Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009068.1 Hibiscus syriacus cultivar Beakdansim tig00112495_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: 670922
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:293014 original size:14 final size:14
Alignment explanation
Indices: 292995--293084 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
292985 TTGAAATGAA
292995 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
293009 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
293028 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
293042 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
293061 AATCGCAACGAGAG
1 AATCGCAACGAGAG
293075 AATCGCAACG
1 AATCGCAACG
293085 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 30 0.50
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:293027 original size:33 final size:33
Alignment explanation
Indices: 292987--293101 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
292977 TCTTTTGGTT
292987 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
293020 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
293053 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
293086 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
293102 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:293033 original size:19 final size:19
Alignment explanation
Indices: 293009--293106 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
292999 GCAACGAGAG
293009 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
293028 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
293042 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
293061 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
293075 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
293094 AATCGCAATGCGA
1 AATCGCAACGCGA
293107 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:293150 original size:33 final size:33
Alignment explanation
Indices: 293102--293182 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
293092 AAAATCGCAA
**
293102 TGCGATTTTGGTTTCGCGTTGCGATTCTCTAGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
*
293135 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
293168 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
293183 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
Found at i:293170 original size:14 final size:14
Alignment explanation
Indices: 293118--293174 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
293108 TTTGGTTTCG
293118 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
293132 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
293151 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
293165 CGTTGCGATT
1 CGTTGCGATT
293175 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:293215 original size:41 final size:41
Alignment explanation
Indices: 293158--293235 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
293148 TCGCGTTGCG
*
293158 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
293199 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
293236 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:293220 original size:20 final size:21
Alignment explanation
Indices: 293159--293234 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
293149 CGCGTTGCGA
293159 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
293180 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
293200 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
293221 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
293235 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:293356 original size:33 final size:33
Alignment explanation
Indices: 293314--293384 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
293304 AATACTAACT
*
293314 TGAAAATCGCAACGAGAGAATAACAACGCGAAA
1 TGAAAATCGCAACGACAGAATAACAACGCGAAA
***
293347 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAACAACGCGAAA
293380 TGAAA
1 TGAAA
293385 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAACAACGCGAAA
Found at i:293618 original size:22 final size:22
Alignment explanation
Indices: 293566--293620 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
293556 TGGTTGTGAG
**
293566 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
293588 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
293610 GGATTTCTTCG
1 GGATTTCTTCG
293621 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:293792 original size:20 final size:20
Alignment explanation
Indices: 293767--293920 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
293757 CTTTAAATAT
293767 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
293787 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
293809 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
293828 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
293848 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
293868 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
293888 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
293908 CGCGTTGCGATTT
1 CGCGTTGCGATTT
293921 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:293894 original size:40 final size:40
Alignment explanation
Indices: 293766--293920 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
293756 GCTTTAAATA
*
293766 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
293807 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
293847 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
293887 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
293921 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:293937 original size:21 final size:21
Alignment explanation
Indices: 293907--293989 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
293897 ATTTTCATAT
*
293907 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
293928 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
293949 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
293970 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
293990 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:293980 original size:42 final size:43
Alignment explanation
Indices: 293887--293985 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
293877 ATTTATGTGT
* *
293887 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
293928 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
293970 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
293986 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:294777 original size:18 final size:17
Alignment explanation
Indices: 294756--294797 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
294746 TATTAAATTA
*
294756 AATAATTATTGTAAAGAT
1 AATAATTATTATAAA-AT
294774 AATAATTATTATAAAAT
1 AATAATTATTATAAAAT
294791 -ATAATTA
1 AATAATTA
294798 GATTGATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.30
17 2 0.09
18 14 0.61
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (17 bp):
AATAATTATTATAAAAT
Found at i:311441 original size:13 final size:13
Alignment explanation
Indices: 311423--311448 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
311413 GTAAATCTTA
311423 ATTTCTTTTATTT
1 ATTTCTTTTATTT
311436 ATTTCTTTTATTT
1 ATTTCTTTTATTT
311449 GTGGTTATGT
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:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTCTTTTATTT
Found at i:313148 original size:29 final size:29
Alignment explanation
Indices: 313106--313164 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
313096 ATTTTCACCT
313106 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
313135 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
313164 A
1 A
313165 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:329979 original size:31 final size:31
Alignment explanation
Indices: 329941--330035 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
329931 AGAGTCGAGG
329941 GTTTACCTATG-TCTTTCGGGACATATGGACA
1 GTTTACCTATGTTC-TTCGGGACATATGGACA
* * *
329972 GTTTACCTATGTTCTACGGGACATATGAATA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
* *
330003 GTTTACCTAGGTTCTTC-GGACCTATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
330033 GTT
1 GTT
330036 GTCGAGGTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 13 0.24
