Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008424.1 Hibiscus syriacus cultivar Beakdansim tig00111207_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: 4198033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 16
Found at i:223966 original size:22 final size:22
Alignment explanation
Indices: 223941--223983 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
223931 GATGGGGAAG
*
223941 GATGTCGTTGGATATAGGAACA
1 GATGTCGTTAGATATAGGAACA
223963 GATGTCGTTAGATATAGGAAC
1 GATGTCGTTAGATATAGGAAC
223984 GGATCGTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (22 bp):
GATGTCGTTAGATATAGGAACA
Found at i:224128 original size:19 final size:18
Alignment explanation
Indices: 224085--224131 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
224075 CAAAACATTT
224085 GTGTTGCGAAACTAAAAC
1 GTGTTGCGAAACTAAAAC
* * *
224103 ATGTTGCGAAATTAAATTC
1 GTGTTGCGAAACTAAA-AC
224122 GTGTTGCGAA
1 GTGTTGCGAA
224132 TTCGAAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (18 bp):
GTGTTGCGAAACTAAAAC
Found at i:224149 original size:20 final size:19
Alignment explanation
Indices: 224124--224196 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
224114 TTAAATTCGT
*
224124 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTGAAAATC-A
*
224144 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAAATCA
* *
224163 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAAAT-C-A
224184 GTTGCGAATTTGA
1 GTTGCGAATTTGA
224197 CTTTTGTGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
19 18 0.38
20 17 0.35
21 13 0.27
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (19 bp):
GTTGCGAATTTGAAAATCA
Found at i:224165 original size:19 final size:20
Alignment explanation
Indices: 224105--224236 Score: 108
Period size: 20 Copynumber: 6.7 Consensus size: 20
224095 ACTAAAACAT
* *
224105 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* * *
224124 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTCGA
224144 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
*
224163 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-CGA
** * *
224184 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAAATTCGA
* * *
224204 GTTGTGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGA
224224 GTTGCGAATTTGA
1 GTTGCGAATTTGA
224237 CTTATATGTT
Statistics
Matches: 90, Mismatches: 18, Indels: 8
0.78 0.16 0.07
Matches are distributed among these distances:
19 28 0.31
20 47 0.52
21 15 0.17
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:224167 original size:39 final size:41
Alignment explanation
Indices: 224105--224196 Score: 109
Period size: 39 Copynumber: 2.3 Consensus size: 41
224095 ACTAAAACAT
* * *
224105 GTTGCGAAATT-AAATTCGTGTTGCGAATTCGAAAAT-CTA
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCCGA
* * *
224144 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCCGA
224184 GTTGCGAATTTGA
1 GTTGCGAATTTGA
224197 CTTTTGTGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 25 0.56
40 20 0.44
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (41 bp):
GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCCGA
Found at i:224268 original size:80 final size:79
Alignment explanation
Indices: 224204--224375 Score: 218
Period size: 80 Copynumber: 2.2 Consensus size: 79
224194 TGACTTTTGT
* * * *
224204 GTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTATATGTTACGATTTACAAATTCATGTTGC
1 GTTGAGAATTTGACTATCGCATTACAAATTTGACTTATATGTTACGATTTACAAATTCATGTTGC
224269 GATTTACAAATTCGC
66 GATTTAC-AATTCGC
* * ** *
224284 GTTGAGAATTTGACTATCGCATTACAAATTTGACTTCTGTGTTACGATTTACAAATTCGCGTTGT
1 GTTGAGAATTTGACTATCGCATTACAAATTTGACTTATATGTTACGATTTACAAATTCATGTTGC
**
224349 GATTTACAGATTCAT
66 GATTTACA-ATTCGC
*
224364 GTTGCGAATTTG
1 GTTGAGAATTTG
224376 GAAAATCACA
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
79 1 0.01
80 78 0.99
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (79 bp):
GTTGAGAATTTGACTATCGCATTACAAATTTGACTTATATGTTACGATTTACAAATTCATGTTGC
GATTTACAATTCGC
Found at i:224271 original size:20 final size:20
Alignment explanation
Indices: 224242--224281 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
224232 TTTGACTTAT
224242 ATGTTACGATTTACAAATTC
1 ATGTTACGATTTACAAATTC
*
224262 ATGTTGCGATTTACAAATTC
1 ATGTTACGATTTACAAATTC
224282 GCGTTGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTTACGATTTACAAATTC
Found at i:224287 original size:20 final size:20
Alignment explanation
Indices: 224248--224287 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
224238 TTATATGTTA
*
224248 CGATTTACAAATTCATGTTG
1 CGATTTACAAATTCACGTTG
*
224268 CGATTTACAAATTCGCGTTG
1 CGATTTACAAATTCACGTTG
224288 AGAATTTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (20 bp):
CGATTTACAAATTCACGTTG
Found at i:224367 original size:20 final size:20
Alignment explanation
Indices: 224329--224367 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
224319 TCTGTGTTAC
*
224329 GATTTACAAATTCGCGTTGT
1 GATTTACAAATTCACGTTGT
* *
224349 GATTTACAGATTCATGTTG
1 GATTTACAAATTCACGTTG
224368 CGAATTTGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (20 bp):
GATTTACAAATTCACGTTGT
Found at i:224393 original size:21 final size:21
Alignment explanation
Indices: 224369--224412 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
224359 TTCATGTTGC
224369 GAATTTGGAAAATCACAACGT
1 GAATTTGGAAAATCACAACGT
* *
224390 GAATTTGGAAAATCGCAATGT
1 GAATTTGGAAAATCACAACGT
224411 GA
1 GA
224413 TTTACATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (21 bp):
GAATTTGGAAAATCACAACGT
Found at i:224469 original size:20 final size:21
Alignment explanation
Indices: 224420--224473 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
224410 TGATTTACAT
224420 ATTCGCGTTGCGAAATTGGAA
1 ATTCGCGTTGCGAAATTGGAA
* *
224441 ACTAG-GTTGCGAAATTGG-A
1 ATTCGCGTTGCGAAATTGGAA
*
224460 GTTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
224474 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.11
20 21 0.78
21 3 0.11
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTGGAA
Found at i:228599 original size:27 final size:27
Alignment explanation
Indices: 228569--228623 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
228559 TCGGTGCATT
228569 AATGCACCGAATGACATTAGTCAAAAA
1 AATGCACCGAATGACATTAGTCAAAAA
*
228596 AATGCACCGAATGGCATTAGTCAAAAA
1 AATGCACCGAATGACATTAGTCAAAAA
228623 A
1 A
228624 GAGAAGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (27 bp):
AATGCACCGAATGACATTAGTCAAAAA
Found at i:236428 original size:21 final size:22
Alignment explanation
Indices: 236389--236430 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
236379 TGAAAATAAA
*
236389 AAAAATAAAACAAAGAACTTTG
1 AAAAAGAAAACAAAGAACTTTG
*
236411 AAAAAGAAAAGAAA-AACTTT
1 AAAAAGAAAACAAAGAACTTT
236431 TATTAAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.67, C:0.07, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAAAGAAAACAAAGAACTTTG
Found at i:237898 original size:12 final size:12
Alignment explanation
Indices: 237883--237927 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
237873 ACAAACAAGT
*
237883 TCATTTATTAAA
1 TCATTTATTAAC
237895 TCATTTA-TAAGC
1 TCATTTATTAA-C
*
237907 TCATTTATTGAC
1 TCATTTATTAAC
237919 TCATTTATT
1 TCATTTATT
237928 TATGAATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 3 0.10
12 24 0.83
13 2 0.07
ACGTcount: A:0.31, C:0.13, G:0.04, T:0.51
Consensus pattern (12 bp):
TCATTTATTAAC
Found at i:238731 original size:13 final size:13
Alignment explanation
Indices: 238702--238745 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
238692 TAATTTTTTT
* *
238702 ATATTATATATAT
1 ATATTATATAAAA
238715 ATATTATATAAAA
1 ATATTATATAAAA
* *
238728 ATATTTTCTAAAA
1 ATATTATATAAAA
238741 ATATT
1 ATATT
238746 CGGATGTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTATATAAAA
Found at i:238990 original size:14 final size:13
Alignment explanation
Indices: 238968--239030 Score: 60
Period size: 14 Copynumber: 4.8 Consensus size: 13
238958 TCGATTATAT
*
238968 GTTCGTTTATGTTC
1 GTTCATTTATG-TC
238982 GTTCATTTA--T-
1 GTTCATTTATGTC
*
238992 ATTCATTTATGTC
1 GTTCATTTATGTC
239005 TGTTCATTTATGTTC
1 -GTTCATTTATG-TC
239020 GTTCATTTATG
1 GTTCATTTATG
239031 ATCGAACAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
10 8 0.20
11 1 0.02
12 1 0.02
14 29 0.71
15 2 0.05
ACGTcount: A:0.16, C:0.13, G:0.14, T:0.57
Consensus pattern (13 bp):
GTTCATTTATGTC
Found at i:239009 original size:24 final size:23
Alignment explanation
Indices: 238955--239015 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
238945 CGTTAGTGAA
* *
238955 TGTTCGATTATATGTTCGTTTATGT
1 TGTTC-ATT-TATATTCATTTATGT
238980 TCGTTCATTTATATTCATTTATGT
1 T-GTTCATTTATATTCATTTATGT
239004 CTGTTCATTTAT
1 -TGTTCATTTAT
239016 GTTCGTTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 23 0.72
25 5 0.16
26 4 0.12
ACGTcount: A:0.18, C:0.11, G:0.13, T:0.57
Consensus pattern (23 bp):
TGTTCATTTATATTCATTTATGT
Found at i:239326 original size:20 final size:17
Alignment explanation
Indices: 239289--239329 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 17
239279 TGTTTTTTGT
239289 GTTTGTGTTGTTCGTTC
1 GTTTGTGTTGTTCGTTC
239306 GTTTGTGTTCGTTTACGTTC
1 GTTTGTGTT-G-TT-CGTTC
239326 GTTT
1 GTTT
239330 ATAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 1 0.05
19 2 0.10
20 9 0.43
ACGTcount: A:0.02, C:0.12, G:0.27, T:0.59
Consensus pattern (17 bp):
GTTTGTGTTGTTCGTTC
Found at i:250314 original size:22 final size:22
Alignment explanation
Indices: 250285--250329 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
250275 AAAAAATGTT
*
250285 GAAAAAAATAGCAGTTCGAAAAA
1 GAAAAAAA-AACAGTTCGAAAAA
*
250308 GAAAAAAAAACTGTTCGAAAAA
1 GAAAAAAAAACAGTTCGAAAAA
250330 AAAGACATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.62, C:0.09, G:0.16, T:0.13
Consensus pattern (22 bp):
GAAAAAAAAACAGTTCGAAAAA
Found at i:255078 original size:16 final size:16
Alignment explanation
Indices: 255057--255088 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
255047 CCTATTGAGA
255057 TAGCCACAGTTTCCTT
1 TAGCCACAGTTTCCTT
255073 TAGCCACAGTTTCCTT
1 TAGCCACAGTTTCCTT
255089 GAGTCTCTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.12, T:0.38
Consensus pattern (16 bp):
TAGCCACAGTTTCCTT
Found at i:256786 original size:4 final size:4
Alignment explanation
Indices: 256777--256809 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
256767 TGTGCATTTT
256777 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
256810 TATATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:260920 original size:24 final size:23
Alignment explanation
Indices: 260894--260939 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
260884 ACACCCTGCA
260894 TTTTGCACATGCATCATTTTATTAT
1 TTTTGCA-ATGCAT-ATTTTATTAT
*
260919 TTTTGCAATGCATTTTTTATT
1 TTTTGCAATGCATATTTTATT
260940 TTTCTTACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 7 0.35
