Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 26
Found at i:3944 original size:12 final size:12
Alignment explanation
Indices: 3927--3960 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
3917 GTCAGAGAGT
3927 GTCATGCCCAGA
1 GTCATGCCCAGA
3939 GTCATGCCCAGA
1 GTCATGCCCAGA
3951 GTCATGCCCA
1 GTCATGCCCA
3961 TGTCTCCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.18
Consensus pattern (12 bp):
GTCATGCCCAGA
Found at i:4261 original size:41 final size:41
Alignment explanation
Indices: 4216--4364 Score: 201
Period size: 41 Copynumber: 3.6 Consensus size: 41
4206 AAATTGTGGT
* *
4216 GTTTGTATAAAAATACCACTAAAGTATGAGTCTATAGTAGC
1 GTTTGTATAAAAATGCCACTAAAGTACGAGTCTATAGTAGC
** *
4257 GTTTGTGCAAAAATGCCACTAAAGTACGAGTATATAGTAGC
1 GTTTGTATAAAAATGCCACTAAAGTACGAGTCTATAGTAGC
* * *
4298 GTTTGTGTAAAAATGCCACTAAAGTACGTGTCTATAGCAGC
1 GTTTGTATAAAAATGCCACTAAAGTACGAGTCTATAGTAGC
*
4339 GTTTGTATAAAAACGCCA-TGAAAGTA
1 GTTTGTATAAAAATGCCACT-AAAGTA
4365 TTACTTTATA
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 1 0.01
41 95 0.99
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (41 bp):
GTTTGTATAAAAATGCCACTAAAGTACGAGTCTATAGTAGC
Found at i:4375 original size:41 final size:40
Alignment explanation
Indices: 4313--4417 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
4303 TGTAAAAATG
* * *
4313 CCACTAAAGTACGT-GTCTATAGCAG-CGTTTGTATAAAAACG
1 CCACTAAAGTAC-TACTTTATAGC-GTCGTTTGTAT-AAAACA
*
4354 CCA-TGAAAGTATTACTTTATAGCGTCGTTTGTATAAAACA
1 CCACT-AAAGTACTACTTTATAGCGTCGTTTGTATAAAACA
4394 CCACTAAAGTACTACTTTATAGCG
1 CCACTAAAGTACTACTTTATAGCG
4418 GCATCTTTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
40 29 0.53
41 26 0.47
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (40 bp):
CCACTAAAGTACTACTTTATAGCGTCGTTTGTATAAAACA
Found at i:4375 original size:82 final size:81
Alignment explanation
Indices: 4216--4405 Score: 206
Period size: 82 Copynumber: 2.3 Consensus size: 81
4206 AAATTGTGGT
* * * *
4216 GTTTGTATAAAAATACCACTAAAGTATGAGTCTATAGTAGCGTTTGTGCAAAAATGCCACTAAAG
1 GTTTGTATAAAAAT-CCACTAAAGTACGAGTCTATAGCAGCGTTTGTACAAAAACGCCACTAAAG
*
4281 TACGAGTATATAGTAG-C
65 TACGACTATATAG-AGTC
* * *
4298 GTTTGTGTAAAAATGCCACTAAAGTACGTGTCTATAGCAGCGTTTGTATAAAAACGCCA-TGAAA
1 GTTTGTATAAAAAT-CCACTAAAGTACGAGTCTATAGCAGCGTTTGTACAAAAACGCCACT-AAA
** * *
4362 GTATTACTTTATAGCGTC
64 GTACGACTATATAGAGTC
4380 GTTTGTATAAAACA-CCACTAAAGTAC
1 GTTTGTATAAAA-ATCCACTAAAGTAC
4406 TACTTTATAG
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
81 14 0.15
82 76 0.84
83 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (81 bp):
GTTTGTATAAAAATCCACTAAAGTACGAGTCTATAGCAGCGTTTGTACAAAAACGCCACTAAAGT
ACGACTATATAGAGTC
Found at i:4431 original size:40 final size:40
Alignment explanation
Indices: 4265--4448 Score: 124
Period size: 41 Copynumber: 4.5 Consensus size: 40
4255 GCGTTTGTGC
* * * ** * *
4265 AAAAATGCCACTAAAGTACGAGTATATAGTAGCGTTTGTGT
1 AAAAA-GCCACTAAAGTACTACTTTATAGCGGCATTTGTAT
* * * *
4306 AAAAATGCCACTAAAGTACGT-GTCTATAGCAGCGTTTGTAT
1 AAAAA-GCCACTAAAGTAC-TACTTTATAGCGGCATTTGTAT
* * *
4347 AAAAACGCCA-TGAAAGTATTACTTTATAGCGTCGTTTGTAT
1 AAAAA-GCCACT-AAAGTACTACTTTATAGCGGCATTTGTAT
4388 AAAACA-CCACTAAAGTACTACTTTATAGCGGCATCTTTGTA-
1 AAAA-AGCCACTAAAGTACTACTTTATAGCGGCA--TTTGTAT
* *
4429 AAAATGCCACTATAGTACTA
1 AAAAAGCCACTAAAGTACTA
4449 GTCTTCGATG
Statistics
Matches: 120, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
40 24 0.20
41 89 0.74
42 7 0.06
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (40 bp):
AAAAAGCCACTAAAGTACTACTTTATAGCGGCATTTGTAT
Found at i:7374 original size:16 final size:16
Alignment explanation
Indices: 7350--7383 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7340 CAAAATAATG
*
7350 TAATTATAAATAATAA
1 TAATAATAAATAATAA
*
7366 TAATAATAATTAATAA
1 TAATAATAAATAATAA
7382 TA
1 TA
7384 TTTTTTCGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAATAAATAATAA
Found at i:11749 original size:68 final size:67
Alignment explanation
Indices: 11640--11803 Score: 249
Period size: 68 Copynumber: 2.4 Consensus size: 67
11630 AACAAAATGA
* *
11640 AAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGACTAAGTGCCTTTGAGGCCTAGCTGTGCATT
1 AAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTTGAGGCCTAACTGTGCATT
11705 TGG
66 T-G
*
11708 AAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATT
1 AAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTTGAGGCCTAACTGTGCATT
11773 TG
66 TG
* * *
11775 ACATAAA-GTGTTAATTATGCCTGTTAGAT
1 A-AGAAAGGTGTCAATTATGCCAGTTAGAT
11804 AAACGGTTAA
Statistics
Matches: 89, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
67 22 0.25
68 67 0.75
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (67 bp):
AAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTTGAGGCCTAACTGTGCATT
TG
Found at i:11891 original size:81 final size:79
Alignment explanation
Indices: 11757--11968 Score: 289
Period size: 81 Copynumber: 2.6 Consensus size: 79
11747 GTGCCTTTGA
* * * * *
11757 GGCCTAACTGTGCATTTGACATAAAGTGTTAATTATGCCTGTTAGATAAACGGTTAAAGACCGTT
1 GGCCTAGCTGTGCATTTGA-ATAATGTGTTAATTATGCCAGTTAGATGAACGGTTAAAGACCATT
11822 GAGTAAAAGATAAAT
65 GAGTAAAAGATAAAT
* *
11837 GGCCTAGCTGTGCATTTGGAATAATGGTGTTAATTATGCCAGTTAGATGAACGGTTAGAGATCAT
1 GGCCTAGCTGTGCATTT-GAATAAT-GTGTTAATTATGCCAGTTAGATGAACGGTTAAAGACCAT
11902 TGAGTAAAAGATAAAT
64 TGAGTAAAAGATAAAT
* * *
11918 GGCCTAGCTGTACATTTTGAAGAAATGTGTCAATTATGCCAGTTAGATGAA
1 GGCCTAGCTGTGCA-TTTGAA-TAATGTGTTAATTATGCCAGTTAGATGAA
11969 AGGCTAAGTG
Statistics
Matches: 118, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
80 20 0.17
81 92 0.78
82 6 0.05
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (79 bp):
GGCCTAGCTGTGCATTTGAATAATGTGTTAATTATGCCAGTTAGATGAACGGTTAAAGACCATTG
AGTAAAAGATAAAT
Found at i:12107 original size:149 final size:149
Alignment explanation
Indices: 11837--12266 Score: 556
Period size: 149 Copynumber: 2.9 Consensus size: 149
11827 AAAGATAAAT
* * * * * * * * * *
11837 GGCCTAGCTGTGCATTTGGAATAATGGTGTTAATTATGCCAGTTAGATGAACGGTTAGAGATCAT
1 GGCCTAACTGTGCATTTGAAAGAAAGGTGTCAATTATACCAGTTAGATGAACGATTAAAGACCGT
* *
11902 TGAGTAAAAGATAAATGGCCTAGCTGTACATTTTGAAGAAATGTGTCAATTATGCCAGTTAGATG
66 TGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAATGTGTCAATTATGCCAGTTAGATG
* *
11967 AAAGGCTAAGTGTCTTTTA
131 AAAGGCTAAGTGCCTTTGA
* * * * * *
11986 GGCCTTACTGTGCATTTGACAGAAAGGTTTCTATTATACTAGTTAGATGAACAATTAAAGACCGT
1 GGCCTAACTGTGCATTTGAAAGAAAGGTGTCAATTATACCAGTTAGATGAACGATTAAAGACCGT
* * * *
12051 TGAG-AATAAGATAAATGGCCTAGGTGTGTATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGAT
66 TGAGTAA-AAGATAAATGGCCTAGCTGTGCATTTGGAAGAAATGTGTCAATTATGCCAGTTAGAT
*
12115 GAAAGGTTAAGTGCCTTTGA
130 GAAAGGCTAAGTGCCTTTGA
* *
12135 GGCCTAACTGTGCATTTGAAAGAAATGTGTCAATTATTCCAGTTAGATGAACGATTAAAGACCGT
1 GGCCTAACTGTGCATTTGAAAGAAAGGTGTCAATTATACCAGTTAGATGAACGATTAAAGACCGT
* * * * *
12200 TGAGTAAAATATAAATGGTCTAGCTGTGCATTTGGCAGAAATGTGTTAATTATGCCTGTTAGATG
66 TGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAATGTGTCAATTATGCCAGTTAGATG
12265 AA
131 AA
12267 TGGTTAAAGA
Statistics
Matches: 238, Mismatches: 41, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
148 2 0.01
149 234 0.98
150 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (149 bp):
GGCCTAACTGTGCATTTGAAAGAAAGGTGTCAATTATACCAGTTAGATGAACGATTAAAGACCGT
TGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAATGTGTCAATTATGCCAGTTAGATG
AAAGGCTAAGTGCCTTTGA
Found at i:12277 original size:81 final size:81
Alignment explanation
Indices: 12135--12347 Score: 300
Period size: 81 Copynumber: 2.6 Consensus size: 81
12125 GTGCCTTTGA
* ** *
12135 GGCCTAACTGTGCATTTGAAAGAAATGTGTCAATTATTCCAGTTAGATGAACGATTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGT
*
12200 TGAGTAAAATATAAAT
66 TGAGTAAAAGATAAAT
* * * * *
12216 GGTCTAGCTGTGCATTTGGCAGAAATGTGTTAATTATGCCTGTTAGATGAATGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGT
12281 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * *
12297 GGCCTAGCTGTGCATTTGGCAGAAAAGTCTCAATCATGCAAGTTAGATGAA
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAA
12348 AAGTAAATGT
Statistics
Matches: 115, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 115 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (81 bp):
GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGT
TGAGTAAAAGATAAAT
Found at i:12465 original size:49 final size:46
Alignment explanation
Indices: 12404--12521 Score: 146
Period size: 49 Copynumber: 2.5 Consensus size: 46
12394 GGATAAACGG
* * *
12404 TGCATAAGTGGTATGAAAGGATGTCATATAGATATAAAATGTACAACAA
1 TGCATAATTGGTATGAAAGGATGTCATAAAG-GA-AAAATGTA-AACAA