31 40 0.73
32 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACA
Found at i:333407 original size:31 final size:31
Alignment explanation
Indices: 333372--333431 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
333362 AATTCGGTGA
333372 ATTCAATATGTCCTTCTCACTAGGAACTCTC
1 ATTCAATATGTCCTTCTCACTAGGAACTCTC
*
333403 ATTCAATATGTCCTTCTCATTAGGAACTC
1 ATTCAATATGTCCTTCTCACTAGGAACTC
333432 CCAAACTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.37
Consensus pattern (31 bp):
ATTCAATATGTCCTTCTCACTAGGAACTCTC
Found at i:346935 original size:31 final size:31
Alignment explanation
Indices: 346900--346961 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
346890 TTTTAGTACC
346900 CAATTCATCTGTTTCTACTTTTGTCGTCTTT
1 CAATTCATCTGTTTCTACTTTTGTCGTCTTT
346931 CAATTCATCTGTTTCTACTTTTGTCGTCTTT
1 CAATTCATCTGTTTCTACTTTTGTCGTCTTT
346962 TCATTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.13, C:0.23, G:0.10, T:0.55
Consensus pattern (31 bp):
CAATTCATCTGTTTCTACTTTTGTCGTCTTT
Found at i:350044 original size:101 final size:101
Alignment explanation
Indices: 349869--350072 Score: 408
Period size: 101 Copynumber: 2.0 Consensus size: 101
349859 CGATTCCCTG
349869 CAAGCTAATTACGGCAGCTGAAGCAGCTAAGATGGGGTCAGCTGAGTGGTGAGGGTTGCTGGCGA
1 CAAGCTAATTACGGCAGCTGAAGCAGCTAAGATGGGGTCAGCTGAGTGGTGAGGGTTGCTGGCGA
349934 AGCCTTTTCTTCCGCTGATAACGGCTCTAAAGAAGC
66 AGCCTTTTCTTCCGCTGATAACGGCTCTAAAGAAGC
349970 CAAGCTAATTACGGCAGCTGAAGCAGCTAAGATGGGGTCAGCTGAGTGGTGAGGGTTGCTGGCGA
1 CAAGCTAATTACGGCAGCTGAAGCAGCTAAGATGGGGTCAGCTGAGTGGTGAGGGTTGCTGGCGA
350035 AGCCTTTTCTTCCGCTGATAACGGCTCTAAAGAAGC
66 AGCCTTTTCTTCCGCTGATAACGGCTCTAAAGAAGC
350071 CA
1 CA
350073 CAACCGGCAA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 103 1.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (101 bp):
CAAGCTAATTACGGCAGCTGAAGCAGCTAAGATGGGGTCAGCTGAGTGGTGAGGGTTGCTGGCGA
AGCCTTTTCTTCCGCTGATAACGGCTCTAAAGAAGC
Found at i:353375 original size:14 final size:14
Alignment explanation
Indices: 353353--353409 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
353343 CGTTCGTGAA
*
353353 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
353367 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
*
353381 C--AT--TTATGTT
1 CGTTTGGTTATGTT
* *
353391 CGTTCGATTATGTT
1 CGTTTGGTTATGTT
353405 CGTTT
1 CGTTT
353410 ATGTTCATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
10 8 0.24
12 1 0.03
14 25 0.74
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:353381 original size:24 final size:24
Alignment explanation
Indices: 353354--353428 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
353344 GTTCGTGAAC
* * *
353354 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
353378 GTTCATTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
353402 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
353426 GTT
1 GTT
353429 TAACACAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
23 1 0.02
24 43 0.98
ACGTcount: A:0.13, C:0.11, G:0.20, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:353421 original size:38 final size:37
Alignment explanation
Indices: 353353--353428 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 37
353343 CGTTCGTGAA
*
353353 CGTTCGGTTATGTTCGTTTGGTTATGTTCATTTATGTT
1 CGTTCGATTATGTTCGTTTGGTTA-GTTCATTTATGTT
*
353391 CGTTCGATTATGTTCGTTTATGTTCA-TTCATTTATGTT
1 CGTTCGATTATGTTCGTTT-GGTT-AGTTCATTTATGTT
353429 TAACACAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 30 0.88
39 3 0.09
40 1 0.03
ACGTcount: A:0.13, C:0.12, G:0.20, T:0.55
Consensus pattern (37 bp):
CGTTCGATTATGTTCGTTTGGTTAGTTCATTTATGTT
Found at i:354506 original size:16 final size:16
Alignment explanation
Indices: 354483--354555 Score: 128
Period size: 16 Copynumber: 4.6 Consensus size: 16
354473 GGGTCTCCAA
*
354483 CGTTTATGTTTGTGTT
1 CGTTTATGTTCGTGTT
*
354499 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
354515 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
354531 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
354547 CGTTTATGT
1 CGTTTATGT
354556 ATTAAATGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 54 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:355471 original size:22 final size:21
Alignment explanation
Indices: 355441--355521 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
355431 AAATACGGTA
355441 AAATTGAGTTGCGAAATTAGC
1 AAATTGAGTTGCGAAATTAGC
* * *
355462 GAATTCGAGTTGCG-AATTTGA
1 AAATT-GAGTTGCGAAATTAGC
* * *
355483 AAATTGAGTTACGAATTTGGC
1 AAATTGAGTTGCGAAATTAGC
*
355504 AAATTCGTGTTGCGAAAT
1 AAATT-GAGTTGCGAAAT
355522 GTAAATTCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
20 7 0.15
21 22 0.48
22 17 0.37
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (21 bp):
AAATTGAGTTGCGAAATTAGC
Found at i:355487 original size:42 final size:42
Alignment explanation
Indices: 355440--355519 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
355430 TAAATACGGT
* *
355440 AAAATTGAGTTGCGAAATTAGCGAATTCGAGTTGCGAATTTG
1 AAAATTGAGTTACGAAATTAGCAAATTCGAGTTGCGAATTTG
* * *
355482 AAAATTGAGTTACGAATTTGGCAAATTCGTGTTGCGAA
1 AAAATTGAGTTACGAAATTAGCAAATTCGAGTTGCGAA
355520 ATGTAAATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (42 bp):
AAAATTGAGTTACGAAATTAGCAAATTCGAGTTGCGAATTTG
Found at i:355497 original size:20 final size:20
Alignment explanation
Indices: 355440--355561 Score: 75
Period size: 20 Copynumber: 5.9 Consensus size: 20
355430 TAAATACGGT
*
355440 AAAATTGAGTTGCGAAATTAG
1 AAAATTGAGTTGCG-AATTTG
**
355461 CGAATTCGAGTTGCGAATTTG
1 AAAATT-GAGTTGCGAATTTG
*
355482 AAAATTGAGTTACGAATTTGG
1 AAAATTGAGTTGCGAATTT-G
* * *
355503 CAAATTCGTGTTGCGAA-ATG
1 AAAATT-GAGTTGCGAATTTG
* ** *
355523 TAAATTCTTGTTGCGAATTCG
1 AAAATT-GAGTTGCGAATTTG
* *
355544 AAAACTGTGTTGCGAATT
1 AAAATTGAGTTGCGAATT
355562 CGTTGATTAT
Statistics
Matches: 80, Mismatches: 17, Indels: 9
0.75 0.16 0.08
Matches are distributed among these distances:
20 39 0.49
21 25 0.31
22 16 0.20
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (20 bp):
AAAATTGAGTTGCGAATTTG
Found at i:355752 original size:2 final size:2
Alignment explanation
Indices: 355747--355791 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
355737 GTTATTTTTA
355747 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
355788 AT AT
1 AT AT
355792 TCAAACACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:357482 original size:16 final size:16
Alignment explanation
Indices: 357463--357493 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
357453 TTTTAAAACA
357463 ATTTTAAAGAAAAATC
1 ATTTTAAAGAAAAATC
357479 ATTTTAAAGAAAAAT
1 ATTTTAAAGAAAAAT
357494 GGTCTGCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (16 bp):
ATTTTAAAGAAAAATC
Found at i:359923 original size:91 final size:93
Alignment explanation
Indices: 359766--359934 Score: 261
Period size: 91 Copynumber: 1.8 Consensus size: 93
359756 TGTTGAAGAC
* *
359766 GACACTGCTCATCCGCGATGAAGAGAATCTTGGTCATCTTTAGGAAAGATGATAACATGGTTCCA
1 GACACTGCTCATCCGCGATGAAGAGAATCTTGGCCATCTTTAGGAAAGATGATAACACGGTTCCA
*
359831 CTCTGCTGGGGACATCTGGCCGAGGGAT
66 CTCTGCTGCGGACATCTGGCCGAGGGAT
* * * *
359859 GACACTTCTCATCCGCGATGAAGAG-TTC-TGGCCATCTTTAGGAATGATGCTAACACGGTTCCA
1 GACACTGCTCATCCGCGATGAAGAGAATCTTGGCCATCTTTAGGAAAGATGATAACACGGTTCCA
359922 CTCTGCTGCGGAC
66 CTCTGCTGCGGAC
359935 GGCTGGTTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
91 43 0.62
92 2 0.03
93 24 0.35
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.25
Consensus pattern (93 bp):
GACACTGCTCATCCGCGATGAAGAGAATCTTGGCCATCTTTAGGAAAGATGATAACACGGTTCCA
CTCTGCTGCGGACATCTGGCCGAGGGAT
Found at i:360086 original size:130 final size:128
Alignment explanation
Indices: 359844--360329 Score: 650
Period size: 130 Copynumber: 3.7 Consensus size: 128
359834 TGCTGGGGAC
* ** * * * *
359844 ATCTGGCCGAGGGATGACACTTCTCATCCGCGATGAAGAGTTCTGGCCATCTTTAGGAATGATGC
1 ATCTGGTCG-GGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATC--TA--AA-GGTGA
* * * *
359909 TAACACGGTTCC-ACTCTGCTGCGGACGGCTGGTTATCTGAGGTTGACACGGCTCATACGTGATG
60 TAACACGGTTCCTAC-GTGATGAGGACGGCTGGTTATCTAAGGTTGACACGGCTCATACGTGATG
359973 AAGAG
124 AAGAG
* *** *
359978 TTCTGGTCAGGGGATGACATTACTCATACATGATGAAGAGTTCTTGGCCATCTAAAGGTGATAAC