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.57
Consensus pattern (23 bp):
TTTTGCAATGCATATTTTATTAT
Found at i:268607 original size:54 final size:54
Alignment explanation
Indices: 268539--269053 Score: 589
Period size: 54 Copynumber: 9.7 Consensus size: 54
268529 TGAAGCAAAT
* * * *
268539 GAAGATTGTCCGAGTTCCTACTCCCTAGAGAAAGAGGGAGTGAACCCATTGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
268593 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * *
268647 GAATATTGTTTGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGACA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * * *
268701 GAAGATTGTTCAAGTTTCTACTCCCTAAAGAAAGAGGAAGTGAACCCGTTGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * ** * * *
268755 GAAGATTATTTGTTTTCCTACTCCCTAAAGAAAGAGGGAGTGAACCCATAGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* ** * ** * *
268809 TAAGATCATTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGAGAACTTGTAGCCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * * * ** *
268863 GAAGATTGATCGAGTTCATACACTCTAAAGAAAGAGGGAGCGAACCTATTTGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * * * *
268917 GAAGATTATTTGAGTACCTACT--C------AAGAGGGAGCAAACCCGTAGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* *
268963 GAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTAGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* *
269017 GAAGATTGTTTGAGTTCCTACTACCTAAAGAAA-AGGG
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGG
269054 TTGGTAGAAT
Statistics
Matches: 386, Mismatches: 67, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
46 36 0.09
48 1 0.00
52 1 0.00
53 4 0.01
54 344 0.89
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (54 bp):
GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
Found at i:269018 original size:100 final size:100
Alignment explanation
Indices: 268856--269038 Score: 267
Period size: 100 Copynumber: 1.8 Consensus size: 100
268846 GAGAGAACTT
* * * *
268856 GTAGCCAGAAGATTGATCGAGTTCATACACTCTAAAGAAAGAGGGAGCGAACCTATTTGCAGAAG
1 GTAGCCAGAAGATCGATCGAGTTCATACACCCTAAAGAAAGAGGGAGCGAACCCATTAGCAGAAG
268921 ATTATTTGAGTACCTACTCAAGAGGGAGCAAACCC
66 ATTATTTGAGTACCTACTCAAGAGGGAGCAAACCC
* * * * *
268956 GTAGGCAGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTAGCAGAAG
1 GTAGCCAGAAGATCGATCGAGTTCATACACCCTAAAGAAAGAGGGAGCGAACCCATTAGCAGAAG
* *
269021 ATTGTTTGAGTTCCTACT
66 ATTATTTGAGTACCTACT
269039 ACCTAAAGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 72 1.00
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (100 bp):
GTAGCCAGAAGATCGATCGAGTTCATACACCCTAAAGAAAGAGGGAGCGAACCCATTAGCAGAAG
ATTATTTGAGTACCTACTCAAGAGGGAGCAAACCC
Found at i:270914 original size:4 final size:4
Alignment explanation
Indices: 270907--270972 Score: 132
Period size: 4 Copynumber: 16.5 Consensus size: 4
270897 TTATGCATGC
270907 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
270955 ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT AT
270973 TATATAATTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 62 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:274698 original size:35 final size:35
Alignment explanation
Indices: 274643--274711 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
274633 TACGTGCAGG
** * *
274643 GGGAACAGATTTTCCGTGGGGGTTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
274678 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCC
274712 ACCTAAATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.25
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
Found at i:274871 original size:19 final size:19
Alignment explanation
Indices: 274847--274892 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
274837 GTTCCGGAAT
274847 AATCAAAGGATTATAAATG
1 AATCAAAGGATTATAAATG
*
274866 AATCAAAGGATTATAATTG
1 AATCAAAGGATTATAAATG
274885 AATCAAAG
1 AATCAAAG
274893 CAAGGCTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (19 bp):
AATCAAAGGATTATAAATG
Found at i:275338 original size:31 final size:31
Alignment explanation
Indices: 275296--275436 Score: 237
Period size: 31 Copynumber: 4.5 Consensus size: 31
275286 AGGGTCGAGG
*
275296 GTTTACATATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
275327 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
275358 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
275389 GTTTACCTATGTTCTTCGGGACATTTGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
275420 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
275437 AGAATCTATG
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:275447 original size:62 final size:62
Alignment explanation
Indices: 275306--275451 Score: 204
Period size: 62 Copynumber: 2.4 Consensus size: 62
275296 GTTTACATAT
* * * *
275306 GTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTAT
1 GTTCTTCAGAACATATGGACTGTTTACCTATGTTCTTCAGGACATATGGACTGATTACCTAG
* * * *
275368 GTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATTTGGACTGATTACCTAG
1 GTTCTTCAGAACATATGGACTGTTTACCTATGTTCTTCAGGACATATGGACTGATTACCTAG
275430 GTTCTTCAGAATC-TATGGACTG
1 GTTCTTCAGAA-CATATGGACTG
275452 GTCATTCGGG
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
62 76 0.99
63 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (62 bp):
GTTCTTCAGAACATATGGACTGTTTACCTATGTTCTTCAGGACATATGGACTGATTACCTAG
Found at i:281284 original size:2 final size:2
Alignment explanation
Indices: 281232--281270 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
281222 CTCTATAATC
281232 AT AT AT 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 AT AT AT A
281271 AAAGTAGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:281767 original size:421 final size:429
Alignment explanation
Indices: 280975--281805 Score: 1028
Period size: 438 Copynumber: 1.9 Consensus size: 429
280965 ATTCTTATAG
* * *
280975 TTAATCTTATACCCATGAACCAAACACATCCGAGAGATGTGATGTACATGTATCTAAAAATAATC
1 TTAATCTTATACCCATGAACCAAACACATCCAAGAGATGTGACGTACACGTATCTAAAAATAATC
* * ** * *
281040 ACATTATAATCTTAAATGAACAATCCATGTTCAAACCTTAAAATGATATTATTGAGAGAAATGTC
66 ACATTATAATCTTAAATAAACAATCCATCTTCAAACCTTAAAACAAAATTATTGAGAGAAATATC
* *
281105 CACGAAGCTGGTAAATGAACAATATGATAGTCCAATGAAGATTAAATATAGAAGAAAGGGAAACA
131 CACGAAGCTGGTAAATGAACAATATGAAAGTCCAATCAAGATTAAATATAGAAGAAAGGGAAACA
* * * *
281170 ATAAAATAATTTCTTATAACAGTAAGTGCATAGTCGATTTCAGAATCATATACTCTATAATCATA
196 AAAAAATAATTTCTTATAAAAATAAGTGCATAGTCGATTTCAAAATCATATACTCTATAATC---
* * *
281235 TATATATATATATATATATATATATATATATATATAAAAGTAGAATATATGTTGAATTTGATTGT
258 ---A-ATATATATATATATATATACATATATATAT---AGTAGAATAAATGTTGAAATTGATTGT
* *
281300 ATCAATTAAGAATTATTCTTTAATATCTTTAAATATTTCGTTTTCAT-GATAGGAGAAACAATAA
316 ATCAATTAAGAATTATTCTTTAATATCCTTAAATATTTCGTTTTCATAG-TAGAAGAAACAATAA
* *
281364 TTTATGTGAA-GATAATTGGCCACGCAATTTTCAAACCTCCAACCTTGTGT
380 CTTATGT-AAGGAGAATTGGCCACGCAATTTTCAAACCTCCAACCTTGTGT
* * *
281414 TTAATCTTATATCCATGAACCAAACCCATCCAAGAGATGTGACGTACACGTATGT-AAAATAA-C
1 TTAATCTTATACCCATGAACCAAACACATCCAAGAGATGTGACGTACACGTATCTAAAAATAATC
* * * * *
281477 TACATTATACTCTTAAATAAAGAATTCATCTTTAAACCTTGAAACAAAATTATTGAGA-AGAATA
66 -ACATTATAATCTTAAATAAACAATCCATCTTCAAACCTTAAAACAAAATTATTGAGAGA-AATA
* * * *
281541 TCCATGAA-CATGGTAAATGAACGATGTGAAAGTCCAATCAAGATTAAATATAGAATAAAGGGAA
129 TCCACGAAGC-TGGTAAATGAACAATATGAAAGTCCAATCAAGATTAAATATAGAAGAAAGGGAA
* * *
281605 ACAAAAAAATAATTTCATTTTAAAAATAATTGTATAG-CTGATTTCAAAATCATATACTCTATAA
193 ACAAAAAAATAATTTC-TTATAAAAATAAGTGCATAGTC-GATTTCAAAATCATATACTCTATAA
*
281669 TC-A-A-AT-TA-ATATATATACAT-T-TATAT-GTAGAATAAATGTTGAAATTGATTGTGTCAA
256 TCAATATATATATATATATATACATATATATATAGTAGAATAAATGTTGAAATTGATTGTATCAA
* *
281726 TTTAGAATTATTCTTTAATA-CCTTACAATATTTCTTTTTCATAGTAGAAGAAACAATAACTTAT
321 TTAAGAATTATTCTTTAATATCCTTA-AATATTTCGTTTTCATAGTAGAAGAAACAATAACTTAT
281790 GTAAGGAGAATTGGCC
385 GTAAGGAGAATTGGCC
281806 TATGCAAGTA
Statistics
Matches: 344, Mismatches: 40, Indels: 34
0.82 0.10 0.08
Matches are distributed among these distances:
420 6 0.02
421 92 0.27
422 1 0.00
425 5 0.01
426 1 0.00
427 11 0.03
428 2 0.01
429 2 0.01
430 1 0.00
431 1 0.00
437 3 0.01
438 129 0.38
439 90 0.26
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (429 bp):
TTAATCTTATACCCATGAACCAAACACATCCAAGAGATGTGACGTACACGTATCTAAAAATAATC
ACATTATAATCTTAAATAAACAATCCATCTTCAAACCTTAAAACAAAATTATTGAGAGAAATATC
CACGAAGCTGGTAAATGAACAATATGAAAGTCCAATCAAGATTAAATATAGAAGAAAGGGAAACA
AAAAAATAATTTCTTATAAAAATAAGTGCATAGTCGATTTCAAAATCATATACTCTATAATCAAT
ATATATATATATATATACATATATATATAGTAGAATAAATGTTGAAATTGATTGTATCAATTAAG
AATTATTCTTTAATATCCTTAAATATTTCGTTTTCATAGTAGAAGAAACAATAACTTATGTAAGG
AGAATTGGCCACGCAATTTTCAAACCTCCAACCTTGTGT
Found at i:283942 original size:39 final size:40
Alignment explanation
Indices: 283883--283982 Score: 107
Period size: 40 Copynumber: 2.5 Consensus size: 40
283873 GTCTAGACAT
* *
283883 ATTTT-CCCTAAGCACAAAGCAAAGG-AGCAT-ACGGTAAA
1 ATTTTCCCCTATGCACGAAGCAAAGGTAGCATGA-GGTAAA
* * *
283921 ATTTTCCCCTATGCATGAAGCAAAGGTGGCATGAGGTAAG
1 ATTTTCCCCTATGCACGAAGCAAAGGTAGCATGAGGTAAA
* *
283961 GTTTTTCCCTATGCACGAAGCA
1 ATTTTCCCCTATGCACGAAGCA
283983 TATGATCCTA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 5 0.10
39 17 0.33
40 28 0.55
41 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (40 bp):
ATTTTCCCCTATGCACGAAGCAAAGGTAGCATGAGGTAAA
Found at i:289158 original size:17 final size:18
Alignment explanation
Indices: 289136--289182 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
289126 TATAGAATTG
*
289136 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
289153 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
289171 GATTCCAATTCC
1 GATTCCAATTCC
289183 CTCATAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:289821 original size:44 final size:42
Alignment explanation
Indices: 289704--289866 Score: 129
Period size: 42 Copynumber: 3.8 Consensus size: 42
289694 CACTATTTTA
* * *
289704 TTTTTTATATTTATAATTGAGGTCACTAATTTTTATAATCACA-
1 TTTTTTAT-TTTATAATTGAGCTC-CTAATTTTTACAATCCCAT
* * *
289747 -CTTTTATCTTTATAACTGGGC-CCATAAATTTTT-CAATCCCACT
1 TTTTTTAT-TTTATAATTGAGCTCC-T-AATTTTTACAATCCCA-T
*
289790 TTTTTTATATTTATAATTGATGACT-CTAATTTTTTACAATCTCAT
1 TTTTTTAT-TTTATAATTGA-G-CTCCTAA-TTTTTACAATCCCAT
*
289835 TTTTTTCTTTTATAATTGAGCTCCTAATTTTT
1 TTTTTTATTTTATAATTGAGCTCCTAATTTTT
289867 TTCATTCTCA
Statistics
Matches: 96, Mismatches: 13, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
40 1 0.01
41 8 0.08
42 30 0.31
43 5 0.05
44 28 0.29
45 15 0.16
46 9 0.09
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (42 bp):
TTTTTTATTTTATAATTGAGCTCCTAATTTTTACAATCCCAT
Found at i:289863 original size:43 final size:42
Alignment explanation
Indices: 289704--290074 Score: 194
Period size: 43 Copynumber: 8.7 Consensus size: 42
289694 CACTATTTTA
* * *
289704 TTTTTTATATTTATAATTGAGGTCACTAATTTTTAT-AATCACAC
1 TTTTTTCT-TTTATAATTGAGCTC-CTAATTTTT-TCAATCTCAC
* * * * *
289748 TTTTATC-TTTATAACTGGGC-CCATAAATTTTTCAATCCCAC
1 TTTTTTCTTTTATAATTGAGCTCC-TAATTTTTTCAATCTCAC