* *
12453 TGCATAATTGGTATGAATGGATGTCATAAAGGAAAAATGTAAACAG
1 TGCATAATTGGTATGAAAGGATGTCATAAAGGAAAAATGTAAACAA
* *
12499 TACATAATGGGTATGAAAGGATG
1 TGCATAATTGGTATGAAAGGATG
12522 CCCAAATGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
46 24 0.39
47 8 0.13
48 1 0.02
49 28 0.46
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (46 bp):
TGCATAATTGGTATGAAAGGATGTCATAAAGGAAAAATGTAAACAA
Found at i:12521 original size:46 final size:49
Alignment explanation
Indices: 12413--12521 Score: 143
Period size: 46 Copynumber: 2.3 Consensus size: 49
12403 GTGCATAAGT
* * * *
12413 GGTATGAAAGGATGTCATATAGATATAAAATGTACAACAATGCATAATT
1 GGTATGAAAGGATGTCATAAAGAGATAAAATGTACAACAATACATAATG
* *
12462 GGTATGAATGGATGTCATAAAG-GA-AAAATGTA-AACAGTACATAATG
1 GGTATGAAAGGATGTCATAAAGAGATAAAATGTACAACAATACATAATG
12508 GGTATGAAAGGATG
1 GGTATGAAAGGATG
12522 CCCAAATGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
46 24 0.45
47 8 0.15
48 1 0.02
49 20 0.38
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (49 bp):
GGTATGAAAGGATGTCATAAAGAGATAAAATGTACAACAATACATAATG
Found at i:22181 original size:22 final size:23
Alignment explanation
Indices: 22151--22193 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
22141 GGTCGTTTAA
22151 TTCTCGGTCAACACCAGTCAAAG
1 TTCTCGGTCAACACCAGTCAAAG
* *
22174 TTCT-GGTCAACGCCGGTCAA
1 TTCTCGGTCAACACCAGTCAA
22194 TGCAGGTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (23 bp):
TTCTCGGTCAACACCAGTCAAAG
Found at i:25932 original size:68 final size:68
Alignment explanation
Indices: 25858--26024 Score: 271
Period size: 68 Copynumber: 2.5 Consensus size: 68
25848 ACAAAATGAA
* *
25858 AGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAAGCCTAGCTGTGCATTT
1 AGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAAGCCTAACTATGCATTT
*
25923 GGC
66 GAC
* *
25926 AGAAAGGTGTCAATTATGCCAGCTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTATGCATTT
1 AGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAAGCCTAACTATGCATTT
25991 GAC
66 GAC
* *
25994 AAAAAGGTGTCAATTATGCCTGTTAGATGAA
1 AGAAAGGTGTCAATTATGCCAGTTAGATGAA
26025 CGGTTAAAGA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 91 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (68 bp):
AGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAAGCCTAACTATGCATTT
GAC
Found at i:26119 original size:81 final size:81
Alignment explanation
Indices: 25974--26267 Score: 444
Period size: 81 Copynumber: 3.6 Consensus size: 81
25964 GTGCCTTTGA
* * * * * * *
25974 GGCCTAACTATGCATTTGACAAAAAGGTGTCAATTATGCCTGTTAGATGAACGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTATCAATTATGCCAGTTAGATGAACGGTTAGAGACCGT
*
26039 TGAGTTAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * *
26055 GTCCTAGTTGTGCATTTGTCAGAAAGGTATCAATTATGCCAGTTAGATGAACGGTTAGAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTATCAATTATGCCAGTTAGATGAACGGTTAGAGACCGT
26120 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* *
26136 GGCCTAGCTGTGTATTTGGCAGAAAGGTATCAATTATGCCAGTTAGATGAACAGTTAGAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTATCAATTATGCCAGTTAGATGAACGGTTAGAGACCGT
26201 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * *
26217 GGCCTAGCTATGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTATCAATTATGCCAGTTAGATGAA
26268 AGGCTAAGTG
Statistics
Matches: 194, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 194 1.00
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (81 bp):
GGCCTAGCTGTGCATTTGGCAGAAAGGTATCAATTATGCCAGTTAGATGAACGGTTAGAGACCGT
TGAGTAAAAGATAAAT
Found at i:27341 original size:81 final size:82
Alignment explanation
Indices: 27194--27648 Score: 453
Period size: 81 Copynumber: 5.6 Consensus size: 82
27184 TACTTAACTT
* * * * * * * *
27194 GCATATTTGACACTTTTCTGTCCAA-GGCATAGTTAGTCAATTATTCTTTTACTCAACA-GTGCT
1 GCATAATTGACACCTTTCT-ACCAATTGCATAGTTAGGCCATTATCCTTTTACTCAACATGTGTT
27257 TAACCATTCAGCTAACCA
65 TAACCATTCAGCTAACCA
* * * *
27275 GCATAATTGACACATTTCTACCAATTGCATAGTTAGACCATTATCATTTTACTCAA-ATGTATTT
1 GCATAATTGACACCTTTCTACCAATTGCATAGTTAGGCCATTATCCTTTTACTCAACATGTGTTT
** * *
27339 AACTGTTCATCTAA-CT
66 AACCATTCAGCTAACCA
* * *
27355 GACATAATTGACACCTTTCTGA-TAATTGCACATTTAGGCCATTATCCTTTTACTCAACA-GTGT
1 G-CATAATTGACACCTTTCT-ACCAATTGCATAGTTAGGCCATTATCCTTTTACTCAACATGTGT
**
27418 TTAACC-TTTTGCTAACCA
64 TTAACCATTCAGCTAACCA
* * * * *
27436 ACATAATTGACACATTTCTACTAATTGCACAGTTAGGCCATTATCCTTTTACTCAA-ATGTATTT
1 GCATAATTGACACCTTTCTACCAATTGCATAGTTAGGCCATTATCCTTTTACTCAACATGTGTTT
* * * **
27500 AACCGTTCATCAAACTG
66 AACCATTCAGCTAACCA
* *
27517 GCATAATTGACACCTTTCTACCAATTGCATAGTTAGGCCATTATCATTCTACTCAACATG-GTTT
1 GCATAATTGACACCTTTCTACCAATTGCATAGTTAGGCCATTATCCTTTTACTCAACATGTGTTT
* *
27581 AACCATTTAGCTAATCTA
66 AACCATTCAGCTAA-CCA
* * * *
27599 -CATAATTGACACCTTTCTTCCAATTACATTGTTAGTCCATTATCCTTTTA
1 GCATAATTGACACCTTTCTACCAATTGCATAGTTAGGCCATTATCCTTTTA
27649 TTTTGGACTA
Statistics
Matches: 309, Mismatches: 54, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
79 2 0.01
80 73 0.24
81 227 0.73
82 7 0.02
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (82 bp):
GCATAATTGACACCTTTCTACCAATTGCATAGTTAGGCCATTATCCTTTTACTCAACATGTGTTT
AACCATTCAGCTAACCA
Found at i:27464 original size:161 final size:162
Alignment explanation
Indices: 27224--27648 Score: 577
Period size: 161 Copynumber: 2.6 Consensus size: 162
27214 TCCAAGGCAT
* * * * * *
27224 AGTTAGTCAATTATTCTTTTACTCAACAGTGCTTAACCATTCAGCTAACCAGCATAATTGACACA
1 AGTTAGGCCATTATCCTTTTACTCAACAGTGTTTAACCATTTAGCTAACCAACATAATTGACACA
* * *
27289 TTTCTACCAATTGCATAGTTAGACCATTATCATTTTACTCAAATGTATTTAACTGTTCATCTAAC
66 TTTCTACCAATTGCATAGTTAGACCATTATCCTTTTACTCAAATGTATTTAACCGTTCATCAAAC
*
27354 TGACATAATTGACACCTTTCTGA-TAATTGCAC
131 TGACATAATTGACACCTTTCT-ACCAATTGCAC
* *
27386 ATTTAGGCCATTATCCTTTTACTCAACAGTGTTTAACC-TTTTGCTAACCAACATAATTGACACA
1 AGTTAGGCCATTATCCTTTTACTCAACAGTGTTTAACCATTTAGCTAACCAACATAATTGACACA
* * *
27450 TTTCTACTAATTGCACAGTTAGGCCATTATCCTTTTACTCAAATGTATTTAACCGTTCATCAAAC
66 TTTCTACCAATTGCATAGTTAGACCATTATCCTTTTACTCAAATGTATTTAACCGTTCATCAAAC
* *
27515 TGGCATAATTGACACCTTTCTACCAATTGCAT
131 TGACATAATTGACACCTTTCTACCAATTGCAC
* * * *
27547 AGTTAGGCCATTATCATTCTACTCAACA-TGGTTTAACCATTTAGCTAATCTACATAATTGACAC
1 AGTTAGGCCATTATCCTTTTACTCAACAGT-GTTTAACCATTTAGCTAACCAACATAATTGACAC
* * * * *
27611 CTTTCTTCCAATTACATTGTTAGTCCATTATCCTTTTA
65 ATTTCTACCAATTGCATAGTTAGACCATTATCCTTTTA
27649 TTTTGGACTA
Statistics
Matches: 230, Mismatches: 30, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
160 2 0.01
161 142 0.62
162 86 0.37
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (162 bp):
AGTTAGGCCATTATCCTTTTACTCAACAGTGTTTAACCATTTAGCTAACCAACATAATTGACACA
TTTCTACCAATTGCATAGTTAGACCATTATCCTTTTACTCAAATGTATTTAACCGTTCATCAAAC
TGACATAATTGACACCTTTCTACCAATTGCAC
Found at i:27921 original size:54 final size:54
Alignment explanation
Indices: 27812--28610 Score: 1163
Period size: 54 Copynumber: 14.8 Consensus size: 54
27802 TATAAAGTAG
* *
27812 TTCATCAACTCATGATGAATTCCGT-GAATTTGCACACATAGTGCCTGTACAGTTA
1 TTCATCAACTCATGATGAATTCCGTGGAA--TGCACACTTAGTGCCTGTACGGTTA
* ** *
27867 TTCATCAACCCATGATGAATTATGTGGAATGCACACGTAGTGCCTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACGGTTA
* * * *
27921 TTCATCAACGCATGATGAATTCCATAGAATGCACACTTAGTGCTTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACGGTTA
* * * * *
27975 TTCATCAACTCATTATGAATTCCATAGAATACACACTTAGTGCTTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACGGTTA
*
28029 TTCATCAACTCATGATGAATTTCGTGGAATGCACACTTAGTGCCTGTA-GTGTTA
1 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACG-GTTA
** *
28083 TTCATCAACTCATGATGAATTTTGTGGAATGCACACTTAGTGTCTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACGGTTA
* * **
28137 TCCATCACCTCATGATGAATTATGTGGAATGCACACTTAGTGCCTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACGGTTA
* * *
28191 -TCTATCAACTCAAGATGAATTTCGTGGAATGCACACTTAGTTCCTGTACGGTTA
1 TTC-ATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACGGTTA
* * *
28245 TTCATCAACTCATGATGAATTCCATGGAATACACACTTAGTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACGGTTA
*
28299 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTCTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACGGTTA
* *
28353 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGTCTGAACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACGGTTA
* * * *
28407 TTCATCAACTCATGATGAATTCCATGGAATGCACACTTAATGCATGTATGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACGGTTA
* *
28461 TTCATGAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTATGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACGGTTA
* *
28515 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCATGTATGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACGGTTA
* *
28569 TTCATCAACTCATAATGAATTTCGTGGAATGCACACTTAGTG
1 TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTG
28611 TCTTTTGGTA
Statistics
Matches: 679, Mismatches: 60, Indels: 11
0.91 0.08 0.01
Matches are distributed among these distances:
53 2 0.00
54 649 0.96
55 25 0.04
56 3 0.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (54 bp):
TTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCCTGTACGGTTA
Found at i:28996 original size:19 final size:19
Alignment explanation
Indices: 28974--29022 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
28964 ACTATGCTAT
28974 GGTATCGATACTCTATCAC
1 GGTATCGATACTCTATCAC
28993 GGTATCGATACTCTATCAC
1 GGTATCGATACTCTATCAC
* *
29012 AGTATTGATAC
1 GGTATCGATAC
29023 CATTTTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (19 bp):
GGTATCGATACTCTATCAC
Found at i:30160 original size:81 final size:81
Alignment explanation
Indices: 30035--30235 Score: 267
Period size: 81 Copynumber: 2.5 Consensus size: 81
30025 CCTAACTGTG
* * * * *
30035 CATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAAGATCGTCGAGAAAAAGAT
1 CATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTCGAGAAAAAGAT
*
30100 AAATGGCCTAGCTGTA
66 AAATGGCCTAGATGTA
* ** * * *
30116 CATTTGGTAGAAATTTGTCAATTATGCCAGTTAGATGAACGGTTAGAGACCGTTGAGTAAAAGAT
1 CATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTCGAGAAAAAGAT
*
30181 AAATGGCCTAGATGTG
66 AAATGGCCTAGATGTA
* *
30197 CATTTGGCAGAAAAGTGTCAATCATGCAAGTTAGATGAA
1 CATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAA
30236 AAGTAAATGT
Statistics
Matches: 103, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 103 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (81 bp):
CATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTCGAGAAAAAGAT
AAATGGCCTAGATGTA
Found at i:30172 original size:149 final size:149
Alignment explanation
Indices: 29900--30172 Score: 343
Period size: 149 Copynumber: 1.8 Consensus size: 149
29890 TGGCAAAAAT
* * * * *
29900 GTGTCAAATATGCCAGTTTGATGAACGGTTAAAGACCGTTGAGTAAAAGATGAATGTCCTAGCTG
1 GTGTCAAATATGCCAGTTAGATGAACGGTTAAAGACCGTCGAGAAAAAGATAAATGGCCTAGCTG
** * * * *
29965 TGTATTTGGCTTAAAGGTATCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAA
66 TACATTTGGCTGAAAGGTATCAATTATGCCAGTTAGATGAAAGGCTAAGTACCGTTGAGGCCTAA
30030 CTGTGCATTTGACATAAAG
131 CTGTGCATTTGACATAAAG
* * *
30049 GTGTCAATTATGCCAGTTAGATGAATGGTTAAAGATCGTCGAGAAAAAGATAAATGGCCTAGCTG
1 GTGTCAAATATGCCAGTTAGATGAACGGTTAAAGACCGTCGAGAAAAAGATAAATGGCCTAGCTG
** * * *
30114 TACATTTGG-TAGAAATTTGTCAATTATGCCAGTTAGATGAACGGTTAGAG-ACCGTTGAG
66 TACATTTGGCT-GAAAGGTATCAATTATGCCAGTTAGATGAAAGGCTA-AGTACCGTTGAG
30173 TAAAAGATAA
Statistics
Matches: 103, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
148 1 0.01
149 100 0.97
150 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (149 bp):
GTGTCAAATATGCCAGTTAGATGAACGGTTAAAGACCGTCGAGAAAAAGATAAATGGCCTAGCTG
TACATTTGGCTGAAAGGTATCAATTATGCCAGTTAGATGAAAGGCTAAGTACCGTTGAGGCCTAA
CTGTGCATTTGACATAAAG
Found at i:30472 original size:17 final size:17
Alignment explanation
Indices: 30450--30491 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
30440 TGTTGTCCAT
30450 AATGATTATAAAAGATA
1 AATGATTATAAAAGATA
30467 AATGATTATAAAAGATA
1 AATGATTATAAAAGATA
30484 AATGATTA
1 AATGATTA
30492 ATGGGCACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (17 bp):
AATGATTATAAAAGATA
Found at i:30810 original size:27 final size:27
Alignment explanation
Indices: 30780--30833 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
30770 GTTGATTTCA
30780 CGTATAGGTAAAGGAAAAGATTAATTG
1 CGTATAGGTAAAGGAAAAGATTAATTG
*
30807 CGTATAGGTAAAGGAAAATATTAATTG
1 CGTATAGGTAAAGGAAAAGATTAATTG
30834 AGTAAGGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.28
Consensus pattern (27 bp):
CGTATAGGTAAAGGAAAAGATTAATTG
Found at i:33546 original size:26 final size:26
Alignment explanation
Indices: 33511--33575 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
33501 CACCACAAAC
33511 TGCCTTAGCTCGCTGGCTCCTCTTGGA
1 TGCC-TAGCTCGCTGGCTCCTCTTGGA
*
33538 TGCCTAGCTCGTTGGCTCCTCTTGGA
1 TGCCTAGCTCGCTGGCTCCTCTTGGA
33564 TGCCTAGCTCGC
1 TGCCTAGCTCGC
33576 AACTCCTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 32 0.89
27 4 0.11
ACGTcount: A:0.08, C:0.34, G:0.26, T:0.32
Consensus pattern (26 bp):
TGCCTAGCTCGCTGGCTCCTCTTGGA
Found at i:46591 original size:13 final size:13
Alignment explanation
Indices: 46573--46598 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46563 TTATAGGTGT
46573 GAAAATGGTGATG
1 GAAAATGGTGATG
46586 GAAAATGGTGATG
1 GAAAATGGTGATG
46599 AACATATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (13 bp):
GAAAATGGTGATG
Found at i:50313 original size:17 final size:17
Alignment explanation
Indices: 50291--50323 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
50281 CGGCTTTAAA
50291 AAATGGTTAGGGTATAG
1 AAATGGTTAGGGTATAG
*
50308 AAATGGTTATGGTATA
1 AAATGGTTAGGGTATA
50324 TGATACGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (17 bp):
AAATGGTTAGGGTATAG
Found at i:52254 original size:28 final size:26
Alignment explanation
Indices: 52222--52278 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
52212 GAAAATCAGA
*
52222 AAAGAAATTGAAACACTCAAAAAGAAAG
1 AAAGAAA-TCAAACACTCAAAAAG-AAG
* *
52250 AAAGAAATCCAGCACTCAAAAAGAAG
1 AAAGAAATCAAACACTCAAAAAGAAG
52276 AAA
1 AAA
52279 AATAAAGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
27 13 0.50
28 7 0.27
ACGTcount: A:0.63, C:0.14, G:0.14, T:0.09
Consensus pattern (26 bp):
AAAGAAATCAAACACTCAAAAAGAAG
Found at i:53607 original size:24 final size:23
Alignment explanation
Indices: 53563--53608 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
53553 CATTTGACAT
**
53563 TTCAAAAGATGTACCTCTTGAAA
1 TTCAAAAGATGTACCAATTGAAA
*
53586 TTCAAAAGAATGTGCCAATTGAA
1 TTCAAAAG-ATGTACCAATTGAA
53609 GTACCAAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (23 bp):
TTCAAAAGATGTACCAATTGAAA
Found at i:55450 original size:91 final size:91
Alignment explanation
Indices: 55290--55471 Score: 283
Period size: 91 Copynumber: 2.0 Consensus size: 91
55280 TCTAGAACAC
*
55290 CCATGTGCCTTGCATATGACCAGCCCTCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATA
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATA
55355 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
** * * * * *
55381 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATA
*
55446 AAGAGTTCTCTCCCTATTTGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
55472 TATCAACTAC
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.30
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATA
AAGAGTTCTCTCCCTATTCGGCCAAG
Found at i:56912 original size:13 final size:13
Alignment explanation
Indices: 56894--56919 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56884 TTATAGGCGT
56894 GAAAATGGTGATG
1 GAAAATGGTGATG
56907 GAAAATGGTGATG
1 GAAAATGGTGATG
56920 AACAGATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (13 bp):
GAAAATGGTGATG
Found at i:58595 original size:30 final size:31
Alignment explanation
Indices: 58554--58613 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
58544 ATAGGCTGCC
**
58554 ATGATATCTAAATGATACGCAAACATAATAA
1 ATGATATCTAAAACATACGCAAACATAATAA
* *
58585 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATACGCAAACATAATA
58614 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACATACGCAAACATAATAA
Found at i:61390 original size:24 final size:25
Alignment explanation
Indices: 61325--61390 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
61315 TTGTGAATCA
*
61325 CCAAAAGTCATGATTATTGGTTCTT
1 CCAAAAGTCATGATTTTTGGTTCTT
*
61350 -CAAAAGTCA-CATCTTTTGGTT-TT
1 CCAAAAGTCATGAT-TTTTGGTTCTT
*
61373 CCAAAAGCCATGATTTTT
1 CCAAAAGTCATGATTTTT
61391 TAATAATCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
23 4 0.12
24 28 0.82
25 2 0.06
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (25 bp):
CCAAAAGTCATGATTTTTGGTTCTT
Found at i:62949 original size:27 final size:26
Alignment explanation
Indices: 62919--62975 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
62909 TAAGAACATA
* *
62919 AAATGATTAATA-AAGGAAGATTAAATG
1 AAATGATAAATATAA-GAA-ATGAAATG
62946 AAATGATAAATATAAGAAATGAAATG
1 AAATGATAAATATAAGAAATGAAATG
62972 AAAT
1 AAAT
62976 AAAGGAAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 11 0.41
27 14 0.52
28 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.25