1 ATCTGGTC-GGGGATGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTAAAGGTGATAAC
* *
360043 ACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAG
64 ACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGTTGACACGGCTCATACGTGATGAAGAG
* *
360108 GTCTGGTCGAGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACA
1 ATCTGGTCG-GGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACA
*
360173 CGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAG
65 CGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGTTGACACGGCTCATACGTGATGAAGAG
* *
360237 ATATGGTCTGGGGAATGACACGGCTCATACGTGATGAAGAGTTATGGCCATCTAAAGGTGATAAC
1 ATCTGGTC-GGGG-ATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAAC
360302 ACGGTTCCTACGTGATGAGGACGGCTGG
64 ACGGTTCCTACGTGATGAGGACGGCTGG
360330 CCATCTTTAG
Statistics
Matches: 318, Mismatches: 28, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
129 92 0.29
130 177 0.56
131 4 0.01
133 2 0.01
134 34 0.11
135 9 0.03
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (128 bp):
ATCTGGTCGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACAC
GGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGTTGACACGGCTCATACGTGATGAAGAG
Found at i:360138 original size:40 final size:42
Alignment explanation
Indices: 359943--360277 Score: 188
Period size: 40 Copynumber: 7.9 Consensus size: 42
359933 ACGGCTGGTT
* *
359943 ATCTGAGG-TTGACACGGCTCATACGTGATGAAGAGTTCTGG
1 ATCTGAGGAATGACACGGCTCATACGTGATGAAGAGGTCTGG
* * *** * *
359984 -TCAG-GGGATGACATTACTCATACATGATGAAGAGTTCTTGG
1 ATCTGAGGAATGACACGGCTCATACGTGATGAAGAGGTC-TGG
* * * * * *
360025 CCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG-CTGG
1 --ATCT-GAGG-AATGACACGGCTCATACGTGATGAAGA-GGTCTGG
* * *
360071 TTATCTAAGG-GTGACACGGCTCCTACGTGATGAAGAGGTCTGG
1 --ATCTGAGGAATGACACGGCTCATACGTGATGAAGAGGTCTGG
*
360114 -TC-GAGGAATGACACGGCTCATACGTGATGAAGAGTTCTGG
1 ATCTGAGGAATGACACGGCTCATACGTGATGAAGAGGTCTGG
* * * * * *
360154 CCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG-CTGG
1 --ATCT-GAGG-AATGACACGGCTCATACGTGATGAAGA-GGTCTGG
* * *
360200 TTATCT-ATGG-TTGACACGGCTCATACGTGATGAAGAGATATGG
1 --ATCTGA-GGAATGACACGGCTCATACGTGATGAAGAGGTCTGG
*
360243 -TCTGGGGAATGACACGGCTCATACGTGATGAAGAG
1 ATCTGAGGAATGACACGGCTCATACGTGATGAAGAG
360278 TTATGGCCAT
Statistics
Matches: 227, Mismatches: 45, Indels: 44
0.72 0.14 0.14
Matches are distributed among these distances:
39 5 0.02
40 65 0.29
41 29 0.13
42 3 0.01
43 52 0.23
44 3 0.01
45 9 0.04
46 39 0.17
47 21 0.09
48 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.25
Consensus pattern (42 bp):
ATCTGAGGAATGACACGGCTCATACGTGATGAAGAGGTCTGG
Found at i:360321 original size:259 final size:262
Alignment explanation
Indices: 359845--360329 Score: 712
Period size: 259 Copynumber: 1.9 Consensus size: 262
359835 GCTGGGGACA
* ** * *
359845 TCTGGCCGAGGGATGACACTTCTCATCCGCGATGAAGAGTTCTGGCCATCTTTAGGAATGATGCT
1 TCTGGCCGAGGAATGACACGGCTCATACGCGATGAAGAGTTCTGGCCATC-TTA-GAATGATGAT
* *
359910 AACACGGTTCCACTCTGCTGCGGACGGCTGGTTATCTGAGGTTGACACGGCTCATACGTGATGAA
64 AACACGGTTCCACTCTGATGAGGACGGCTGGTTATCTGAGGTTGACACGGCTCATACGTGATGAA
* * ** *
359975 GAGTTCTGGTCAGGGGATGACATTACTCATACATGATGAAGAGTTCTTGGCCATCTAAAGGTGAT
129 GAGATATGGTCAGGGGATGACACGACTCATACATGATGAAGAGTTCATGGCCATCTAAAGGTGAT
360040 AACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAA
194 AACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAA
360105 GAGG
259 GAGG
* * *
360109 TCTGGTCGAGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATC-TA-AA-GGTGATAA
1 TCTGGCCGAGGAATGACACGGCTCATACGCGATGAAGAGTTCTGGCCATCTTAGAATGATGATAA
*
360171 CACGGTTCCTAC-GTGATGAGGACGGCTGGTTATCT-ATGGTTGACACGGCTCATACGTGATGAA
66 CACGGTTCC-ACTCTGATGAGGACGGCTGGTTATCTGA-GGTTGACACGGCTCATACGTGATGAA
* * *
360234 GAGATATGGTCTGGGGAATGACACGGCTCATACGTGATGAAGAGTT-ATGGCCATCTAAAGGTGA
129 GAGATATGGTCAGGGG-ATGACACGACTCATACATGATGAAGAGTTCATGGCCATCTAAAGGTGA
360298 TAACACGGTTCCTACGTGATGAGGACGGCTGG
193 TAACACGGTTCCTACGTGATGAGGACGGCTGG
360330 CCATCTTTAG
Statistics
Matches: 199, Mismatches: 19, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
258 1 0.01
259 123 0.62
260 29 0.15
262 2 0.01
264 44 0.22
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (262 bp):
TCTGGCCGAGGAATGACACGGCTCATACGCGATGAAGAGTTCTGGCCATCTTAGAATGATGATAA
CACGGTTCCACTCTGATGAGGACGGCTGGTTATCTGAGGTTGACACGGCTCATACGTGATGAAGA
GATATGGTCAGGGGATGACACGACTCATACATGATGAAGAGTTCATGGCCATCTAAAGGTGATAA
CACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAAGA
GG
Found at i:360331 original size:46 final size:44
Alignment explanation
Indices: 360008--360335 Score: 207
Period size: 46 Copynumber: 7.5 Consensus size: 44
359998 TACTCATACA
* * *
360008 TGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACG
1 TGATGAAGAG-GC-TGGCCATCT-AAGGTGATGACACGGCTCCTACG
* **
360055 TGATGAGGACGGCTGGTTATCTAAGG-G-TGACACGGCTCCTACG
1 TGATGAAGA-GGCTGGCCATCTAAGGTGATGACACGGCTCCTACG
* * *
360098 TGATGAAGAGGTCTGG---TC-GAGG-AATGACACGGCTCATACG
1 TGATGAAGAGG-CTGGCCATCTAAGGTGATGACACGGCTCCTACG
* * *
360138 TGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACG
1 TGATGAAGAG-GCTGGCCATCT-AAGGTGATGACACGGCTCCTACG
* ** * *
360184 TGATGAGGACGGCTGGTTATCTATGGT--TGACACGGCTCATACG
1 TGATGAAGA-GGCTGGCCATCTAAGGTGATGACACGGCTCCTACG
** * *
360227 TGATGAAGAGATATGG---TCT--GGGGAATGACACGGCTCATACG
1 TGATGAAGAG-GCTGGCCATCTAAGGTG-ATGACACGGCTCCTACG
** * *
360268 TGATGAAGAGTTATGGCCATCTAAAGGTGATAACACGGTTCCTACG
1 TGATGAAGAG-GCTGGCCATCT-AAGGTGATGACACGGCTCCTACG
*
360314 TGATGAGGACGGCTGGCCATCT
1 TGATGAAGA-GGCTGGCCATCT
360336 TTAGGAGTTA
Statistics
Matches: 223, Mismatches: 36, Indels: 45
0.73 0.12 0.15
Matches are distributed among these distances:
38 2 0.01
39 3 0.01
40 34 0.15
41 31 0.14
42 3 0.01
43 52 0.23
44 4 0.02
45 11 0.05
46 68 0.30
47 14 0.06
48 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (44 bp):
TGATGAAGAGGCTGGCCATCTAAGGTGATGACACGGCTCCTACG
Found at i:360388 original size:28 final size:28
Alignment explanation
Indices: 360368--360436 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 28
360358 AAACCAAATT
360368 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
360396 AAAGATTTGTTTCAAGAA-AAACATACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
360424 AAAGACTTTGTTT
1 AAAGA-TTTGTTT
360437 GTTTTGTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 28 0.76
29 9 0.24
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:361292 original size:31 final size:31
Alignment explanation
Indices: 361257--361322 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
361247 AGAGACAAAA
*
361257 TTTTGTTTCCAAAGAAACAAACTCAAAGATT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATT
**
361288 TTTTGTTTCAAAAGAAACACTCTCAAAGATT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATT
361319 TTTT
1 TTTT
361323 CACAAAATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (31 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGATT
Found at i:361328 original size:29 final size:31
Alignment explanation
Indices: 361267--361329 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
361257 TTTTGTTTCC
**
361267 AAAGAAACAAACTCAAAGATTTTTTGTTTCA
1 AAAGAAACAAACTCAAAGATTTTTTGTCACA
**
361298 AAAGAAACACTCTCAAAGA-TTTTT-TCACA
1 AAAGAAACAAACTCAAAGATTTTTTGTCACA
361327 AAA
1 AAA
361330 TTGTCTCAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 6 0.21
30 5 0.18
31 17 0.61
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.29
Consensus pattern (31 bp):
AAAGAAACAAACTCAAAGATTTTTTGTCACA
Found at i:361383 original size:52 final size:51
Alignment explanation
Indices: 361309--361409 Score: 168
Period size: 52 Copynumber: 2.0 Consensus size: 51
361299 AAGAAACACT
361309 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAACACTTTGTTTCAGA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGAC-A-ACTTTGTTTCAGA
*
361362 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAACTTTGTTTCA
361410 AAATAAATAG
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
50 11 0.23
51 1 0.02
52 27 0.57
53 8 0.17
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (51 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAACTTTGTTTCAGA
Found at i:361466 original size:28 final size:29
Alignment explanation