* *
289789 TTTTTTTATATTTATAATTGATGACT-CTAATTTTTTACAATCTCAT
1 -TTTTTTCT-TTTATAATTGA-G-CTCCTAATTTTTT-CAATCTCAC
*
289835 TTTTTTCTTTTATAATTGAGCTCCTAATTTTTTTCATTCTCA-
1 TTTTTTCTTTTATAATTGAGCTCCTAA-TTTTTTCAATCTCAC
* * * * *
289877 ---TTACCTTTATAATTGTGGCCCCTAATTTTTT-AAT-TTAC
1 TTTTTTCTTTTATAATTG-AGCTCCTAATTTTTTCAATCTCAC
* **
289915 TTTTTATC-TTTATAATTGAGGCCCCTAATTTTTTCAAAATCAC
1 TTTTT-TCTTTTATAATTGA-GCTCCTAATTTTTTCAATCTCAC
* * *
289958 TTTTTACTTTT-TAAATTGAGGTCCCTAATTTTTTTAATCTCAC
1 TTTTTTCTTTTAT-AATTGAGCT-CCTAATTTTTTCAATCTCAC
* * * * * *
290001 CTATTACCTTTATAATTGAGATCCCTAATTATTTT-AACCAT-AC
1 TTTTTTCTTTTATAATTGAGCT-CCTAATT-TTTTCAATC-TCAC
* * *
290044 TTTTTACTTTTATAATTTAAGCCCCTAATTT
1 TTTTTTCTTTTATAA-TTGAGCTCCTAATTT
290075 AATCATTTTC
Statistics
Matches: 257, Mismatches: 43, Indels: 56
0.72 0.12 0.16
Matches are distributed among these distances:
37 2 0.01
38 2 0.01
39 19 0.07
40 9 0.04
41 41 0.16
42 24 0.09
43 94 0.37
44 41 0.16
45 16 0.06
46 9 0.04
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (42 bp):
TTTTTTCTTTTATAATTGAGCTCCTAATTTTTTCAATCTCAC
Found at i:289867 original size:44 final size:44
Alignment explanation
Indices: 289775--289878 Score: 124
Period size: 44 Copynumber: 2.3 Consensus size: 44
289765 GGCCCATAAA
*
289775 TTTTTCAATCCCACTTTTTTTATATTTATAATTGATGACTCTAAT
1 TTTTTCAATCTCA-TTTTTTTATATTTATAATTGATGACTCTAAT
*
289820 TTTTTACAATCTCATTTTTTTCT-TTTATAATTGA-G-CTCCTAATT
1 TTTTT-CAATCTCATTTTTTTATATTTATAATTGATGACT-CTAA-T
*
289864 TTTTTCATTCTCATT
1 TTTTTCAATCTCATT
289879 ACCTTTATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
42 2 0.04
43 14 0.26
44 17 0.32
45 13 0.25
46 7 0.13
ACGTcount: A:0.23, C:0.16, G:0.04, T:0.57
Consensus pattern (44 bp):
TTTTTCAATCTCATTTTTTTATATTTATAATTGATGACTCTAAT
Found at i:289906 original size:39 final size:40
Alignment explanation
Indices: 289843--289950 Score: 121
Period size: 41 Copynumber: 2.7 Consensus size: 40
289833 ATTTTTTTCT
* *
289843 TTTATAATTGAGCTCCTAATTTTTTTCA-TT-CTCATTACC
1 TTTATAATTGGGCCCCTAA-TTTTTTCATTTACTCATTACC
* ** *
289882 TTTATAATTGTGGCCCCTAATTTTTTAATTTACTTTTTATC
1 TTTATAATTG-GGCCCCTAATTTTTTCATTTACTCATTACC
289923 TTTATAATTGAGGCCCCTAATTTTTTCA
1 TTTATAATTG-GGCCCCTAATTTTTTCA
289951 AAATCACTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 17 0.29
40 9 0.16
41 32 0.55
ACGTcount: A:0.23, C:0.18, G:0.07, T:0.52
Consensus pattern (40 bp):
TTTATAATTGGGCCCCTAATTTTTTCATTTACTCATTACC
Found at i:289962 original size:124 final size:129
Alignment explanation
Indices: 289791--290074 Score: 316
Period size: 124 Copynumber: 2.2 Consensus size: 129
289781 AATCCCACTT
* * * * * * *
289791 TTTTTATATTTATAATTGATGACTCTAATTTTTTACAATCTCATTTTT-TTCTTTTATAATTGAG
1 TTTTTATCTTTATAATTGAAGCCCCTAATTTTTTAAAATCACATTTTTACT-TTTTA-AATTGAG
* * * * **
289855 CT-CCTAATTTTTTTCAT-TC-TC-ATTACCTTTATAATTGTGGCCCCTAATT-TTTTAA-TTTA
64 CTCCCTAATTTTTTTAATCTCACCTATTACCTTTATAATTGAGACCCCTAATTATTTTAACCATA
289914 C
129 C
* *
289915 TTTTTATCTTTATAATTGAGGCCCCTAATTTTTTCAAAATCAC-TTTTTACTTTTTAAATTGAGG
1 TTTTTATCTTTATAATTGAAGCCCCTAATTTTTT-AAAATCACATTTTTACTTTTTAAATTGAGC
*
289979 TCCCTAATTTTTTTAATCTCACCTATTACCTTTATAATTGAGATCCCTAATTATTTTAACCATAC
65 TCCCTAATTTTTTTAATCTCACCTATTACCTTTATAATTGAGACCCCTAATTATTTTAACCATAC
*
290044 TTTTTA-CTTTTATAATTTAAGCCCCTAATTT
1 TTTTTATC-TTTATAATTGAAGCCCCTAATTT
290075 AATCATTTTC
Statistics
Matches: 134, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
123 8 0.06
124 54 0.40
125 9 0.07
126 1 0.01
127 25 0.19
128 7 0.05
129 30 0.22
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (129 bp):
TTTTTATCTTTATAATTGAAGCCCCTAATTTTTTAAAATCACATTTTTACTTTTTAAATTGAGCT
CCCTAATTTTTTTAATCTCACCTATTACCTTTATAATTGAGACCCCTAATTATTTTAACCATAC
Found at i:290019 original size:86 final size:85
Alignment explanation
Indices: 289882--290074 Score: 223
Period size: 86 Copynumber: 2.3 Consensus size: 85
289872 TCTCATTACC
* * * * * *
289882 TTTATAATTGTGGCCCCTAATTTTTTAATTTACTTTTTATCTTTATAATTGAGGCCCCTAATT-T
1 TTTATAATTGAGGCCCCTAATTTTTTAATTCACCTATTACCTTTATAATTGAGACCCCTAATTAT
289946 TTTCAA-AATCACTTTTTACTT
66 TTT-AACAAT-ACTTTTTACTT
* *
289967 TTTA-AATTGAGGTCCCTAATTTTTTTAATCTCACCTATTACCTTTATAATTGAGATCCCTAATT
1 TTTATAATTGAGGCCCCTAA-TTTTTTAAT-TCACCTATTACCTTTATAATTGAGACCCCTAATT
*
290031 ATTTTAACCATACTTTTTAC-T
64 ATTTTAACAATACTTTTTACTT
* *
290052 TTTATAATTTAAGCCCCTAATTT
1 TTTATAATTGAGGCCCCTAATTT
290075 AATCATTTTC
Statistics
Matches: 91, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
84 13 0.14
85 21 0.23
86 51 0.56
87 6 0.07
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (85 bp):
TTTATAATTGAGGCCCCTAATTTTTTAATTCACCTATTACCTTTATAATTGAGACCCCTAATTAT
TTTAACAATACTTTTTACTT
Found at i:292396 original size:16 final size:16
Alignment explanation
Indices: 292375--292405 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
292365 GGGAAACAAT
*
292375 AAAATAATTTCATATA
1 AAAATAATTGCATATA
292391 AAAATAATTGCATAT
1 AAAATAATTGCATAT
292406 TCGATTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (16 bp):
AAAATAATTGCATATA
Found at i:292446 original size:19 final size:19
Alignment explanation
Indices: 292422--292470 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
292412 TCAAAATCAT
292422 ATACTCTATAATCAAATTA
1 ATACTCTATAATCAAATTA
292441 ATACTCTATAATCAAATTA
1 ATACTCTATAATCAAATTA
292460 ATACTCTATAA
1 ATACTCTATAA
292471 ATATAAAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (19 bp):
ATACTCTATAATCAAATTA
Found at i:292879 original size:32 final size:32
Alignment explanation
Indices: 292838--292922 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
292828 TAACACTGTT
* * *
292838 TTAAGGATATATATAACATGTTAATAAAAACA
1 TTAAGGATATATATAAAATATTAACAAAAACA
*
292870 TTAAGGATATATATAAAATATTAACAAAAATA
1 TTAAGGATATATATAAAATATTAACAAAAACA
* *
292902 GTAAGGATTTATA-AATAATAT
1 TTAAGGATATATATAA-AATAT
292923 CGTATAGTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 2 0.04
32 44 0.96
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (32 bp):
TTAAGGATATATATAAAATATTAACAAAAACA
Found at i:294271 original size:301 final size:307
Alignment explanation
Indices: 293708--294282 Score: 790
Period size: 301 Copynumber: 1.9 Consensus size: 307
293698 TCTTAGTAAT
* *
293708 ATGAATATATTGCATAATCGTATTCTTATATTTAATCCTATATTCATGAACCAAACGCATCCGAG
1 ATGAATATATTGCATAATCGTATTCTTATAGTTAATCCTATATCCATGAACCAAACGCATCCGAG
* * * *
293773 AGATGTGGTATACATGAATCAAAAAAGAACTACATTATACTCTTAAATAAAGAATCTATGATCAA
66 AGA----G-ATACA-GAATCAAAAAAGAAATACATTACACTCATAAATAAAGAATCCATGATCAA
** * * * *
293838 ACCTTGAAATTTAGATTATTGAGAGAAATATCCACGAAGCTGGTAAATGAAAGGTCTAAAATTCC
125 ACCTTGAAATCGAGATTATTGAGAGAAATATACACGAAACTGGTAAATGAAAAGTCTAAAAGTCC
* * * *
293903 AATCAAGATTGAATATAGAGAAAATGGAAACAATAAAATAATTTCATATAAATTTAATTGCATAG
190 AATCAAGATTAAATATAGAGAAAAGGGAAACAATAAAATAATTTCACATAAAATTAATTGCATAG
*
293968 TCGATTTCAGAATCATATACTCTATAATCAAATTAATACTGTATAAATATAAA
255 TCGATTTCAAAATCATATACTCTATAATCAAATTAATACTGTATAAATATAAA
*
294021 ATGAATATATTGCATAATCGTATTCTTATAGTTAATCTTATATCCATGAACCAAACGCATCCGA-
1 ATGAATATATTGCATAATCGTATTCTTATAGTTAATCCTATATCCATGAACCAAACGCATCCGAG
* * * *
294085 A-A-A-A-A-AATCTAAAAATAAATATATTACACTCATAAATAAAGAATCCATGTTCAAACCTTG
66 AGAGATACAGAATCAAAAAAGAAATACATTACACTCATAAATAAAGAATCCATGATCAAACCTTG
*
294145 AAA-CGAGATTATTGAGAGAAATATACACGAAACTGGTAAATGAAAAGTCTAAAAAGTCCCATCA
131 AAATCGAGATTATTGAGAGAAATATACACGAAACTGGTAAATGAAAAGTCT-AAAAGTCCAATCA
*
294209 AGATTAAATATAGA-AGAAAGGGAAACAATAAAATAATTTCACATAAAAATT-ATTGTATAGTCG
195 AGATTAAATATAGAGA-AAAGGGAAACAATAAAATAATTTCACAT-AAAATTAATTGCATAGTCG
294272 ATTTCAAAATC
258 ATTTCAAAATC
294283 TTTTTTTATT
Statistics
Matches: 235, Mismatches: 24, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
300 43 0.18
301 121 0.51
302 5 0.02
303 1 0.00
304 1 0.00
305 1 0.00
311 1 0.00
312 1 0.00
313 61 0.26
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (307 bp):
ATGAATATATTGCATAATCGTATTCTTATAGTTAATCCTATATCCATGAACCAAACGCATCCGAG
AGAGATACAGAATCAAAAAAGAAATACATTACACTCATAAATAAAGAATCCATGATCAAACCTTG
AAATCGAGATTATTGAGAGAAATATACACGAAACTGGTAAATGAAAAGTCTAAAAGTCCAATCAA
GATTAAATATAGAGAAAAGGGAAACAATAAAATAATTTCACATAAAATTAATTGCATAGTCGATT
TCAAAATCATATACTCTATAATCAAATTAATACTGTATAAATATAAA
Found at i:296805 original size:23 final size:23
Alignment explanation
Indices: 296746--296829 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
296736 AAATCTTATA
*
296746 TGGCACTACGGTACATTTCTACG
1 TGGCACTACGGTGCATTTCTACG
* *
296769 CGGCACTACAGTGCATTTCTACG
1 TGGCACTACGGTGCATTTCTACG
* *
296792 TGGCACTTCGGTGCAAATTCTAC-
1 TGGCACTACGGTGC-ATTTCTACG
* *
296815 TGGAACTTCGGTGCA
1 TGGCACTACGGTGCA
296830 ATTTATATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
22 1 0.02
23 44 0.85
24 7 0.13
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCATTTCTACG
Found at i:298727 original size:106 final size:106
Alignment explanation
Indices: 298542--298749 Score: 407
Period size: 106 Copynumber: 2.0 Consensus size: 106
298532 GTATGGCAAG
298542 GAAAATCGAGGCAATACTTTACTACCTCTTTATGCTTTATGGAACATGTTAATATTGGTAAATGC
1 GAAAATCGAGGCAATACTTTACTACCTCTTTATGCTTTATGGAACATGTTAATATTGGTAAATGC
298607 ATGAATAAGATAATGTTGGTCACTTTTGTGGAGTTGACACT
66 ATGAATAAGATAATGTTGGTCACTTTTGTGGAGTTGACACT
*
298648 GAAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGGAACATGTTAATATTGGTAAATGC
1 GAAAATCGAGGCAATACTTTACTACCTCTTTATGCTTTATGGAACATGTTAATATTGGTAAATGC
298713 ATGAATAAGATAATGTTGGTCACTTTTGTGGAGTTGA
66 ATGAATAAGATAATGTTGGTCACTTTTGTGGAGTTGA
298750 TAAATTTATA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 101 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (106 bp):
GAAAATCGAGGCAATACTTTACTACCTCTTTATGCTTTATGGAACATGTTAATATTGGTAAATGC
ATGAATAAGATAATGTTGGTCACTTTTGTGGAGTTGACACT
Found at i:301018 original size:43 final size:43
Alignment explanation
Indices: 300957--301248 Score: 428
Period size: 43 Copynumber: 6.8 Consensus size: 43
300947 TTAATTACCG
* * *
300957 TTACAGTTCTCTCAGGTCCCTTTGCTGTGTGTAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
301000 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
301043 TTACAGTTCCCCCAGGTCCCTTTACTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
301086 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGATAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* **
301129 TTACAGTTCTCCCAATTTCCC-TTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTC-CCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
301172 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
301214 TTACAGTTTCCCCAGG-CTCTTTTGCTATGTGCAAG
1 TTACAGTTCCCCCAGGTC-CCTTTGCTGTGTGCAAG
301249 TATAAGACCT
Statistics
Matches: 226, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
41 6 0.03
42 30 0.13
43 182 0.81
44 8 0.04
ACGTcount: A:0.17, C:0.27, G:0.24, T:0.32
Consensus pattern (43 bp):
TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:305060 original size:2 final size:2
Alignment explanation
