTTCAATATGACAAAACAGGTA-AAACACCCTAGATATGTTG-AA--GGTATCGATACTT
* *
345245 TTCTAAGTATATGCACCAAAGTATCGGTACTTTAGGAATTTAAAAGAATTGCAATAATAGCGCCT
127 TTATAAGTATATGCACCAAAGTATCGGTACTTTAGGAATTGAAAAGAATTGCAATAATAGCGCCT
345310 AT
192 AT
* *
345312 AAAGTATCGATACCTTAGACAAATGTATCGATACATGACAATATAACAGGTTAAAATTTGACAAA
1 AAAGTATCGATACCTTACACAAATGTATCGATACATAACAATATAACAGGTTAAAATTTGACAAA
** *
345377 ATTGGTTTCAATATGACAAAACCGGTAAAACACTCCTAGATATGTTGAAGGTATCGATACTTTTA
66 ATCAGTTTCAATATGACAAAACAGGTAAAACAC-CCTAGATATGTTGAAGGTATCGATACTTTTA
* * *
345442 TAAGTATATGTATCATAGTATCGGTACTTTAGGAATTGAAAAGAA
130 TAAGTATATGCACCAAAGTATCGGTACTTTAGGAATTGAAAAGAA
345487 ATGAAAAAAA
Statistics
Matches: 148, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
193 3 0.02
194 132 0.89
195 2 0.01
196 6 0.04
197 5 0.03
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (193 bp):
AAAGTATCGATACCTTACACAAATGTATCGATACATAACAATATAACAGGTTAAAATTTGACAAA
ATCAGTTTCAATATGACAAAACAGGTAAAACACCCTAGATATGTTGAAGGTATCGATACTTTTAT
AAGTATATGCACCAAAGTATCGGTACTTTAGGAATTGAAAAGAATTGCAATAATAGCGCCTAT
Found at i:347111 original size:222 final size:224
Alignment explanation
Indices: 346611--347378 Score: 1125
Period size: 225 Copynumber: 3.4 Consensus size: 224
346601 TTGATAAAGA
* * * ** * *
346611 TTGATAACAAATCAAGTAATTAATCGGTTATGTTATCGTCGGATTTCTAAGTTTTCATCAGCTTA
1 TTGATAACAAATCAAATAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACTTA
** *
346676 AACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACCGATAACAAATTAAATAATTA
66 AACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTA
* * ** * * *
346741 ACCTATTTTGTTATC-TTCAGATTTCTAAGGCCTTATTAGCTTAAAAAGACGTTATCTATTATGT
131 ACCTATTTTATTATCGTT-GGATTTCTAAGGCCACATCAGCTTAAAAGGA-GCTATCTATTATGT
346805 TACATAAGCGCTACCTAATATGTTATTATGG
194 TACATAAGCGCTACCTAATATGTTATTATGG
* * *
346836 TTGATAACAAATCAAATAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCGTCAGCTTA
1 TTGATAACAAATCAAATAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACTTA
* *
346901 AACTTTTGTAACATTTTAGGTGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTA
66 AACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTA
**
346966 ACCT-TTTT-TTATCGTTGGATTTCTAAGGCCACATCAGCTTAAAAGGAGCTATCTATTACATTA
131 ACCTATTTTATTATCGTTGGATTTCTAAGGCCACATCAGCTTAAAAGGAGCTATCTATTATGTTA
347029 CATAAGCGCTACCTAATATGTTATTATGG
196 CATAAGCGCTACCTAATATGTTATTATGG
347058 TTGATAACAAATCAAATAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACTTA
1 TTGATAACAAATCAAATAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACTTA
* * *
347123 AACTTTGGTAATATTTTAGGCGTTACCTAATATATTGATAATACTAATAACATATTAAGTAATTA
66 AACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTA
* *
347188 ACCTATTTTATTATCGTCGAATTTCTAAGG-CACCATCAGCTTTAAAAAGGCA-CTATCTATTAT
131 ACCTATTTTATTATCGTTGGATTTCTAAGGCCA-CATCAGC-TT-AAAAGG-AGCTATCTATTAT
347251 GTTACATAAGCGCTACCTAATATGTTATTATGG
192 GTTACATAAGCGCTACCTAATATGTTATTATGG
* * *
347284 TTGATAACAAATCAAATAATTAACTGATTAT-ATATCGTCAGATTTCTAAGGCTCCATCAACTTA
1 TTGATAACAAATCAAATAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACTTA
* * *
347348 AACTTTGGTAATATTTTTGACGTTACCTAAT
66 AACTTTGGTAACATTTTAGGCGTTACCTAAT
347379 GTCGTAACCG
Statistics
Matches: 500, Mismatches: 36, Indels: 14
0.91 0.07 0.03
Matches are distributed among these distances:
222 168 0.34
223 37 0.07
224 31 0.06
225 185 0.37
226 78 0.16
227 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (224 bp):
TTGATAACAAATCAAATAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACTTA
AACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTA
ACCTATTTTATTATCGTTGGATTTCTAAGGCCACATCAGCTTAAAAGGAGCTATCTATTATGTTA
CATAAGCGCTACCTAATATGTTATTATGG
Found at i:348064 original size:17 final size:17
Alignment explanation
Indices: 348042--348074 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
348032 TTTATATGAC
348042 TATATAATAAT-AATAAA
1 TATAT-ATAATCAATAAA
348059 TATATATAATCAATAA
1 TATATATAATCAATAA
348075 TAATTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
TATATATAATCAATAAA
Found at i:348084 original size:23 final size:23
Alignment explanation
Indices: 348031--348084 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
348021 GATTATATAT
348031 ATTTATATGACTATATAATAATA
1 ATTTATATGACTATATAATAATA
**
348054 ATAAATAT-A-TATAATCAATAATA
1 ATTTATATGACTAT-AT-AATAATA
348077 ATTTATAT
1 ATTTATAT
348085 TAAATCTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 3 0.12
23 19 0.76
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTTATATGACTATATAATAATA
Found at i:348880 original size:15 final size:15
Alignment explanation
Indices: 348862--348898 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
348852 TATTATTTTC
*
348862 ATATTATTTATATGT
1 ATATTATTTATATAT
348877 ATATTA--TATATAT
1 ATATTATTTATATAT
348890 ATATTATTT
1 ATATTATTT
348899 TATTTTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 12 0.63
15 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
ATATTATTTATATAT
Found at i:348914 original size:15 final size:14
Alignment explanation
Indices: 348892--348931 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
348882 ATATATATAT
348892 ATTATTTTATTTTC
1 ATTATTTTATTTTC
348906 ATGTATTTTA-TTTC
1 AT-TATTTTATTTTC
348920 ATTA-TTTATTTT
1 ATTATTTTATTTT
348932 TCTGTTAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.17
13 5 0.21
14 8 0.33
15 7 0.29
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (14 bp):
ATTATTTTATTTTC
Found at i:352211 original size:15 final size:15
Alignment explanation
Indices: 352191--352221 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
352181 TAATACCTTT
352191 TGCATACATGCATTA
1 TGCATACATGCATTA
*
352206 TGCATACATTCATTA
1 TGCATACATGCATTA
352221 T
1 T
352222 TCATTGCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (15 bp):
TGCATACATGCATTA
Found at i:359560 original size:29 final size:27
Alignment explanation
Indices: 359527--359602 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 27
359517 ATGCTTGAAG
359527 AAAAAATGAAAAAAATGAA-AATGAAAGAA
1 AAAAAATGAAAAAAA-GAAGAA-G-AAGAA
359556 AAAAAATGAAAAAAGAGAAGAAGAAGAA
1 AAAAAATGAAAAAA-AGAAGAAGAAGAA
*
359584 GAAAAA-GAAAAAAA-AAGAA
1 AAAAAATGAAAAAAAGAAGAA
359603 AAAAAAGAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 7 0.16
28 10 0.23
29 18 0.41
30 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (27 bp):
AAAAAATGAAAAAAAGAAGAAGAAGAA
Found at i:359608 original size:9 final size:9
Alignment explanation
Indices: 359527--359610 Score: 78
Period size: 9 Copynumber: 9.0 Consensus size: 9
359517 ATGCTTGAAG
*
359527 AAAAAATGA
1 AAAAAAAGA
*
359536 AAAAAATGA
1 AAAAAAAGA
*
359545 AAATGAAAGA
1 AAA-AAAAGA
359555 AAAAAAATGA
1 AAAAAAA-GA
*
359565 AAAAAGAGA
1 AAAAAAAGA
* *
359574 AGAAGAAGA
1 AAAAAAAGA
*
359583 AGAAAAAGAA
1 AAAAAAAG-A
359593 AAAAAAAGA
1 AAAAAAAGA
359602 AAAAAAAGA
1 AAAAAAAGA
359611 GGGTCAAGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
9 40 0.63
10 23 0.37
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:361286 original size:24 final size:23
Alignment explanation
Indices: 361243--361287 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
361233 GTTCATAATG
*
361243 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
361266 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
361288 AACTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:361286 original size:113 final size:113
Alignment explanation
Indices: 361098--361763 Score: 686
Period size: 113 Copynumber: 5.8 Consensus size: 113
361088 CATCATTCGG
* ** *
361098 TGGATCAGCAGTGCCATTTAGAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * ** *
361163 CATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGG
66 CATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGA
* * *
361211 TGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* *
361276 CATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTTGA
66 CATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGA
* * * *
361324 TGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * *
361389 CATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGA
66 CATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGA
* * *
361437 TGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAAATTGTCATCTGAAGAA-GAAG-A-AA
1 TGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAG-AA--CTCATCTGAAGAAGGAAGAAGAA
* * * * *
361499 -TTCATAATGATAAGAATTTGTTCAACCTTTTGCTCAAATCCATTACTTAA
63 GTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGA
* ** * *
361549 TGGATCAGCTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-A--AA-AAGAAGTT
1 TGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * * *
361610 CACAATGAGAAGAGTTTGTTCAACCTTTGGCAT-AATTCTATCA-TAGAAGGAGATAGAA
66 CATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTC-ATCACT---------T-G-A
* * * * * * *
361668 TAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGT
1 T-GGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
** *
361733 TCATAATGAGAAGAGCTTATTCAACCTTTTG
65 TCATAATGAGAAGAATTTGTTCAACCTTTTG
361764 AATGACTCTA
Statistics
Matches: 472, Mismatches: 58, Indels: 35
0.84 0.10 0.06
Matches are distributed among these distances:
107 3 0.01
108 8 0.02
109 42 0.09
111 2 0.00
112 72 0.15
113 241 0.51
114 3 0.01
115 4 0.01
116 12 0.03
117 1 0.00
119 2 0.00
120 45 0.10
121 1 0.00
123 2 0.00
124 34 0.07
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
TGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
CATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGA
Found at i:361782 original size:124 final size:121
Alignment explanation
Indices: 361563--361851 Score: 358
Period size: 124 Copynumber: 2.4 Consensus size: 121
361553 TCAGCTTTTT
361563 CAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAAGAAA-AAGAAGTTCACAATGAGAAGAG
1 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAGAG
* * * * * * *
361624 TTTGTTCAACCTTTGGCATAATTCTATCATAGAAGGAGATA-GAAT-AGCATCAACCTTTC
66 CTTATTCAACCTTTGGAATAACTCTATCACAGAAGGAAATATG--TCAACATCAACC---C
*
361683 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAG
1 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAGAG
* * *
361748 CTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATATGTCAACATCATCCC
66 CTTATTCAACCTTTGGAATAACTCTATCACAGAAGGAAATATGTCAACATCAACCC
* *
361804 CAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-AGAGAAGAA
1 CAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAA
361852 TTTATTCAAC
Statistics