Consensus pattern (26 bp):
AAATGATAAATATAAGAAATGAAATG
Found at i:90633 original size:20 final size:20
Alignment explanation
Indices: 90608--90656 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
90598 CTTGGAATCC
90608 CTTGTTGATGTTGGGATTAA
1 CTTGTTGATGTTGGGATTAA
90628 CTTGTTGATGTTGGGATTAA
1 CTTGTTGATGTTGGGATTAA
*
90648 CTTGCTGAT
1 CTTGTTGAT
90657 TTATTTTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.08, G:0.29, T:0.45
Consensus pattern (20 bp):
CTTGTTGATGTTGGGATTAA
Found at i:93757 original size:10 final size:10
Alignment explanation
Indices: 93742--93770 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
93732 AAGTTCATCC
93742 ATTCATGCAT
1 ATTCATGCAT
93752 ATTCATGCAT
1 ATTCATGCAT
93762 ATTCATGCA
1 ATTCATGCA
93771 AGAAGACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (10 bp):
ATTCATGCAT
Found at i:96768 original size:2 final size:2
Alignment explanation
Indices: 96761--96785 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
96751 TGGTAGCGGA
96761 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
96786 AGTTGGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:100017 original size:2 final size:2
Alignment explanation
Indices: 100010--100034 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
100000 TGGTAGCGGA
100010 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
100035 AGTTTGATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:113192 original size:182 final size:182
Alignment explanation
Indices: 112885--113251 Score: 716
Period size: 182 Copynumber: 2.0 Consensus size: 182
112875 AAGTTGGAAT
112885 ATGAAACATCATTAACAATGTGAATGAATGTACAAGATTCAATAAGGTTCATGAATTGAATTTGG
1 ATGAAACATCATTAACAATGTGAATGAATGTACAAGATTCAATAAGGTTCATGAATTGAATTTGG
112950 TTCGTTGAAACTTCCCTTTCATAAGGTTCATTGGATCTTGAATATGAACTGAATGTAATTCGAAT
66 TTCGTTGAAACTTCCCTTTCATAAGGTTCATTGGATCTTGAATATGAACTGAATGTAATTCGAAT
113015 GTCAAAGAGCACATGCTTTGGAATACCAAACGTTACAACCTTTGGAACTTCA
131 GTCAAAGAGCACATGCTTTGGAATACCAAACGTTACAACCTTTGGAACTTCA
*
113067 ATGAAACATCATTAACAATGTGAATGAATGTACAAGATTCATTAAGGTTCATGAATTGAATTTGG
1 ATGAAACATCATTAACAATGTGAATGAATGTACAAGATTCAATAAGGTTCATGAATTGAATTTGG
*
113132 TTCGTTGAAACTTCCCTTTCATAAGGTTCATTGGATCTTTAATATGAACTGAATGTAATTCGAAT
66 TTCGTTGAAACTTCCCTTTCATAAGGTTCATTGGATCTTGAATATGAACTGAATGTAATTCGAAT
113197 GTCAAAGAGCACATGCTTTGGAATACCAAACGTTACAACCTTTGGAACTTCA
131 GTCAAAGAGCACATGCTTTGGAATACCAAACGTTACAACCTTTGGAACTTCA
113249 ATG
1 ATG
113252 GATAAATGTG
Statistics
Matches: 183, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 183 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (182 bp):
ATGAAACATCATTAACAATGTGAATGAATGTACAAGATTCAATAAGGTTCATGAATTGAATTTGG
TTCGTTGAAACTTCCCTTTCATAAGGTTCATTGGATCTTGAATATGAACTGAATGTAATTCGAAT
GTCAAAGAGCACATGCTTTGGAATACCAAACGTTACAACCTTTGGAACTTCA
Found at i:127404 original size:27 final size:28
Alignment explanation
Indices: 127374--127435 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
127364 CTTTTCTTTG
* *
127374 CTTTTTTTCTTTTTGAATG-TTGAATTT
1 CTTTTTTTCTTTTAGAATGCTTCAATTT
* *
127401 CTTTCTTTCTTTTAGAGTGCTTCAATTT
1 CTTTTTTTCTTTTAGAATGCTTCAATTT
127429 CTTTTTT
1 CTTTTTT
127436 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.13, C:0.13, G:0.10, T:0.65
Consensus pattern (28 bp):
CTTTTTTTCTTTTAGAATGCTTCAATTT
Found at i:142395 original size:27 final size:27
Alignment explanation
Indices: 142365--142426 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
142355 CTTTTCTTTG
*
142365 CTTTTCTTCTTTTTGAATGC-CGAATTT
1 CTTTTCTTCTTTTGGAATGCTC-AATTT
*
142392 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAATGC-TCAATTT
142420 CTTTTCT
1 CTTTTCT
142427 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 7 0.24
29 5 0.17
ACGTcount: A:0.11, C:0.19, G:0.11, T:0.58
Consensus pattern (27 bp):
CTTTTCTTCTTTTGGAATGCTCAATTT
Found at i:144334 original size:29 final size:30
Alignment explanation
Indices: 144290--144348 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
144280 GTTAGCTTTA
**
144290 TATTATGTTTACATATGTTTTAGAT-TCAT
1 TATTATGTTTACATATCATTTAGATATCAT
144319 TATTATGTTTGA-ATATCATTTAGATATCAT
1 TATTATGTTT-ACATATCATTTAGATATCAT
144349 GGCAGTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.53
Consensus pattern (30 bp):
TATTATGTTTACATATCATTTAGATATCAT
Found at i:149500 original size:15 final size:16
Alignment explanation
Indices: 149480--149516 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
149470 GATTAGAATA
149480 AAATAAATGAAAGAT-
1 AAATAAATGAAAGATG
149495 AAATAAATGAAAGATG
1 AAATAAATGAAAGATG
149511 AAATAA
1 AAATAA
149517 GATAATAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.19
Consensus pattern (16 bp):
AAATAAATGAAAGATG
Found at i:150826 original size:2 final size:2
Alignment explanation
Indices: 150819--150845 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
150809 TGGTAGCGGA
150819 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
150846 GTTGGTGATA
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:156227 original size:11 final size:11
Alignment explanation
Indices: 156203--156247 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
156193 TTGGTGCTAG
156203 AAACAAGATAA
1 AAACAAGATAA
* *
156214 AAATAAGATTA
1 AAACAAGATAA
156225 AAACAAGATAA
1 AAACAAGATAA
156236 AGAA-AAGATAA
1 A-AACAAGATAA
156247 A
1 A
156248 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:156231 original size:22 final size:22
Alignment explanation
Indices: 156203--156244 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
156193 TTGGTGCTAG
156203 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
156225 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
156245 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:163753 original size:68 final size:68
Alignment explanation
Indices: 163644--163781 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
163634 ATCCTTGGCC
163644 GAATAGTCCTTGTGTCCCCTCAAGTTGGCGCCAAATTGGGTGGGAAATGATGCTTGGTCGAATAG
1 GAATAGTCCTTGTGTCCCCTCAAGTTGGCGCCAAATTGGGTGGGAAATGATGCTTGGTCGAATAG
163709 GGA
66 GGA
163712 GAATAGTCCTTGTGTCCCCTCAAGTTGGCGCCAAATTGGGTGGGAAATGATGCTTGGTCGAATAG
1 GAATAGTCCTTGTGTCCCCTCAAGTTGGCGCCAAATTGGGTGGGAAATGATGCTTGGTCGAATAG
163777 GGA
66 GGA
163780 GA
1 GA
163782 GAGCTCTTCA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (68 bp):
GAATAGTCCTTGTGTCCCCTCAAGTTGGCGCCAAATTGGGTGGGAAATGATGCTTGGTCGAATAG
GGA
Found at i:165619 original size:22 final size:20
Alignment explanation
Indices: 165591--165637 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 20
165581 TAAAGGGGAT
165591 AATAATATAAGTAATGAAAAGA
1 AATAA-ATAAGT-ATGAAAAGA
*
165613 AAT-AATAAGTATGAAATGA
1 AATAAATAAGTATGAAAAGA
165632 AATAAA
1 AATAAA
165638 GAAAGAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 11 0.48
20 8 0.35
21 1 0.04
22 3 0.13
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (20 bp):
AATAAATAAGTATGAAAAGA
Found at i:165626 original size:19 final size:20
Alignment explanation
Indices: 165597--165636 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
165587 GGATAATAAT
165597 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
165617 ATAAGT-ATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
165636 A
1 A
165637 AGAAAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:166088 original size:20 final size:21
Alignment explanation
Indices: 166049--166088 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
166039 GAAACCCCTT
166049 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
*
166070 TGAAAATACGTGA-TTTTAA
1 TGAAAATACATGACTTTTAA
166089 TAAACATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:170266 original size:26 final size:26
Alignment explanation
Indices: 170237--170291 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
170227 TTTTTTTCTT
*
170237 TGCTTTGCTTTTCTTCTTT-TTTTGAG
1 TGCTTTGCATTT-TTCTTTCTTTTGAG
*
170263 TGC--TGGATTTTTCTTTCTTTTGAG
1 TGCTTTGCATTTTTCTTTCTTTTGAG
170287 TGCTT
1 TGCTT
170292 CACTTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
23 6 0.25
24 15 0.62
26 3 0.12
ACGTcount: A:0.05, C:0.15, G:0.18, T:0.62
Consensus pattern (26 bp):
TGCTTTGCATTTTTCTTTCTTTTGAG
Found at i:176485 original size:2 final size:2
Alignment explanation
Indices: 176478--176502 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
176468 TGGTAGTGGA
176478 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
176503 AGTTGGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:179755 original size:2 final size:2
Alignment explanation
Indices: 179748--179780 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
179738 TGGTAGTGGA