Indices: 305053--305085 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
305043 CTCTATAATC
305053 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
305086 AGTACAATAA
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:308343 original size:2 final size:2
Alignment explanation
Indices: 308336--308367 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
308326 AATCAAATTA
308336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
308368 AGTAGAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:313556 original size:48 final size:48
Alignment explanation
Indices: 313478--313572 Score: 111
Period size: 48 Copynumber: 2.0 Consensus size: 48
313468 GAAGAAGTTG
* *
313478 ATGATGCAGGAGTCTCCCATGGAGTCGAGGTGATCAATAATGAGGTTA
1 ATGATGCAGAAGTCTCCCATGAAGTCGAGGTGATCAATAATGAGGTTA
* * * * *
313526 ATGATGGAGAAGT-TCCTCATGAAGTTGAGGTGGTCACTTATGAGGTT
1 ATGATGCAGAAGTCTCC-CATGAAGTCGAGGTGATCAATAATGAGGTT
313573 CAGTATAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 3 0.08
48 36 0.92
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.28
Consensus pattern (48 bp):
ATGATGCAGAAGTCTCCCATGAAGTCGAGGTGATCAATAATGAGGTTA
Found at i:321872 original size:5 final size:5
Alignment explanation
Indices: 321862--321887 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
321852 ATGAAAAAAG
321862 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
321888 AAAGAGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:321903 original size:15 final size:14
Alignment explanation
Indices: 321841--321890 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
321831 GGCTATGTTT
*
321841 AAAAAAAA-AAGATG
1 AAAAAAAAGAA-AAG
*
321855 AAAAAAGAGAAAAG
1 AAAAAAAAGAAAAG
321869 AAAAGAAAAGAAAAG
1 AAAA-AAAAGAAAAG
321884 AAAAAAA
1 AAAAAAA
321891 GAGAGATGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 16 0.52
15 15 0.48
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAAAAAAGAAAAG
Found at i:322707 original size:36 final size:36
Alignment explanation
Indices: 322667--322739 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
322657 TTAGGAATGG
* * *
322667 ATTAGCTGCT-AAAGATAAGGTTGGAATTTGAATTTT
1 ATTAGATGCTGAAA-ATAAGGATGGAATTTAAATTTT
*
322703 ATTAGATGCTGAAAATAAGGATGTAATTTAAATTTT
1 ATTAGATGCTGAAAATAAGGATGGAATTTAAATTTT
322739 A
1 A
322740 AATAAAAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 29 0.91
37 3 0.09
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.38
Consensus pattern (36 bp):
ATTAGATGCTGAAAATAAGGATGGAATTTAAATTTT
Found at i:322754 original size:16 final size:18
Alignment explanation
Indices: 322733--322772 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
322723 ATGTAATTTA
322733 AATTTTAAATAA-AA-GG
1 AATTTTAAATAAGAAGGG
*
322749 AATTTTAGATAAGAAGGG
1 AATTTTAAATAAGAAGGG
322767 AATTTT
1 AATTTT
322773 TCAATGGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 2 0.10
18 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.35
Consensus pattern (18 bp):
AATTTTAAATAAGAAGGG
Found at i:342640 original size:24 final size:24
Alignment explanation
Indices: 342613--342689 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
342603 TTTGAAAAAA
342613 AAAGAAAAAAAGAAAAAGAATAAG
1 AAAGAAAAAAAGAAAAAGAATAAG
* *
342637 AAAGGAAAAAAGAATAAG-AT---
1 AAAGAAAAAAAGAAAAAGAATAAG
* *
342657 AAAGAAAAAAATAAAAA-ATAAAAG
1 AAAGAAAAAAAGAAAAAGA-ATAAG
342681 AAAGAAAAA
1 AAAGAAAAA
342690 TGAAATGAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
20 14 0.33
21 1 0.02
23 2 0.05
24 25 0.60
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAAAGAAAAAGAATAAG
Found at i:345106 original size:64 final size:64
Alignment explanation
Indices: 344966--345180 Score: 204
Period size: 64 Copynumber: 3.3 Consensus size: 64
344956 CTTGAAACTT
* * *
344966 AAATCTTTGAGATTGTTTTTCTTGAAACAAAATTTATTCTCACTTGAGACAGTTTCCTTAAGACA
1 AAATATTTGAGATTGTTTTTCTT-AAA-AAAAATTAGTCTCACTTGAGACAGTTTCCTTAAGACA
*
345031 T
64 C
* * * * * *
345032 GAACACTTGAGATTGTTTTTATTAAAAAAAATT-GTCTCACTTGAGACATTCTTTCTTAAGACAC
1 AAATATTTGAGATTGTTTTTCTTAAAAAAAATTAGTCTCACTTGAGACAGT-TTCCTTAAGACAC
* *
345096 AAATATTTGAGATTGTTTTTCTTAAAAACAAATTTCA-TTTCGCTTGAGACAGTTTTCCCTTGAA
1 AAATATTTGAGATTGTTTTTCTTAAAAA-AAA-TT-AGTCTCACTTGAGACAG-TTT-CCTT-AA
345160 -ACAC
60 GACAC
*
345164 AAAT-TTTGAAATTGTTT
1 AAATATTTGAGATTGTTT
345181 CACTCGGAAC
Statistics
Matches: 122, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
63 15 0.12
64 41 0.34
65 6 0.05
66 20 0.16
67 26 0.21
68 12 0.10
69 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (64 bp):
AAATATTTGAGATTGTTTTTCTTAAAAAAAATTAGTCTCACTTGAGACAGTTTCCTTAAGACAC
Found at i:346943 original size:22 final size:22
Alignment explanation
Indices: 346867--346944 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
346857 TATTTTAGTC
346867 ATTGTTTATTTCTTATTTAGCT
1 ATTGTTTATTTCTTATTTAGCT
346889 ATTGTTCTTTTATTT-TATGCATTTTAG-T
1 ATTG----TTTATTTCT-T--A-TTTAGCT
346917 CATTGTTTATTTCTTATTTAGCT
1 -ATTGTTTATTTCTTATTTAGCT
346940 ATTGT
1 ATTGT
346945 ACATTTATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 22
0.67 0.00 0.33
Matches are distributed among these distances:
22 14 0.31
23 2 0.04
25 9 0.20
26 9 0.20
28 2 0.04
29 9 0.20
ACGTcount: A:0.18, C:0.09, G:0.10, T:0.63
Consensus pattern (22 bp):
ATTGTTTATTTCTTATTTAGCT
Found at i:346987 original size:51 final size:51
Alignment explanation
Indices: 346741--346971 Score: 302
Period size: 51 Copynumber: 4.5 Consensus size: 51
346731 CTTAATGTGA
* * * * *
346741 TTCTTTCAATTTATGCATTTTAGTCACTATTTATTTCTGATTTAGCTAATG
1 TTCTTTTATTTTATGCATTTTAGTCACTGTTTATTTCTTATTTAGCTATTG
* * * * *
346792 TTCTTTTATTTTATGCATTTTAGTCACTATATA-TTGTTGTTTAACTATTG
1 TTCTTTTATTTTATGCATTTTAGTCACTGTTTATTTCTTATTTAGCTATTG
* * *
346842 TTCTTTTAATTTATGTATTTTAGTCATTGTTTATTTCTTATTTAGCTATTG
1 TTCTTTTATTTTATGCATTTTAGTCACTGTTTATTTCTTATTTAGCTATTG
*
346893 TTCTTTTATTTTATGCATTTTAGTCATTGTTTATTTCTTATTTAGCTATTG
1 TTCTTTTATTTTATGCATTTTAGTCACTGTTTATTTCTTATTTAGCTATTG
* * *
346944 TACATTTATTTTATGCATTTTATTCACT
1 TTCTTTTATTTTATGCATTTTAGTCACT
346972 TTCACTTTTT
Statistics
Matches: 157, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
50 40 0.25
51 117 0.75
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.59
Consensus pattern (51 bp):
TTCTTTTATTTTATGCATTTTAGTCACTGTTTATTTCTTATTTAGCTATTG
Found at i:347080 original size:18 final size:17
Alignment explanation
Indices: 347048--347081 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
347038 ATTTCTTTTC
*
347048 ATATTATTTTTTATTTG
1 ATATTATTTTATATTTG
347065 ATATTGATTTTATATTT
1 ATATT-ATTTTATATTT
347082 TTTTGGTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
ATATTATTTTATATTTG
Found at i:348899 original size:20 final size:20
Alignment explanation
Indices: 348644--348904 Score: 90
Period size: 20 Copynumber: 11.6 Consensus size: 20
348634 AATAAAATGA
*
348644 ATGAAATGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
*
348664 ATGAAAGGATGCCATGAATAAAATGC
1 ATGAAAGGATG-CAT---T--AAGGC
*
348690 ATGAAAGCATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
* * **
348710 ATGAAATGATGCCATAAAAAAATAC
1 ATGAAAGGATG-CAT----TAAGGC
* *
348735 ATGAAATGATGCATTGAGGC
1 ATGAAAGGATGCATTAAGGC
* *
348755 ATGAATGGATGCCATGAATAAATTGC
1 ATGAAAGGATG-CAT---T-AA-GGC
* *
348781 TTGAAAGGATGCATTAAGTC
1 ATGAAAGGATGCATTAAGGC
* **
348801 AGGAAAGGATGCCATGAATAAAATAC
1 ATGAAAGGATG-CAT---T--AAGGC
348827 ATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
* *
348847 ACGAAAGGATGCCATGAATAAAATGC
1 ATGAAAGGATG-CAT---T--AAGGC
348873 ATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
*
348893 ATAAAAGGATGC
1 ATGAAAGGATGC
348905 CATGAATAAA
Statistics
Matches: 179, Mismatches: 33, Indels: 58
0.66 0.12 0.21
Matches are distributed among these distances:
20 72 0.40
21 17 0.09
22 4 0.02
24 7 0.04
25 27 0.15
26 52 0.29
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
ATGAAAGGATGCATTAAGGC
Found at i:348942 original size:183 final size:183
Alignment explanation
Indices: 348624--349127 Score: 678
Period size: 183 Copynumber: 2.7 Consensus size: 183
348614 GTGTCTTTAT
*
348624 GGATGCCTTGAATAAAATGA-ATGAAATGATGCATTAAGGCATGAAAGGATGCCATGAATAAAAT
1 GGATGCCATGAATAAAAT-ACATGAAATGATGCATTAAGGCATGAAAGGATGCCATGAATAAAAT
* *
348688 GCATGAAAGCATGCATTAAGGCATGAAATGATGCCAT-AAAAAAAT-ACATGAAATGATGCATTG
65 GCATGAAAGGATGCATTAAGGCATGAAATGATGCCATGAATAAAATGA-ATGAAATGATGCATT-
* * * * **
348751 AGGCATGAATGGAT-GC-CATGAATAAATTGCTTGAAAGGATGCATTAAGTCAGGAAA
128 AAGCATGAATGGATGGCGCA--AATAAAATGCATGAAAGGATACATTAAGGAAGGAAA
* *
348807 GGATGCCATGAATAAAATACATGAAAGGATGCATTAAGGCACGAAAGGATGCCATGAATAAAATG
1 GGATGCCATGAATAAAATACATGAAATGATGCATTAAGGCATGAAAGGATGCCATGAATAAAATG
* *
348872 CATGAAAGGATGCATTAAGGCATAAAAGGATGCCATGAATAAAATGAATGAAATGATGCATTAAG
66 CATGAAAGGATGCATTAAGGCATGAAATGATGCCATGAATAAAATGAATGAAATGATGCATTAAG
* * * *
348937 CATGAAAGGATGGCGCAAATAAAATGCATGAATGGATATATTAAGGAATGAAA
131 CATGAATGGATGGCGCAAATAAAATGCATGAAAGGATACATTAAGGAAGGAAA
* * * *
348990 GGATTCCATAAATAAAATACTTGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATG
1 GGATGCCATGAATAAAATACATGAAATGATGCATTAAGGCATGAAAGGATGCCATGAATAAAATG
* * * *
349055 CATTAAAGGATGCATTAAGGCATGAAATGATGCAATGAATAAAATGCAAT-CAAGGATGCATTAA
66 CATGAAAGGATGCATTAAGGCATGAAATGATGCCATGAATAAAATG-AATGAAATGATGCATTAA
349119 GGCATGAAT
130 -GCATGAAT
349128 AAAATGCATG
Statistics
Matches: 284, Mismatches: 30, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
182 1 0.00
183 246 0.87
184 34 0.12
185 3 0.01
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (183 bp):
GGATGCCATGAATAAAATACATGAAATGATGCATTAAGGCATGAAAGGATGCCATGAATAAAATG
CATGAAAGGATGCATTAAGGCATGAAATGATGCCATGAATAAAATGAATGAAATGATGCATTAAG
CATGAATGGATGGCGCAAATAAAATGCATGAAAGGATACATTAAGGAAGGAAA
Found at i:349025 original size:229 final size:229
Alignment explanation
Indices: 348624--349123 Score: 677
Period size: 229 Copynumber: 2.2 Consensus size: 229
348614 GTGTCTTTAT
* * * *
348624 GGATGCCTTGAATAAAATGAATGAAATGATGCATTAAGGCATGAAAGGATGCCATGAATAAAATG
1 GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCATGAATAAAATG
* * * *
348689 CATGAAAGCATGCATTAAGGCATGAAATGATGCCATAAAAAAATACATGAAATGATGCATTGAGG
66 AATGAAAGCATGCATTAAGGCATGAAAGGATGCCATAAAAAAATACATGAAATGATACATTAAGG
* * * * * * *
348754 CATGAATGGATGCCATGAATAAATTGCTTGAAAGGATGCATTAAGTCAGGAAAGGATGCCATGAA
131 AATGAAAGGATGCCATAAATAAAATACTTGAAAGGATGCATTAAGGCAGGAAAGGATGCCATAAA
348819 TAAAATACATGAAAGGATGCATTAAGGCACGAAA
196 TAAAATACATGAAAGGATGCATTAAGGCACGAAA
348853 GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCATGAATAAAATG
1 GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCATGAATAAAATG
* * *
348918 AATGAAATG-ATGCATTAA-GCATGAAAGGATGGCGCA-AATAAAATGCATG-AATGGATATATT
66 AATGAAA-GCATGCATTAAGGCATGAAAGGAT-GC-CATAAAAAAATACATGAAAT-GATACATT
* * *
348979 AAGGAATGAAAGGATTCCATAAATAAAATACTTGAAATGATGCATTAAGGCATGAAAGGATGCCA
127 AAGGAATGAAAGGATGCCATAAATAAAATACTTGAAAGGATGCATTAAGGCAGGAAAGGATGCCA
* * *