Matches: 149, Mismatches: 13, Indels: 13
0.85 0.07 0.07
Matches are distributed among these distances:
120 32 0.21
121 12 0.08
122 34 0.23
123 8 0.05
124 62 0.42
125 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (121 bp):
CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAGAG
CTTATTCAACCTTTGGAATAACTCTATCACAGAAGGAAATATGTCAACATCAACCC
Found at i:362057 original size:3 final size:3
Alignment explanation
Indices: 361993--362044 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
361983 TTCATTTAAA
361993 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
362037 TAT TAT TA
1 TAT TAT TA
362045 ATAAATATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 3 0.07
3 42 0.91
4 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:362526 original size:12 final size:12
Alignment explanation
Indices: 362509--362535 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
362499 GAGAGAGAAA
362509 AAGAAAAAAAAC
1 AAGAAAAAAAAC
362521 AAGAAAAAAAAC
1 AAGAAAAAAAAC
362533 AAG
1 AAG
362536 CAAACCAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAC
Found at i:364552 original size:225 final size:224
Alignment explanation
Indices: 364145--364737 Score: 700
Period size: 225 Copynumber: 2.6 Consensus size: 224
364135 CGGTTACGAC
* * * * **
364145 ACCTAATATGATGATAATATTGAAAACAAATTAAATAATTAACCTATTTTGTTATCGTCAGATCG
1 ACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCA-ATTT
* * * * *
364210 CTAAGGCCACATCA-ATTTAAAAAGGTGTTA-TCTATTACATTATATAAGCGCTACCTAATATGT
65 CTAA-GCC-CATTAGCTTTAAAAAGGAGCTACT-TATTACGTTATATAAGCGCTACCTAATATGT
* * * * *
364273 TATTTTGGTTGATAACAAATTAAGTAATTAACTGGTTATGTTTTCGTCGGATTTCTAAGACTCTA
127 TATTATGGTTGATAACAAATCAAGTAATTAACTGGTTATATTATCGTCGGATTTCTAAGACTCCA
** * **
364338 -CCGCTTAAACTTT-AGTATCA-TTTTAGGT-GTT
192 TCAACTTAAAATTTGACAAT-ATTTTTA-GTCGTT
*
364369 ACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTATTATCGTCTAATTT
1 ACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTC-AATTT
*
364434 CTAATGTCCCATTAGCTTTAAAAAGGCGCTACTTATTACGTTATATAAGCGCTACCTAATATGTT
65 CTAA-G-CCCATTAGCTTTAAAAAGGAGCTACTTATTACGTTATATAAGCGCTACCTAATATGTT
* * *
364499 ATTATAGTTGATAACAAATCAAGTAATTAAGC-GGTTATATTATCGTTGGATTTCTAAGGCTCCA
128 ATTATGGTTGATAACAAATCAAGTAATTAA-CTGGTTATATTATCGTCGGATTTCTAAGACTCCA
364563 TCAACTTAAAATTTGACAATATTTTTAGTCGTT
192 TCAACTTAAAATTTGACAATATTTTTAGTCGTT
* *
364596 ACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACTTATTTTGTTATCGTCGGATTT
1 ACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTC-AATTT
* * * * *
364661 CTAAGCTTCATTAGC-TTAAAAATGAGCTACTTATTACGTTTTATAAGTGCTACTTAATAAT-TT
65 CTAAGC-CCATTAGCTTTAAAAAGGAGCTACTTATTACGTTATATAAGCGCTACCTAAT-ATGTT
*
364724 ATTATGGTTAATAA
128 ATTATGGTTGATAA
364738 TATTTCCGGT
Statistics
Matches: 320, Mismatches: 38, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
224 65 0.20
225 154 0.48
226 25 0.08
227 76 0.24
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (224 bp):
ACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAATTTC
TAAGCCCATTAGCTTTAAAAAGGAGCTACTTATTACGTTATATAAGCGCTACCTAATATGTTATT
ATGGTTGATAACAAATCAAGTAATTAACTGGTTATATTATCGTCGGATTTCTAAGACTCCATCAA
CTTAAAATTTGACAATATTTTTAGTCGTT
Found at i:364683 original size:109 final size:109
Alignment explanation
Indices: 364486--364681 Score: 254
Period size: 109 Copynumber: 1.8 Consensus size: 109
364476 ATATAAGCGC
* * * * *
364486 TACCTAATATGTT-ATTATAGTTGATAACAAATCAAGTAATTAAGC-GGTTATATTATCGTTGGA
1 TACCTAATATGTTGATAATA-CTGATAACAAATTAAGTAATTAA-CTGATTATATTATCGTCGGA
* *
364549 TTTCTAAGGCTCCATCAACTTAAAATTTGACAATATTTTTAGTCGT
64 TTTCTAAGGCTCCATTAGCTTAAAATTTGACAATATTTTTAGTCGT
* * *
364595 TACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACTTATTTTGTTATCGTCGGATT
1 TACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACTGATTATATTATCGTCGGATT
*
364660 TCTAA-GCTTCATTAGCTTAAAA
66 TCTAAGGCTCCATTAGCTTAAAA
364682 ATGAGCTACT
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
108 15 0.20
109 54 0.73
110 5 0.07
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (109 bp):
TACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACTGATTATATTATCGTCGGATT
TCTAAGGCTCCATTAGCTTAAAATTTGACAATATTTTTAGTCGT
Found at i:364886 original size:17 final size:17
Alignment explanation
Indices: 364864--364902 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
364854 TTCGTTATCA
364864 ATTTTAACCAATTAC-CT
1 ATTTT-ACCAATTACACT
*
364881 ATTTTATCAATTACACT
1 ATTTTACCAATTACACT
364898 ATTTT
1 ATTTT
364903 TTAATAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTTACCAATTACACT
Found at i:368462 original size:31 final size:30
Alignment explanation
Indices: 368427--368603 Score: 149
Period size: 31 Copynumber: 5.7 Consensus size: 30
368417 GAGCATCTTG
*
368427 GGGCCTAAGAGCCTACCCAAGAAAGTTCTCA
1 GGGCC-AAGAGCCTACCCAAGAAAGATCTCA
*
368458 GGGCCACAGGGCCTACCCAAGAAAGATCTCA
1 GGGCCA-AGAGCCTACCCAAGAAAGATCTCA
* * * *
368489 GGGCCGTAGGGCCTACCCAAGAATGATCTTA
1 GGGCC-AAGAGCCTACCCAAGAAAGATCTCA
* *
368520 GGGCCATGAGGCCTACCCAAGAAAAATC-CTA
1 GGGCCAAGA-GCCTACCCAAGAAAGATCTC-A
* * * **
368551 GGGCCGCAGGGCCTACCCAAGAATGATCTTG
1 GGGCC-AAGAGCCTACCCAAGAAAGATCTCA
* *
368582 GGGCCGCATAGCCTACCCAAGA
1 GGGCC-AAGAGCCTACCCAAGA
368604 GTCACATTAG
Statistics
Matches: 120, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
30 2 0.02
31 117 0.98
32 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.27, T:0.14
Consensus pattern (30 bp):
GGGCCAAGAGCCTACCCAAGAAAGATCTCA
Found at i:368524 original size:62 final size:62
Alignment explanation
Indices: 368437--368603 Score: 212
Period size: 62 Copynumber: 2.7 Consensus size: 62
368427 GGGCCTAAGA
* * * * *
368437 GCCTACCCAAGAAAGTTCTCAGGGCCACAGGGCCTACCCAAGAAAGAT-CTCAGGGCCGTAGG
1 GCCTACCCAAGAATGATCTTAGGGCCACAGGGCCTACCCAAGAAAAATCCT-AGGGCCGCAGG
*
368499 GCCTACCCAAGAATGATCTTAGGGCCA-TGAGGCCTACCCAAGAAAAATCCTAGGGCCGCAGG
1 GCCTACCCAAGAATGATCTTAGGGCCACAG-GGCCTACCCAAGAAAAATCCTAGGGCCGCAGG
* * **
368561 GCCTACCCAAGAATGATCTTGGGGCCGCATAGCCTACCCAAGA
1 GCCTACCCAAGAATGATCTTAGGGCCACAGGGCCTACCCAAGA
368604 GTCACATTAG
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
61 1 0.01
62 88 0.97
63 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (62 bp):
GCCTACCCAAGAATGATCTTAGGGCCACAGGGCCTACCCAAGAAAAATCCTAGGGCCGCAGG
Found at i:368614 original size:93 final size:93
Alignment explanation
Indices: 368420--368603 Score: 228
Period size: 93 Copynumber: 2.0 Consensus size: 93
368410 CCTAAGGGAG
* * * *
368420 CATCTTGGGGCC-TAAGAGCCTACCCAAGAAAGTTCTCAGGGCCACAGGGCCTACCCAAGAAAGA
1 CATCTTAGGGCCATGAG-GCCTACCCAAGAAAATCCTCAGGGCCACAGGGCCTACCCAAGAAAGA
* *
368484 TCTCAGGGCCGTAGGGCCTACCCAAGAAT
65 TCTCAGGGCCGCAGAGCCTACCCAAGAAT
* * *
368513 GATCTTAGGGCCATGAGGCCTACCCAAGAAAAATCCT-AGGGCCGCAGGGCCTACCCAAGAATGA
1 CATCTTAGGGCCATGAGGCCTACCCAAG-AAAATCCTCAGGGCCACAGGGCCTACCCAAGAAAGA
** *
368577 TCTTGGGGCCGCATAGCCTACCCAAGA
65 TCTCAGGGCCGCAGAGCCTACCCAAGA
368604 GTCACATTAG
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
93 68 0.88
94 9 0.12
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.15
Consensus pattern (93 bp):
CATCTTAGGGCCATGAGGCCTACCCAAGAAAATCCTCAGGGCCACAGGGCCTACCCAAGAAAGAT
CTCAGGGCCGCAGAGCCTACCCAAGAAT
Found at i:370650 original size:18 final size:18
Alignment explanation
Indices: 370627--370665 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
370617 AGTCGGCTTA
370627 GCTTGGCTCAACGACTCG
1 GCTTGGCTCAACGACTCG
**
370645 GCTTGGCTCGGCGACTCG
1 GCTTGGCTCAACGACTCG
370663 GCT
1 GCT
370666 CAGTGGCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.33, G:0.33, T:0.23
Consensus pattern (18 bp):
GCTTGGCTCAACGACTCG
Found at i:370726 original size:39 final size:39
Alignment explanation
Indices: 370643--370732 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
370633 CTCAACGACT
* * *
370643 CGGCTTGGCTCGGCGACTCGGCTCAGTGGCTCAACTCGG
1 CGGCTCGGCTCGACGACTCGGCTCAGTGACTCAACTCGG
* * **
370682 TGGCTCTGCTCGACGACTCGGCTCAGTGACTC-GGTGCGG
1 CGGCTCGGCTCGACGACTCGGCTCAGTGACTCAACT-CGG
370721 CGGCTCGGCTCG
1 CGGCTCGGCTCG
370733 GTGGCTCAGC
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
38 1 0.02
39 40 0.98
ACGTcount: A:0.09, C:0.33, G:0.37, T:0.21
Consensus pattern (39 bp):
CGGCTCGGCTCGACGACTCGGCTCAGTGACTCAACTCGG
Found at i:370738 original size:13 final size:13
Alignment explanation
Indices: 370644--370744 Score: 60
Period size: 13 Copynumber: 7.8 Consensus size: 13
370634 TCAACGACTC
* *
370644 GGCTTGGCTCGGC
1 GGCTCGGCTCGGT
* *
370657 GACTCGGCTCAGT
1 GGCTCGGCTCGGT
**
370670 GGCTCAACTCGGT
1 GGCTCGGCTCGGT
* **
370683 GGCTCTGCTCGAC
1 GGCTCGGCTCGGT
* *
370696 GACTCGGCTCAGT
1 GGCTCGGCTCGGT
* *
370709 GACTCGG-TGCGGC
1 GGCTCGGCT-CGGT
370722 GGCTCGGCTCGGT
1 GGCTCGGCTCGGT
*
370735 GGCTCAGCTC
1 GGCTCGGCTC
370745 AGACCGGTCC
Statistics
Matches: 64, Mismatches: 22, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
12 1 0.02
13 62 0.97
14 1 0.02
ACGTcount: A:0.09, C:0.33, G:0.37, T:0.22
Consensus pattern (13 bp):
GGCTCGGCTCGGT
Found at i:370767 original size:19 final size:19
Alignment explanation
Indices: 370743--370780 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
370733 GTGGCTCAGC
*
370743 TCAGACCGGTCCAGTCGGT
1 TCAGACCAGTCCAGTCGGT
*
370762 TCAGACTAGTCCAGTCGGT
1 TCAGACCAGTCCAGTCGGT
370781 CAACTGGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.29, T:0.24
Consensus pattern (19 bp):
TCAGACCAGTCCAGTCGGT
Found at i:371595 original size:30 final size:28
Alignment explanation
Indices: 371539--371603 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
371529 TTTTTTTCTA
*
371539 AAAAATTAGGGTTTAACTAAAACTTTTG
1 AAAAATTAGGGCTTAACTAAAACTTTTG
371567 AAAAATTGAGAGGCTTAA-TAAGAACTTTT-
1 AAAAATT-AG-GGCTTAACTAA-AACTTTTG
*
371596 AAATATTA
1 AAAAATTA
371604 TGGGAGGGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 8 0.25
29 11 0.34
30 13 0.41
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (28 bp):
AAAAATTAGGGCTTAACTAAAACTTTTG
Found at i:374819 original size:18 final size:18
Alignment explanation
Indices: 374791--374845 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
374781 ACTTCATTCC
*
374791 CTTTG-TTGAGTCCTCAT
1 CTTTGCTTGAGTCTTCAT
*
374808 CTTTGCTTGAGTCTTTAT
1 CTTTGCTTGAGTCTTCAT
*
374826 CTTTGCTTAAGTCTTCAT
1 CTTTGCTTGAGTCTTCAT
374844 CT
1 CT
374846 CATGACAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.13, C:0.22, G:0.15, T:0.51
Consensus pattern (18 bp):
CTTTGCTTGAGTCTTCAT
Found at i:381094 original size:18 final size:18
Alignment explanation