179748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
179781 AGTTGGTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:181908 original size:26 final size:26
Alignment explanation
Indices: 181872--181939 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
181862 ATGAACCCAC
* *
181872 ATGCAAGGCACATGGGGGCTGGTCAT
1 ATGCAAGGCACATGGGGGATGATCAT
*
181898 ATGCAAGGCACATGGGGGATTATCAT
1 ATGCAAGGCACATGGGGGATGATCAT
* *
181924 ATACAAAGCACATGGG
1 ATGCAAGGCACATGGG
181940 TGTTCTAGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.31, C:0.18, G:0.32, T:0.19
Consensus pattern (26 bp):
ATGCAAGGCACATGGGGGATGATCAT
Found at i:183185 original size:19 final size:21
Alignment explanation
Indices: 183142--183193 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
183132 GAAACCCCTT
183142 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
183163 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
183182 TGAAGATACATG
1 TGAAAATACATG
183194 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:187112 original size:19 final size:21
Alignment explanation
Indices: 187069--187118 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
187059 GAAACCCCTT
187069 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
187090 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
187109 TGAAGATACA
1 TGAAAATACA
187119 AGCTCTTGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 11 0.39
20 4 0.14
21 13 0.46
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:197301 original size:28 final size:26
Alignment explanation
Indices: 197248--197304 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
197238 TTCTTTGCTT
* *
197248 TTTCTTCTTTTGAGTGCTGGATTTTC
1 TTTCTTCTTTTGAGTGCTGCAATTTC
*
197274 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTT-GAGTGCTGCAATTTC
197302 TTT
1 TTT
197305 TTTAAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 7 0.27
28 15 0.58
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.60
Consensus pattern (26 bp):
TTTCTTCTTTTGAGTGCTGCAATTTC
Found at i:198075 original size:23 final size:22
Alignment explanation
Indices: 198045--198087 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
198035 TAGGTGCTGG
198045 AAACAAGATAAAAAACAATATTA
1 AAACAAGATAAAAAA-AATATTA
*
198068 AAACAAGATAAATAAAATAT
1 AAACAAGATAAAAAAAATAT
198088 AAAGGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.19
Consensus pattern (22 bp):
AAACAAGATAAAAAAAATATTA
Found at i:204039 original size:28 final size:26
Alignment explanation
Indices: 203986--204042 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 26
203976 TTCTTTGTTT
*
203986 TTTCTTCTTTTGAGTGCTGAATTTTC
1 TTTCTTCTTTTGAGTGCTCAATTTTC
204012 TTTCTTTCTTTTGGAGTGCTTCAA-TTTC
1 TTTC-TTCTTTT-GAGTGC-TCAATTTTC
204040 TTT
1 TTT
204043 TTTGAATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
27 7 0.26
28 13 0.48
29 3 0.11
ACGTcount: A:0.11, C:0.16, G:0.14, T:0.60
Consensus pattern (26 bp):
TTTCTTCTTTTGAGTGCTCAATTTTC
Found at i:221144 original size:11 final size:12
Alignment explanation
Indices: 221114--221159 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
221104 TTGGTGCTGG
221114 AAACAAGATAAA
1 AAACAAGATAAA
* *
221126 AAATAAGAT-TA
1 AAACAAGATAAA
221137 AAACAAGATAAA
1 AAACAAGATAAA
*
221149 GAA-AAGATAAA
1 AAACAAGATAAA
221160 GGAATTACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:221144 original size:23 final size:22
Alignment explanation
Indices: 221114--221156 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
221104 TTGGTGCTGG
221114 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
221137 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
221157 AAAGGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:232820 original size:19 final size:19
Alignment explanation
Indices: 232779--232828 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
232769 CGGCCAAGAG
* ** *
232779 CATGTATATTCATTTAAAT
1 CATGTATTTTCATAAAAAA
232798 CATGTATTTTCATAAAAAA
1 CATGTATTTTCATAAAAAA
*
232817 CATGTACTTTCA
1 CATGTATTTTCA
232829 AAAGAGGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAA
Found at i:237508 original size:32 final size:33
Alignment explanation
Indices: 237467--237533 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
237457 TGACAATATT
237467 TTCTATCCAT-TTCAATTCTT-ATCATTTCCTTTC
1 TTCTATCCATATTCAATT-TTAATCATTT-CTTTC
*
237500 TTCT-TCCATATTCCATTTTAATCATTTCTTTC
1 TTCTATCCATATTCAATTTTAATCATTTCTTTC
237532 TT
1 TT
237534 TTAATTTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.18, C:0.25, G:0.00, T:0.57
Consensus pattern (33 bp):
TTCTATCCATATTCAATTTTAATCATTTCTTTC
Found at i:238946 original size:13 final size:13
Alignment explanation
Indices: 238924--238953 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
238914 ACTAAACACC
238924 TTTC-ACATACCT
1 TTTCAACATACCT
238936 TTTCAACATACCT
1 TTTCAACATACCT
238949 TTTCA
1 TTTCA
238954 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:244536 original size:12 final size:11
Alignment explanation
Indices: 244522--244564 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
244512 TTTGCAATTC
244522 TTTTATCTTTT
1 TTTTATCTTTT
* *
244533 CTTTATCTTGT
1 TTTTATCTTTT
*
244544 TTTAATCTTATT
1 TTTTATCTT-TT
244556 TTTTATCTT
1 TTTTATCTT
244565 GTTTCCAGCA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTTATCTTTT
Found at i:244564 original size:23 final size:21
Alignment explanation
Indices: 244522--244568 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
244512 TTTGCAATTC
244522 TTTTATCTTTTCTTTATCTTG
1 TTTTATCTTTTCTTTATCTTG
*
244543 TTTTAATCTTATTTTTTATCTTG
1 TTTT-ATCTT-TTCTTTATCTTG
244566 TTT
1 TTT
244569 CCAGCACCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.17
22 5 0.22
23 14 0.61
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTTATCTTTTCTTTATCTTG
Found at i:244927 original size:9 final size:9
Alignment explanation
Indices: 244899--244941 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
244889 TTTTTTATAC
244899 AAAAAAACA
1 AAAAAAACA
**
244908 AAAAAGGCA
1 AAAAAAACA
244917 AAAAAAACA
1 AAAAAAACA
244926 AAAAAAA-A
1 AAAAAAACA
244934 ACAAAAAA
1 A-AAAAAA
244942 GCCAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 2 0.07
9 27 0.93
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:244933 original size:11 final size:11
Alignment explanation
Indices: 244916--244941 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
244906 CAAAAAAGGC
244916 AAAAAAAACAA
1 AAAAAAAACAA
244927 AAAAAAAACAA
1 AAAAAAAACAA
244938 AAAA
1 AAAA
244942 GCCAAAATTT
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:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:248404 original size:40 final size:41
Alignment explanation
Indices: 248345--248425 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 41
248335 GTTACAAGAC
248345 TTGTATGCAAAAGAGGATTTCAAGACTACAAGAAATCAGTT
1 TTGTATGCAAAAGAGGATTTCAAGACTACAAGAAATCAGTT
248386 TTGTATGC-AAAGAGGATTTCAAGACTACAAGAAATCAGTT
1 TTGTATGCAAAAGAGGATTTCAAGACTACAAGAAATCAGTT
248426 CCTACAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 32 0.80
41 8 0.20
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (41 bp):
TTGTATGCAAAAGAGGATTTCAAGACTACAAGAAATCAGTT
Found at i:249617 original size:12 final size:11
Alignment explanation
Indices: 249603--249645 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
249593 TTTGGAATTC
249603 TTTTATCTTTT
1 TTTTATCTTTT
* *
249614 CTTTATCTTGT
1 TTTTATCTTTT
*
249625 TTTAATCTTATT
1 TTTTATCTT-TT
249637 TTTTATCTT
1 TTTTATCTT
249646 GTTTCCAGCA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTTATCTTTT
Found at i:249645 original size:23 final size:21
Alignment explanation
Indices: 249603--249649 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
249593 TTTGGAATTC
249603 TTTTATCTTTTCTTTATCTTG
1 TTTTATCTTTTCTTTATCTTG
*
249624 TTTTAATCTTATTTTTTATCTTG
1 TTTT-ATCTT-TTCTTTATCTTG
249647 TTT
1 TTT
249650 CCAGCACCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.17
22 5 0.22
23 14 0.61
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTTATCTTTTCTTTATCTTG
Found at i:250867 original size:23 final size:23
Alignment explanation
Indices: 250822--250867 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
250812 TTATACCTAT
*
250822 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
250845 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
250868 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:254946 original size:23 final size:23
Alignment explanation
Indices: 254916--254959 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
254906 TCTTTATACC