349044 TAAATAAAATGCATTAAAGGATGCATTAAGGCATGAAA
192 TAAATAAAATACATGAAAGGATGCATTAAGGCACGAAA
* * *
349082 TGATGCAATGAATAAAATGCAAT-CAAGGATGCATTAAGGCAT
1 GGATGCCATGAATAAAATGC-ATGAAAGGATGCATTAAGGCAT
349124 GAATAAAATG
Statistics
Matches: 239, Mismatches: 27, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
228 14 0.06
229 220 0.92
230 5 0.02
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (229 bp):
GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCATGAATAAAATG
AATGAAAGCATGCATTAAGGCATGAAAGGATGCCATAAAAAAATACATGAAATGATACATTAAGG
AATGAAAGGATGCCATAAATAAAATACTTGAAAGGATGCATTAAGGCAGGAAAGGATGCCATAAA
TAAAATACATGAAAGGATGCATTAAGGCACGAAA
Found at i:349040 original size:20 final size:20
Alignment explanation
Indices: 349011--349088 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
349001 ATAAAATACT
*
349011 TGAAATGATGCATTAAGGCA
1 TGAAAGGATGCATTAAGGCA
*
349031 TGAAAGGATGCCATAAATAAAATGCA
1 TGAAAGGATG-CAT---T--AAGGCA
*
349057 TTAAAGGATGCATTAAGGCA
1 TGAAAGGATGCATTAAGGCA
*
349077 TGAAATGATGCA
1 TGAAAGGATGCA
349089 ATGAATAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
20 24 0.52
21 3 0.07
22 1 0.02
24 1 0.02
25 3 0.07
26 14 0.30
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.23
Consensus pattern (20 bp):
TGAAAGGATGCATTAAGGCA
Found at i:349126 original size:33 final size:33
Alignment explanation
Indices: 349089--349159 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
349079 AAATGATGCA
*
349089 ATGAATAAAATGCAAT-CAAGGATGCATTAAGGC
1 ATGAATAAAATGC-ATGAAAGGATGCATTAAGGC
*
349122 ATGAATAAAATGCATGAAATGATGCATTAAGGC
1 ATGAATAAAATGCATGAAAGGATGCATTAAGGC
349155 ATGAA
1 ATGAA
349160 AGGATGCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.06
33 33 0.94
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (33 bp):
ATGAATAAAATGCATGAAAGGATGCATTAAGGC
Found at i:349139 original size:46 final size:46
Alignment explanation
Indices: 348624--349126 Score: 647
Period size: 46 Copynumber: 11.0 Consensus size: 46
348614 GTGTCTTTAT
* * *
348624 GGATGCCTTGAATAAAATGAATGAAATGATGCATTAAGGCATGAAA
1 GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATGAAA
*
348670 GGATGCCATGAATAAAATGCATGAAAGCATGCATTAAGGCATGAAA
1 GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATGAAA
* * * * * *
348716 TGATGCCAT-AAAAAAATACATGAAATGATGCATTGAGGCATGAAT
1 GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATGAAA
* * * *
348761 GGATGCCATGAATAAATTGCTTGAAAGGATGCATTAAGTCAGGAAA
1 GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATGAAA
* *
348807 GGATGCCATGAATAAAATACATGAAAGGATGCATTAAGGCACGAAA
1 GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATGAAA
*
348853 GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATAAAA
1 GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATGAAA
* *
348899 GGATGCCATGAATAAAATGAATGAAATGATGCATTAA-GCATGAAA
1 GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATGAAA
* ** *
348944 GGATGGCGCA--AATAAAATGCATGAATGGATATATTAAGGAATGAAA
1 GGAT-GC-CATGAATAAAATGCATGAAAGGATGCATTAAGGCATGAAA
* * * * *
348990 GGATTCCATAAATAAAATACTTGAAATGATGCATTAAGGCATGAAA
1 GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATGAAA
* *
349036 GGATGCCATAAATAAAATGCATTAAAGGATGCATTAAGGCATGAAA
1 GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATGAAA
* * *
349082 TGATGCAATGAATAAAATGCAAT-CAAGGATGCATTAAGGCATGAA
1 GGATGCCATGAATAAAATGC-ATGAAAGGATGCATTAAGGCATGAA
349127 TAAAATGCAT
Statistics
Matches: 395, Mismatches: 55, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
44 2 0.01
45 72 0.18
46 317 0.80
47 4 0.01
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.22
Consensus pattern (46 bp):
GGATGCCATGAATAAAATGCATGAAAGGATGCATTAAGGCATGAAA
Found at i:349158 original size:20 final size:21
Alignment explanation
Indices: 349133--349172 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
349123 TGAATAAAAT
*
349133 GCATGAAATGATG-CATTAAG
1 GCATGAAAGGATGCCATTAAG
349153 GCATGAAAGGATGCCATTAA
1 GCATGAAAGGATGCCATTAA
349173 TAAAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (21 bp):
GCATGAAAGGATGCCATTAAG
Found at i:351383 original size:2 final size:2
Alignment explanation
Indices: 351376--351417 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
351366 TGTCATAAAG
351376 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
351416 AT
1 AT
351418 TATGGTTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:353564 original size:20 final size:20
Alignment explanation
Indices: 353538--353589 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
353528 TGATTCAATC
*
353538 GGTATCGATACCGAAGGGGTA
1 GGTATCGATACCGAA-GGGAA
353559 -GTATCGATACCGAAGGGAA
1 GGTATCGATACCGAAGGGAA
353578 GGTATCGATACC
1 GGTATCGATACC
353590 ATTTTAAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.31, C:0.17, G:0.33, T:0.19
Consensus pattern (20 bp):
GGTATCGATACCGAAGGGAA
Found at i:353665 original size:22 final size:19
Alignment explanation
Indices: 353620--353684 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 19
353610 AATGGTATTA
*
353620 ATACCATAGTAGAGTATTG
1 ATACCATAGTAGAGTATCG
*
353639 GTACCATAGTATAGTAGTATCG
1 ATACCATAG--TAG-AGTATCG
* *
353661 ATACCATGGTAGGGGTATCG
1 ATACCATAGTA-GAGTATCG
353681 ATAC
1 ATAC
353685 TATGGAGTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 8 0.22
20 12 0.32
21 4 0.11
22 13 0.35
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (19 bp):
ATACCATAGTAGAGTATCG
Found at i:353836 original size:13 final size:13
Alignment explanation
Indices: 353818--353889 Score: 67
Period size: 13 Copynumber: 5.5 Consensus size: 13
353808 TTATGGATGC
353818 CATGAAAAAAATG
1 CATGAAAAAAATG
**
353831 CATG-AAAGGATG
1 CATGAAAAAAATG
353843 CCATGAAAAAAATG
1 -CATGAAAAAAATG
*
353857 CATG-AAAAGATG
1 CATGAAAAAAATG
* *
353869 CCATGAATAAAGTG
1 -CATGAAAAAAATG
353883 CATGAAA
1 CATGAAA
353890 GGATGCCATA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
12 13 0.28
13 22 0.48
14 11 0.24
ACGTcount: A:0.51, C:0.11, G:0.21, T:0.17
Consensus pattern (13 bp):
CATGAAAAAAATG
Found at i:353848 original size:26 final size:26
Alignment explanation
Indices: 353812--353915 Score: 156
Period size: 26 Copynumber: 4.0 Consensus size: 26
353802 GTGTCTTTAT
353812 GGATGCCATGAAAAAAATGCATGAAA
1 GGATGCCATGAAAAAAATGCATGAAA
353838 GGATGCCATGAAAAAAATGCATGAAA
1 GGATGCCATGAAAAAAATGCATGAAA
* * *
353864 AGATGCCATGAATAAAGTGCATGAAA
1 GGATGCCATGAAAAAAATGCATGAAA
*
353890 GGATGCCAT-AAATAAAGTGCATGAAA
1 GGATGCCATGAAA-AAAATGCATGAAA
353916 TGAGGCATTA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
25 2 0.03
26 70 0.97
ACGTcount: A:0.48, C:0.12, G:0.23, T:0.17
Consensus pattern (26 bp):
GGATGCCATGAAAAAAATGCATGAAA
Found at i:353933 original size:20 final size:20
Alignment explanation
Indices: 353908--354231 Score: 182
Period size: 20 Copynumber: 14.7 Consensus size: 20
353898 TAAATAAAGT
* *
353908 GCATGAAATGAGGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
353928 GCATGAAAGGACGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
353948 GCATGAAAGGATACATTAAT
1 GCATGAAAGGATGCATTAAG
353968 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
353988 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
354014 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
354034 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
354060 G-ATTGAAAGGATGCATTAAG
1 GCA-TGAAAGGATGCATTAAG
* * *
354080 GCGTGAAAGTATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
354106 GCATGAATGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
354126 GCATGAGAGGATGACATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
354152 GCATGAAATGATGTATTAAG
1 GCATGAAAGGATGCATTAAG
* * * * *
354172 GAATGAAACGAAGCCTCGAATAAAAT
1 GCATGAAA-G--G-AT-GCAT-TAAG
354198 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
354218 GCATGAAAGGATGC
1 GCATGAAAGGATGC
354232 CATGAATAAA
Statistics
Matches: 236, Mismatches: 36, Indels: 64
0.70 0.11 0.19
Matches are distributed among these distances:
20 131 0.56
21 15 0.06
22 5 0.02
23 2 0.01
24 5 0.02
25 16 0.07
26 62 0.26
ACGTcount: A:0.44, C:0.10, G:0.25, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:353965 original size:40 final size:41
Alignment explanation
Indices: 353881--354271 Score: 241
Period size: 46 Copynumber: 8.7 Consensus size: 41
353871 ATGAATAAAG
* *
353881 TGCATGAAAGGATGCCATAAATAAAGTGCATGAAATGA-GGCATTAA
1 TGCATGAAAGGATG-CAT---T-AAG-GCATGAAAGGATGACATTAA
* *
353927 GGCATGAAAGGACGCATTAAGGCATGAAAGGAT-ACATTAA
1 TGCATGAAAGGATGCATTAAGGCATGAAAGGATGACATTAA
*
353967 TGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAA
1 TGCATGAAAGGATGCATTAAGGCATGAAAGGATGACAT---T--AA
*
354013 TGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAA
1 TGCATGAAAGGATGCATTAAGGCATGAAAGGATGACAT---T--AA
* * *
354059 TG-ATTGAAAGGATGCATTAAGGCGTGAAAGTATGCCATAAATAAAA
1 TGCA-TGAAAGGATGCATTAAGGCATGAAAGGATGACAT---T--AA
* *
354105 TGCATGAATGGATGCATTAAGGCATGAGAGGATGACATAAATAAAA
1 TGCATGAAAGGATGCATTAAGGCATGAAAGGATGACAT---T--AA
* * * * *
354151 TGCATGAAATGATGTATTAAGGAATGAAACGAAGCCTCGA-ATAAAA
1 TGCATGAAAGGATGCATTAAGGCATGAAA-G--G-AT-GACAT-TAA
*
354197 TGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATGAATAAAA
1 TGCATGAAAGGATGCATTAAGGCATGAAAGGATGACAT---T--AA
* *
354243 TGCATGAAAGGATGCAATAAAGCATGAAA
1 TGCATGAAAGGATGCATTAAGGCATGAAA
354272 TGACGCCATA
Statistics
Matches: 297, Mismatches: 29, Indels: 38
0.82 0.08 0.10
Matches are distributed among these distances:
40 47 0.16
41 7 0.02
42 4 0.01
43 1 0.00
44 2 0.01
45 5 0.02
46 222 0.75
47 2 0.01
48 1 0.00
49 1 0.00
50 3 0.01
51 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.25, T:0.20
Consensus pattern (41 bp):
TGCATGAAAGGATGCATTAAGGCATGAAAGGATGACATTAA
Found at i:354032 original size:46 final size:46
Alignment explanation
Indices: 353928--354290 Score: 490
Period size: 46 Copynumber: 8.0 Consensus size: 46
353918 AGGCATTAAG
* *
353928 GCATGAAAGGACGCATTAAGGCATGAAAGGAT-ACAT---T--AAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
353968 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
354014 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
* *
354060 G-ATTGAAAGGATGCATTAAGGCGTGAAAGTATGCCATAAATAAAAT
1 GCA-TGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
* * *
354106 GCATGAATGGATGCATTAAGGCATGAGAGGATGACATAAATAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
* * * * * *
354152 GCATGAAATGATGTATTAAGGAATGAAACGAAGCC-TCGAATAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCAT-AAATAAAAT
*
354198 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATGAATAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
* * * *
354244 GCATGAAAGGATGCAATAAAGCATGAAATGACGCCATAAATAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
354290 G
1 G
354291 AAATTTAAAG
Statistics
Matches: 285, Mismatches: 28, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
40 31 0.11
41 3 0.01
44 1 0.00
45 2 0.01
46 246 0.86
47 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.20