Indices: 381058--381115 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
381048 ATTAAAAGTA
* *
381058 TAAATTTTT-TAAAACCT
1 TAAATTTTTCTCAAATCT
381075 TAAATTTTTCTCAAATCT
1 TAAATTTTTCTCAAATCT
***
381093 TAAAATAAATCTCAAATCT
1 T-AAATTTTTCTCAAATCT
381112 TAAA
1 TAAA
381116 ATGAATCCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 9 0.26
18 10 0.29
19 15 0.44
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATTTTTCTCAAATCT
Found at i:381105 original size:19 final size:19
Alignment explanation
Indices: 381083--381127 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
381073 CTTAAATTTT
381083 TCTCAAATCTTAAAATAAA
1 TCTCAAATCTTAAAATAAA
*
381102 TCTCAAATCTTAAAATGAA
1 TCTCAAATCTTAAAATAAA
*
381121 TCCCAAA
1 TCTCAAA
381128 AATTTGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (19 bp):
TCTCAAATCTTAAAATAAA
Found at i:381545 original size:23 final size:23
Alignment explanation
Indices: 381506--381550 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
381496 TTAAATATAA
*
381506 AAATATTTTAAAGTTTTTTAAAT
1 AAATATTTTAAAGTTTTATAAAT
*
381529 AAAT-TTTTAAATTTTTTATAAA
1 AAATATTTTAAA-GTTTTATAAA
381551 CGTAACGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
AAATATTTTAAAGTTTTATAAAT
Found at i:383187 original size:45 final size:45
Alignment explanation
Indices: 383134--383462 Score: 509
Period size: 45 Copynumber: 7.3 Consensus size: 45
383124 ATCCTATGAT
*
383134 CTCGTAAGCTTATTTTATCAATATACTTACCATTTATTCCATAAG
1 CTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAG
* * *
383179 CTCATAAGCTAATTTTACCAATATACTTACCATTTATCCCATAAG
1 CTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAG
* *
383224 CTCGTAAGCTTGTTTTACCAATATACTTA-CATTTTTTTCCATAAG
1 CTCGTAAGCTTATTTTACCAATATACTTACCA-TTTATTCCATAAG
* * *
383269 CTCATAAGCTTATTTTACCAATATACTTACCTTTTATTTCATAAG
1 CTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAG
* *
383314 CTCATAAGCTTATTTTACCAATATACTTACCATTTATTCCATTAG
1 CTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAG
* *
383359 CTCGTAAGCTTATTTTACTAATATACTTATCATTTATTCCATAAG
1 CTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAG
*
383404 CTCGTAAGCTTATTTTACCAATATACTTGCCA-TTATTCCATAAG
1 CTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAG
383448 CTCGTAAGCTTATTT
1 CTCGTAAGCTTATTT
383463 GCATGCTTAC
Statistics
Matches: 258, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
44 29 0.11
45 228 0.88
46 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (45 bp):
CTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAG
Found at i:387689 original size:59 final size:58
Alignment explanation
Indices: 387576--387697 Score: 133
Period size: 59 Copynumber: 2.1 Consensus size: 58
387566 GATTTTAAAG
* ** *
387576 AAATAAATTTAACGATTTATTTATTTCCTTCAAAATATAATCATACTTGATTCCCAAGA
1 AAATAAATTTAACGATTTATTTATTT-CTTCAAAATAGAATCATACAAGATTCCCAAAA
*
387635 AAATAAATTTAACGATTTATTTCCTTT-TAT-AAACA-AGAATCATACAAGATTTCCCAAAA
1 AAATAAATTTAACGATTTATTT-ATTTCT-TCAAA-ATAGAATCATACAAGA-TTCCCAAAA
387694 AAAT
1 AAAT
387698 TCAATGATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
58 15 0.28
59 36 0.67
60 3 0.06
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (58 bp):
AAATAAATTTAACGATTTATTTATTTCTTCAAAATAGAATCATACAAGATTCCCAAAA
Found at i:387747 original size:39 final size:39
Alignment explanation
Indices: 387690--388041 Score: 384
Period size: 39 Copynumber: 8.8 Consensus size: 39
387680 AAGATTTCCC
* * * *
387690 AAAA-AAATTCAATGATTTATTTCCTGTTACAAAATAGA
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
387728 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
* * * *
387767 AAACTAAATCCAATGATTTATTTTCTTTTACAAAATAGAA
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAG-G
** *
387807 AAAATAAATTTAACGATTTATTTCCTTTTACAAAACAGG
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
387846 AAAATAAATCAACAATTTGTTCGATTTATTTCCTTTTACAAAATAGG
1 AAAATAAATC--CAA------CGATTTATTTCCTTTTACAAAATAGG
* ** * * *
387893 AAACTAAATCCAATAATTTATTTTCTTGTACAAAACAGG
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
**
387932 AAAATAAATCCAAC-ATTTTATTTCCTTTTACAAACCAGG
1 AAAATAAATCCAACGA-TTTATTTCCTTTTACAAAATAGG
* * * * *
387971 AAACTAAATTCTATGATTTATTTCCTTTTTCAAAATAGG
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
388010 AAAATAAATCCAACGATTTATTTCCTTTTACA
1 AAAATAAATCCAACGATTTATTTCCTTTTACA
388042 TATTAGAATC
Statistics
Matches: 261, Mismatches: 41, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
38 5 0.02
39 184 0.70
40 33 0.13
41 2 0.01
45 3 0.01
47 34 0.13
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.36
Consensus pattern (39 bp):
AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
Found at i:387872 original size:47 final size:48
Alignment explanation
Indices: 387820--387911 Score: 150
Period size: 47 Copynumber: 1.9 Consensus size: 48
387810 ATAAATTTAA
387820 CGATTTATTTCCTTTTACAAAACAGGAAAATAAAT-CAACAATTTGTT
1 CGATTTATTTCCTTTTACAAAACAGGAAAATAAATCCAACAATTTGTT
* * *
387867 CGATTTATTTCCTTTTACAAAATAGGAAACTAAATCCAATAATTT
1 CGATTTATTTCCTTTTACAAAACAGGAAAATAAATCCAACAATTT
387912 ATTTTCTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 33 0.80
48 8 0.20
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (48 bp):
CGATTTATTTCCTTTTACAAAACAGGAAAATAAATCCAACAATTTGTT
Found at i:387900 original size:126 final size:118
Alignment explanation
Indices: 387705--388041 Score: 401
Period size: 126 Copynumber: 2.8 Consensus size: 118
387695 AATTCAATGA
* * * * *
387705 TTTATTTCCTGTTACAAAATAGAAAAATAAA-TCCAACGATTTATTTCCTTTTACAAAATAGGAA
1 TTTATTTCCTTTTACAAAACAGGAAAATAAATTCTATCGATTTATTTCCTTTTACAAAATAGGAA
* **
387769 ACTAAATCCAATGATTTATTTTCTTTTACAAAATAGAAAAAATAAATTTAACGA-
66 ACTAAATCCAATGATTTATTTTCTTTTACAAAACAG-AAAAATAAATCCAAC-AT
* *
387823 TTTATTTCCTTTTACAAAACAGGAAAATAAATCAACAATTTGTTCGATTTATTTCCTTTTACAAA
1 TTTATTTCCTTTTACAAAACAGGAAAATAAAT------TCT-ATCGATTTATTTCCTTTTACAAA
* * *
387888 ATAGGAAACTAAATCCAATAATTTATTTTCTTGTACAAAACAGGAAAATAAATCCAACAT
59 ATAGGAAACTAAATCCAATGATTTATTTTCTTTTACAAAACAGAAAAATAAATCCAACAT
* * *
387948 TTTATTTCCTTTTACAAACCAGGAAACTAAATTCTAT-GATTTATTTCCTTTTTCAAAATAGGAA
1 TTTATTTCCTTTTACAAAACAGGAAAATAAATTCTATCGATTTATTTCCTTTTACAAAATAGGAA
* * *
388012 AATAAATCCAACGATTTATTTCCTTTTACA
66 ACTAAATCCAATGATTTATTTTCTTTTACA
388042 TATTAGAATC
Statistics
Matches: 187, Mismatches: 23, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
117 51 0.27
118 29 0.16
119 2 0.01
124 1 0.01
125 43 0.23
126 61 0.33
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (118 bp):
TTTATTTCCTTTTACAAAACAGGAAAATAAATTCTATCGATTTATTTCCTTTTACAAAATAGGAA
ACTAAATCCAATGATTTATTTTCTTTTACAAAACAGAAAAATAAATCCAACAT
Found at i:387903 original size:165 final size:165
Alignment explanation
Indices: 387703--388028 Score: 433
Period size: 165 Copynumber: 2.0 Consensus size: 165
387693 AAAATTCAAT
* * *
387703 GATTTATTTCCTGTTACAAAATAGAAAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGGA
1 GATTTATTTCCTGTTACAAAATAGAAAAATAAATCCAACAATTTATTTCCTTGTACAAAACAGGA
* * * *
387768 AACTAAATCCAATGA-TTTATTTTCTTTTACAAAATAGAAAAAATAAATT-TAACGATTTATTTC
66 AAATAAATCCAA-CATTTTATTTCCTTTTACAAAACAG-AAAAATAAATTCT-ACGATTTATTTC
387831 CTTTTACAAAACAGGAAAATAAAT-CAACAATTTGTTC
128 CTTTTACAAAACAGGAAAATAAATCCAACAATTTGTTC
* * * * *
387868 GATTTATTTCCTTTTACAAAATAGGAAACTAAATCCAATAATTTATTTTCTTGTACAAAACAGGA
1 GATTTATTTCCTGTTACAAAATAGAAAAATAAATCCAACAATTTATTTCCTTGTACAAAACAGGA
* * * *
387933 AAATAAATCCAACATTTTATTTCCTTTTACAAACCAGGAAACTAAATTCTATGATTTATTTCCTT
66 AAATAAATCCAACATTTTATTTCCTTTTACAAAACAGAAAAATAAATTCTACGATTTATTTCCTT
* * *
387998 TTTCAAAATAGGAAAATAAATCCAACGATTT
131 TTACAAAACAGGAAAATAAATCCAACAATTT
388029 ATTTCCTTTT
Statistics
Matches: 139, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
164 43 0.31
165 96 0.69
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.36
Consensus pattern (165 bp):
GATTTATTTCCTGTTACAAAATAGAAAAATAAATCCAACAATTTATTTCCTTGTACAAAACAGGA
AAATAAATCCAACATTTTATTTCCTTTTACAAAACAGAAAAATAAATTCTACGATTTATTTCCTT
TTACAAAACAGGAAAATAAATCCAACAATTTGTTC
Found at i:388275 original size:97 final size:97
Alignment explanation
Indices: 387986--388345 Score: 453
Period size: 97 Copynumber: 3.8 Consensus size: 97
387976 AAATTCTATG
* * *
387986 ATTTATTTCCTTTTTCAAAATAGGAAAATAAATCCAACGATTTATTTCCTTTTACATATTAGAAT
1 ATTTATTTCCTTTTTCAAAACAGGAAAATAAATCCAACGATTTATTTCCTTTTACAAATCAGAAT
388051 CATACAAGATTCTTAGGAAAATAAATTTACCA
66 CATACAAGATTCTTAGGAAAATAAATTTACCA
* * * * * *
388083 ATTTATTTCCTTTTTTAAAACATGAAAATAAATTCTATGA--T-TTT--TTTTACATATCAGAAT
1 ATTTATTTCCTTTTTCAAAACAGGAAAATAAATCCAACGATTTATTTCCTTTTACAAATCAGAAT
*
388143 CATACAAGATTCTTAGGAAAACAAATTTACCA
66 CATACAAGATTCTTAGGAAAATAAATTTACCA
* * * *
388175 ATTTATTTCTTTTTTCAAAACAAGAAAATAAATTCTACGATTTATTTCCTTTTACAAATCAGAAT
1 ATTTATTTCCTTTTTCAAAACAGGAAAATAAATCCAACGATTTATTTCCTTTTACAAATCAGAAT
*** * * * *
388240 CATGTGAGATTCTCAAGAAAATAAATCTAACA
66 CATACAAGATTCTTAGGAAAATAAATTTACCA
* *
388272 ATTTATTTCCTTTTACAAAAACAGGAAAATAAATCCAACGATTTATTTCCTTTTAAAAAT-AGAA
1 ATTTATTTCCTTTTTC-AAAACAGGAAAATAAATCCAACGATTTATTTCCTTTTACAAATCAGAA
*
388336 TCATATAAGA
65 TCATACAAGA
388346 AAATAAATTC
Statistics
Matches: 228, Mismatches: 29, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
92 82 0.36
94 4 0.02
95 4 0.02
97 99 0.43
98 39 0.17
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (97 bp):
ATTTATTTCCTTTTTCAAAACAGGAAAATAAATCCAACGATTTATTTCCTTTTACAAATCAGAAT
CATACAAGATTCTTAGGAAAATAAATTTACCA
Found at i:388533 original size:57 final size:58
Alignment explanation
Indices: 388388--388749 Score: 181
Period size: 57 Copynumber: 6.4 Consensus size: 58
388378 TGATCCCAAG
* * * * *
388388 AAAATAAACTTAACAACTTATTTCCTTTAACAAAATAAAAATCATTTAGGATTCTCATG
1 AAAATAAATTTAACAATTTATTT-CTTTTACAAAATAAAAATCATTTAAGATTCTCATA
* * *
388447 AAAATAATTTTAACAATTTATTAACTTTTAC-ACA-AAAAATCATTTAAGATTCTCATA
1 AAAATAAATTTAACAATTTATT-TCTTTTACAAAATAAAAATCATTTAAGATTCTCATA
* ** *
388504 AAAATAAATTTAATAATTTATTTCTTTTTA-ATGGAT-ATAATCA--T---A---TCA-A
1 AAAATAAATTTAACAATTTATTTC-TTTTACA-AAATAAAAATCATTTAAGATTCTCATA
** * *
388553 GAAAATAAATTCGACAATTTATTT-TTCTTACAAAGTTAAAATCATTTAAGATT-TCCA-A
1 -AAAATAAATTTAACAATTTATTTCTT-TTACAAAATAAAAATCATTTAAGATTCT-CATA
* * * * * * *
388611 GGAAATAAATTCAACAAATTATTT-TCCTTACAAAGTTAGAATCA-TTAAGATTCTCA-A
1 -AAAATAAATTTAACAATTTATTTCT-TTTACAAAATAAAAATCATTTAAGATTCTCATA
* * * * * * *
388668 GGAAATAAATTCAACAATCTATTT-TCTTTACAAAGTTAGAATCATTAAAGATTCTCA-A
1 -AAAATAAATTTAACAATTTATTTCT-TTTACAAAATAAAAATCATTTAAGATTCTCATA
* *