254916 TATAGATACTTA-TTTCATATGT
1 TATAGATACTTATTTTCATATGT
*
254938 TATATGATAGTTATTTTCATAT
1 TATA-GATACTTATTTTCATAT
254960 ATATATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 7 0.37
24 8 0.42
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (23 bp):
TATAGATACTTATTTTCATATGT
Found at i:254964 original size:23 final size:23
Alignment explanation
Indices: 254916--254965 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
254906 TCTTTATACC
*
254916 TATA-GATACTTATTTCATATGT
1 TATATGATACTTATTTCATATGA
*
254938 TATATGATAGTTATTTTCATAT-A
1 TATATGATACTTA-TTTCATATGA
254961 TATAT
1 TATAT
254966 ATTATACCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 12 0.50
24 8 0.33
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (23 bp):
TATATGATACTTATTTCATATGA
Found at i:256992 original size:23 final size:24
Alignment explanation
Indices: 256950--257002 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
256940 TTTCTTTCTT
256950 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
256974 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
256997 TTTCTT
1 TTTCTT
257003 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:261460 original size:56 final size:58
Alignment explanation
Indices: 261374--261488 Score: 216
Period size: 56 Copynumber: 2.0 Consensus size: 58
261364 AGTAAATTTT
261374 ACTTGTTTGGCGTCGGCTGCAAATGGTGAGTAGGAAGGGAAAAT-AAA-ATAATTGAA
1 ACTTGTTTGGCGTCGGCTGCAAATGGTGAGTAGGAAGGGAAAATAAAATATAATTGAA
261430 ACTTGTTTGGCGTCGGCTGCAAATGGTGAGTAGGAAGGGAAAATAAAATATAATTGAA
1 ACTTGTTTGGCGTCGGCTGCAAATGGTGAGTAGGAAGGGAAAATAAAATATAATTGAA
261488 A
1 A
261489 GGGTGGCTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
56 44 0.77
57 3 0.05
58 10 0.18
ACGTcount: A:0.37, C:0.09, G:0.30, T:0.25
Consensus pattern (58 bp):
ACTTGTTTGGCGTCGGCTGCAAATGGTGAGTAGGAAGGGAAAATAAAATATAATTGAA
Found at i:281702 original size:31 final size:30
Alignment explanation
Indices: 281662--281719 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
281652 AAAAAAAATT
*
281662 GAAATTGAAAA-TATAGTGATTAAATTAGAA
1 GAAATTGAAAATTA-AGTAATTAAATTAGAA
*
281692 GAAATTTGAAAGTTAAGTAATTAAATTA
1 GAAA-TTGAAAATTAAGTAATTAAATTA
281720 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 4 0.17
31 18 0.75
32 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.33
Consensus pattern (30 bp):
GAAATTGAAAATTAAGTAATTAAATTAGAA
Found at i:282069 original size:21 final size:22
Alignment explanation
Indices: 282025--282070 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
282015 TTTATTTACG
282025 AAAATAATATTTTTCACATAAGAT
1 AAAATAATATTTTT--CATAAGAT
*
282049 AAAATAATATTTTT-ATCAGAT
1 AAAATAATATTTTTCATAAGAT
282070 A
1 A
282071 CCCTTTCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
24 14 0.67
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (22 bp):
AAAATAATATTTTTCATAAGAT
Found at i:282616 original size:3 final size:3
Alignment explanation
Indices: 282608--282674 Score: 77
Period size: 3 Copynumber: 23.3 Consensus size: 3
282598 TTACTCATCC
* * *
282608 TAT TAT TAT TAT AAT TA- TCT TAT CAT TAT T-T TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
282654 TAT TAT T-T TAT TAC TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
282675 CTTACATAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 5 0.09
3 48 0.91
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:282653 original size:23 final size:23
Alignment explanation
Indices: 282609--282674 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
282599 TACTCATCCT
* *
282609 ATTATTATTATAATTA-TCTTATC
1 ATTATT-TTATTATTATTATTATC
*
282632 ATTATTTTATTATTATTATTATT
1 ATTATTTTATTATTATTATTATC
*
282655 ATTATTTTATTACTATTATT
1 ATTATTTTATTATTATTATT
282675 CTTACATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.21
23 30 0.79
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTATTTTATTATTATTATTATC
Found at i:282664 original size:20 final size:20
Alignment explanation
Indices: 282608--282674 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
282598 TTACTCATCC
* * *
282608 TATTATTATTATAATTATCT
1 TATTATTATTATTATTTTAT
*
282628 TATCATTATT-TTA--TTAT
1 TATTATTATTATTATTTTAT
282645 TATTATTATTATTATTTTAT
1 TATTATTATTATTATTTTAT
*
282665 TACTATTATT
1 TATTATTATT
282675 CTTACATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 11 0.29
18 3 0.08
19 2 0.05
20 22 0.58
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATTATTATTATTTTAT
Found at i:282857 original size:11 final size:10
Alignment explanation
Indices: 282837--282870 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
282827 ATTGGAGTGC
282837 AAAAAGAAAA
1 AAAAAGAAAA
*
282847 GAAAAGAAAA
1 AAAAAGAAAA
282857 AAAGAAGAAAA
1 AAA-AAGAAAA
282868 AAA
1 AAA
282871 TTCAGAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:298574 original size:18 final size:18
Alignment explanation
Indices: 298551--298585 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
298541 ACAACACTTA
298551 CCACGACAACACCATTTG
1 CCACGACAACACCATTTG
298569 CCACGACAACACCATTT
1 CCACGACAACACCATTT
298586 ACTTCACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.40, G:0.09, T:0.17
Consensus pattern (18 bp):
CCACGACAACACCATTTG
Found at i:298924 original size:23 final size:21
Alignment explanation
Indices: 298881--298928 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
298871 CAGGGTTAGT
* *
298881 AAAAAAATCAAAAAAATAAGA
1 AAAAAAAACAAAAAAAAAAGA
298902 AAAAAAAACAAAAGAAAGAAAGA
1 AAAAAAAACAAAA-AAA-AAAGA
298925 AAAA
1 AAAA
298929 TGTTTAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.52
22 3 0.13
23 8 0.35
ACGTcount: A:0.83, C:0.04, G:0.08, T:0.04
Consensus pattern (21 bp):
AAAAAAAACAAAAAAAAAAGA
Found at i:307614 original size:25 final size:24
Alignment explanation
Indices: 307565--307610 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
307555 CTCCAATTCA
307565 TATGCTCCAGATGTTTTTCTGCAG
1 TATGCTCCAGATGTTTTTCTGCAG
307589 TATGCTCCAGATGTTTTTCTGC
1 TATGCTCCAGATGTTTTTCTGC
307611 CAGTTCCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (24 bp):
TATGCTCCAGATGTTTTTCTGCAG
Found at i:317293 original size:36 final size:36
Alignment explanation
Indices: 317216--317331 Score: 153
Period size: 36 Copynumber: 3.2 Consensus size: 36
317206 ATTTAGAAGT
* *
317216 TGGTGATAATATAGGCGTGAT-ATGGTGATGAAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
** *
317251 CAGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
317287 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGG-TGATGGAATA
317324 TGGTGATG
1 TGGTGATG
317332 GAAATAGTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
35 18 0.26
36 36 0.51
37 16 0.23
ACGTcount: A:0.31, C:0.04, G:0.34, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:322941 original size:13 final size:13
Alignment explanation
Indices: 322923--322983 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
322913 TATAGGCGTG
322923 ATATGGTGATGAA
1 ATATGGTGATGAA
*
322936 ATATGGTGATGAT
1 ATATGGTGATGAA
* *
322949 ATA-GGCG-TGAT
1 ATATGGTGATGAA
*
322960 A-ATGGTGATGGA
1 ATATGGTGATGAA
*
322972 CTATGGTGATGA
1 ATATGGTGATGA
322984 TATAGGCGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
10 1 0.03
11 8 0.21
12 5 0.13
13 24 0.63
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.31
Consensus pattern (13 bp):
ATATGGTGATGAA
Found at i:322977 original size:36 final size:36
Alignment explanation
Indices: 322904--323019 Score: 171
Period size: 36 Copynumber: 3.2 Consensus size: 36
322894 ATTTAGAAGT
* *
322904 TGGTGATAATATAGGCGTGAT-ATGGTGATGAAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
322939 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
322975 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGG-TGATGGAATA
323012 TGGTGATG
1 TGGTGATG
323020 GAAATAGTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
35 20 0.27
36 38 0.51
37 16 0.22
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:325624 original size:35 final size:36
Alignment explanation
Indices: 325568--325635 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
325558 ATACAATCTG
325568 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
325604 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
325636 ACTTGTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:326136 original size:24 final size:24
Alignment explanation
Indices: 326081--326129 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
326071 AGTGCAAAAG
* *
326081 AAAGAAAAGAAAAAGAAGAATCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
*
326105 AAAGCAAAGAAAAAG-TGAAGCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