Consensus pattern (46 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
Found at i:354213 original size:12 final size:12
Alignment explanation
Indices: 354196--354258 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
354186 CTCGAATAAA
354196 ATGCATGAAAGG
1 ATGCATGAAAGG
*
354208 ATGCAT-TAA-G
1 ATGCATGAAAGG
354218 --GCATGAAAGG
1 ATGCATGAAAGG
**
354228 ATGCCATGAATAAA
1 ATG-CATGAA-AGG
354242 ATGCATGAAAGG
1 ATGCATGAAAGG
354254 ATGCA
1 ATGCA
354259 ATAAAGCATG
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 2 0.05
11 2 0.05
12 13 0.33
13 12 0.31
14 4 0.10
ACGTcount: A:0.43, C:0.11, G:0.27, T:0.19
Consensus pattern (12 bp):
ATGCATGAAAGG
Found at i:354282 original size:20 final size:20
Alignment explanation
Indices: 354198--354283 Score: 55
Period size: 20 Copynumber: 4.0 Consensus size: 20
354188 CGAATAAAAT
* * *
354198 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGACGCAATAAA
*
354218 GCATGAAAGGATGCCATGAATAAAA
1 GCATGAAAGGACG-C---AAT-AAA
*
354243 TGCATGAAAGGATGCAATAAA
1 -GCATGAAAGGACGCAATAAA
* *
354264 GCATGAAATGACGCCATAAA
1 GCATGAAAGGACGCAATAAA
354284 TAAAATGAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
20 30 0.55
21 4 0.07
22 3 0.05
24 2 0.04
25 3 0.05
26 13 0.24
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.17
Consensus pattern (20 bp):
GCATGAAAGGACGCAATAAA
Found at i:382275 original size:55 final size:55
Alignment explanation
Indices: 382144--382594 Score: 523
Period size: 55 Copynumber: 8.3 Consensus size: 55
382134 TTTTGCAAAT
* * * * * * *
382144 ATAGTGTCAATACGGTAATTCACATACTCATTATGAATTACATGGGG-TG-A-AC
1 ATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * ** * ** **
382196 AAAGTACCAATATGGTAATTCATAAACTCATTATGAATTAAGTGGTATTGCACAC
1 ATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * * *
382251 ATAGTGGCAATATATAAATTCATAAACTCATTATGAATTTTGTGGGGTTGCACAC
1 ATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * * ** * *
382306 ATACTGTCAATACAAAAATTTGTAAACTCATTATGAATTTCGTGGGGTTGTACAA
1 ATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
** * * *
382361 ATAGTGTTAATACGGAAATTCATAAACTCATTATGAATTTCGTCGGGTTGCACAT
1 ATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* *
382416 ATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGATGCACAC
1 ATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
382471 ATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
1 ATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * * *
382526 AAAGTCCCAGTAC-GAAAATTAATAAACTCATTATGAATTTCGTGGGGTTGCACAC
1 ATAGTGCCAATACAG-AAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
382581 ATAGTGCCAATACA
1 ATAGTGCCAATACA
382595 TAATTTGCAA
Statistics
Matches: 342, Mismatches: 52, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
52 37 0.11
53 2 0.01
54 2 0.01
55 301 0.88
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (55 bp):
ATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
Found at i:388741 original size:83 final size:83
Alignment explanation
Indices: 388590--388757 Score: 214
Period size: 83 Copynumber: 2.0 Consensus size: 83
388580 ATACCTTAAA
* *
388590 GGTGTTTTTCCAACAAAATCCCTAATAGAGTAATATTTTAGCGGTGTTTATAGCACAAACCTCAG
1 GGTGCTTTTCCAACAAAATCCCTAATAGAGTAATAATTTAGCGGTGTTTATAGCACAAACCTCAG
*
388655 AATATGGTTGTTTATAGT
66 AATAGGGTTGTTTATAGT
* * * ** *
388673 GGTGCTTTTCCAAC-AAATGCCAC-AATAGAGTAGTAATTTAGTGGTGTTTATAGCATAAATGTT
1 GGTGCTTTTCCAACAAAAT-CC-CTAATAGAGTAATAATTTAGCGGTGTTTATAGCACAAACCTC
*
388736 GGAATAGGGTTGTTTATAGT
64 AGAATAGGGTTGTTTATAGT
388756 GG
1 GG
388758 CATTTTTCAA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
82 4 0.05
83 68 0.93
84 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (83 bp):
GGTGCTTTTCCAACAAAATCCCTAATAGAGTAATAATTTAGCGGTGTTTATAGCACAAACCTCAG
AATAGGGTTGTTTATAGT
Found at i:388765 original size:83 final size:82
Alignment explanation
Indices: 388594--388783 Score: 211
Period size: 83 Copynumber: 2.3 Consensus size: 82
388584 CTTAAAGGTG
*
388594 TTTTTCCAACAAAATCCCTAATAGAGTAATATTTTAGCGGTGTTTATAGCACAAACCTCAGAATA
1 TTTTTCCAAC-AAATCCCTAATAGAGTAATAATTTAGCGGTGTTTATAGCACAAACCTCAGAATA
* **
388659 TGGTTGTTTATAGTGGTG
65 GGGTTGTTTATAGTGGCA
* * * * ** **
388677 CTTTTCCAACAAATGCCAC-AATAGAGTAGTAATTTAGTGGTGTTTATAGCATAAATGTTGGAAT
1 TTTTTCCAACAAAT-CC-CTAATAGAGTAATAATTTAGCGGTGTTTATAGCACAAACCTCAGAAT
388741 AGGGTTGTTTATAGTGGCA
64 AGGGTTGTTTATAGTGGCA
* *
388760 TTTTTCAAACAAATACCGTAATAG
1 TTTTTCCAACAAAT-CCCTAATAG
388784 GGTTGTTTAT
Statistics
Matches: 88, Mismatches: 16, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
82 4 0.05
83 83 0.94
84 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (82 bp):
TTTTTCCAACAAATCCCTAATAGAGTAATAATTTAGCGGTGTTTATAGCACAAACCTCAGAATAG
GGTTGTTTATAGTGGCA
Found at i:389293 original size:21 final size:22
Alignment explanation
Indices: 389242--389294 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
389232 CGTTTTACTG
*
389242 ATTTATTGCTTGGGAGCAATGT
1 ATTTACTGCTTGGGAGCAATGT
* * *
389264 -CTTACTGCTTGGTAGCAGTGT
1 ATTTACTGCTTGGGAGCAATGT
389285 ATTTA-TGCTT
1 ATTTACTGCTT
389295 TCGAATAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.43
Consensus pattern (22 bp):
ATTTACTGCTTGGGAGCAATGT
Found at i:389322 original size:22 final size:22
Alignment explanation
Indices: 389291--389343 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
389281 GTGTATTTAT
*
389291 GCTTTCGAATAGAAAAATAATA
1 GCTTTTGAATAGAAAAATAATA
*
389313 GCTTTTGAATAGGAAAATAATA
1 GCTTTTGAATAGAAAAATAATA
389335 GCTTTTGAA
1 GCTTTTGAA
389344 AACGTGAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (22 bp):
GCTTTTGAATAGAAAAATAATA
Found at i:392688 original size:21 final size:22
Alignment explanation
Indices: 392664--392712 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
392654 AGCCGAAAAT
* *
392664 GAAGCAAG-GGAAGCAGATAGA
1 GAAGCAAGCGGAAGCACAAAGA
*
392685 GAAGC-TGCGGAAGCACAAAGA
1 GAAGCAAGCGGAAGCACAAAGA
392706 GAAGCAA
1 GAAGCAA
392713 CATATATAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.47, C:0.14, G:0.35, T:0.04
Consensus pattern (22 bp):
GAAGCAAGCGGAAGCACAAAGA
Found at i:393737 original size:55 final size:55
Alignment explanation
Indices: 393655--394111 Score: 592
Period size: 55 Copynumber: 8.3 Consensus size: 55
393645 TTTTTGTAGT
* *
393655 GTGCCAATACGGTAATTCATAAACTCATTATGAATTAT-GTGGGGTTGCACACATA
1 GTGCCAATACAGAAATTCATAAACTCATTATGAATT-TCGTGGGGTTGCACACATA
* * * *
393710 GTGCCAATATATAAATTCAAAAACTCATTTTGAATTTCGTGGGGTTGCACACATA
1 GTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATA
* * * * *
393765 GTGCCAATACGGAAATTCATAAAATCATTATGAATTTTGTGGGGTTGTAAACATA
1 GTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATA
* * *
393820 GTGCCGATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGATGCACACATA
1 GTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATA
* ** * * * *
393875 ATGCCAATATGGAAATTCATAAACTCATTATGAATTTCATAGGGTTGTACACAAA
1 GTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATA
* * *
393930 GTGCCAATACATAAATTCATAAACTCATTATGAATTTCGTTGGGTTACACACATA
1 GTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATA
* * *
393985 GTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGAGTTGCAGACGTA
1 GTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATA
* * * *
394040 GTGCCAGTACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTACACATATA
1 GTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATA
* * *
394095 TTGCTAATACATAAATT
1 GTGCCAATACAGAAATT
394112 GAAACATATA
Statistics
Matches: 345, Mismatches: 56, Indels: 2
0.86 0.14 0.00
Matches are distributed among these distances:
54 1 0.00
55 344 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (55 bp):
GTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATA
Found at i:397816 original size:6 final size:6
Alignment explanation
Indices: 397792--397897 Score: 54
Period size: 6 Copynumber: 16.8 Consensus size: 6
397782 AAAAAACATT
* * * *
397792 GAAAAGA GAGAAA -AAAAA GAAAAA GAAAAT G-ATAG GAAAAAA GAAAAA
1 GAAAA-A GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G-AAAAA GAAAAA
* * * * *
397840 GAAAATAA GAATAATA GAAAGA GAAAAA GAAAAG GAACAA GAGAAAA GGAAAG
1 G-AAA-AA GAA-AA-A GAAAAA GAAAAA GAAAAA GAAAAA GA-AAAA GAAAAA
397893 GAAAA
1 GAAAA
397898 TGAATGAAAA
Statistics
Matches: 75, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
5 7 0.09
6 42 0.56
7 18 0.24
8 8 0.11
ACGTcount: A:0.72, C:0.01, G:0.23, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:397819 original size:24 final size:24
Alignment explanation
Indices: 397792--397866 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
397782 AAAAAACATT
397792 GAAAA-GAGAGAAAAAAAAGAAAAA
1 GAAAATGAGAG-AAAAAAAGAAAAA
* *
397816 GAAAATGATAGGAAAAAAGAAAAA
1 GAAAATGAGAGAAAAAAAGAAAAA
* * *
397840 GAAAAT-A-AGAATAATAGAAAGA
1 GAAAATGAGAGAAAAAAAGAAAAA
397862 GAAAA
1 GAAAA
397867 AGAAAAGGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
22 16 0.36
23 1 0.02
24 23 0.52
25 4 0.09
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (24 bp):
GAAAATGAGAGAAAAAAAGAAAAA
Found at i:397881 original size:20 final size:19
Alignment explanation
Indices: 397858--397895 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
397848 GAATAATAGA
397858 AAGAGAAAAAGAAAAGGAAC
1 AAGAG-AAAAGAAAAGGAAC
*
397878 AAGAGAAAAGGAAAGGAA
1 AAGAGAAAAGAAAAGGAA
397896 AATGAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.68, C:0.03, G:0.29, T:0.00
Consensus pattern (19 bp):
AAGAGAAAAGAAAAGGAAC
Found at i:405670 original size:6 final size:6
Alignment explanation
Indices: 405659--405743 Score: 68
Period size: 6 Copynumber: 13.5 Consensus size: 6
405649 AAAAGAGAGA
*
405659 AAAAAG AAAAAG AAAATG ATAGGAAA- AAAAATG AACAAGAG AAAAAG
1 AAAAAG AAAAAG AAAAAG A-A--AAAG AAAAA-G AA-AA-AG AAAAAG
*
405706 AAAAAAG AAAAA- AGAAAG AAAAAG AAAAAG -AAAAG AAA
1 -AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
405744 GAAAAATGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
5 12 0.18
6 32 0.49
7 12 0.18
8 6 0.09
9 3 0.05
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:405703 original size:15 final size:13
Alignment explanation
Indices: 405684--405754 Score: 58
Period size: 15 Copynumber: 5.2 Consensus size: 13
405674 ATGATAGGAA
*
405684 AAAAAATGAACAAG
1 AAAAAA-GAAAAAG
405698 AGAAAAAGAAAAAAG
1 A-AAAAAG-AAAAAG
405713 AAAAAAG--AAAG
1 AAAAAAGAAAAAG
405724 -AAAAAGAAAAAG
1 AAAAAAGAAAAAG
405736 AAAAGAAAGAAAAATG
1 -AAA-AAAGAAAAA-G
405752 AAA
1 AAA
405755 TAAGGGTTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
10 6 0.12
11 4 0.08
12 4 0.08
14 10 0.21
15 23 0.48
16 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:405708 original size:24 final size:24
Alignment explanation
Indices: 405692--405739 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
405682 AAAAAAAATG
405692 AACAAGAGAAAAAGAAAAAAGAAAA
1 AACAA-AGAAAAAGAAAAAAGAAAA
*
405717 AAGAAAGAAAAAG-AAAAAGAAAA
1 AACAAAGAAAAAGAAAAAAGAAAA