388726 AGAAATAAATTCAACAATCTATTT
1 A-AAATAAATTTAACAATTTATTT
388750 TCCTTACGAA
Statistics
Matches: 251, Mismatches: 31, Indels: 43
0.77 0.10 0.13
Matches are distributed among these distances:
48 2 0.01
49 5 0.02
50 30 0.12
52 1 0.00
53 1 0.00
55 1 0.00
56 2 0.01
57 99 0.39
58 85 0.34
59 25 0.10
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (58 bp):
AAAATAAATTTAACAATTTATTTCTTTTACAAAATAAAAATCATTTAAGATTCTCATA
Found at i:388705 original size:115 final size:114
Alignment explanation
Indices: 388549--388768 Score: 320
Period size: 115 Copynumber: 1.9 Consensus size: 114
388539 TATAATCATA
* * * *
388549 TCAAGAAAATAAATTCGACAATTTATTTTTCTTACAAAGTTAAAATCATTTAAGATT-TCCAAGG
1 TCAAGAAAATAAATTCAACAATCTATTTTTCTTACAAAGTTAAAATCATTAAAGATTCT-CAAAG
388613 AAATAAATTCAACAAAT-TATTTTCCTTACAAAGTTAGAATCATTAAGATTC
65 AAATAAATTCAAC-AATCTATTTTCCTTACAAAG-TAGAATCATTAAGATTC
* *
388664 TCAAGGAAATAAATTCAACAATCTA-TTTTCTTTACAAAGTTAGAATCATTAAAGATTCTCAAAG
1 TCAAGAAAATAAATTCAACAATCTATTTTTC-TTACAAAGTTAAAATCATTAAAGATTCTCAAAG
*
388728 AAATAAATTCAACAATCTATTTTCCTTACGAAGTAGAATCA
65 AAATAAATTCAACAATCTATTTTCCTTACAAAGTAGAATCA
388769 ATGCAAGATT
Statistics
Matches: 95, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
114 16 0.17
115 78 0.82
116 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (114 bp):
TCAAGAAAATAAATTCAACAATCTATTTTTCTTACAAAGTTAAAATCATTAAAGATTCTCAAAGA
AATAAATTCAACAATCTATTTTCCTTACAAAGTAGAATCATTAAGATTC
Found at i:388778 original size:58 final size:58
Alignment explanation
Indices: 388549--388768 Score: 313
Period size: 58 Copynumber: 3.8 Consensus size: 58
388539 TATAATCATA
* * * * *
388549 TCAAGAAAATAAATTCGACAATTTATTTTTCTTACAAAGTTAAAATCATTTAAGATT-
1 TCAAGGAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTC
388606 TCCAAGGAAATAAATTCAACAAAT-TATTTTCCTTACAAAGTTAGAATCA-TTAAGATTC
1 T-CAAGGAAATAAATTCAAC-AATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTC
* *
388664 TCAAGGAAATAAATTCAACAATCTATTTTCTTTACAAAGTTAGAATCATTAAAGATTC
1 TCAAGGAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTC
* *
388722 TCAAAGAAATAAATTCAACAATCTATTTTCCTTACGAAG-TAGAATCA
1 TCAAGGAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCA
388769 ATGCAAGATT
Statistics
Matches: 149, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
56 3 0.02
57 59 0.40
58 84 0.56
59 3 0.02
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (58 bp):
TCAAGGAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTC
Found at i:389023 original size:45 final size:43
Alignment explanation
Indices: 388924--389076 Score: 173
Period size: 45 Copynumber: 3.4 Consensus size: 43
388914 TTAATTATGT
* * *
388924 CAACCTAATATTCAAAAGGAACTAATCCTTTGATTTTA-TTTTCAG
1 CAACC-AATAATCAAAA-GAAATAATCCTTTGATTTTACTTTT-GG
* *
388969 CAATCCAATAATCGAAAGAAAATAATCCTTTGCTTTTACTTTTGG
1 CAA-CCAATAATCAAAAG-AAATAATCCTTTGATTTTACTTTTGG
*
389014 CAACACAATAATCAAAAGAAATGAATCCTTTGATTTTACTTTTGA
1 CAAC-CAATAATCAAAAGAAAT-AATCCTTTGATTTTACTTTTGG
389059 CAACCCAATAATCAAAAG
1 CAA-CCAATAATCAAAAG
389077 CCTTGACTTA
Statistics
Matches: 94, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
44 6 0.06
45 81 0.86
46 7 0.07
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (43 bp):
CAACCAATAATCAAAAGAAATAATCCTTTGATTTTACTTTTGG
Found at i:391454 original size:95 final size:96
Alignment explanation
Indices: 391281--391483 Score: 223
Period size: 95 Copynumber: 2.1 Consensus size: 96
391271 CCTGTTGTAG
* ** *
391281 GTATCGATACCAAGAGAAAGGTATTGATACCAGGGAATTCCAAAATGTCGAAATGGTATCGATAT
1 GTATCGATACCAAGAGAAAGGTATCGATACCAGGGAATTCCAAAATGTAAAAATGGCATCGATAT
* * *
391346 TGAAAGGGAGTATTGGTA-TAATAGTATCGAA
66 AGAAAGGGAGTATTGATACT-ATAGTATAGAA
* * * * * * *
391377 GTATTGATACTAAGAGAAAGGTATCGATACTA-TGAATTGCAGAATGTAAAAATGGCATCTATAC
1 GTATCGATACCAAGAGAAAGGTATCGATACCAGGGAATTCCAAAATGTAAAAATGGCATCGATA-
*
391441 TAG-AAGGGTGTATTGATACTATAGTATAGAA
65 TAGAAAGGGAGTATTGATACTATAGTATAGAA
*
391472 GTATCGACACCA
1 GTATCGATACCA
391484 TGGTAGGGGT
Statistics
Matches: 87, Mismatches: 18, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
95 56 0.64
96 31 0.36
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (96 bp):
GTATCGATACCAAGAGAAAGGTATCGATACCAGGGAATTCCAAAATGTAAAAATGGCATCGATAT
AGAAAGGGAGTATTGATACTATAGTATAGAA
Found at i:391903 original size:45 final size:45
Alignment explanation
Indices: 391833--392202 Score: 510
Period size: 45 Copynumber: 8.2 Consensus size: 45
391823 GTTTTCATTA
* * *
391833 CATAAATGAAATGCATAATGATGCATTAAAGGCATAAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
391878 CATAAATGAAATGCACAACGGTGCATTAAAGGCATGAAGGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
391923 CATAAATGAAATTCATAACGGTGCATTAAAGGCACGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
391968 CATAAATAAAATGCATAACGGTGAATTAAAGGCATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
392013 CATAAATAAAATGCATAACAGTGCATTAAAGGCATGAAAGGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
392058 CGTAAATGAAATGCATAACGGTGCATTAAAGAG-AAGAAAAGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAG-GCATGAAAGGATGC
*
392103 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATG-
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* ** * *
392147 CATAAATGAAATGCACAAATGTGCAATAAAGGCATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*
392192 CATAATTGAAA
1 CATAAATGAAA
392203 ATAATGAATA
Statistics
Matches: 287, Mismatches: 35, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
44 39 0.14
45 247 0.86
46 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
Found at i:398490 original size:95 final size:96
Alignment explanation
Indices: 398335--398534 Score: 280
Period size: 95 Copynumber: 2.1 Consensus size: 96
398325 ACTGCTATAG
* * *
398335 GTATCAATACCAAGAGAAAATTATTGATATCAGGGAATTCCAGAATGTCGAAATGATATCGATA-
1 GTATCGATACCAAGAGAAAATTATTGATATCAGGGAATTACAGAATGTAGAAATGATATCGATAC
* *
398399 TTGAAAGGGAGTATCGATACCATAGTATAGAA
66 TAG-AAGGGAGCATCGATACCATAGTATAGAA
* * *
398431 GTATCGATACTAAGAGAAAGA-TATTGATATCA-TGAATTACAGAATGTAGAAATGGTATCGATA
1 GTATCGATACCAAGAGAAA-ATTATTGATATCAGGGAATTACAGAATGTAGAAATGATATCGATA
*
398494 CTAGAAGGGCGCATCGATACCATAGTATAGAA
65 CTAGAAGGGAGCATCGATACCATAGTATAGAA
398526 GTATCGATA
1 GTATCGATA
398535 ACATGGTAGG
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
95 62 0.67
96 30 0.32
97 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (96 bp):
GTATCGATACCAAGAGAAAATTATTGATATCAGGGAATTACAGAATGTAGAAATGATATCGATAC
TAGAAGGGAGCATCGATACCATAGTATAGAA
Found at i:398952 original size:45 final size:45
Alignment explanation
Indices: 398887--399212 Score: 499
Period size: 45 Copynumber: 7.2 Consensus size: 45
398877 GTTTTAATTA
* *
398887 CATAAATGAAATGCATAACGGTGCCTTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
*
398932 CATAAATGAAATGCACAACGGTGCATTAAAGGCATGAAAGGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
* *
398977 CATAAATGAAATGCATAACGGTGCATTAAAGGAATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
* *
399022 CATAAATGAAATGCATAACGGTGCATTAAAGGAATGAAATGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
* *
399067 CATAAATTAAATGCATAACGGTGCATTAAAGGTATGAAAGGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
* * *
399112 CGTAAATGAAATGCATAACGGTGCATTAAAGACATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
** ** *
399157 CATAAATGAAATGCGCAAATGTGCATTAAAGGCATGAAATGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
399202 CATAAATGAAA
1 CATAAATGAAA
399213 ATAATGAATA
Statistics
Matches: 257, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 257 1.00
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
Found at i:404790 original size:24 final size:24
Alignment explanation
Indices: 404765--404897 Score: 160
Period size: 24 Copynumber: 5.5 Consensus size: 24
404755 AAACTGAGAT
* * *
404765 ATCAAAAATCAAAACAGAATTCAT
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
404789 ATCATATATCAGAATAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
404813 ATCAGAAATCAGAACATAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
404837 ATCAGAAATCAGAACATAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
404861 ATCAGAAATCAGAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAG
404885 ATC-GAAAATCAGA
1 ATCAG-AAATCAGA
404898 TAAAACATTC
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
23 1 0.01
24 94 0.99
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:404819 original size:12 final size:11
Alignment explanation
Indices: 404796--404880 Score: 62
Period size: 12 Copynumber: 7.2 Consensus size: 11
404786 CATATCATAT
*
404796 ATCAGAATAGA
1 ATCAGAACAGA
*
404807 ATCCAGATCAGAA
1 AT-CAGAACAG-A
*
404820 ATCAGAACATA
1 ATCAGAACAGA
*
404831 ATTCAGATCAGAA
1 A-TCAGAACAG-A
*
404844 ATCAGAACATA
1 ATCAGAACAGA
*
404855 ATTCAGATCAGAA
1 A-TCAGAACAG-A
404868 ATCAGAACAGA
1 ATCAGAACAGA
404879 AT
1 AT
404881 TCAAATCGAA
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
11 9 0.16
12 41 0.72
13 7 0.12
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (11 bp):
ATCAGAACAGA
Found at i:410164 original size:23 final size:23
Alignment explanation
Indices: 410134--410179 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
410124 TGTAAGTGAG
410134 TATTGATGGTTTTATATATCAAA
1 TATTGATGGTTTTATATATCAAA
410157 TATTGATGGTTTTATATATCAAA
1 TATTGATGGTTTTATATATCAAA
410180 CATCAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (23 bp):
TATTGATGGTTTTATATATCAAA
Found at i:411005 original size:25 final size:25
Alignment explanation
Indices: 410972--411029 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
410962 ATTTTAAAAT
410972 TAAGTTAATAATAA-AATATATTTAA
1 TAAGTTAATAATAACAA-ATATTTAA
*
410997 TAAGTTAAT-ATAACAAATATTTTA
1 TAAGTTAATAATAACAAATATTTAA
411021 -AAGTTAATA
1 TAAGTTAATA
411030 TATATATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 8 0.27
24 11 0.37
25 11 0.37
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (25 bp):
TAAGTTAATAATAACAAATATTTAA
Found at i:411032 original size:25 final size:26
Alignment explanation
Indices: 410972--411033 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
410962 ATTTTAAAAT
410972 TAAGTTAATA-ATAAAATATATTTAA
1 TAAGTTAATATATAAAATATATTTAA
410997 TAAGTTAATATA-ACAAATAT-TTT-A
1 TAAGTTAATATATA-AAATATATTTAA
411021 -AAGTTAATATATA
1 TAAGTTAATATATA
411034 TATAAAATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.32
24 2 0.06
25 14 0.41
26 7 0.21
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (26 bp):
TAAGTTAATATATAAAATATATTTAA