Indices: 361406--361529 Score: 132
Period size: 29 Copynumber: 4.4 Consensus size: 29
361396 ACAACTTTGT
* *
361406 TTCAAAATAAATAGACTCAAAGAT-TTT-
1 TTCAAAAGAAACAGACTCAAAGATATTTA
361433 TTCAAAAGAAACA-ACTCAAAGATATTTA
1 TTCAAAAGAAACAGACTCAAAGATATTTA
* * * *
361461 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAGACTCAAAGATATTTA
*
361490 TTCAAAAGGAACAGACTCAAAG--ATTTA
1 TTCAAAAGAAACAGACTCAAAGATATTTA
*
361517 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
361530 TGTCTCCAGA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
26 10 0.12
27 19 0.23
28 21 0.25
29 33 0.40
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.26
Consensus pattern (29 bp):
TTCAAAAGAAACAGACTCAAAGATATTTA
Found at i:361489 original size:29 final size:29
Alignment explanation
Indices: 361420--361515 Score: 135
Period size: 29 Copynumber: 3.4 Consensus size: 29
361410 AAATAAATAG
*
361420 ACTCAAAGA-TTTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
361446 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
* *
361475 ACTCCAAGATTTTTATTCAAAAGGAACAG
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
361504 ACTCAAAGATTT
1 ACTCAAAGATTT
361516 ATCTCAAGAG
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
26 9 0.15
27 3 0.05
28 11 0.18
29 38 0.62
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTCAAAAGGAACAA
Found at i:361537 original size:57 final size:54
Alignment explanation
Indices: 361406--361529 Score: 133
Period size: 57 Copynumber: 2.2 Consensus size: 54
361396 ACAACTTTGT
* * * *
361406 TTCAAAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCCAAGATTTTTTCAAAAGAAACAACTCAAAGA-ATTTA
* *
361461 TTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAGACTCAAAG-ATTTA
1 TTCAAAAGAAACAAACTCCAAGA-TTTT-TTCAAAAGAAACA-ACTCAAAGAATTTA
*
361517 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
361530 TGTCTCCAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
55 18 0.32
56 10 0.18
57 21 0.37
58 8 0.14
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.26
Consensus pattern (54 bp):
TTCAAAAGAAACAAACTCCAAGATTTTTTCAAAAGAAACAACTCAAAGAATTTA
Found at i:361941 original size:36 final size:36
Alignment explanation
Indices: 361825--361948 Score: 103
Period size: 36 Copynumber: 3.5 Consensus size: 36
361815 TCTCAAAGGA
* ** *
361825 AAAATGTCTCAAGCGAGATGAAATTTG-CTTTA-AG
1 AAAACGTCTCAAGCGAGACAAAATTTGTTTTTAGAG
* **
361859 ATATA-GTCTCAAATGAGACAAAATTTGTTTTTAGAG
1 A-AAACGTCTCAAGCGAGACAAAATTTGTTTTTAGAG
** *
361895 AAATTGTCTCAAGCGAGACAAAGTTTGTTTTT-GAG
1 AAAACGTCTCAAGCGAGACAAAATTTGTTTTTAGAG
*
361930 AAAACGATCTCAAGTGAGA
1 AAAACG-TCTCAAGCGAGA
361949 TCAACTTTGT
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
34 19 0.27
35 14 0.20
36 38 0.54
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (36 bp):
AAAACGTCTCAAGCGAGACAAAATTTGTTTTTAGAG
Found at i:361960 original size:36 final size:36
Alignment explanation
Indices: 361864--361948 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
361854 TTAAGATATA
* **
361864 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
361900 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
361935 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
361949 TCAACTTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:362079 original size:105 final size:101
Alignment explanation
Indices: 361900--362132 Score: 292
Period size: 105 Copynumber: 2.3 Consensus size: 101
361890 TAGAGAAATT
*
361900 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
* *
361964 GTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
64 GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
362002 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
362066 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
362107 GTCTCAAGCGAGACGAAGTTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
362133 AAGAGAATTT
Statistics
Matches: 115, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 4 0.03
105 78 0.68
106 5 0.04
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:362146 original size:36 final size:36
Alignment explanation
Indices: 362106--362187 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
362096 AAAGGAAAAA
* * *
362106 TGTCTCAAGCGAGACGAAGTTTG-TTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAA-AGAAAT
* * *
362142 TGTCTTAAGTGATACAAACTTTGTTTTTAAAGAAAT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
362178 TGTCTCAAGC
1 TGTCTCAAGC
362188 AAAACAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
Found at i:362195 original size:36 final size:36
Alignment explanation
Indices: 362106--362200 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 36
362096 AAAGGAAAAA
* * * *
362106 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
* * * *
362142 TGTCTTAAGTGATACAAACTTTGTTTTTAA-AGAAAT
1 TGTCTCAAGCGAAACAAAATTTG-TTTTAAGAGAAAT
*
362178 TGTCTCAAGCAAAACAAAATTTG
1 TGTCTCAAGCGAAACAAAATTTG
362201 AGAAAACGAT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
36 41 0.87
37 6 0.13
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.35
Consensus pattern (36 bp):
TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
Found at i:362222 original size:273 final size:268
Alignment explanation
Indices: 361697--362299 Score: 811
Period size: 273 Copynumber: 2.2 Consensus size: 268
361687 TTTCAAGTAC
* * * * *
361697 AACAAATT-TAAATTTGTATCTCAGA-GAAAAATGTCTCAAGCGAAACGAAATTTGTTTCGAAAT
1 AACAAATTCGAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAAAG
361760 AAACAACAATATCAAGTGAGATTTTGTTTTAAGTGAAACAAATTCAAAATTAGTATCTCAAAGGA
66 AAACAACAATATCAAGTGAGATTTTGTTTTAAGTGAAACAAATTCAAAATTAGTATCTCAAAGGA
* *
361825 AAAATGTCTCAAGCGAGATGAAATTTGCTTTAAGATATAGTCTCAAATGAGACAAAATTTGTTTT
131 AAAATGTCTCAAGCGAGACGAAATTTGCTTTAAGAAATAGTCTCAAATGAGACAAAATTTGTTTT
* * * *
361890 TAGAGAAATTGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACT
196 TAAAGAAATTGTCTCAAGCAAAACAAA-----TATTTGAGAAAACGATCTCAAGTGAGATCAACT
361955 TTGTTTAATGTGA
256 TTGTTTAATGTGA
* * *
361968 AACAAATTCGAAATTTGGATCTCAAAGGGAAAAGGTCTCAAGCGAGACGAAATTTGTTTTGAAAG
1 AACAAATTCGAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAAAG
* * *
362033 AAACAACAATCT-AAGGTGAGATTAATTTTGTTTTAAGTGAATCAAATTCAAAATTTGTATCTCA
66 AAACAACAATATCAA-GTGAG----ATTTTGTTTTAAGTGAAACAAATTCAAAATTAGTATCTCA
* * * * * * *
362097 AAGGAAAAATGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATTTGTCTTAAGTGATACAAACT
126 AAGGAAAAATGTCTCAAGCGAGACGAAATTTGCTTTAAGA-AA-TAGTCTCAAATGAGACAAAAT
362162 TTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAA-ATTTGAGAAAACGATCTCAAGTGAGATCAA
189 TTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAATATTTGAGAAAACGATCTCAAGTGAGATCAA
362226 CTTTGTTTAATGTGA
254 CTTTGTTTAATGTGA
* * * *
362241 ATCAAATTCGAAATTTGTATCTC-AAGGAAAAATGTCTCCAGTGAGACGGAATTTGTTTT
1 AACAAATTCGAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTT
362300 TCAAGAAATT
Statistics
Matches: 292, Mismatches: 31, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
271 8 0.03
272 47 0.16
273 114 0.39
277 75 0.26
278 1 0.00
279 47 0.16
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (268 bp):
AACAAATTCGAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAAAG
AAACAACAATATCAAGTGAGATTTTGTTTTAAGTGAAACAAATTCAAAATTAGTATCTCAAAGGA
AAAATGTCTCAAGCGAGACGAAATTTGCTTTAAGAAATAGTCTCAAATGAGACAAAATTTGTTTT
TAAAGAAATTGTCTCAAGCAAAACAAATATTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTT
TAATGTGA
Found at i:362243 original size:168 final size:166
Alignment explanation
Indices: 362048--362366 Score: 423
Period size: 167 Copynumber: 1.9 Consensus size: 166
362038 ACAATCTAAG
* *
362048 GTGAGATTAATTTTGTTTTAAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCA
1 GTGAGATCAACTTTGTTTTAAGTGAATCAAATTCAAAATTTGTATCTC-AAGGAAAAATGTCTCA
* ** * *
362113 AGCGAGAC-GAAGTTTG-TTTT-AAGAGAATTTGTCTTAAGTGATACAAACTTTGTTTTTAAAGA
65 AGCGAGACGGAA-TTTGTTTTTCAAGA-AA-TTGTCTCAAACGAGACAAAATTTGTTTTT--AGA
*
362175 AA-TTGTCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
125 AAGCTGTCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
* *
362216 GTGAGATCAACTTTG-TTTAATGTGAATCAAATTCGAAATTTGTATCTCAAGGAAAAATGTCTCC
1 GTGAGATCAACTTTGTTTTAA-GTGAATCAAATTCAAAATTTGTATCTCAAGGAAAAATGTCTCA
*