405740 GAAAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.45
24 8 0.36
25 4 0.18
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAGAAAAAGAAAAAAGAAAA
Found at i:405709 original size:21 final size:19
Alignment explanation
Indices: 405656--405754 Score: 71
Period size: 21 Copynumber: 5.0 Consensus size: 19
405646 TTGAAAAGAG
405656 AGAAAAAAGAAAAA-GAAA
1 AGAAAAAAGAAAAATGAAA
*
405674 ATGATAGGAAA-AAAAATGAACA
1 A-GA-A-AAAAGAAAAATGAA-A
*
405696 AGAGAAAAAGAAAAAAGAAA
1 AGA-AAAAAGAAAAATGAAA
*
405716 A-AAGAAAGAAAAA-GAAAA
1 AGAAAAAAGAAAAATG-AAA
405734 AGAAAAGAAAGAAAAATGAAA
1 AG-AAA-AAAGAAAAATGAAA
405755 TAAGGGTTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
17 1 0.02
18 15 0.23
19 3 0.05
20 13 0.20
21 29 0.45
22 3 0.05
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (19 bp):
AGAAAAAAGAAAAATGAAA
Found at i:405727 original size:42 final size:44
Alignment explanation
Indices: 405620--405728 Score: 104
Period size: 43 Copynumber: 2.5 Consensus size: 44
405610 GAGCATCATT
* *
405620 GAAAAAA-AAAACA-AAACAAAAAAACATTGAAAAGAGAGAAAA
1 GAAAAAAGAAAAAAGAAAGAAAAAAACATTGAAAAGAGAGAAAA
* * *
405662 AAGAAAAAG-AAAATGATAGGAAAAAAA-A-TGAACAAGAGA-AAAA
1 GA-AAAAAGAAAAAAGA-AAGAAAAAAACATTGAA-AAGAGAGAAAA
405705 GAAAAAAGAAAAAAGAAAGAAAAA
1 GAAAAAAGAAAAAAGAAAGAAAAA
405729 GAAAAAGAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
42 14 0.26
43 23 0.43
44 8 0.15
45 8 0.15
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.05
Consensus pattern (44 bp):
GAAAAAAGAAAAAAGAAAGAAAAAAACATTGAAAAGAGAGAAAA
Found at i:405754 original size:11 final size:11
Alignment explanation
Indices: 405649--405754 Score: 71
Period size: 11 Copynumber: 9.7 Consensus size: 11
405639 AAAAACATTG
*
405649 AAAAGAGAGAA
1 AAAAGAAAGAA
405660 AAAAGAAA-AA
1 AAAAGAAAGAA
*
405670 GAAAATGATAGGAA
1 -AAAA-GA-AAGAA
*
405684 AAAA-AATGAA
1 AAAAGAAAGAA
*
405694 CAAGAGAAA-AA
1 -AAAAGAAAGAA
*
405705 GAAA-AAAGAA
1 AAAAGAAAGAA
405715 AAAAGAAAG-A
1 AAAAGAAAGAA
405725 AAAAGAAA-AA
1 AAAAGAAAGAA
405735 GAAAAGAAAGAA
1 -AAAAGAAAGAA
*
405747 AAATGAAA
1 AAAAGAAA
405755 TAAGGGTTTA
Statistics
Matches: 75, Mismatches: 9, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
9 3 0.04
10 23 0.31
11 36 0.48
12 6 0.08
13 5 0.07
14 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (11 bp):
AAAAGAAAGAA
Found at i:408552 original size:15 final size:16
Alignment explanation
Indices: 408527--408556 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
408517 CTTTGATAAC
408527 ATTCATTTCCATTTCA
1 ATTCATTTCCATTTCA
408543 ATTC-TTTCCATTTC
1 ATTCATTTCCATTTC
408557 CATTTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTCATTTCCATTTCA
Found at i:408797 original size:25 final size:25
Alignment explanation
Indices: 408769--408817 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
408759 GCTGCAACAA
*
408769 AAGAAACAAAAAAAGATAAAGAAAG
1 AAGAAACAAAAAAAGAGAAAGAAAG
* *
408794 AAGAAATACAAAAAGAGAAAGAAA
1 AAGAAACAAAAAAAGAGAAAGAAA
408818 AGACTCCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (25 bp):
AAGAAACAAAAAAAGAGAAAGAAAG
Found at i:409114 original size:17 final size:17
Alignment explanation
Indices: 409092--409125 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
409082 TATCCTACCC
409092 CTATACCATAACCATTT
1 CTATACCATAACCATTT
*
409109 CTATACCCTAACCATTT
1 CTATACCATAACCATTT
409126 TTTTAAGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (17 bp):
CTATACCATAACCATTT
Found at i:415620 original size:64 final size:64
Alignment explanation
Indices: 415493--415675 Score: 163
Period size: 64 Copynumber: 2.8 Consensus size: 64
415483 ACATAAATCT
* * * * * * *
415493 TTGAGATTGTTTCTCTCAAAACAAAATCTCGTCTCACTTGAGATAGTCTTCCTTTATAAACAAAC
1 TTGAGATTGTTTTTCT-TAAA-AAAATCT-GTCTTACTTGAGACAGTTTTCCTTAAGAAACAAAC
415558 AC
63 AC
* **
415560 TTGAGATTGTTTTTCTTAAAAAAATCTGTCTTACTTGAGACAGTTTTCCTTAAGACACAAACGT
1 TTGAGATTGTTTTTCTTAAAAAAATCTGTCTTACTTGAGACAGTTTTCCTTAAGAAACAAACAC
* * *
415624 TTAAGATTCTTTTTCTTACAAACAAAT-T-TCATTTCACTTGAGACAATTTTCC
1 TTGAGATTGTTTTTCTTA-AAA-AAATCTGTC--TT-ACTTGAGACAGTTTTCC
415676 CTCAAAACAA
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
64 47 0.48
65 11 0.11
66 9 0.09
67 31 0.32
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (64 bp):
TTGAGATTGTTTTTCTTAAAAAAATCTGTCTTACTTGAGACAGTTTTCCTTAAGAAACAAACAC
Found at i:419758 original size:629 final size:631
Alignment explanation
Indices: 418639--419879 Score: 2155
Period size: 629 Copynumber: 2.0 Consensus size: 631
418629 AGGTAGGACT
*
418639 TGCGATAAGTATACCTTGTTTATATTGGCGTGATATTTATGTCATATATCATATGTTTGACATAT
1 TGCGATAAGTATACCTTGTTTATATTGGCGTGATATTTATGTCATATATCATATATTTGACATAT
* * *
418704 TCTGAATATGTAAAATGTTGAATATAAAATAAATTGATCACTGATTGTTACATATGATGTTTATC
66 TCTAAATATGTAAAAGGTTGAATATAAAATAAATTGAGCACTGATTGTTACATATGATGTTTATC
* * * *
418769 ATGAACATATATGATATTTAACATGAATGATATTTCGGGTATAAACTTCCCAACGATATATTATG
131 ATGAACATAAATGATATTTAACATGAACGATATTTCGGGTATAAACTGCCCAACGATAAATTATG
* *
418834 ATAATATACTTTCCCATGGATGGATCAAATAAAATAGATTGTATGCCCAAGTAAGTCATTGAAGG
196 ATAATATACTTTCCCATGGATGGATCAAATAAAATAGACTATATGCCCAAGTAAGTCATTGAAGG
* *
418899 ACATGGTGTAATTACCATGACATAGAGTCTAGCAGTTGCATAATCAAATTAGCACTAATGTGTAA
261 ACATGGTGTAATTACCATGACATAGAGTCAAGCAGCTGCATAATCAAATTAGCACTAATGTGTAA
*
418964 GGATATTTAGTGCAGCACTATAGTGTGTAAGGGCACTAAGTGCATATGGTGGACACGACCTTATG
326 GGACATTTAGTGCAGCACTATAGTGTGTAAGGGCACTAAGTGCATATGGTGGACACGACCTTATG
*
419029 TGTATTAGCACTTCGGTGAATATTTGACTCGAATACTCAGGGTCTTCATAGATTTACGTTTGGAC
391 TGTATTAGCACTTCGGTGAATATTTGACTCGAATACCCAGGGTCTTCATAGATTTACGTTTGGAC
* * * *
419094 TTTGGTTTATTTATTATTAAATAATAAATAGACAAATAAGCTTACGATCTTATGGGATAAATGAC
456 TATGGTTTATTTATTAATAAATAATAAACAGACAAATAAGCTTACGATCTTATAGGATAAATGAC
419159 AAGTATATTGGTAAGAAACTTTATATTCAGTTATATCATGTTAATTTATGGTAACATGGTTGAAA
521 AAGTATATTGGTAAGAAACTTTATATTCAGTTATATCATGTTAATTTATGGTAACATGGTTGAAA
*
419224 TGCAGGTAAAGTTATC-TA-TGCATTGCACTCACTTTGAAATTATA
586 TGCAGGTAAAGTGATCATATTGCATTGCACTCACTTTGAAATTATA
*
419268 TGCGATAAGTATACCTTGTTTATATTGGTGTGATATTTATGTCATATATCATATATTTGACATAT
1 TGCGATAAGTATACCTTGTTTATATTGGCGTGATATTTATGTCATATATCATATATTTGACATAT
* **
419333 TCTAAATATGTCAAAGGTTGAATATAAAATGCATTGAGCACTGATTGTTACATATGATGTTTATC
66 TCTAAATATGTAAAAGGTTGAATATAAAATAAATTGAGCACTGATTGTTACATATGATGTTTATC
* *
419398 ATGAACATAAATGATATTTAACATGAACGATATTTCGGGTATAAACTGCCCAATGTTAAATTATG
131 ATGAACATAAATGATATTTAACATGAACGATATTTCGGGTATAAACTGCCCAACGATAAATTATG
* *
419463 ATAATTTACTTTCTCATGGATGGATCAAATAAAATAGACTATATGCCCAAGTAAGTCATTGAAGG
196 ATAATATACTTTCCCATGGATGGATCAAATAAAATAGACTATATGCCCAAGTAAGTCATTGAAGG
**
419528 ACATGGTGTAATTATGATGACATAGAGTCAAGCAGCTGCATAATCAAATTAGCACTAATGTGTAA
261 ACATGGTGTAATTACCATGACATAGAGTCAAGCAGCTGCATAATCAAATTAGCACTAATGTGTAA
* *
419593 GGACATTTAGTGCAGCACTATAGTGTGTAAGGGCACTAGGTGCATATGGTGGGCACGACCTTATG
326 GGACATTTAGTGCAGCACTATAGTGTGTAAGGGCACTAAGTGCATATGGTGGACACGACCTTATG
*
419658 TGTATTAGCACTTCGGTGAATATTTGACTCGAATACCCAGGGTCTTCATAGATTTACGTTTGGGC
391 TGTATTAGCACTTCGGTGAATATTTGACTCGAATACCCAGGGTCTTCATAGATTTACGTTTGGAC
419723 TATGGTTTATTTATTAATAAA-AGATAAACAGACAAATAAGCTTACGATCTTATAGGATAAATGA
456 TATGGTTTATTTATTAATAAATA-ATAAACAGACAAATAAGCTTACGATCTTATAGGATAAATGA
*
419787 CAAGTATATTGGTAAGAAACTTTATATTCGGTTATATCATGTTAATTTATGGTAACATGGTTGAA
520 CAAGTATATTGGTAAGAAACTTTATATTCAGTTATATCATGTTAATTTATGGTAACATGGTTGAA
419852 ATGCAGGTAAAGTGATCATATTGCATTG
585 ATGCAGGTAAAGTGATCATATTGCATTG
419880 AATATTATTA
Statistics
Matches: 576, Mismatches: 33, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
628 1 0.00
629 566 0.98
630 2 0.00
631 7 0.01
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (631 bp):
TGCGATAAGTATACCTTGTTTATATTGGCGTGATATTTATGTCATATATCATATATTTGACATAT
TCTAAATATGTAAAAGGTTGAATATAAAATAAATTGAGCACTGATTGTTACATATGATGTTTATC
ATGAACATAAATGATATTTAACATGAACGATATTTCGGGTATAAACTGCCCAACGATAAATTATG
ATAATATACTTTCCCATGGATGGATCAAATAAAATAGACTATATGCCCAAGTAAGTCATTGAAGG
ACATGGTGTAATTACCATGACATAGAGTCAAGCAGCTGCATAATCAAATTAGCACTAATGTGTAA
GGACATTTAGTGCAGCACTATAGTGTGTAAGGGCACTAAGTGCATATGGTGGACACGACCTTATG
TGTATTAGCACTTCGGTGAATATTTGACTCGAATACCCAGGGTCTTCATAGATTTACGTTTGGAC
TATGGTTTATTTATTAATAAATAATAAACAGACAAATAAGCTTACGATCTTATAGGATAAATGAC
AAGTATATTGGTAAGAAACTTTATATTCAGTTATATCATGTTAATTTATGGTAACATGGTTGAAA
TGCAGGTAAAGTGATCATATTGCATTGCACTCACTTTGAAATTATA
Found at i:428945 original size:24 final size:24
Alignment explanation
Indices: 428888--428948 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
428878 ATATAATTTA
*
428888 CACTGAAGTACCACGTAGAATATG
1 CACTGAAGTGCCACGTAGAATATG
428912 CACTGAAGTGCCACGTAGAATATG
1 CACTGAAGTGCCACGTAGAATATG
*
428936 CATTGAAGTGCCA
1 CACTGAAGTGCCA
428949 TATAGATTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (24 bp):
CACTGAAGTGCCACGTAGAATATG
Found at i:428994 original size:24 final size:24
Alignment explanation
Indices: 428946--429005 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
428936 CATTGAAGTG
*
428946 CCATATAG-ATTTGTCCCGAATGA
1 CCATATAGAATTTGTCCCGAAGGA
*
428969 CCATATAGAATTTGTCCTGAAGGA
1 CCATATAGAATTTGTCCCGAAGGA
* *
428993 CCACATATAATTT
1 CCATATAGAATTT
429006 TGCCCAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 8 0.25
24 24 0.75
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (24 bp):
CCATATAGAATTTGTCCCGAAGGA
Found at i:434265 original size:3 final size:3
Alignment explanation
Indices: 434257--434305 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
434247 CACATATGTT
434257 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
434305 T
1 T
434306 GTCTCACTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:434879 original size:13 final size:13
Alignment explanation
Indices: 434861--434885 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
434851 AATCAATTTT
434861 TTTTAAAAATAAA
1 TTTTAAAAATAAA
434874 TTTTAAAAATAA
1 TTTTAAAAATAA
434886 TGATAATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TTTTAAAAATAAA
Found at i:440956 original size:155 final size:156
Alignment explanation
Indices: 440673--440978 Score: 506
Period size: 155 Copynumber: 2.0 Consensus size: 156
440663 TCAAATTCAG
* * *
440673 AAACCATAGTAATCCCTCCAGCCCAACACATCATAATGTGTAGGTTCCCCATAACCATACACCCA
1 AAACCATAGTAATCCCTCCAACCAAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
440738 CAGTCACATCGAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCAAGTATACTTCCTCCAACAA
66 CAGTCACATCGAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCAAGTATACTTCCTCCAACAA
440803 TACCCCCCAAATAAAACATTTATCAA
131 TACCCCCCAAATAAAACATTTATCAA
*
440829 AAACCATAGTAATCCCTCCAACCAAACACATCATAATGTGTAGGTTCCCCAGAGCCATACA-CCA
1 AAACCATAGTAATCCCTCCAACCAAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
* ** * *
440893 CTGTCACATCGAGTAAGGCCCTGAGCACAAAGCCGAGGAGTTTGCAAGTTTTCTTCCTCCAACAA
66 CAGTCACATCGAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCAAGTATACTTCCTCCAACAA
* *
440958 TACCCTCCAAATAAAATATTT
131 TACCCCCCAAATAAAACATTT
440979 TATGTTCGTA
Statistics