Found at i:415467 original size:3 final size:3
Alignment explanation
Indices: 415459--415513 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
415449 TCTAATTTGA
415459 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
415507 TAT TAT T
1 TAT TAT T
415514 TTGCTATCGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:430422 original size:186 final size:188
Alignment explanation
Indices: 430097--430470 Score: 734
Period size: 187 Copynumber: 2.0 Consensus size: 188
430087 GGCATAATTA
430097 GTCATATCAAAAGAATCTAAATGCACCATGTATATGTTTCCTATTCTATGACCAACAAGCATAAT
1 GTCATATCAAAAGAATCTAAATGCACCATGTATATGTTTCCTATTCTATGACCAACAAGCATAAT
430162 CCGATTAGATGCAATGTCATGACTTTACAACCATTAATTTCAAATAAGACATTGAATCCTTTATC
66 CCGATTAGATGCAATGTCATGACTTTACAACCATTAATTTCAAATAAGACATTGAATCCTTTATC
430227 GCATAATTGACTAATACTC-ATAGATTATGCTTTAATCCATTCACATATAAAACATTT
131 GCATAATTGACTAATACTCAATAGATTATGCTTTAATCCATTCACATATAAAACATTT
430284 GTCATATCAAAAGAATCTAAATGCACCATGTATATGTTTCCTATTCTATGACCAACAAGCATAAT
1 GTCATATCAAAAGAATCTAAATGCACCATGTATATGTTTCCTATTCTATGACCAACAAGCATAAT
430349 CCGA-TAGATGCAATGTCATGACTTTACAACCATTAATTTCAAATAAGACATTGAATCCTTTATC
66 CCGATTAGATGCAATGTCATGACTTTACAACCATTAATTTCAAATAAGACATTGAATCCTTTATC
430413 GCATAATTGACTAATACTCAATAGATTATGCTTTAATCCATTCACATATAAAACATTT
131 GCATAATTGACTAATACTCAATAGATTATGCTTTAATCCATTCACATATAAAACATTT
430471 TTAATTTGTA
Statistics
Matches: 186, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
186 79 0.42
187 107 0.58
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (188 bp):
GTCATATCAAAAGAATCTAAATGCACCATGTATATGTTTCCTATTCTATGACCAACAAGCATAAT
CCGATTAGATGCAATGTCATGACTTTACAACCATTAATTTCAAATAAGACATTGAATCCTTTATC
GCATAATTGACTAATACTCAATAGATTATGCTTTAATCCATTCACATATAAAACATTT
Found at i:433510 original size:12 final size:12
Alignment explanation
Indices: 433493--433532 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
433483 TTGTCGTTTC
*
433493 CCGTCCCCGTCT
1 CCGTCCCCGTAT
433505 CCGTCCCCGTAT
1 CCGTCCCCGTAT
*
433517 CCGTCCCTGTAT
1 CCGTCCCCGTAT
433529 CCGT
1 CCGT
433533 ATCAGTGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.05, C:0.50, G:0.17, T:0.28
Consensus pattern (12 bp):
CCGTCCCCGTAT
Found at i:433757 original size:22 final size:22
Alignment explanation
Indices: 433702--433743 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
433692 ATTGAACTAT
433702 ATATAAACTATATAATTTATTA
1 ATATAAACTATATAATTTATTA
* *
433724 ATATAAATTATATAGTTTAT
1 ATATAAACTATATAATTTAT
433744 ATAGTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATAAACTATATAATTTATTA
Found at i:433826 original size:8 final size:8
Alignment explanation
Indices: 433810--433879 Score: 51
Period size: 8 Copynumber: 9.1 Consensus size: 8
433800 ATGAATACTA
*
433810 AAGTCTAT
1 AAGTATAT
433818 AAGTATAT
1 AAGTATAT
433826 AA-TATA-
1 AAGTATAT
* *
433832 AAATATAA
1 AAGTATAT
433840 AAGTATAT
1 AAGTATAT
433848 AAAGTATAT
1 -AAGTATAT
*
433857 ATA-CATAT
1 A-AGTATAT
433865 AAG--TAT
1 AAGTATAT
433871 AAGTATAT
1 AAGTATAT
433879 A
1 A
433880 TATAAACTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
6 8 0.16
7 9 0.18
8 25 0.49
9 9 0.18
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (8 bp):
AAGTATAT
Found at i:433833 original size:22 final size:20
Alignment explanation
Indices: 433775--433833 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 20
433765 GAATTATATA
433775 TATAATATAT-ATATAAAG-
1 TATAATATATAATATAAAGT
433793 TATAAT-TATGAATACTAAAGT
1 TATAATATAT-AATA-TAAAGT
433814 CTATAAGTATATAATATAAA
1 -TATAA-TATATAATATAAA
433834 ATATAAAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 3 0.09
18 6 0.18
19 3 0.09
20 5 0.15
22 9 0.26
23 5 0.15
24 3 0.09
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (20 bp):
TATAATATATAATATAAAGT
Found at i:433843 original size:22 final size:22
Alignment explanation
Indices: 433818--433907 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
433808 TAAAGTCTAT
433818 AAGTATATAATATAAAATATAA
1 AAGTATATAATATAAAATATAA
433840 AAGTATATAAAGTATATATACATATAAGTA
1 AAGTATAT-AA-TATA-A-A-ATAT-A--A
*
433870 TAAGTATAT-ATATAAACTATAA
1 -AAGTATATAATATAAAATATAA
433892 AACGTATATATATATA
1 AA-GTATATA-ATATA
433908 TATATATATA
Statistics
Matches: 55, Mismatches: 1, Indels: 22
0.71 0.01 0.28
Matches are distributed among these distances:
21 2 0.04
22 15 0.27
23 2 0.04
24 10 0.18
25 4 0.07
26 2 0.04
27 5 0.09
28 5 0.09
29 1 0.02
30 1 0.02
31 8 0.15
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (22 bp):
AAGTATATAATATAAAATATAA
Found at i:433855 original size:59 final size:53
Alignment explanation
Indices: 433815--433917 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 53
433805 TACTAAAGTC
433815 TATAAGTATATAATATAAAATATAAAA-GTATATAAAGTATATATACATATAAG
1 TATAAGTATAT-ATATAAAATATAAAACGTATATAAAGTATATATACATATAAG
* * *
433868 TATAAGTATATATATAAACTATAAAACGTATATATA-TATATATATATATA
1 TATAAGTATATATATAAAATATAAAACGTATATAAAGTATATATACATATA
433918 TTGTTATGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 27 0.59
53 19 0.41
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (53 bp):
TATAAGTATATATATAAAATATAAAACGTATATAAAGTATATATACATATAAG
Found at i:435446 original size:2 final size:2
Alignment explanation
Indices: 435439--435465 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
435429 ATGGGTGATG
435439 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
435466 AAGTATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:435503 original size:8 final size:8
Alignment explanation
Indices: 435486--435583 Score: 120
Period size: 8 Copynumber: 13.1 Consensus size: 8
435476 ATAACGATTA
435486 AAGTATAT
1 AAGTATAT
*
435494 AAGCATAT
1 AAGTATAT
435502 AA-TATA-
1 AAGTATAT
435508 AAGTATAT
1 AAGTATAT
435516 AAGTAT-T
1 AAGTATAT
*
435523 AAATATA-
1 AAGTATAT
435530 AAGTATAT
1 AAGTATAT
*
435538 AAGCATAT
1 AAGTATAT
435546 AA-TATA-
1 AAGTATAT
435552 AAGTATAT
1 AAGTATAT
435560 AAGTAT-T
1 AAGTATAT
435567 AAGTATAT
1 AAGTATAT
435575 AAGTATAT
1 AAGTATAT
435583 A
1 A
435584 TATAAACTAC
Statistics
Matches: 77, Mismatches: 6, Indels: 14
0.79 0.06 0.14
Matches are distributed among these distances:
6 4 0.05
7 33 0.43
8 40 0.52
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (8 bp):
AAGTATAT
Found at i:435509 original size:22 final size:21
Alignment explanation
Indices: 435484--435583 Score: 137
Period size: 22 Copynumber: 4.5 Consensus size: 21
435474 TTATAACGAT
435484 TAAAGTATATAAGCATATAATA
1 TAAAGTATATAAGCAT-TAATA
*
435506 TAAAGTATATAAGTATTAAATA
1 TAAAGTATATAAGCATT-AATA
435528 TAAAGTATATAAGCATATAATA
1 TAAAGTATATAAGCAT-TAATA
*
435550 TAAAGTATATAAGTATTAAGTA
1 TAAAGTATATAAGCATTAA-TA
435572 TATAAGTATATA
1 TA-AAGTATATA
435584 TATAAACTAC
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
21 4 0.06
22 57 0.80
23 10 0.14
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (21 bp):
TAAAGTATATAAGCATTAATA
Found at i:435532 original size:44 final size:44
Alignment explanation
Indices: 435484--435583 Score: 182
Period size: 44 Copynumber: 2.2 Consensus size: 44
435474 TTATAACGAT
435484 TAAAGTATATAAGCATATAATATAAAGTATATAAGTATTAAATA
1 TAAAGTATATAAGCATATAATATAAAGTATATAAGTATTAAATA
*
435528 TAAAGTATATAAGCATATAATATAAAGTATATAAGTATTAAGTA
1 TAAAGTATATAAGCATATAATATAAAGTATATAAGTATTAAATA
435572 TATAAGTATATA
1 TA-AAGTATATA
435584 TATAAACTAC
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 45 0.83
45 9 0.17
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (44 bp):
TAAAGTATATAAGCATATAATATAAAGTATATAAGTATTAAATA
Found at i:435570 original size:15 final size:15
Alignment explanation
Indices: 435486--435580 Score: 106
Period size: 15 Copynumber: 6.4 Consensus size: 15
435476 ATAACGATTA
*
435486 AAGTATATAAGCATAT
1 AAGTAT-TAAGTATAT
*
435502 AA-TATAAAGTATAT
1 AAGTATTAAGTATAT
*
435516 AAGTATTAAATATA-
1 AAGTATTAAGTATAT
*
435530 AAGTATATAAGCATAT
1 AAGTAT-TAAGTATAT
*
435546 AA-TATAAAGTATAT
1 AAGTATTAAGTATAT
435560 AAGTATTAAGTATAT
1 AAGTATTAAGTATAT
435575 AAGTAT
1 AAGTAT
435581 ATATATAAAC
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
14 24 0.36
15 38 0.58
16 4 0.06
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.35
Consensus pattern (15 bp):
AAGTATTAAGTATAT
Found at i:435623 original size:14 final size:15
Alignment explanation
Indices: 435598--435917 Score: 88
Period size: 13 Copynumber: 22.3 Consensus size: 15
435588 AACTACAAAG
435598 TATATATATATACTT
1 TATATATATATACTT
435613 TATAT-TATATAC-T
1 TATATATATATACTT
* *
435626 TATACACTTTAGT-CTT
1 TATATA-TATA-TACTT
*
435642 TATA-AT-TATACTC
1 TATATATATATACTT
*
435655 TATATATACATA--T
1 TATATATATATACTT
*
435668 AATATACT-TATA-TT
1 TATATA-TATATACTT
** *
435682 T-TATAT-TATTGTA
1 TATATATATATACTT
* *
435695 TATATATATATGCAT
1 TATATATATATACTT
435710 TATACTA-A-A-ACTT
1 TATA-TATATATACTT
*
435723 ATATATATATATAC-A
1 -TATATATATATACTT
* * *
435738 CACACACTTATATACTT
1 TATATA--TATATACTT
435755 TATAT-TATATAC-T
1 TATATATATATACTT
* *
435768 TATATACTTTATTCTT
1 TATATA-TATATACTT
*
435784 TATA-AT-TATTCTTT
1 TATATATATATAC-TT
435798 TGATTATATAATATAC-T
1 T-A-TATAT-ATATACTT
*
435815 TATA-CT-TATACTT
1 TATATATATATACTT
*
435828 TATAT-TAT-TA-TA
1 TATATATATATACTT
* *
435840 TATGTATATATAATT
1 TATATATATATACTT
435855 TATACTA-A-A-ACTT
1 TATA-TATATATACTT
*
435868 TATATATATATA-TA
1 TATATATATATACTT
435882 TATATACTTATATACTT
1 TATATA--TATATACTT
435899 TATAT-TATATACTT
1 TATATATATATACTT
435913 GTATA
1 -TATA
435918 CTTTATATTA
Statistics
Matches: 227, Mismatches: 35, Indels: 86
0.65 0.10 0.25
Matches are distributed among these distances:
12 17 0.07
13 61 0.27
14 59 0.26
15 41 0.18
16 33 0.15
17 12 0.05
19 4 0.02
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.50
Consensus pattern (15 bp):
TATATATATATACTT
Found at i:435623 original size:22 final size:22
Alignment explanation
Indices: 435598--435687 Score: 66
Period size: 22 Copynumber: 4.2 Consensus size: 22
435588 AACTACAAAG
435598 TATATATATATACTTTATATTA
1 TATATATATATACTTTATATTA
* *
435620 TATACT-TATACACTTTAGTCTT-
1 TATA-TATATATACTTTA-TATTA
*
435642 TATA-AT-TATACTCTATA-TA
1 TATATATATATACTTTATATTA
* *
435661 TACATATAATATAC-TTATATTT
1 TATATAT-ATATACTTTATATTA
435683 TATAT
1 TATAT
435688 TATTGTATAT
Statistics
Matches: 51, Mismatches: 9, Indels: 16
0.67 0.12 0.21
Matches are distributed among these distances:
18 1 0.02
19 4 0.08
20 9 0.18
21 5 0.10
22 28 0.55
23 4 0.08
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (22 bp):
TATATATATATACTTTATATTA
Found at i:435765 original size:142 final size:144
Alignment explanation