326128 AA
1 AA
326130 TTGCAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAGCAAAGAAAAAGAAGAAGCAA
Found at i:328995 original size:24 final size:21
Alignment explanation
Indices: 328960--329002 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
328950 GGCTCATTCT
*
328960 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
328983 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
329003 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:332314 original size:35 final size:35
Alignment explanation
Indices: 332218--332327 Score: 130
Period size: 35 Copynumber: 3.1 Consensus size: 35
332208 GTTTGGATCG
*
332218 TATCAATCACCATCTTCCATCACCATTTTCATGCCTA
1 TATC-ATCACCATCTTCCATCACCA-TTTCACGCCTA
* * * *
332255 TAACATCACCATCTTCCATTACCATTGCACGCTTA
1 TATCATCACCATCTTCCATCACCATTTCACGCCTA
* * *
332290 TATCCTTACCATCTTCTATCACCATTTCACGCCTA
1 TATCATCACCATCTTCCATCACCATTTCACGCCTA
332325 TAT
1 TAT
332328 AACCACCTAT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 39 0.64
36 19 0.31
37 3 0.05
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.35
Consensus pattern (35 bp):
TATCATCACCATCTTCCATCACCATTTCACGCCTA
Found at i:332986 original size:16 final size:16
Alignment explanation
Indices: 332947--333005 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
332937 GAGTTATAAG
332947 TTATCTTCACTTTC-TTA
1 TTAT-TTCA-TTTCTTTA
*
332964 CTATTTCATTTCTTTA
1 TTATTTCATTTCTTTA
* * *
332980 TTCTTTCATTTTTTTC
1 TTATTTCATTTCTTTA
332996 TTATTTCATT
1 TTATTTCATT
333006 ACCATATCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
15 4 0.11
16 28 0.80
17 3 0.09
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTCATTTCTTTA
Found at i:335046 original size:35 final size:36
Alignment explanation
Indices: 335007--335086 Score: 126
Period size: 35 Copynumber: 2.2 Consensus size: 36
334997 AAATGGAATT
**
335007 TGGTGATGATATAGGCGTGAT-ATGATGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGATGATGGAAGA
*
335042 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGATGATGGAAGA
335078 TGGTGATGA
1 TGGTGATGA
335087 ACATATTGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 21 0.51
36 20 0.49
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGATGATGGAAGA
Found at i:339008 original size:24 final size:24
Alignment explanation
Indices: 338954--339009 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
338944 GAAAAATCAG
338954 AAAAG-AAACACTCAAAAAGAAGA
1 AAAAGAAAACACTCAAAAAGAAGA
**
338977 AATTGAAAACACTC-AAAAGAAGAA
1 AAAAGAAAACACTCAAAAAGAAG-A
339001 AAAAGAAAA
1 AAAAGAAAA
339010 GTTGGAAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.70, C:0.11, G:0.12, T:0.07
Consensus pattern (24 bp):
AAAAGAAAACACTCAAAAAGAAGA
Found at i:340258 original size:24 final size:21
Alignment explanation
Indices: 340224--340266 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
340214 TGCACAAGAT
*
340224 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
340246 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
340267 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:350211 original size:22 final size:22
Alignment explanation
Indices: 350183--350226 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
350173 CATCTTCCAT
350183 TATCACGCCTATATCATCACCA
1 TATCACGCCTATATCATCACCA
350205 TATCACGCCTATATCATCACCA
1 TATCACGCCTATATCATCACCA
350227 AATTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.27
Consensus pattern (22 bp):
TATCACGCCTATATCATCACCA
Found at i:358902 original size:17 final size:17
Alignment explanation
Indices: 358867--358902 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
358857 TTGCATCGGC
*
358867 TATAGAAATGGTTAGGG
1 TATAGAAATGGATAGGG
*
358884 TATAGAAATGGATATGG
1 TATAGAAATGGATAGGG
358901 TA
1 TA
358903 AAGGTGGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (17 bp):
TATAGAAATGGATAGGG
Found at i:359212 original size:5 final size:6
Alignment explanation
Indices: 359198--359236 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
359188 GTATGAGTTA
*
359198 TTTTCT TTTTCT TTTTGT TTTTCT TCTTTCT TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TT
359237 ATGTTGCAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:359442 original size:18 final size:17
Alignment explanation
Indices: 359400--359451 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
359390 TGCACAATAT
359400 AAAGAAAT-AAATGATG
1 AAAGAAATAAAATGATG
*
359416 AAATGGAAATAAGAATTATG
1 AAA--GAAATAA-AATGATG
*
359436 AAAGAAATAAATTGAT
1 AAAGAAATAAAATGAT
359452 AAGAGATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 3 0.10
17 4 0.14
18 12 0.41
19 1 0.03
20 9 0.31
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (17 bp):
AAAGAAATAAAATGATG
Found at i:360033 original size:19 final size:20
Alignment explanation
Indices: 359994--360037 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
359984 GAAACTCCTT
*
359994 TGAAAATATATGATTTTTTAA
1 TGAAAATACATGA-TTTTTAA
360015 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
360034 TGAA
1 TGAA
360038 TATGCATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
21 12 0.55
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:360538 original size:36 final size:35
Alignment explanation
Indices: 360444--360549 Score: 133
Period size: 35 Copynumber: 3.0 Consensus size: 35
360434 ATTGGTGGTT
* ** *
360444 ATATAGGCGTGAAATAGTGATAAAAGATGGTAATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
* *
360479 ATATAGGCGTGCAATGGTAATGGAAGATGGTGAT-
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
360513 ATTATAGGCGTGAAAATGGTGATGGAAGATGGTGATG
1 A-TATAGGCGTG-AAATGGTGATGGAAGATGGTGATG
360550 TTTAGGTAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 1 0.02
35 38 0.63
36 21 0.35
ACGTcount: A:0.36, C:0.04, G:0.34, T:0.26
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
Found at i:365503 original size:20 final size:22
Alignment explanation
Indices: 365468--365509 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
365458 CATGCTTAAT
365468 CATTCATTTCTTAGCTCATATG
1 CATTCATTTCTTAGCTCATATG
365490 CATTCA-TT-TTAGCTCATATG
1 CATTCATTTCTTAGCTCATATG
365510 TCTTACACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.60
21 2 0.10
22 6 0.30
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (22 bp):
CATTCATTTCTTAGCTCATATG
Found at i:375251 original size:24 final size:21
Alignment explanation
Indices: 375216--375258 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
375206 GGCACATTCT
*
375216 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
375239 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
375259 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:376151 original size:13 final size:13
Alignment explanation
Indices: 376133--376192 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
376123 TATAGGCGTG
376133 ATATGGTGATGGA
1 ATATGGTGATGGA
376146 ATATGGTGAT-GA
1 ATATGGTGATGGA
376158 TATATGG-G-T-G-
1 -ATATGGTGATGGA
376168 ATAATGGTGATGGA
1 AT-ATGGTGATGGA
*
376182 CTATGGTGATG
1 ATATGGTGATG
376193 ATATAGTCGT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
9 2 0.05
10 4 0.10
11 3 0.08
12 4 0.10
13 26 0.65
14 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.37, T:0.33
Consensus pattern (13 bp):
ATATGGTGATGGA
Found at i:376187 original size:36 final size:35
Alignment explanation
Indices: 376114--376218 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 35
376104 ATTTATAAGT
* *
376114 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGG-GTGATAATGGTGATGGACTA
376149 TGGTGATGATATATGGGTGATAATGGTGATGGACTA
1 TGGTGATGATATA-GGGTGATAATGGTGATGGACTA
*
376185 TGGTGATGATATAGTCGTGATAATGGTGATGGAC
1 TGGTGATGATATAG-GGTGATAATGGTGATGGAC
376219 AGATTGTATC
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
35 18 0.28
36 46 0.72
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.32
Consensus pattern (35 bp):
TGGTGATGATATAGGGTGATAATGGTGATGGACTA
Found at i:377865 original size:26 final size:26
Alignment explanation
Indices: 377826--377882 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
377816 TATCTTTTGT
377826 ATTCCCAAAAGTCACTTCTCCTAAAC
1 ATTCCCAAAAGTCACTTCTCCTAAAC
* *
377852 ATTCCCAAAGGTCACTTCTCCTAAAT
1 ATTCCCAAAAGTCACTTCTCCTAAAC
377878 ATTCC
1 ATTCC
377883 TTTTGGCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (26 bp):
ATTCCCAAAAGTCACTTCTCCTAAAC
Found at i:397307 original size:9 final size:9
Alignment explanation
Indices: 397295--397346 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
397285 TTTTTTTGAA
397295 TTTTTGGCT
1 TTTTTGGCT
397304 TTTTTGGCTTT
1 TTTTTGGC--T
**
397315 TTTTTGTTT
1 TTTTTGGCT