Matches: 139, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
155 82 0.59
156 57 0.41
ACGTcount: A:0.35, C:0.31, G:0.13, T:0.21
Consensus pattern (156 bp):
AAACCATAGTAATCCCTCCAACCAAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
CAGTCACATCGAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCAAGTATACTTCCTCCAACAA
TACCCCCCAAATAAAACATTTATCAA
Found at i:441090 original size:24 final size:24
Alignment explanation
Indices: 441010--441092 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
441000 CAAAAATAAA
* *
441010 AACATAATTCAGGTCAGATATCAT
1 AACAGAATTCATGTCAGATATCAT
* *
441034 AACAGAATCCATGTCATATATCAT
1 AACAGAATTCATGTCAGATATCAT
* *
441058 AACAGAATTCATGTCAGGTAACAT
1 AACAGAATTCATGTCAGATATCAT
441082 AACAGAATTCA
1 AACAGAATTCA
441093 AATTGGAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (24 bp):
AACAGAATTCATGTCAGATATCAT
Found at i:443028 original size:30 final size:30
Alignment explanation
Indices: 442992--443065 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
442982 ATTTGACTTT
442992 TTGGTCAAAGTCAAAGATCAA-AGGGTTGAC
1 TTGGTCAAAGTCAAAGATCAACA-GGTTGAC
*
443022 TTGGTCAAAGTCAAAGGTCAACAGGTTGAC
1 TTGGTCAAAGTCAAAGATCAACAGGTTGAC
* *
443052 TAGGCCAAAGTCAA
1 TTGGTCAAAGTCAA
443066 CGAGTTGACC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 39 0.98
31 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (30 bp):
TTGGTCAAAGTCAAAGATCAACAGGTTGAC
Found at i:444600 original size:13 final size:13
Alignment explanation
Indices: 444582--444607 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
444572 CAAAGAATTA
444582 CTAGAAGCAATCT
1 CTAGAAGCAATCT
444595 CTAGAAGCAATCT
1 CTAGAAGCAATCT
444608 GGAAGAATGA
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:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
CTAGAAGCAATCT
Found at i:447244 original size:6 final size:6
Alignment explanation
Indices: 447233--447272 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
447223 CGACACCCCC
*
447233 AAGCAA AAGCAA AAACAA AAGCAA AAGCAA AAGCAA AAGC
1 AAGCAA AAGCAA AAGCAA AAGCAA AAGCAA AAGCAA AAGC
447273 TTCACGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.68, C:0.17, G:0.15, T:0.00
Consensus pattern (6 bp):
AAGCAA
Found at i:448124 original size:15 final size:14
Alignment explanation
Indices: 448088--448127 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
448078 TTGAAAGGAC
**
448088 TAAAATTTAAATGT
1 TAAAATTTAAATAA
448102 TAAAATTTAAATAA
1 TAAAATTTAAATAA
448116 TAGAAATTTAAA
1 TA-AAATTTAAA
448128 GGGAAGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (14 bp):
TAAAATTTAAATAA
Found at i:449706 original size:6 final size:6
Alignment explanation
Indices: 449697--449737 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
449687 AAGAAAAGAA
*
449697 AAAAAT -AAAAT AAAAAT --AAAT AAAAAT AAAAAT AATAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
449738 CTCAAAGGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
4 4 0.13
5 5 0.16
6 22 0.71
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:449717 original size:10 final size:10
Alignment explanation
Indices: 449656--449726 Score: 56
Period size: 11 Copynumber: 6.8 Consensus size: 10
449646 AATATTAGAT
449656 AAAAT-AATA
1 AAAATAAATA
*
449665 ATAATAAATA
1 AAAATAAATA
*
449675 TTAAATAAATCA
1 -AAAATAAAT-A
*
449687 AAGAA-AAGAAA
1 AA-AATAA-ATA
449698 AAAATAAAATA
1 AAAAT-AAATA
449709 AAAATAAATA
1 AAAATAAATA
449719 AAAATAAA
1 AAAATAAA
449727 AATAATAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
9 4 0.08
10 19 0.39
11 20 0.41
12 6 0.12
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (10 bp):
AAAATAAATA
Found at i:449721 original size:22 final size:22
Alignment explanation
Indices: 449697--449737 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
449687 AAGAAAAGAA
449697 AAAAAT-AAAATAAAAATAAAT
1 AAAAATAAAAATAAAAATAAAT
*
449718 AAAAATAAAAATAATAATAA
1 AAAAATAAAAATAAAAATAA
449738 CTCAAAGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAAATAAAAATAAAAATAAAT
Found at i:449733 original size:15 final size:15
Alignment explanation
Indices: 449690--449734 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
449680 TAAATCAAAG
*
449690 AAAAGAAAAA-AAT-
1 AAAATAAAAATAATA
449703 AAAATAAAAATAAATA
1 AAAATAAAAAT-AATA
449719 AAAATAAAAATAATA
1 AAAATAAAAATAATA
449734 A
1 A
449735 TAACTCAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 9 0.32
15 8 0.29
16 11 0.39
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (15 bp):
AAAATAAAAATAATA
Found at i:449737 original size:33 final size:36
Alignment explanation
Indices: 449661--449737 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 36
449651 TAGATAAAAT
*
449661 AATAATAAT-AAATATTAAATAAATCAAAGAAAAGA
1 AATAATAATAAAATATAAAATAAATCAAAGAAAAGA
449696 AA-AA-AATAAAATA-AAAATAAAT-AAA-AATAA-A
1 AATAATAATAAAATATAAAATAAATCAAAGAA-AAGA
449727 AATAATAATAA
1 AATAATAATAA
449738 CTCAAAGGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
31 5 0.14
32 7 0.19
33 16 0.43
34 7 0.19
35 2 0.05
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (36 bp):
AATAATAATAAAATATAAAATAAATCAAAGAAAAGA
Found at i:451075 original size:26 final size:24
Alignment explanation
Indices: 451044--451112 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 24
451034 GGACCTGAAA
** *
451044 AAAAAAGAAATAAAATTAAATGAAT
1 AAAAAA-AAATAAAAAAAAATAAAT
451069 AAGAAAAATAATAAATAAAAAATAAAT
1 AA-AAAAA-AATAAA-AAAAAATAAAT
451096 AAAAAAAAAATAAAAAA
1 -AAAAAAAAATAAAAAA
451113 TCATTTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
25 6 0.16
26 16 0.43
27 13 0.35
28 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (24 bp):
AAAAAAAAATAAAAAAAAATAAAT
Found at i:451086 original size:7 final size:7
Alignment explanation
Indices: 451072--451113 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
451062 AATGAATAAG
451072 AAAAATA
1 AAAAATA
*
451079 ATAAATA
1 AAAAATA
451086 AAAAATA
1 AAAAATA
*
451093 AATAAAAA
1 AA-AAATA
451101 AAAAATA
1 AAAAATA
451108 AAAAAT
1 AAAAAT
451114 CATTTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAAAATA
Found at i:451094 original size:11 final size:11
Alignment explanation
Indices: 451073--451113 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
451063 ATGAATAAGA
451073 AAAATAATAAAT
1 AAAA-AATAAAT
451085 AAAAAATAAAT
1 AAAAAATAAAT
*
451096 AAAAAAAAAAT
1 AAAAAATAAAT
451107 AAAAAAT
1 AAAAAAT
451114 CATTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 23 0.85
12 4 0.15
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:451201 original size:2 final size:2
Alignment explanation
Indices: 451191--451250 Score: 86
Period size: 2 Copynumber: 30.5 Consensus size: 2
451181 TTTTTTAAAC
* *
451191 TA TA T- TA TA TA TA TA TA TA TA TA GA TA TA TA GA 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
*
451232 TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
451251 TAAAAATTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:451294 original size:37 final size:37
Alignment explanation
Indices: 451232--451508 Score: 158
Period size: 37 Copynumber: 7.6 Consensus size: 37
451222 GATATATATA
* * *
451232 TATATATATAAATATATATTAAAAATTGTTTT-TAAAAC
1 TATATAT-TATATATATTTTAAAAA-TGTTTTCAAAAAC
* *
451270 TATTTATTATATATATTTTTAAAATGTTTTCAAAAAC
1 TATATATTATATATATTTTAAAAATGTTTTCAAAAAC
451307 TATATA-T-TATATA---T----A--TTTTCAAAAAC
1 TATATATTATATATATTTTAAAAATGTTTTCAAAAAC
* * *
451333 AT-TATATTATATAGT-TTTCAAAATGT-TTTTTAAAAAC
1 -TATATATTATATA-TATTTTAAAA-ATGTTTTCAAAAAC
* * *
451370 CATATACTATATA-AGTTTTAAAAATGTTTTTTTAAAAAATC
1 TATATATTATATATA-TTTTAAAAATG---TTTTCAAAAA-C
* * *
451411 TATATAATATATACATTTTCAAAAATCATTTTC-AAAAC
1 TATATATTATATATATTTT-AAAAAT-GTTTTCAAAAAC
* *
451449 TAAATATTATATATATTTTCAAAATGTTTTC-AAAAC
1 TATATATTATATATATTTTAAAAATGTTTTCAAAAAC
* *
451485 TATATAATATATATATTTCAAAAA
1 TATATATTATATATATTTTAAAAA
451509 CTATTTTTAA
Statistics
Matches: 187, Mismatches: 27, Indels: 52
0.70 0.10 0.20
Matches are distributed among these distances:
26 15 0.08
27 2 0.01
28 5 0.03
29 1 0.01
32 1 0.01
35 6 0.03
36 38 0.20
37 56 0.30
38 23 0.12
39 4 0.02
40 13 0.07
41 16 0.09
42 7 0.04
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (37 bp):
TATATATTATATATATTTTAAAAATGTTTTCAAAAAC
Found at i:451311 original size:63 final size:63
Alignment explanation
Indices: 451244--451375 Score: 144
Period size: 63 Copynumber: 2.1 Consensus size: 63
451234 TATATATAAA
** *
451244 TATATATTAAAAAT-TGTTTTTAAAACTATT-TATTATATATATTTTTAAAATG-TTTTCAAAAA
1 TATATATTAAAAATAT-TTTCAAAAAC-ATTATATTATATA-ATTTTCAAAATGTTTTTCAAAAA
451306 C
63 C
* * * *
451307 TATATATTATATATATTTTCAAAAACATTATATTATATAGTTTTCAAAATGTTTTTTAAAAAC
1 TATATATTAAAAATATTTTCAAAAACATTATATTATATAATTTTCAAAATGTTTTTCAAAAAC
*
451370 CATATA
1 TATATA
451376 CTATATAAGT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
62 13 0.22
63 44 0.76
64 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (63 bp):
TATATATTAAAAATATTTTCAAAAACATTATATTATATAATTTTCAAAATGTTTTTCAAAAAC
Found at i:451355 original size:24 final size:26
Alignment explanation
Indices: 451293--451355 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
451283 TATTTTTAAA
451293 ATGTTTTCAAAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATATTATAT
*
451319 ATATTTTCAAAAAC-ATTATATTATAT
1 ATGTTTTCAAAAACTA-TATATTATAT
451345 A-GTTTTCAAAA
1 ATGTTTTCAAAA
451356 TGTTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 10 0.29
26 24 0.71
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (26 bp):
ATGTTTTCAAAAACTATATATTATAT
Found at i:451421 original size:39 final size:38
Alignment explanation
Indices: 451322--451421 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 38
451312 ATTATATATA
* * *
451322 TTTTCAAAAACAT-TATATTATAT-AGTTTTCAAAATGT
1 TTTTTAAAAA-ATCTATATAATATAAGTTTTAAAAATGT
*
451359 TTTTT-AAAAA-CCATATACTATATAAGTTTTAAAAATGTT
1 TTTTTAAAAAATCTATATA--ATATAAGTTTTAAAAATG-T
451398 TTTTTAAAAAATCTATATAATATA
1 TTTTTAAAAAATCTATATAATATA
451422 TACATTTTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
35 5 0.10
36 4 0.08
37 8 0.16
38 12 0.24
39 11 0.22
40 5 0.10
41 6 0.12
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (38 bp):
TTTTTAAAAAATCTATATAATATAAGTTTTAAAAATGT
Found at i:451461 original size:38 final size:37
Alignment explanation
Indices: 451405--451520 Score: 137
Period size: 36 Copynumber: 3.1 Consensus size: 37
451395 GTTTTTTTAA
* *
451405 AAAATCTATATAATATATACATTTTCAAAAATCATTTTC
1 AAAA-CTAAATAATATATATATTTTCAAAAAT-ATTTTC
* *
451444 AAAACTAAATATTATATATATTTTC-AAAATGTTTTC
1 AAAACTAAATAATATATATATTTTCAAAAATATTTTC
* *
451480 AAAACTATATAATATATATA-TTTCAAAAACTATTTTT
1 AAAACTAAATAATATATATATTTTCAAAAA-TATTTTC
451517 AAAA
1 AAAA
451521 AAACGAAAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
35 4 0.06
36 27 0.40
37 14 0.21
38 18 0.27
39 4 0.06
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.41
Consensus pattern (37 bp):
AAAACTAAATAATATATATATTTTCAAAAATATTTTC
Done.