Indices: 435604--435922 Score: 450
Period size: 144 Copynumber: 2.2 Consensus size: 144
435594 AAAGTATATA
*
435604 TATATACTTTATATTATATACTTATACACTTTAGTCTTTATAATTATAC-TCT-A-TATATACAT
1 TATATACTTTATATTATATACTTATATACTTTAGTCTTTATAATTATACTTCTGATTATATA-AT
* * *
435666 ATA-ATATACTTATATTTTATATTATTGTATATATATATATGCA-TTATACTAAAACTTATATAT
65 ATACATATACTTATACTTTATATTATTATATATATATATAT-AATTTATACTAAAACTT-TATAT
435729 ATATATACACACACACT
128 ATATATACACACACACT
* * *
435746 TATATACTTTATATTATATACTTATATACTTTATTCTTTATAATTATTCTTTTGATTATATAATA
1 TATATACTTTATATTATATACTTATATACTTTAGTCTTTATAATTATACTTCTGATTATATAATA
* *
435811 TACTTATACTTATACTTTATATTATTATATATGTATATATAATTTATACTAAAACTTTATATATA
66 TACATATACTTATACTTTATATTATTATATATATATATATAATTTATACTAAAACTTTATATATA
* * * *
435876 TATATATATATACT
131 TATACACACACACT
*
435890 TATATACTTTATATTATATACTTGTATACTTTA
1 TATATACTTTATATTATATACTTATATACTTTA
435923 TATTATTACA
Statistics
Matches: 158, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
142 46 0.29
143 2 0.01
144 57 0.36
145 53 0.34
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (144 bp):
TATATACTTTATATTATATACTTATATACTTTAGTCTTTATAATTATACTTCTGATTATATAATA
TACATATACTTATACTTTATATTATTATATATATATATATAATTTATACTAAAACTTTATATATA
TATACACACACACT
Found at i:435768 original size:22 final size:22
Alignment explanation
Indices: 435743--436066 Score: 136
Period size: 22 Copynumber: 14.9 Consensus size: 22
435733 ATACACACAC
435743 ACTTATATACTTTATATTATAT
1 ACTTATATACTTTATATTATAT
*
435765 ACTTATATACTTTAT-TCTTTAT
1 ACTTATATACTTTATAT-TATAT
*
435787 AATTAT-T-CTTT-TGATTATAT
1 ACTTATATACTTTAT-ATTATAT
*
435807 A---ATATAC-TTATACT-TAT
1 ACTTATATACTTTATATTATAT
* *
435824 ACTT-TATATTATTATA-TATGT
1 ACTTATATACT-TTATATTATAT
* * *
435845 A--TATATAATTTATACTA-AA
1 ACTTATATACTTTATATTATAT
*
435864 ACTTTATATA-TATATATATATAT
1 AC-TTATATACTTTATAT-TATAT
435887 ACTTATATACTTTATATTATAT
1 ACTTATATACTTTATATTATAT
*
435909 ACTTGTATACTTTATATTATTACAT
1 ACTTATATACTTTATATTA-T--AT
* * *
435934 ACCTATAGACACTTTATACTA-A-
1 A-CT-TATATACTTTATATTATAT
*
435956 AGCTTTAATATA-TATATATATATAT
1 A-C-TT-ATATACTTTATAT-TATAT
* *
435981 ACTTTTATATTTTATATTATAT
1 ACTTATATACTTTATATTATAT
* *
436003 A-TGTATATACTTTAGTCTT-TGT
1 ACT-TATATACTTTA-TATTATAT
*
436025 A-AT-TATACTTTATA-TATAT
1 ACTTATATACTTTATATTATAT
*
436044 AATATACCTATACTTTATATTAT
1 ACT-TA--TATACTTTATATTAT
436067 TATATAAAGT
Statistics
Matches: 229, Mismatches: 33, Indels: 77
0.68 0.10 0.23
Matches are distributed among these distances:
17 6 0.03
18 6 0.03
19 18 0.08
20 26 0.11
21 19 0.08
22 92 0.40
23 28 0.12
24 13 0.06
25 7 0.03
26 2 0.01
27 12 0.05
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (22 bp):
ACTTATATACTTTATATTATAT
Found at i:435850 original size:44 final size:42
Alignment explanation
Indices: 435802--435981 Score: 108
Period size: 40 Copynumber: 4.2 Consensus size: 42
435792 TTCTTTTGAT
*
435802 TATATA-ATATACTTATACTTATACTTTATATTATTATATATG
1 TATATATATATACTTATACTTATACTTTATA-TATTATATATA
* *
435844 TATATATA-AT--TTATACTAAAACTTTATATA-TATATATA
1 TATATATATATACTTATACTTATACTTTATATATTATATATA
*
435882 TATATACTTATATACTTTATATTATATACTTGTATACT-TTATATTATTA
1 TATATA--TATATAC-TTATACT-TATACTT-TATA-TATTATA-TA-TA
* * * *
435931 CATACCTATAGACACTTTATAC-TAAAGCTTTA-ATA-TATATATA
1 TATA--TATATATAC-TTATACTTATA-CTTTATATATTATATATA
435974 TATATATA
1 TATATATA
435982 CTTTTATATT
Statistics
Matches: 109, Mismatches: 12, Indels: 35
0.70 0.08 0.22
Matches are distributed among these distances:
38 13 0.12
39 2 0.02
40 18 0.17
41 6 0.06
42 8 0.07
43 6 0.06
44 8 0.07
45 10 0.09
46 5 0.05
47 10 0.09
48 5 0.05
49 16 0.15
51 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (42 bp):
TATATATATATACTTATACTTATACTTTATATATTATATATA
Found at i:435869 original size:40 final size:38
Alignment explanation
Indices: 435802--435887 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
435792 TTCTTTTGAT
* * *
435802 TATATA-ATAT-ACTTATACTTATACTTTATATTATTATA
1 TATATATATATAATTTATACTAAAACTTTATA-TA-TATA
*
435840 TATGTATATATAATTTATACTAAAACTTTATATATATA
1 TATATATATATAATTTATACTAAAACTTTATATATATA
435878 TATATATATA
1 TATATATATA
435888 CTTATATACT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 18 0.44
39 6 0.15
40 17 0.41
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (38 bp):
TATATATATATAATTTATACTAAAACTTTATATATATA
Found at i:435924 original size:15 final size:15
Alignment explanation
Indices: 435743--435924 Score: 85
Period size: 14 Copynumber: 12.6 Consensus size: 15
435733 ATACACACAC
435743 ACTTATATACTTTAT
1 ACTTATATACTTTAT
435758 A-TTATATACTTATAT
1 ACTTATATACTT-TAT
*
435773 ACTT-TATTCTTTAT
1 ACTTATATACTTTAT
*
435787 AATTAT-T-CTTT-T
1 ACTTATATACTTTAT
*
435799 GA-TTATATA--ATAT
1 -ACTTATATACTTTAT
435812 AC-T-TATAC-TTAT
1 ACTTATATACTTTAT
435824 ACTTTATATTA-TTATAT
1 AC-TTATA-TACTT-TAT
* *
435841 ATGTATATATAATTTAT
1 A-CT-TATATACTTTAT
*
435858 AC-TA-AAACTTTAT
1 ACTTATATACTTTAT
435871 A-TATATATA-TATATAT
1 ACT-TATATACT-T-TAT
435887 ACTTATATACTTTAT
1 ACTTATATACTTTAT
435902 A-TTATATACTTGTAT
1 ACTTATATACTT-TAT
435917 ACTT-TATA
1 ACTTATATA
435925 TTATTACATA
Statistics
Matches: 131, Mismatches: 9, Indels: 54
0.68 0.05 0.28
Matches are distributed among these distances:
11 4 0.03
12 13 0.10
13 15 0.11
14 33 0.25
15 29 0.22
16 18 0.14
17 13 0.10
18 6 0.05
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (15 bp):
ACTTATATACTTTAT
Found at i:436001 original size:94 final size:93
Alignment explanation
Indices: 435821--436016 Score: 277
Period size: 94 Copynumber: 2.1 Consensus size: 93
435811 TACTTATACT
* ** * *
435821 TATACTTTATATTATTATATATGTATATATAATTTATACTAAAACTTTATATATATATATATATA
1 TATACTTTATATTATTACATACCTATAGACAATTTATACTAAAACTTTATATATATATATATATA
*
435886 TACTTATATACTTTATATTATATACT-TG
66 TACTTATATACTTTATATTATATA-TGTA
* *
435914 TATACTTTATATTATTACATACCTATAGACACTTTATACTAAAGCTTTAATATATATATATATAT
1 TATACTTTATATTATTACATACCTATAGACAATTTATACTAAAACTTT-ATATATATATATATAT
* *
435979 ATACTTTTATATTTTATATTATATATGTA
65 ATACTTATATACTTTATATTATATATGTA
436008 TATACTTTA
1 TATACTTTA
436017 GTCTTTGTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
93 42 0.46
94 49 0.54
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.51
Consensus pattern (93 bp):
TATACTTTATATTATTACATACCTATAGACAATTTATACTAAAACTTTATATATATATATATATA
TACTTATATACTTTATATTATATATGTA
Found at i:436031 original size:30 final size:30
Alignment explanation
Indices: 435866--436015 Score: 92
Period size: 30 Copynumber: 4.8 Consensus size: 30
435856 ATACTAAAAC
* *
435866 TTTATATATATATATATATATACTTATATAC
1 TTTATAT-TATATATATATATACTTTTATAT
*
435897 TTTATATTATATACT-TGTATAC-TTTATAT
1 TTTATATTATATA-TATATATACTTTTATAT
* * ** * *
435926 TAT-TA-CATACCTATAGACACTTTATACTAAAGCT
1 TTTATATTATATATATATATACTTT-TA-T--A--T
*
435960 TTAATATATATATATATATATACTTTTATAT
1 TTTATAT-TATATATATATATACTTTTATAT
*
435991 TTTATATTATATATGTATATACTTT
1 TTTATATTATATATATATATACTTT
436016 AGTCTTTGTA
Statistics
Matches: 88, Mismatches: 19, Indels: 25
0.67 0.14 0.19
Matches are distributed among these distances:
26 1 0.01
27 7 0.08
28 4 0.05
29 9 0.10
30 30 0.34
31 15 0.17
32 1 0.01
33 1 0.01
34 2 0.02
35 3 0.03
36 2 0.02
37 13 0.15
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (30 bp):
TTTATATTATATATATATATACTTTTATAT
Found at i:436055 original size:24 final size:23
Alignment explanation
Indices: 436028--436072 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
436018 TCTTTGTAAT
436028 TATACTTTATATATATAATATACC
1 TATACTTTATAT-TATAATATACC
*
436052 TATACTTTATATTATTATATA
1 TATACTTTATATTATAATATA
436073 AAGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (23 bp):
TATACTTTATATTATAATATACC
Found at i:436154 original size:7 final size:7
Alignment explanation
Indices: 436100--436154 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
436090 ACTAAAACTT
436100 TATAT-A
1 TATATAA
436106 TATATATA
1 TATATA-A
436114 TATATAA
1 TATATAA
436121 -AGTATAAA
1 TA-TAT-AA
*
436129 TATAAAA
1 TATATAA
436136 TATATAA
1 TATATAA
*
436143 CATATAA
1 TATATAA
436150 TATAT
1 TATAT
436155 TTAAAGTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
6 6 0.15
7 22 0.55
8 11 0.28
9 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (7 bp):
TATATAA
Found at i:436201 original size:24 final size:24
Alignment explanation
Indices: 436174--436252 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 24
436164 TAGTATAAAG
*
436174 TATACATACTTTATAGTTTATATA
1 TATATATACTTTATAGTTTATATA
* *
436198 TATATACACTTTATAATTTA-A-A
1 TATATATACTTTATAGTTTATATA
* *
436220 GTATATATACCTTATAGTTTTTATA
1 -TATATATACTTTATAGTTTATATA
436245 TATATATA
1 TATATATA
436253 TATATTATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
22 1 0.02
23 17 0.38
24 26 0.58
25 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (24 bp):
TATATATACTTTATAGTTTATATA
Found at i:436252 original size:51 final size:47
Alignment explanation
Indices: 436169--436268 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 47
436159 AGTTTTAGTA
*
436169 TAAAGTATACATACTTTATAGTTTATATATATATACACTT-TATAATT
1 TAAAGTATACATACCTTATAGTTTATATATATATACA-TTATATAATT
* *
436216 TAAAGTATATATACCTTATAGTTTTTATATATATATATATATTATATAATT
1 TAAAGTATACATACCTTATAG---TT-TATATATATATACATTATATAATT
436267 TA
1 TA
436269 TTGTTTACAC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
47 19 0.42
50 4 0.09
51 22 0.49
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (47 bp):
TAAAGTATACATACCTTATAGTTTATATATATATACATTATATAATT
Found at i:436284 original size:49 final size:47
Alignment explanation
Indices: 436169--436284 Score: 110
Period size: 49 Copynumber: 2.4 Consensus size: 47
436159 AGTTTTAGTA
* * *
436169 TAAAGTATACATACTTTATAGTTTATATATATATACACTTTATAATT
1 TAAAGTATATACACTTTATAGTTTATATATATATACAATTTATAATT
* * *
436216 TAAAGTATATATACCTTATAGTTTTTATATATATATATATATTATATAATT
1 TAAAGTATATACACTTTATAG--TTTATATATATATACA-ATT-TATAATT
**
436267 TATTGT-T-TACACTTTATA
1 TAAAGTATATACACTTTATA
436285 TATATACTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
47 19 0.33
49 24 0.42
50 3 0.05
51 11 0.19
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (47 bp):
TAAAGTATATACACTTTATAGTTTATATATATATACAATTTATAATT
Found at i:436883 original size:2 final size:2
Alignment explanation
Indices: 436864--436897 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
436854 AAAGTATAAG
* *
436864 TA TA TA TG TA TA TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
436898 AAGTATAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:436890 original size:14 final size:14