* *
397324 TTTTTTGTT
1 TTTTTGGCT
397333 TTTTTGGCT
1 TTTTTGGCT
397342 TTTTT
1 TTTTT
397347 TTCATTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 28 0.80
11 7 0.20
ACGTcount: A:0.00, C:0.06, G:0.15, T:0.79
Consensus pattern (9 bp):
TTTTTGGCT
Found at i:397308 original size:10 final size:10
Alignment explanation
Indices: 397295--397347 Score: 65
Period size: 10 Copynumber: 5.5 Consensus size: 10
397285 TTTTTTTGAA
397295 TTTTTGGC-T
1 TTTTTGGCTT
397304 TTTTTGGCTT
1 TTTTTGGCTT
* *
397314 TTTTTTGTTT
1 TTTTTGGCTT
*
397324 TTTTTTG-TT
1 TTTTTGGCTT
397333 TTTTTGGCTT
1 TTTTTGGCTT
397343 TTTTT
1 TTTTT
397348 TCATTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
9 16 0.41
10 23 0.59
ACGTcount: A:0.00, C:0.06, G:0.15, T:0.79
Consensus pattern (10 bp):
TTTTTGGCTT
Found at i:397327 original size:29 final size:29
Alignment explanation
Indices: 397295--397358 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
397285 TTTTTTTGAA
**
397295 TTTTTGGCTTTTTTGGCTTTTTTTTGTTT
1 TTTTTGGCTTTTTTGGCTTTTTTTTCATT
* *
397324 TTTTTTGTTTTTTTGGCTTTTTTTTCATT
1 TTTTTGGCTTTTTTGGCTTTTTTTTCATT
397353 TTTTTG
1 TTTTTG
397359 AAAAAAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.02, C:0.06, G:0.14, T:0.78
Consensus pattern (29 bp):
TTTTTGGCTTTTTTGGCTTTTTTTTCATT
Found at i:397355 original size:38 final size:38
Alignment explanation
Indices: 397285--397358 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
397275 TCGTTTGCAA
*
397285 TTTTTTTGAATTTTTGGCTTTTTTGGCTTTTTTTTGTT
1 TTTTTTTGAATTTTTGGCTTTTTTGGCATTTTTTTGTT
** **
397323 TTTTTTTGTTTTTTTGGCTTTTTTTTCATTTTTTTG
1 TTTTTTTGAATTTTTGGCTTTTTTGGCATTTTTTTG
397359 AAAAAAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.04, C:0.05, G:0.14, T:0.77
Consensus pattern (38 bp):
TTTTTTTGAATTTTTGGCTTTTTTGGCATTTTTTTGTT
Found at i:409687 original size:205 final size:204
Alignment explanation
Indices: 409336--409745 Score: 779
Period size: 205 Copynumber: 2.0 Consensus size: 204
409326 GAAGACTAAA
409336 GCCATGAACAAAGTTGAAAGATGAGTTTCACGTGAGAAACAAATAACAGTGGAGGGAGATCAAAA
1 GCCATGAACAAAGTTGAAAGATGAGTTTCACGTGAGAAACAAATAACAGTGGAGGGAGATCAAAA
409401 TGAAAATAACAAAATTGATGTGAGAAACGTTTGAGTCGAAAATGAGAAAGTTGAAAAGATTGAAT
66 TGAAAATAACAAAATTGATGTGAGAAACGTTTGAGTCGAAAATGAGAAAGTTGAAAAGATTGAAT
409466 TTGGGAGCAAAGGGGGAAGTACGTGTGGAAGAGAAAAAGAAAAGATTCCAAGTGAGGTTGTGGTT
131 TTGGGAGCAAAGGGGGAAGTACGTGTGGAAGAGAAAAAGAAAAGATTCCAAGTGAGGTTGTGGTT
409531 AAATGATAC
196 AAATGATAC
409540 GCCATGAACAAAGTTGAAAGATGAGTTTCACAGTGAGAAACAAATAACAGTGGAGGGAGATCAAA
1 GCCATGAACAAAGTTGAAAGATGAGTTTCAC-GTGAGAAACAAATAACAGTGGAGGGAGATCAAA
409605 ATGAAAATAACAAAA-TGATGTGAGAAACCG-TTGAGTCGAAAAATGAGAAAGTTGAAAAGATTG
65 ATGAAAATAACAAAATTGATGTGAGAAA-CGTTTGAGTCG-AAAATGAGAAAGTTGAAAAGATTG
409668 AATTTGGGAGCAAAGGGGGAAGTACGTGTGGAAGAGAAAAAGAAAAGATTCCAAGTGAGGTTGTG
128 AATTTGGGAGCAAAGGGGGAAGTACGTGTGGAAGAGAAAAAGAAAAGATTCCAAGTGAGGTTGTG
409733 GTTAAATGATAC
193 GTTAAATGATAC
409745 G
1 G
409746 ATCCAAACTA
Statistics
Matches: 203, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
204 51 0.25
205 152 0.75
ACGTcount: A:0.43, C:0.08, G:0.29, T:0.20
Consensus pattern (204 bp):
GCCATGAACAAAGTTGAAAGATGAGTTTCACGTGAGAAACAAATAACAGTGGAGGGAGATCAAAA
TGAAAATAACAAAATTGATGTGAGAAACGTTTGAGTCGAAAATGAGAAAGTTGAAAAGATTGAAT
TTGGGAGCAAAGGGGGAAGTACGTGTGGAAGAGAAAAAGAAAAGATTCCAAGTGAGGTTGTGGTT
AAATGATAC
Found at i:420266 original size:22 final size:22
Alignment explanation
Indices: 420240--420281 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
420230 TATTTATAGT
*
420240 TATGATGATGATATTATGAATG
1 TATGAAGATGATATTATGAATG
* *
420262 TATGAAGTTGTTATTATGAA
1 TATGAAGATGATATTATGAA
420282 CCACATATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (22 bp):
TATGAAGATGATATTATGAATG
Found at i:430463 original size:33 final size:33
Alignment explanation
Indices: 430420--430492 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
430410 ACAATGATGT
* *
430420 TGGGGACGCACCGCTCGGTATGATGGACGCTGC
1 TGGGGCCGCACCGCTCGGCATGATGGACGCTGC
* *
430453 TGGGGCCGCACCGCTCGGCATGATGGATGTTGC
1 TGGGGCCGCACCGCTCGGCATGATGGACGCTGC
430486 TGGGGCC
1 TGGGGCC
430493 ACACATGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.12, C:0.27, G:0.41, T:0.19
Consensus pattern (33 bp):
TGGGGCCGCACCGCTCGGCATGATGGACGCTGC
Found at i:438549 original size:59 final size:59
Alignment explanation
Indices: 438450--438586 Score: 186
Period size: 59 Copynumber: 2.3 Consensus size: 59
438440 CAGCAGGCTG
* * **
438450 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGTACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTATAGATGGTGGACACGACCTTATGTGT
* ** *
438509 CATATTCGGGACTGTACTTAAGGATACCTAGTATAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTATAGATGGTGGACACGACCTTATGTGT
438568 CATATTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
438587 CGGTGCTTAT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 1 0.02
59 64 0.98
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTATAGATGGTGGACACGACCTTATGTGT
Found at i:438781 original size:47 final size:45
Alignment explanation
Indices: 438687--438808 Score: 146
Period size: 44 Copynumber: 2.8 Consensus size: 45
438677 GTAAGCATAC
* * *
438687 AAATAAGCTTACGAGCTTTTGGAAT-AATGGCAAGTCTATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
* *
438731 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATGGGTA
438778 AAATAAG----CGAGCTTATGGAATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
438809 GGATTTTATA
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
41 11 0.16
43 13 0.19
44 23 0.33
46 1 0.01
47 22 0.31
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
Found at i:440506 original size:6 final size:6
Alignment explanation
Indices: 440495--440523 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
440485 AACACCCATA
440495 GGTCAT GGTCAT GGTCAT GGTCAT GGTCA
1 GGTCAT GGTCAT GGTCAT GGTCAT GGTCA
440524 CGATTATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.31
Consensus pattern (6 bp):
GGTCAT
Found at i:441629 original size:6 final size:6
Alignment explanation
Indices: 441620--441718 Score: 62
Period size: 6 Copynumber: 16.5 Consensus size: 6
441610 GAAAAAAAAC
* * * *
441620 AAAAGA AAAA-A AATAGA AGAAGA AAAA-A AATAGA AAAAGA AAATGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
* * * *
441666 AAATGA AGAAGAAA AAAATGA AAACGA GAAAG- AAAAGA AAAAGA GAAAA-A
1 AAAAGA A-AA-AGA AAAA-GA AAAAGA AAAAGA AAAAGA AAAAGA -AAAAGA
441716 AAA
1 AAA
441719 TGAGAGATGA
Statistics
Matches: 72, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
5 15 0.21
6 43 0.60
7 12 0.17
8 2 0.03
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.05
Consensus pattern (6 bp):
AAAAGA
Found at i:441629 original size:14 final size:13
Alignment explanation
Indices: 441610--441662 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
441600 TTATAAGAAG
441610 GAAAAAAAACAAAA
1 GAAAAAAAA-AAAA
*
441624 GAAAAAAAATAGAA
1 GAAAAAAAA-AAAA
*
441638 GAAGAAAAAAAATA
1 GAA-AAAAAAAAAA
441652 GAAAAAGAAAA
1 GAAAAA-AAAA
441663 TGAAAATGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 3 0.09
14 24 0.73
15 6 0.18
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (13 bp):
GAAAAAAAAAAAA
Found at i:441642 original size:17 final size:17
Alignment explanation
Indices: 441604--441683 Score: 94
Period size: 17 Copynumber: 4.8 Consensus size: 17
441594 TATATATTAT
* *
441604 AAGAAGGAAAAAAA-AC
1 AAGAAGAAAAAAAATAG
441620 AA-AAGAAAAAAAATAG
1 AAGAAGAAAAAAAATAG
441636 AAGAAGAAAAAAAATAG
1 AAGAAGAAAAAAAATAG
*
441653 AAAAAGAAAATGAAAAT-G
1 AAGAAGAAAA--AAAATAG
441671 AAGAAGAAAAAAA
1 AAGAAGAAAAAAA
441684 TGAAAACGAG
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
15 10 0.18
16 8 0.14
17 23 0.41
18 10 0.18
19 5 0.09
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.05
Consensus pattern (17 bp):
AAGAAGAAAAAAAATAG
Found at i:441674 original size:35 final size:34
Alignment explanation
Indices: 441604--441717 Score: 114
Period size: 34 Copynumber: 3.4 Consensus size: 34
441594 TATATATTAT
* *
441604 AAGAAGGAAAAAAA-A-CAAAAGAAAA-AAAATAG
1 AAGAAGAAAAAAAATAGAAAAAGAAAAGAAAAT-G
441636 AAGAAGAAAAAAAATAGAAAAAGAAAATGAAAATG
1 AAGAAGAAAAAAAATAGAAAAAGAAAA-GAAAATG
*
441671 AAGAAG-AAAAAAAT-GAAAACGAGAAAGAAAA-G
1 AAGAAGAAAAAAAATAGAAAAAGA-AAAGAAAATG
*
441703 AAAAAGAGAAAAAAA
1 AAGAAGA-AAAAAAA
441718 ATGAGAGATG
Statistics
Matches: 71, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
32 19 0.27
33 13 0.18
34 27 0.38
35 7 0.10
36 5 0.07
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (34 bp):
AAGAAGAAAAAAAATAGAAAAAGAAAAGAAAATG
Done.