362280 AGTGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGCT
65 AGCGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGCT
* *
362345 GTCTCAAGCGAGACAAAATTTG
130 GTCTCAAGCAAAACAAAATTTG
362367 CTTTGAAATA
Statistics
Matches: 133, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
165 5 0.04
166 21 0.16
167 55 0.41
168 48 0.36
169 4 0.03
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (166 bp):
GTGAGATCAACTTTGTTTTAAGTGAATCAAATTCAAAATTTGTATCTCAAGGAAAAATGTCTCAA
GCGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGCTG
TCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
Found at i:362323 original size:36 final size:35
Alignment explanation
Indices: 362290--362406 Score: 148
Period size: 35 Copynumber: 3.3 Consensus size: 35
362280 AGTGAGACGG
*
362290 AATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAA
1 AATTTGTTTTT-AAGAAATTGTCTCAAGCGAGACAA
*
362326 AATTTGTTTTT-AGAAAGCTGTCTCAAGCGAGACAA
1 AATTTGTTTTTAAGAAA-TTGTCTCAAGCGAGACAA
* *
362361 AATTTGCTTTGAA-ATAATTGTCTCAAGCGAGACAAA
1 AATTTGTTTTTAAGA-AATTGTCTCAAGCGAGAC-AA
362397 AATTTGTTTT
1 AATTTGTTTT
362407 AAAATTCTCA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
34 5 0.07
35 41 0.58
36 25 0.35
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (35 bp):
AATTTGTTTTTAAGAAATTGTCTCAAGCGAGACAA
Found at i:362957 original size:4 final size:4
Alignment explanation
Indices: 362948--362997 Score: 59
Period size: 4 Copynumber: 13.0 Consensus size: 4
362938 TTTATGTATC
* * *
362948 ATGT ATGT ATG- -TGT ATGT ATGT ATAT ATGT ATGT ATGT GTTT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
362994 ATGT
1 ATGT
362998 TTTCTCAATC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
4 36 0.95
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
ATGT
Found at i:364853 original size:26 final size:23
Alignment explanation
Indices: 364822--364892 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 23
364812 TCAAGGTAGA
364822 AAGAATATTTCAAGGTCTCAAAG
1 AAGAATATTTCAAGGTCTCAAAG
* *
364845 AGAGGGAATGTTTCAAGG--TCGAA-
1 A-A--GAATATTTCAAGGTCTCAAAG
364868 AAGAATATTTCAAGGTCTCAAAG
1 AAGAATATTTCAAGGTCTCAAAG
364891 AA
1 AA
364893 ATAGAATGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
20 12 0.32
22 5 0.13
23 4 0.11
24 5 0.13
26 12 0.32
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.24
Consensus pattern (23 bp):
AAGAATATTTCAAGGTCTCAAAG
Found at i:364878 original size:20 final size:20
Alignment explanation
Indices: 364810--364884 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
364800 AAATGCAATG
*
364810 TTTCAAGGTAG-AAAGAATA
1 TTTCAAGGTCGAAAAGAATA
* *
364829 TTTCAAGGTCTCAAAGAGAGGGAATG
1 TTTCAAGG--TCGAA-A-A--GAATA
364855 TTTCAAGGTCGAAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
364875 TTTCAAGGTC
1 TTTCAAGGTC
364885 TCAAAGAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.18
20 14 0.32
21 1 0.02
22 2 0.05
23 2 0.05
24 5 0.11
26 12 0.27
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.27
Consensus pattern (20 bp):
TTTCAAGGTCGAAAAGAATA
Found at i:364898 original size:26 final size:25
Alignment explanation
Indices: 364821--364899 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 25
364811 TTCAAGGTAG
364821 AAAGAATATTTCAAGGTCTCAAAGA
1 AAAGAATATTTCAAGGTCTCAAAGA
** *
364846 GAGGGAATGTTTCAAGG--TC---GA
1 -AAAGAATATTTCAAGGTCTCAAAGA
364867 AAAGAATATTTCAAGGTCTCAAAGA
1 AAAGAATATTTCAAGGTCTCAAAGA
364892 AATAGAAT
1 AA-AGAAT
364900 GTCAAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 4 0.10
26 18 0.44
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (25 bp):
AAAGAATATTTCAAGGTCTCAAAGA
Found at i:364900 original size:46 final size:45
Alignment explanation
Indices: 364806--364901 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 45
364796 AAATAAATGC
* *
364806 AATGTTTCAAGGTAGAAAGAATATTTCAAGGTCTCAAAGAGAGGG
1 AATGTTTCAAGGTAGAAAGAATATTTCAAGGTCTCAAAGAAAGAG
* *
364851 AATGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAAATAG
1 AATGTTTCAAGGTAG-AAAGAATATTTCAAGGTCTCAAAGAAAGAG
364897 AATGT
1 AATGT
364902 CAAAAATTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 14 0.30
46 32 0.70
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (45 bp):
AATGTTTCAAGGTAGAAAGAATATTTCAAGGTCTCAAAGAAAGAG
Found at i:367385 original size:31 final size:32
Alignment explanation
Indices: 367329--367390 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
367319 TGACAAAATG
367329 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
367361 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
367391 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:372386 original size:2 final size:2
Alignment explanation
Indices: 372381--372409 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
372371 AAAACGCCAC
372381 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
372410 TTTTGGGCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:377867 original size:35 final size:36
Alignment explanation
Indices: 377802--377882 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 36
377792 AACACAATCA
* * ** *
377802 TCAATTACATTTTAAACCCCAAATTTC-AAAATGCT
1 TCAATTATATTCTAAACCCCAAATCCCAAAAATACT
*
377837 TCAATTATATTCTAAACCTCAAATCCCAAAAATACT
1 TCAATTATATTCTAAACCCCAAATCCCAAAAATACT
*
377873 TTAATTATAT
1 TCAATTATAT
377883 AACCAACCCC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 22 0.58
36 16 0.42
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (36 bp):
TCAATTATATTCTAAACCCCAAATCCCAAAAATACT
Found at i:379229 original size:21 final size:21
Alignment explanation
Indices: 379203--379259 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
379193 ATAATTGGGT
379203 GTTATATAAGCTTAAGGAAAG
1 GTTATATAAGCTTAAGGAAAG
379224 GTTATATAAGCTTAAGGAAAG
1 GTTATATAAGCTTAAGGAAAG
*
379245 CTTATATAAGCTTAA
1 GTTATATAAGCTTAA
379260 AACACCAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (21 bp):
GTTATATAAGCTTAAGGAAAG
Found at i:380607 original size:18 final size:18
Alignment explanation
Indices: 380584--380634 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
380574 GGATTATCAT
* *
380584 TGGTCCTACGGGACATAG
1 TGGTCCTACGAGACATAA
380602 TGGTCCTACGAGACATAA
1 TGGTCCTACGAGACATAA
* *
380620 TGGTCATTCGAGACA
1 TGGTCCTACGAGACA
380635 AAATTCTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (18 bp):
TGGTCCTACGAGACATAA
Found at i:383979 original size:35 final size:35
Alignment explanation
Indices: 383939--384015 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
383929 TTTGTGTATC
*
383939 GATGCATGGGTAGTGCATCGATGCACATGTTAAGG
1 GATGCATGAGTAGTGCATCGATGCACATGTTAAGG
383974 GATGCATGAGTAGTGCATCGATGCACATGTTAAGG
1 GATGCATGAGTAGTGCATCGATGCACATGTTAAGG
384009 GATGCAT
1 GATGCAT
384016 CGATACATTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.26
Consensus pattern (35 bp):
GATGCATGAGTAGTGCATCGATGCACATGTTAAGG
Found at i:383998 original size:19 final size:19
Alignment explanation
Indices: 383936--383998 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 19
383926 TATTTTGTGT
*
383936 ATCGATGCATGGGTAGTGC
1 ATCGATGCATGAGTAGTGC
* **
383955 ATCGATGCA-CA-T-GTTA
1 ATCGATGCATGAGTAGTGC
**
383971 AGGGATGCATGAGTAGTGC
1 ATCGATGCATGAGTAGTGC
383990 ATCGATGCA
1 ATCGATGCA
383999 CATGTTAAGG
Statistics
Matches: 30, Mismatches: 11, Indels: 6
0.64 0.23 0.13
Matches are distributed among these distances:
16 9 0.30
17 2 0.07
18 1 0.03
19 18 0.60
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (19 bp):
ATCGATGCATGAGTAGTGC
Found at i:384693 original size:29 final size:29
Alignment explanation
Indices: 384658--384716 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
384648 AAAAAATACA
384658 AGTAAAAGTGAAAATTTATGTGATACATG
1 AGTAAAAGTGAAAATTTATGTGATACATG
384687 AGTAAAAGTGAAAATTTATGTGATACATG
1 AGTAAAAGTGAAAATTTATGTGATACATG
384716 A
1 A
384717 ATGTGAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (29 bp):
AGTAAAAGTGAAAATTTATGTGATACATG
Found at i:386211 original size:31 final size:31
Alignment explanation
Indices: 386149--386236 Score: 149
Period size: 31 Copynumber: 2.8 Consensus size: 31
386139 ATATGAAATC
386149 TATGTCCCGAAGGACATAGGTAATCCTGTCCA
1 TATGTCCCGAAGGACATAGGTAA-CCTGTCCA
* *
386181 TATGTCCCAAATGACATAGGTAACCTGTCCA
1 TATGTCCCGAAGGACATAGGTAACCTGTCCA
386212 TATGTCCCGAAGGACATAGGTAACC