Alignment explanation
Indices: 436858--436920 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
436848 AACTATAAAG
* *
436858 TATAAGTATATATG
1 TATATGTATATATA
436872 TATATGTATATATA
1 TATATGTATATATA
* *
436886 TATATATATATAAA
1 TATATGTATATATA
*
436900 GTATAATGTACAT-TA
1 -TAT-ATGTATATATA
436915 TATATG
1 TATATG
436921 CATGCATCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
13 3 0.08
14 27 0.68
15 4 0.10
16 6 0.15
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (14 bp):
TATATGTATATATA
Found at i:437023 original size:531 final size:525
Alignment explanation
Indices: 436373--437431 Score: 1593
Period size: 531 Copynumber: 2.0 Consensus size: 525
436363 ATCTATGCAT
*
436373 AAGTATAATGTACATTATATATACATGCATCATATAATCTAACATACATTATATTTGTTTTAATT
1 AAGTATAATGTACATTATATATACATGCATCATATAATCTAACATACATTATATTTATTTTAATT
436438 TTCCCCAACTTTTGAAATTAATGCAATTCAGTACATTTTACAATTTTCCTCACATTTTACAATTT
66 TTCCCCAACTTTTGAAATTAATGCAATTCAGTACATTTTACAATTTTCCTCACATTTTACAATTT
* *
436503 -TTTTATTTGATCATTTTATGTTATTTA-TTGTTTAAATTTTAA-TTTGTAATTTCATATTAGTT
131 CTTTGATTTGATCATTTTAT-TT-TTTATTTATTTAAA-TTTAATTTTGTAATTTCATATT-GTT
436565 CAATTTAGTCCTTCAAATTATATTTGTATCTGAAATTGACCC-TTACTTATTTATATTTTTGTAA
192 CAATTTAGTCCTTCAAATTATATTTGTATCTGAAATTGACCCATT-CTTATTTATATTTTTGTAA
** **
436629 TTTACTTAAAGCCCTATAAAATGTAAATCACATAATAAATTTCTTTTCAGTTTATGTTCACCAAC
256 TTTACTTAAA-AACTATAAAATGTAAATCACATAATAAATTTCTTTTCAAATTATGTTCACCAAC
**
436694 TTTTTAAATGTATGCAATTTAGTCC-TGTTATATTAATATCAGTTTCACATTTTATAATTAATTC
320 TTTTTAAATGTATGCAATTTAGTCCATGTTATATTAATATCAACTT-ACATTTTATAATTAATTC
* *
436758 AATTTCATCCCTCATCAATTCGTGTTGTTTAATTTATTCAATTTTTTATTTCCAATTTCATG-T-
384 AATTTCATCCCTCATCAATGCGTGATGTTTAATTTATTCAATTTTTTATTTCCAATTTCATGTTG
* * *
436821 TT-AATTTGGTACTCTAT-TACATATATAAACTATAAAGTATA-AGTATATATGTATATGTATAT
449 TTCAATTTGGCACTCTATATACATATATAAA-TATAAA-TATATA-TATATATATATATATATAT
436883 ATATATATATATATA
511 ATATATATATATATA
* * *
436898 AAGTATAATGTACATTATATATGCATGCATCATATTAT-TAACATTCATTATATGTATTATATAT
1 AAGTATAATGTACATTATATATACATGCATCATATAATCTAACATACA-T-TA--TA-T-T-TAT
*
436962 TTTAATTTTCCCCAACTTTTGAAATTAATGCAATTCAGT-CAATTTTACAATTTTTCTCACATTT
59 TTTAATTTTCCCCAACTTTTGAAATTAATGCAATTCAGTAC-ATTTTACAATTTTCCTCACATTT
* *
437026 TACAATTTCTTTGATTTGATCCTTTTATTTTTTATTTTATTTAAATTTAATTTTTTAATTTCATA
123 TACAATTTCTTTGATTTGATCATTTTATTTTTTA-TTTATTTAAATTTAATTTTGTAATTTCATA
* *
437091 TTTTTCAATTTAGTCCTTCAAATTATATTTGTATCTGAAATTGACCCATTCTTCTTTATATTTTT
187 TTGTTCAATTTAGTCCTTCAAATTATATTTGTATCTGAAATTGACCCATTCTTATTTATATTTTT
*
437156 GTAATTTACTTAAAAACTATAAAATGTAAATTACATAATAAATTTCTTTTCAAATTATGTTCACC
252 GTAATTTACTTAAAAACTATAAAATGTAAATCACATAATAAATTTCTTTTCAAATTATGTTCACC
*
437221 AACTTTTTAAATGTATGCAATTTAGTCCATTTTTATATTAATATCAACTTACATTTTATAATTAA
317 AACTTTTTAAATGTATGCAATTTAGTCCA-TGTTATATTAATATCAACTTACATTTTATAATTAA
437286 TTCAATTTCATCCCTCATCAATGCGTGATGTTTAATTTATTCAATTTTTTATTTCCAATTTCATG
381 TTCAATTTCATCCCTCATCAATGCGTGATGTTTAATTTATTCAATTTTTTATTTCCAATTTCATG
* * * *
437351 TTTGTTCAATTTGGCACTTTATATATATATATATATATATATATATATATATATATATATATATA
446 -TTGTTCAATTTGGCACTCTATATACATATATAAATATAAATATATATATATATATATATATATA
437416 TATATATATATATATA
510 TATATATATATATATA
437432 TATATATATA
Statistics
Matches: 485, Mismatches: 28, Indels: 33
0.89 0.05 0.06
Matches are distributed among these distances:
524 8 0.02
525 37 0.08
526 2 0.00
528 2 0.00
529 1 0.00
530 80 0.16
531 228 0.47
532 59 0.12
533 1 0.00
534 38 0.08
535 19 0.04
536 10 0.02
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.49
Consensus pattern (525 bp):
AAGTATAATGTACATTATATATACATGCATCATATAATCTAACATACATTATATTTATTTTAATT
TTCCCCAACTTTTGAAATTAATGCAATTCAGTACATTTTACAATTTTCCTCACATTTTACAATTT
CTTTGATTTGATCATTTTATTTTTTATTTATTTAAATTTAATTTTGTAATTTCATATTGTTCAAT
TTAGTCCTTCAAATTATATTTGTATCTGAAATTGACCCATTCTTATTTATATTTTTGTAATTTAC
TTAAAAACTATAAAATGTAAATCACATAATAAATTTCTTTTCAAATTATGTTCACCAACTTTTTA
AATGTATGCAATTTAGTCCATGTTATATTAATATCAACTTACATTTTATAATTAATTCAATTTCA
TCCCTCATCAATGCGTGATGTTTAATTTATTCAATTTTTTATTTCCAATTTCATGTTGTTCAATT
TGGCACTCTATATACATATATAAATATAAATATATATATATATATATATATATATATATATATAT
ATATA
Found at i:437473 original size:14 final size:14
Alignment explanation
Indices: 437456--437618 Score: 70
Period size: 14 Copynumber: 11.3 Consensus size: 14
437446 TATATATATA
437456 TATAAAGTATAAAG
1 TATAAAGTATAAAG
437470 TATATAA-TATAAAG
1 TATA-AAGTATAAAG
* **
437484 TAATAAAGTGT-TTG
1 T-ATAAAGTATAAAG
* *
437498 GATATAAGTATTAAAA
1 TATA-AAGTA-TAAAG
*
437514 TATATAAATAT-AAG
1 TATA-AAGTATAAAG
437528 TATTAAA-TATAAAG
1 TA-TAAAGTATAAAG
*
437542 TATATAAATATATAAG
1 TATA-AAGTATA-AAG
437558 TACTAAAGTATATAA-
1 TA-TAAAGTATA-AAG
*
437573 TATAAAGTATTAAAC
1 TATAAAGTA-TAAAG
* *
437588 TATATATTAT-AAG
1 TATAAAGTATAAAG
*
437601 TATTAAA-TATAAAA
1 TA-TAAAGTATAAAG
437615 TATA
1 TATA
437619 TTAATTATCA
Statistics
Matches: 116, Mismatches: 17, Indels: 33
0.70 0.10 0.20
Matches are distributed among these distances:
13 17 0.15
14 49 0.42
15 26 0.22
16 22 0.19
17 2 0.02
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (14 bp):
TATAAAGTATAAAG
Found at i:437473 original size:22 final size:20
Alignment explanation
Indices: 437370--437553 Score: 136
Period size: 20 Copynumber: 8.8 Consensus size: 20
437360 TTTGGCACTT
* *
437370 TATATATATATATATATATA
1 TATATATATAAATATAAATA
* *
437390 TATATATATATATATATATA
1 TATATATATAAATATAAATA
* *
437410 TATATATATATATATATATA
1 TATATATATAAATATAAATA
* *
437430 TATATATATATATATATATA
1 TATATATATAAATATAAATA
437450 TATATATATAAAGTATAAAGTA
1 TATATATATAAA-TATAAA-TA
*
437472 TATA-ATATAAAGTAATAAAGTG
1 TATATATATAAA-T-ATAAA-TA
* ** *
437494 TTTGGATATAAGTATTAAAATA
1 TATATATATAAATA-T-AAATA
* *
437516 TATAAATATAAGTATTAAATA
1 TATATATATAAATA-TAAATA
*
437537 TAAAGTATATAAATATA
1 TATA-TATATAAATATA
437554 TAAGTACTAA
Statistics
Matches: 144, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
20 71 0.49
21 25 0.17
22 39 0.27
23 9 0.06
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
TATATATATAAATATAAATA
Found at i:437475 original size:2 final size:2
Alignment explanation
Indices: 437370--437459 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
437360 TTTGGCACTT
437370 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
437412 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
437454 TA TA TA
1 TA TA TA
437460 AAGTATAAAG
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:437546 original size:96 final size:93
Alignment explanation
Indices: 437446--437618 Score: 242
Period size: 96 Copynumber: 1.8 Consensus size: 93
437436 TATATATATA
* * * *
437446 TATATATATATATAAAGTA-TAAAGTATATAATATAAAGTAATAAAGTGTTTGGA-TATAAGTAT
1 TATATAAATATAT-AAGTACTAAAGTATATAATATAAAGTAATAAACTATAT--ATTATAAGTAT
437509 TAAAATATATAAATATAAGTATTAAATATAAAG
63 T-AAATATA-AAATATAAGTATTAAATATAAAG
*
437542 TATATAAATATATAAGTACTAAAGTATATAATATAAAGTATTAAACTATATATTATAAGTATTAA
1 TATATAAATATATAAGTACTAAAGTATATAATATAAAGTAATAAACTATATATTATAAGTATTAA
437607 ATATAAAATATA
66 ATATAAAATATA
437619 TTAATTATCA
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
93 7 0.10
94 8 0.11
95 15 0.21
96 40 0.57
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (93 bp):
TATATAAATATATAAGTACTAAAGTATATAATATAAAGTAATAAACTATATATTATAAGTATTAA
ATATAAAATATAAGTATTAAATATAAAG
Found at i:437569 original size:22 final size:21
Alignment explanation
Indices: 437512--437619 Score: 58
Period size: 21 Copynumber: 4.6 Consensus size: 21
437502 TAAGTATTAA
437512 AATATATAA-ATATAAGTATTA
1 AATATA-AATATATAAGTATTA
*
437533 AATATAAAGTATATAAATATATA
1 AATATAAA-TATATAAGTAT-TA
*
437556 AGTACTAAAGTATATAATATAAAGTATTA
1 A--A-T--A-TAAAT-ATAT-AAGTATTA
*
437585 AACTATATAT-TATAAGTATTA
1 AA-TATAAATATATAAGTATTA
437606 AATATAAAATATAT
1 AATAT-AAATATAT
437620 TAATTATCAT
Statistics
Matches: 70, Mismatches: 4, Indels: 25
0.71 0.04 0.25
Matches are distributed among these distances:
20 5 0.07
21 19 0.27
22 15 0.21
23 3 0.04
24 5 0.07
25 2 0.03
26 1 0.01
27 3 0.04
28 2 0.03
29 10 0.14
30 5 0.07
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (21 bp):
AATATAAATATATAAGTATTA
Found at i:437603 original size:21 final size:20
Alignment explanation
Indices: 437381--437618 Score: 99
Period size: 22 Copynumber: 11.6 Consensus size: 20
437371 ATATATATAT
*
437381 ATATATATATATATA-TATATAT
1 ATATATA-ATATA-AGTAT-TAA
*
437403 ATATATATATATATA-TATATAT
1 ATATATA-ATATA-AGTAT-TAA
*
437425 ATATATATATATATA-TATATAT
1 ATATATA-ATATA-AGTAT-TAA
437447 ATATATATATATAAAGTA-TAA
1 ATATATA-ATAT-AAGTATTAA
*
437468 AGTATATAATATAAAGTAATAA
1 A-TATATAATAT-AAGTATTAA
* * *
437490 AGTGTTTGGATATAAGTATTAAA
1 A-TATAT-AATATAAGTATT-AA
437513 ATATATAAATATAAGTATT--
1 ATATAT-AATATAAGTATTAA
437532 A-A-AT-ATA-AAGTA-T--
1 ATATATAATATAAGTATTAA
* *
437545 ATAAAT-ATATAAGTACTAA
1 ATATATAATATAAGTATTAA
437564 AGTATATAATATAAAGTATTAA
1 A-TATATAATAT-AAGTATTAA
*
437586 ACTATATATTATAAGTATTAA
1 A-TATATAATATAAGTATTAA
*
437607 ATATAAAATATA
1 ATATATAATATA
437619 TTAATTATCA
Statistics
Matches: 186, Mismatches: 15, Indels: 32
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.01
14 6 0.03
15 8 0.04
16 5 0.03
17 3 0.02
18 1 0.01
19 2 0.01
20 13 0.07
21 27 0.15
22 109 0.59
23 10 0.05
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (20 bp):
ATATATAATATAAGTATTAA
Found at i:437638 original size:21 final size:20
Alignment explanation
Indices: 437613--437677 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
437603 TTAAATATAA
437613 AATATATTAATTATCATACTT
1 AATATATTAATTATCATA-TT
*
437634 AATATATTAAGTAT-AT-TT
1 AATATATTAATTATCATATT
*
437652 ATTA-ATTTAATTATCATAATT
1 AATATA-TTAATTATCAT-ATT
437673 AATAT
1 AATAT
437678 TTTATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
17 1 0.03
18 12 0.34
19 2 0.06
20 2 0.06
21 18 0.51
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.49
Consensus pattern (20 bp):
AATATATTAATTATCATATT
Found at i:445157 original size:27 final size:27
Alignment explanation
Indices: 445085--445157 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
445075 TAATCTTTAG
*
445085 TTCTTCGA-ATATAAAATGAATTATAGA
1 TTCTTTGACATATAAAA-GAATTATAGA
* * **
445112 TTCTTTTAGATATTCAAGAATTATAGA
1 TTCTTTGACATATAAAAGAATTATAGA
445139 TT-TTTGACATATGAAAAGA
1 TTCTTTGACATAT-AAAAGA
445158 TTAAACCTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 8 0.22
27 22 0.61
28 6 0.17
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (27 bp):
TTCTTTGACATATAAAAGAATTATAGA
Found at i:445827 original size:19 final size:18