1 TATGTCCCGAAGGACATAGGTAACC
386237 CTCGACTCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 31 0.60
32 21 0.40
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (31 bp):
TATGTCCCGAAGGACATAGGTAACCTGTCCA
Found at i:388949 original size:35 final size:35
Alignment explanation
Indices: 388903--388998 Score: 147
Period size: 35 Copynumber: 2.7 Consensus size: 35
388893 AATAGATTAT
* **
388903 GAATTTAAGGTTGGGAATGTAATTGAAGTATTTTG
1 GAATTTGAGGTTTAGAATGTAATTGAAGTATTTTG
388938 GAATTTGAGGTTTAGAATGTAATTGAAGTATTTTG
1 GAATTTGAGGTTTAGAATGTAATTGAAGTATTTTG
* *
388973 GATTTTGGGGTTTAGAATGTAATTGA
1 GAATTTGAGGTTTAGAATGTAATTGA
388999 TGATTGTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (35 bp):
GAATTTGAGGTTTAGAATGTAATTGAAGTATTTTG
Found at i:412116 original size:23 final size:22
Alignment explanation
Indices: 412072--412120 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
412062 AAAATACAAC
*
412072 ATTTATAATTTTTAGTCCTTTA
1 ATTTATAATTTTTAGTCATTTA
*
412094 TATTTATAATTTTT-TTCAATTTA
1 -ATTTATAATTTTTAGTC-ATTTA
412117 ATTT
1 ATTT
412121 TTTAGAAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (22 bp):
ATTTATAATTTTTAGTCATTTA
Found at i:421542 original size:19 final size:19
Alignment explanation
Indices: 421518--421555 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
421508 TGATTCAACA
421518 AAATAATATTTTATAATTT
1 AAATAATATTTTATAATTT
421537 AAATAATATTTTATAATTT
1 AAATAATATTTTATAATTT
421556 TTAATAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATAATATTTTATAATTT
Found at i:421818 original size:3 final size:3
Alignment explanation
Indices: 421783--421840 Score: 53
Period size: 3 Copynumber: 18.3 Consensus size: 3
421773 GTTTATTTAT
* * *
421783 TAA TAA TAGA TAA AAA AAA GTAA AAA TATA TAA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA -TAA TAA TA-A TAA TAA TAA TAA TAA TAA
*
421831 TAA TAC TAA T
1 TAA TAA TAA T
421841 TTATTATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
3 38 0.83
4 8 0.17
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:423692 original size:61 final size:61
Alignment explanation
Indices: 423597--423719 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
423587 GTTAAAAAAA
423597 AATTACTGAATTTATTATTATTTAAATAATAAAATTAATAAAAATTACCTAAAACATTATT
1 AATTACTGAATTTATTATTATTTAAATAATAAAATTAATAAAAATTACCTAAAACATTATT
423658 AATTACTGAATTTATTATTATTTAAATAATAAAATTAATAAAAATTACCTAAAACATTATT
1 AATTACTGAATTTATTATTATTTAAATAATAAAATTAATAAAAATTACCTAAAACATTATT
423719 A
1 A
423720 TTTTTATCTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.41
Consensus pattern (61 bp):
AATTACTGAATTTATTATTATTTAAATAATAAAATTAATAAAAATTACCTAAAACATTATT
Found at i:424462 original size:18 final size:18
Alignment explanation
Indices: 424424--424495 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 18
424414 CAAAGAAAAC
* *
424424 AAATAAGATAAAGAGAATA
1 AAATAA-ATAAAAAAAATA
424443 AAATAAA-AGAAAAAAATA
1 AAATAAATA-AAAAAAATA
* *
424461 AATTAAATAAAATAAAT-
1 AAATAAATAAAAAAAATA
424478 AAATAAGATAAGAAAAAA
1 AAATAA-ATAA-AAAAAA
424496 AATAGTAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
17 6 0.14
18 25 0.58
19 12 0.28
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (18 bp):
AAATAAATAAAAAAAATA
Found at i:424488 original size:27 final size:26
Alignment explanation
Indices: 424424--424488 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
424414 CAAAGAAAAC
424424 AAATAAGATAAAGAGAATAAAATAAA
1 AAATAAGATAAAGAGAATAAAATAAA
* * *
424450 AGAAAAAAATAAATTA-AATAAAATAAA
1 A-AATAAGATAAA-GAGAATAAAATAAA
424477 TAAATAAGATAA
1 -AAATAAGATAA
424489 GAAAAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
26 1 0.03
27 28 0.90
28 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (26 bp):
AAATAAGATAAAGAGAATAAAATAAA
Found at i:424572 original size:40 final size:39
Alignment explanation
Indices: 424518--424597 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 39
424508 TGAAAAAGGA
* *
424518 AAATATATATATATATATACACATCAAAGTATTAATAAAAT
1 AAATAAATATATATATATACACAACAAA-TATTAA-AAAAT
* *
424559 AAATAAAT-TATATATATATACAACAAATATTTAAAAAT
1 AAATAAATATATATATATACACAACAAATATTAAAAAAT
424597 A
1 A
424598 GAAAAGCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 6 0.17
39 5 0.14
40 17 0.49
41 7 0.20
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.34
Consensus pattern (39 bp):
AAATAAATATATATATATACACAACAAATATTAAAAAAT
Found at i:426357 original size:30 final size:30
Alignment explanation
Indices: 426321--426393 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
426311 CCCGAAGGAC
426321 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
426351 CTATCCAGTGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
426381 CTATCCATAGGTC
1 CTATCCAGAGGTC
426394 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:426433 original size:31 final size:31
Alignment explanation
Indices: 426379--426471 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
426369 GATCCTCGGT
* *
426379 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
426410 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
426441 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
426472 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:428442 original size:35 final size:35
Alignment explanation
Indices: 428403--428474 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
428393 CTAAAAAACC
*
428403 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATACAACT
*
428438 CTATTTTAGACTGGTATTTGAGTCCTAATACAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATACAACT
428473 CT
1 CT
428475 TCTTTTTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATACAACT
Found at i:429144 original size:106 final size:105
Alignment explanation
Indices: 428958--429681 Score: 906
Period size: 106 Copynumber: 7.0 Consensus size: 105
428948 TGCATTGTTC
** * * **
428958 CGAGTCCAATATCC-TCTGCCGTGAAGTTGAAATT-AGCTCTGGAACTGAAAAATTGTTTGTTGA
1 CGAGTCCAATATCCTTC-GATGTGAAGTTGAAATTGA-CTCTGAAATTGGGAAATTGTTTGTTGA
* * * *
429021 CAGCCAAT-CGTACCTTCGCTGTGAAGTTGAGCTTGTGATGTCT
64 CAACC-ATCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCT
* * * * *
429064 TGAGTCTAATATCCTTCGATGTGAAGTTAAAATTGACCCTGAAATTGGGAAATTGTATGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
429129 ACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
66 ACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGT-GTCT
* * * * *
429170 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTATTTGTTGAAA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
429235 ACCAGT-CGTCCCTTCGTTGTGAAGTTGAACTTGTG-GTCT
66 ACCA-TCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCT
* * *
429274 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAATTGGGAAATTATTTGCTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
*
429339 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
66 ACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGT-GTCT
* *
429380 CGAGTCCAATATCCTTCG--CT--A-TTG-----G-CTCTGAAATTGGGAGATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
*
429434 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCT
* * *
429475 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTAGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
*
429540 ACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCC
66 ACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCT
* * * * *
429581 CGAGTCCAACATCCTTCGATATGAAGTTGAAATTGGCTATGAAATTGGAAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
*
429646 ACCAGT-TGTCCCTTCGTTGTGAAGTTGAACTTGTGT
66 ACCA-TCCGTCCCTTCGTTGTGAAGTTGAACTTGTGT
429682 TGCTTCGAGT
Statistics
Matches: 545, Mismatches: 52, Indels: 43
0.85 0.08 0.07
Matches are distributed among these distances:
95 81 0.15
96 2 0.00
97 1 0.00
99 1 0.00
100 3 0.01
101 3 0.01
102 1 0.00
104 97 0.18
105 5 0.01
106 346 0.63
107 5 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
ACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCT
Found at i:429520 original size:305 final size:306
Alignment explanation
Indices: 429102--429681 Score: 939
Period size: 305 Copynumber: 1.9 Consensus size: 306
429092 AAAATTGACC
*
429102 CTGAAATTGGGAAATTGTATGTTGACAACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCG
1 CTGAAATTGGGAAATTGTATGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCG
* *
429167 TCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTATTTGTTG
66 TCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTATGAAATTAGGAAATTATTTGTTG
* * *
429232 AAAACCAGT-CGTCCCTTCGTTGTGAAGTTGAACTTGTG-GTCTCGAGTCCAATATCCTTCGATG
131 AAAACCA-TCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCCCGAGTCCAACATCCTTCGATA
* *
429295 TGAAGTTGAAATTGACCCTGAAATTGGGAAATTATTTGCTGACAACCAGCCGTCCCTTCGTTGTG
195 TGAAGTTGAAATTGACCATGAAATTGGAAAATTATTTGCTGACAACCAGCCGTCCCTTCGTTGTG
429360 AAGTTGAACTTGTGTCGTCTCGAGTCCAATATCCTTCGCTATTGGCT
260 AAGTTGAACTTGTGTCGTCTCGAGTCCAATATCCTTCGCTATTGGCT
* * *
429407 CTGAAATTGGGAGATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
1 CTGAAATTGGGAAATTGTATGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCG
* * *
429472 TCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTAGGAAATTGTTTGTTG
66 TCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTATGAAATTAGGAAATTATTTGTTG
*
429537 ACAACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCCGAGTCCAACATCCTTCGATA
131 AAAACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCCCGAGTCCAACATCCTTCGATA
* * * * **
429602 TGAAGTTGAAATTGGCTATGAAATTGGAAAATTGTTTGTTGACAACCAGTTGTCCCTTCGTTGTG
195 TGAAGTTGAAATTGACCATGAAATTGGAAAATTATTTGCTGACAACCAGCCGTCCCTTCGTTGTG
429667 AAGTTGAACTTGTGT
260 AAGTTGAACTTGTGT
429682 TGCTTCGAGT
Statistics
Matches: 251, Mismatches: 21, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
304 1 0.00
305 156 0.62
307 94 0.37
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (306 bp):
CTGAAATTGGGAAATTGTATGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCG
TCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTATGAAATTAGGAAATTATTTGTTG
AAAACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCCCGAGTCCAACATCCTTCGATAT
GAAGTTGAAATTGACCATGAAATTGGAAAATTATTTGCTGACAACCAGCCGTCCCTTCGTTGTGA
AGTTGAACTTGTGTCGTCTCGAGTCCAATATCCTTCGCTATTGGCT
Found at i:430761 original size:51 final size:52
Alignment explanation
Indices: 430699--430798 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
430689 CTTTTTTCTA
* *
430699 TTTTTCA-TTTTTTTCAATTTATGG-CGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTCATTTTTTTTCAACTTA-GGACGCCCTTTCAGGTTTTCACCCTAAACG
* * * *
430750 TTTTTCCTTTTTTTTCGACTTAGGATGCCCTTTCAGGTTTTCATCCTAA
1 TTTTTCATTTTTTTTCAACTTAGGACGCCCTTTCAGGTTTTCACCCTAA
430799 GCAAAGTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
51 8 0.20
52 33 0.80
ACGTcount: A:0.15, C:0.23, G:0.13, T:0.49
Consensus pattern (52 bp):
TTTTTCATTTTTTTTCAACTTAGGACGCCCTTTCAGGTTTTCACCCTAAACG
Found at i:438641 original size:50 final size:52
Alignment explanation
Indices: 438548--438659 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 52
438538 GATAATTACA
** * * *
438548 ATATATAGTAATAATAGACTTATAAGTAAAATATTAAAGAAAT-ATAT-ATAT
1 ATATATA-TAATAATAGAAATATAAGTAAAAAATCAAAGAAATAATATAAAAT
*
438599 ATATATATAATAATA-AAATAT-AGTAAAAAATCAAATGAAAATAATTTAAAAT
1 ATATATATAATAATAGAAATATAAGTAAAAAATCAAA-G-AAATAATATAAAAT
438651 ATATATATA
1 ATATATATA
438660 TATATACGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
48 12 0.24
49 5 0.10
50 12 0.24
51 10 0.20
52 12 0.24
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (52 bp):
ATATATATAATAATAGAAATATAAGTAAAAAATCAAAGAAATAATATAAAAT
Found at i:439107 original size:35 final size:35
Alignment explanation
Indices: 439068--439139 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
439058 CTAAAAAACC
* *
439068 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAATCATAATCCAACT
*
439103 CTATTTTATACTAGTATTTGAATCATAATCCAACT
1 CTATTTTAGACTAGTATTTGAATCATAATCCAACT
439138 CT
1 CT
439140 TCTTTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAATCATAATCCAACT
Found at i:439607 original size:21 final size:22
Alignment explanation
Indices: 439574--439629 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
439564 TTAAAAAATC
* *
439574 TAAAACTTAAAATTATAAACAA
1 TAAACCTTAAAATAATAAACAA
*
439596 TAAACCTT-AAATAATAAATAA
1 TAAACCTTAAAATAATAAACAA
439617 TAAA-CTGTAAAAT
1 TAAACCT-TAAAAT
439630 TCTAAATCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 16 0.55
22 11 0.38
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAACCTTAAAATAATAAACAA
Found at i:441055 original size:21 final size:21
Alignment explanation
Indices: 441028--441261 Score: 253
Period size: 21 Copynumber: 11.1 Consensus size: 21
441018 GATTCGTAAC
* *
441028 GCGAACTTCGATTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
*
441049 GCAAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
* *
441070 GCGAA-TATGTA-AATCGCAAT
1 GCGAACT-TGGACTATCGCAAT
*
441090 GC-AA-TAGTCGACTATCGCAAT
1 GCGAACT--TGGACTATCGCAAT
* *
441111 GTGAACTTGGACTATCGCAAC
1 GCGAACTTGGACTATCGCAAT
*
441132 GCGAACTTAGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
*
441153 GCGAACTTGGACTATCGCATT
1 GCGAACTTGGACTATCGCAAT
*
441174 GCGAACTTGGACTATCGCATT
1 GCGAACTTGGACTATCGCAAT
*
441195 GCGAA-TAAGTCGACTATCGCAAT
1 GCGAACT---TGGACTATCGCAAT
* *
441218 GCGAACTTGGACTATTGTAAT
1 GCGAACTTGGACTATCGCAAT
441239 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
441260 GC
1 GC
441262 AAATATGTAA
Statistics
Matches: 179, Mismatches: 25, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.02
20 14 0.08
21 141 0.79
22 2 0.01
23 18 0.10
24 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (21 bp):
GCGAACTTGGACTATCGCAAT
Found at i:441243 original size:107 final size:104
Alignment explanation
Indices: 441021--441264 Score: 337
Period size: 107 Copynumber: 2.3 Consensus size: 104
441011 GTTTCCAGAT
* * *
441021 TCGTAACGCGAACTTCGATTATCGCAATGCAAACTTGGACTATCGCAATGCGAATATGTAAATCG
1 TCGTAACGCGAACTTAGACTATCGCAATGCAAACTTGGACTATCGCAATGCGAATATGGAAATCG
*
441086 CAATGCAATAGTCGACTATCGCAATGTGAACTTGGACTA
66 CAATGCAATAGTCGACTATCGCAATGCGAACTTGGACTA
* * * *
441125 TCGCAACGCGAACTTAGACTATCGCAATGCGAACTTGGACTATCGCATTGCGAACT-TGGACTAT
1 TCGTAACGCGAACTTAGACTATCGCAATGCAAACTTGGACTATCGCAATGCGAA-TATGGA-AAT
*
441189 CGCATTGCGAATAAGTCGACTATCGCAATGCGAACTTGGACTA
64 CGCAATGC-AAT-AGTCGACTATCGCAATGCGAACTTGGACTA
* * *
441232 TTGTAATGCGAACTTGGACTATCGCAATGCAAA
1 TCGTAACGCGAACTTAGACTATCGCAATGCAAA
441265 TATGTAAATC
Statistics
Matches: 122, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
104 52 0.43
105 10 0.08
106 3 0.02
107 57 0.47
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (104 bp):
TCGTAACGCGAACTTAGACTATCGCAATGCAAACTTGGACTATCGCAATGCGAATATGGAAATCG
CAATGCAATAGTCGACTATCGCAATGCGAACTTGGACTA
Found at i:441303 original size:21 final size:21
Alignment explanation
Indices: 441273--441437 Score: 142
Period size: 21 Copynumber: 7.9 Consensus size: 21
441263 AATATGTAAA
* *
441273 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
441294 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* * *
441315 TTGCGTTGCGATAGTCCCAGT
1 TCGCATTGCGATAGTCCAAGT
* *
441336 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
441356 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
*
441377 TTGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* * *
441398 TCGCGTTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAGT
441421 TCG--TTGCGATAGTCCAA
1 TCGCATTGCGATAGTCCAA
441438 AATCGCAACG
Statistics
Matches: 118, Mismatches: 19, Indels: 16
0.77 0.12 0.10
Matches are distributed among these distances:
19 7 0.06
20 16 0.14
21 83 0.70
22 1 0.01
23 11 0.09
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:442176 original size:21 final size:21
Alignment explanation
Indices: 442151--442316 Score: 137
Period size: 21 Copynumber: 7.8 Consensus size: 21
442141 ATTTTGGACT
*
442151 ATCGCAATGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
442172 ATCGCAATGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
* *
442193 ATCACAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
442214 ATCGCAATGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
442235 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
442256 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
442277 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
442298 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
442317 CCATCGCAAT
Statistics
Matches: 114, Mismatches: 17, Indels: 26