Alignment explanation
Indices: 445803--445900 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 18
445793 AAGATCAAAT
445803 CAAAGAAGAGAAAAAAAAA
1 CAAAGAA-AGAAAAAAAAA
*
445822 CAAAGAAAAAGAAAAAAAA
1 CAAAGAAAGA-AAAAAAAA
*
445841 CAAAG--AGAAAAAAAAG
1 CAAAGAAAGAAAAAAAAA
*
445857 CAAA-AAAAAAAAAAAAA
1 CAAAGAAAGAAAAAAAAA
*
445874 TCAAAGAAA-AAGAACAAAA
1 -CAAAGAAAGAA-AAAAAAA
*
445893 GAAAGAAA
1 CAAAGAAA
445901 AAAGAGATGA
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
16 11 0.17
17 11 0.17
18 15 0.23
19 29 0.44
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (18 bp):
CAAAGAAAGAAAAAAAAA
Found at i:445838 original size:18 final size:18
Alignment explanation
Indices: 445815--445902 Score: 92
Period size: 19 Copynumber: 4.9 Consensus size: 18
445805 AAGAAGAGAA
445815 AAAAAAACAAAGAAAAAG
1 AAAAAAACAAAGAAAAAG
*
445833 AAAAAAAACAAAG-AGAA-
1 -AAAAAAACAAAGAAAAAG
* *
445850 AAAAAAGCAAA-AAAAAA
1 AAAAAAACAAAGAAAAAG
445867 AAAAAAATCAAAGAAAAAG
1 AAAAAAA-CAAAGAAAAAG
* *
445886 AACAAAAGAAAGAAAAA
1 AAAAAAACAAAGAAAAA
445903 AGAGATGATA
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
16 13 0.22
17 6 0.10
18 16 0.28
19 23 0.40
ACGTcount: A:0.83, C:0.06, G:0.10, T:0.01
Consensus pattern (18 bp):
AAAAAAACAAAGAAAAAG
Found at i:445848 original size:35 final size:35
Alignment explanation
Indices: 445808--445903 Score: 124
Period size: 35 Copynumber: 2.7 Consensus size: 35
445798 CAAATCAAAG
445808 AAGAGAAAAAAAAACAAAGAAAAAGAAAAAAAA-CA
1 AAGAGAAAAAAAAACAAAGAAAAA-AAAAAAAATCA
*
445843 AAGAGAAAAAAAAGCAAA-AAAAAAAAAAAAATCA
1 AAGAGAAAAAAAAACAAAGAAAAAAAAAAAAATCA
* *
445877 AAGAAAAAGAACAAAAGAAAGAAAAAA
1 AAGAGAAA-AA-AAAACAAAGAAAAAA
445904 GAGATGATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
33 8 0.15
34 14 0.26
35 19 0.36
36 6 0.11
37 6 0.11
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.01
Consensus pattern (35 bp):
AAGAGAAAAAAAAACAAAGAAAAAAAAAAAAATCA
Found at i:445881 original size:47 final size:45
Alignment explanation
Indices: 445813--445902 Score: 119
Period size: 47 Copynumber: 2.0 Consensus size: 45
445803 CAAAGAAGAG
* *
445813 AAAAAAAAACAAAGAAAAAGAAAAAAAACAAAGAGAAA-AAAAAGC
1 AAAAAAAAAAAAAAAAAAAGAAAAAAAACAAA-AGAAAGAAAAAGC
*
445858 AAAAAAAAAAAAAAAATCAAAGAAAAAGAACAAAAGAAAGAAAAA
1 AAAAAAAAAAAAAAAA--AAAGAAAAAAAACAAAAGAAAGAAAAA
445903 AGAGATGATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
45 14 0.36
46 5 0.13
47 20 0.51
ACGTcount: A:0.83, C:0.06, G:0.10, T:0.01
Consensus pattern (45 bp):
AAAAAAAAAAAAAAAAAAAGAAAAAAAACAAAAGAAAGAAAAAGC
Found at i:445884 original size:1 final size:1
Alignment explanation
Indices: 445813--445873 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
445803 CAAAGAAGAG
* * * * * * **
445813 AAAAAAAAACAAAGAAAAAGAAAAAAAACAAAGAGAAAAAAAAGCAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
445874 TCAAAGAAAA
Statistics
Matches: 45, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:445897 original size:12 final size:11
Alignment explanation
Indices: 445811--445905 Score: 55
Period size: 10 Copynumber: 9.3 Consensus size: 11
445801 ATCAAAGAAG
445811 AGAAA-AAAAA
1 AGAAAGAAAAA
*
445821 ACAAAG-AAAA
1 AGAAAGAAAAA
445831 AG-AA-AAAAA
1 AGAAAGAAAAA
*
445840 ACAAAGAGAAAA
1 AGAAAGA-AAAA
*
445852 A-AAAGCAAAA
1 AGAAAGAAAAA
445862 A-AAA-AAAAA
1 AGAAAGAAAAA
** *
445871 A-AATCAAAGA
1 AGAAAGAAAAA
445881 A-AAAGAACAAA
1 AGAAAGAA-AAA
445892 AGAAAGAAAAA
1 AGAAAGAAAAA
445903 AGA
1 AGA
445906 GATGATAAGT
Statistics
Matches: 67, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
9 14 0.21
10 28 0.42
11 14 0.21
12 11 0.16
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.01
Consensus pattern (11 bp):
AGAAAGAAAAA
Found at i:445905 original size:19 final size:18
Alignment explanation
Indices: 445804--445903 Score: 72
Period size: 15 Copynumber: 5.8 Consensus size: 18
445794 AGATCAAATC
445804 AAAGAAGAGAAAAAAAAACA
1 AAAGAA-AG-AAAAAAAACA
*
445824 AAGAAAAAGAAAAAAAAC-
1 AA-AGAAAGAAAAAAAACA
445842 AAAG--AGAAAAAAAAGC-
1 AAAGAAAGAAAAAAAA-CA
445858 -AA-AAA-AAAAAAAA-A
1 AAAGAAAGAAAAAAAACA
** *
445872 AATCAAAGAAAAAGAACA
1 AAAGAAAGAAAAAAAACA
445890 AAAGAAAGAAAAAA
1 AAAGAAAGAAAAAA
445904 GAGATGATAA
Statistics
Matches: 64, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
15 21 0.33
16 5 0.08
17 8 0.12
18 14 0.22
19 9 0.14
20 4 0.06
21 3 0.05
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.01
Consensus pattern (18 bp):
AAAGAAAGAAAAAAAACA
Found at i:446662 original size:16 final size:15
Alignment explanation
Indices: 446643--446699 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 15
446633 TTTTATTCTC
*
446643 TTTTCTTTTTTCTTTA
1 TTTTCTTTTTT-TTCA
446659 TTTTTCTCTTTTTTTCA
1 -TTTTCT-TTTTTTTCA
446676 TTTT-TTCATTTTTTCA
1 TTTTCTT--TTTTTTCA
446692 TTTTCTTT
1 TTTTCTTT
446700 CTTTCTCTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 1 0.03
15 2 0.06
16 16 0.46
17 11 0.31
18 5 0.14
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTTTTTCA
Found at i:446663 original size:17 final size:17
Alignment explanation
Indices: 446643--446703 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
446633 TTTTATTCTC
446643 TTTTCTTTTTTCTTTAT
1 TTTTCTTTTTTCTTTAT
*
446660 TTTTCTCTTTTT-TTCATT
1 TTTTCT-TTTTTCTTTA-T
446678 TTTTCATTTTTTCATTT-T
1 TTTTC-TTTTTTC-TTTAT
*
446696 CTTTCTTT
1 TTTTCTTT
446704 CTCTAGGCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
17 12 0.33
18 21 0.58
19 1 0.03
20 2 0.06
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTCTTTTTTCTTTAT
Found at i:446679 original size:8 final size:8
Alignment explanation
Indices: 446658--446695 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
446648 TTTTTTCTTT
446658 ATTTTTCTC
1 ATTTTT-TC
*
446667 TTTTTTTC
1 ATTTTTTC
446675 ATTTTTTC
1 ATTTTTTC
446683 ATTTTTTC
1 ATTTTTTC
446691 ATTTT
1 ATTTT
446696 CTTTCTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 22 0.81
9 5 0.19
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTTC
Found at i:447744 original size:37 final size:35
Alignment explanation
Indices: 447703--447830 Score: 116
Period size: 36 Copynumber: 3.6 Consensus size: 35
447693 CAAAGGGTCA
*
447703 TCTCGATTGAGACAAGTTTTCTTAAAAATAAATTTCG
1 TCTCGCTTGAGACAA-TTTTCTTAAAAA-AAATTTCG
* * *
447740 TCTCGCTTGCGACAA-TTTCACTAAAAACAAATTTTG
1 TCTCGCTTGAGACAATTTTC-TTAAAAA-AAATTTCG
* * *
447776 TTTCGCTTGAGACAATTTCTCTCAAAAAAAA-TTCA
1 TCTCGCTTGAGACAATTT-TCTTAAAAAAAATTTCG
* *
447811 TCTTGCTTGAGACATTTTTC
1 TCTCGCTTGAGACAATTTTC
447831 CTTTGATATA
Statistics
Matches: 74, Mismatches: 14, Indels: 9
0.76 0.14 0.09
Matches are distributed among these distances:
34 2 0.03
35 21 0.28
36 29 0.39
37 20 0.27
38 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.38
Consensus pattern (35 bp):
TCTCGCTTGAGACAATTTTCTTAAAAAAAATTTCG
Found at i:448357 original size:131 final size:129
Alignment explanation
Indices: 448104--448493 Score: 413
Period size: 131 Copynumber: 3.0 Consensus size: 129
448094 ATAATTATCC
** * *
448104 CTAAAGATGGCCTTCTATCCTCATCGCATAGGAACCATGTCATCCCCCGAACAGACATCCTCATC
1 CTAAAGATGGCCTTC-ATCCTCATCAAATAGGAACCATGTCATCCCCCGACCAGACCTCCTCATC
* * * * * * ** *
448169 ACGTAGGAGCTGTGTTACCTTTAGATAACTAGTCATCCTCAA-CACGTATAAATCATGTTATCAT
65 ACGTAGGAGC-GTGTCACCCTTAGATAACCAGCCGTCCT-AATCACATAGGAACCATGTTATCAT
448233 CA
128 CA
* *
448235 CTAAAGATGGCCTGTCATCCTCATCAAATAGGAACCATGTCATCCCCCGACCAGACCTCTTTATC
1 CTAAAGATGGCCT-TCATCCTCATCAAATAGGAACCATGTCATCCCCCGACCAGACCTCCTCATC
*
448300 ACATAGGAGTCGTGTCACCCTTAGATAACCAGCCGTCCTAATCACATAGGAACCATGTTATCATC
65 ACGTAGGAG-CGTGTCACCCTTAGATAACCAGCCGTCCTAATCACATAGGAACCATGTTATCATC
*
448365 C
129 A
* * * * * * * *
448366 CTAAAGATGACATACCGTCCTCATCATATAGGAACCGTGTCATCCCTCGACTAGACCTCCTCATC
1 CTAAAGATGGCCT-TCATCCTCATCAAATAGGAACCATGTCATCCCCCGACCAGACCTCCTCATC
* * * * * * * *
448431 ACGTATGAGCCGTGTGACCCCTAGATAACCATCAGTCCTCATCGCATAGGAACCGTGTTATCA
65 ACGTAGGAG-CGTGTCACCCTTAGATAACCAGCCGTCCTAATCACATAGGAACCATGTTATCA
448494 CCATCCCTAA
Statistics
Matches: 218, Mismatches: 38, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
130 2 0.01
131 213 0.98
132 3 0.01
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (129 bp):
CTAAAGATGGCCTTCATCCTCATCAAATAGGAACCATGTCATCCCCCGACCAGACCTCCTCATCA
CGTAGGAGCGTGTCACCCTTAGATAACCAGCCGTCCTAATCACATAGGAACCATGTTATCATCA
Found at i:450906 original size:3 final size:3
Alignment explanation
Indices: 450891--450940 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
450881 TCTACAAAAA
* * * *
450891 TAT TAT T-T AAT TAT TAT TAT TAT TAT TAA TAT TAA TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
450938 TAT
1 TAT
450941 AACATACGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 1 0.03
3 37 0.97
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:453145 original size:43 final size:42
Alignment explanation
Indices: 453120--453299 Score: 261
Period size: 43 Copynumber: 4.2 Consensus size: 42
453110 CGTTTGTTGG
*
453120 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCATTTGTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTT-TCCC
*
453163 ACAAACGCCGTAATAGGTGTTGAGATTTAGCGGCGTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTCCC
*** * * *
453205 ACAAACATTGCAATAGGTTTTGAGATTTAGAGGTGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCG-TTTTCCC
453248 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCG-TTTTCCC
453291 ACAAACGCC
1 ACAAACGCC
453300 ACAAAATGCG
Statistics
Matches: 121, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
42 32 0.26
43 89 0.74
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (42 bp):
ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTCCC
Found at i:453233 original size:85 final size:86
Alignment explanation
Indices: 453129--453296 Score: 275
Period size: 85 Copynumber: 2.0 Consensus size: 86
453119 GACAAACGCC
* *
453129 GCAATAGGTGTTGAGATTTAGCGGCATTTGTCCCACAAACGCCGTAATAGGTGTTGAGATTTAGC
1 GCAATAGGTGTTGAGATTTAGAGGCATTTGTCCCACAAACGCCGCAATAGGTGTTGAGATTTAGC
453194 GGCG-TTTTCCCACAAACATT
66 GGCGTTTTTCCCACAAACATT
* ** *
453214 GCAATAGGTTTTGAGATTTAGAGGTGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATTTAGC
1 GCAATAGGTGTTGAGATTTAGAGGCATTTGTCCCACAAACGCCGCAATAGGTGTTGAGATTTAGC
453279 GGCGTTTTTCCCACAAAC
66 GGCGTTTTTCCCACAAAC
453297 GCCACAAAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
85 63 0.83
86 13 0.17
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (86 bp):
GCAATAGGTGTTGAGATTTAGAGGCATTTGTCCCACAAACGCCGCAATAGGTGTTGAGATTTAGC
GGCGTTTTTCCCACAAACATT
Done.