0.73 0.11 0.17
Matches are distributed among these distances:
19 29 0.25
21 47 0.41
23 38 0.33
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:442209 original size:42 final size:42
Alignment explanation
Indices: 442144--442350 Score: 285
Period size: 42 Copynumber: 5.0 Consensus size: 42
442134 CTTTGCGATT
* *
442144 TTGGACTATCGCAATGAACTTGGAATAAATCGCAATGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAAC
*
442186 TTGGACTATCACAACGAATTTGGAATAAATCGCAATGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAAC
* *
442228 TTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAAC
* * *
442270 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAAC
* *
442312 TTGGACCATCGCAATGCGAATAT-G--TAAATCGCAATGCGA
1 TTGGACTATCGCAA--CGAATTTGGAATAAATCGCAATGCGA
442351 TAGTCGAAGT
Statistics
Matches: 151, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
41 14 0.09
42 131 0.87
43 1 0.01
44 5 0.03
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAAC
Found at i:449061 original size:12 final size:13
Alignment explanation
Indices: 449046--449078 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
449036 AGCACTTATA
449046 AAAAATATTTTT-
1 AAAAATATTTTTG
449058 AAAAATATTTTTG
1 AAAAATATTTTTG
449071 AAAAATAT
1 AAAAATAT
449079 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (13 bp):
AAAAATATTTTTG
Found at i:449685 original size:214 final size:214
Alignment explanation
Indices: 449316--449746 Score: 853
Period size: 214 Copynumber: 2.0 Consensus size: 214
449306 GCGTATCATT
*
449316 ATTTTAGTTTAATGTTCTAACAAGTGAACTAAAATCCATGAACTCACTCTTATAGGTGAATAACA
1 ATTTTAGTTTAATGTTCGAACAAGTGAACTAAAATCCATGAACTCACTCTTATAGGTGAATAACA
449381 GGCAAGTTACGACTCCTGACAATTTTTTTAGTTAATCTGGAAATAAGTTTATATATAAAAATTAA
66 GGCAAGTTACGACTCCTGACAATTTTTTTAGTTAATCTGGAAATAAGTTTATATATAAAAATTAA
449446 GAAAAAAAATCAAATATAAAAATAATTAACTATGAATATCAATTGAAATTGATGATAGTTATTGA
131 GAAAAAAAATCAAATATAAAAATAATTAACTATGAATATCAATTGAAATTGATGATAGTTATTGA
449511 CTAACAAAACATTAGTTTC
196 CTAACAAAACATTAGTTTC
449530 ATTTTAGTTTAATGTTCGAACAAGTGAACTAAAATCCATGAACTCACTCTTATAGGTGAATAACA
1 ATTTTAGTTTAATGTTCGAACAAGTGAACTAAAATCCATGAACTCACTCTTATAGGTGAATAACA
449595 GGCAAGTTACGACTCCTGACAATTTTTTTAGTTAATCTGGAAATAAGTTTATATATAAAAATTAA
66 GGCAAGTTACGACTCCTGACAATTTTTTTAGTTAATCTGGAAATAAGTTTATATATAAAAATTAA
449660 GAAAAAAAATCAAATATAAAAATAATTAACTATGAATATCAATTGAAATTGATGATAGTTATTGA
131 GAAAAAAAATCAAATATAAAAATAATTAACTATGAATATCAATTGAAATTGATGATAGTTATTGA
449725 CTAACAAAACATTAGTTTC
196 CTAACAAAACATTAGTTTC
449744 ATT
1 ATT
449747 AGAGAGAATG
Statistics
Matches: 216, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
214 216 1.00
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (214 bp):
ATTTTAGTTTAATGTTCGAACAAGTGAACTAAAATCCATGAACTCACTCTTATAGGTGAATAACA
GGCAAGTTACGACTCCTGACAATTTTTTTAGTTAATCTGGAAATAAGTTTATATATAAAAATTAA
GAAAAAAAATCAAATATAAAAATAATTAACTATGAATATCAATTGAAATTGATGATAGTTATTGA
CTAACAAAACATTAGTTTC
Found at i:450153 original size:32 final size:32
Alignment explanation
Indices: 450112--450172 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
450102 TCAATGTGAA
* *
450112 ATGAGATCATTGAGGGAGAAATTATGGAAGTG
1 ATGAGATCATTCAGAGAGAAATTATGGAAGTG
450144 ATGAGATCATTCAGAGAGAAATTATGGAA
1 ATGAGATCATTCAGAGAGAAATTATGGAA
450173 ATGAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.30, T:0.25
Consensus pattern (32 bp):
ATGAGATCATTCAGAGAGAAATTATGGAAGTG
Found at i:450569 original size:19 final size:19
Alignment explanation
Indices: 450545--450583 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
450535 AGATGCGACC
450545 TTATTATATAAGTAGGCAG
1 TTATTATATAAGTAGGCAG
450564 TTATTATATAAGTAGGCAG
1 TTATTATATAAGTAGGCAG
450583 T
1 T
450584 AACGGGACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (19 bp):
TTATTATATAAGTAGGCAG
Found at i:451513 original size:23 final size:22
Alignment explanation
Indices: 451476--451545 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 22
451466 TAAAATGTTA
*
451476 AATTATAAAGT-ATTAAACATAT
1 AATTATAAACTAATTAAA-ATAT
*
451498 AATTATAAACTAATTAAAAATCT
1 AATTATAAACTAATT-AAAATAT
* *
451521 AAATATAAATTAATTAAAATAT
1 AATTATAAACTAATTAAAATAT
451543 AAT
1 AAT
451546 ATTTATAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 18 0.45
23 19 0.47
24 3 0.08
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (22 bp):
AATTATAAACTAATTAAAATAT
Found at i:453540 original size:30 final size:29
Alignment explanation
Indices: 453506--453643 Score: 74
Period size: 30 Copynumber: 4.8 Consensus size: 29
453496 AAAAACAACA
453506 ATTTATCAATTATAATAATTAAATTATTTT
1 ATTTAT-AATTATAATAATTAAATTATTTT
* * * *
453536 ATTTATTA-TGTAATAA-T-AATATATACTG
1 ATTTATAATTATAATAATTAAAT-TAT-TTT
* *
453564 ACTTT-T-A-T-TAATAATTAAATTTTTAT
1 A-TTTATAATTATAATAATTAAATTATTTT
** *
453590 ATTTATTAATTATAATAATTAAACCATTCT
1 ATTTA-TAATTATAATAATTAAATTATTTT
* *
453620 AATTATCAATTATAATAATCAAAT
1 ATTTAT-AATTATAATAATTAAAT
453644 CACTTAAATA
Statistics
Matches: 82, Mismatches: 15, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
25 3 0.04
26 10 0.12
27 10 0.12
28 14 0.17
29 6 0.07
30 39 0.48
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (29 bp):
ATTTATAATTATAATAATTAAATTATTTT
Found at i:454890 original size:2 final size:2
Alignment explanation
Indices: 454885--454918 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
454875 ACACACACAC
454885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
454919 CATTTTGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:466128 original size:2 final size:2
Alignment explanation
Indices: 466121--466156 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
466111 AAATCAAACG
466121 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
466157 GGCAATGGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:478041 original size:36 final size:39
Alignment explanation
Indices: 478001--478079 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 39
477991 TTTTTATATT
*
478001 TTTAA-TTTTGTAAAA-AAATTATATAAATATTATA-AA
1 TTTAATTTTTGTAAAAGAAAATATATAAATATTATATAA
* *
478037 TTTAATTTTTTTAAAAGAAAATATATAAATATTTTATAA
1 TTTAATTTTTGTAAAAGAAAATATATAAATATTATATAA
478076 TTTA
1 TTTA
478080 TAATATTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 5 0.14
37 9 0.24
38 17 0.46
39 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (39 bp):
TTTAATTTTTGTAAAAGAAAATATATAAATATTATATAA
Found at i:478099 original size:18 final size:17
Alignment explanation
Indices: 478054--478102 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
478044 TTTTTAAAAG
*
478054 AAAATATATAAATATTTT
1 AAAATATAT-AATATTAT
* *
478072 ATAATTTATAATATTAT
1 AAAATATATAATATTAT
478089 ACAAATATATAATA
1 A-AAATATATAATA
478103 AGGATAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATATATAATATTAT
Found at i:480657 original size:5 final size:5
Alignment explanation
Indices: 480616--480654 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
480606 CGACACGACA
*
480616 CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT CGGCA CGGC
1 CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT CGGC
480655 ACGAGCGGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.03, C:0.41, G:0.41, T:0.15
Consensus pattern (5 bp):
CGGCT
Found at i:482138 original size:5 final size:5
Alignment explanation
Indices: 482102--482135 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
482092 CCGTCCGTCT
* *
482102 CGGCT CGGCA CGGCA CGGCA CGGCA CGGCT CGGC
1 CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGC
482136 TCGTGGTCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.12, C:0.41, G:0.41, T:0.06
Consensus pattern (5 bp):
CGGCA
Found at i:482147 original size:6 final size:6
Alignment explanation
Indices: 482136--482202 Score: 116
Period size: 6 Copynumber: 11.2 Consensus size: 6
482126 ACGGCTCGGC
* *
482136 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
482184 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
482203 AATACGTGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:482502 original size:22 final size:22
Alignment explanation
Indices: 482477--482531 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
482467 TCAGGAGTTA
* *
482477 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
482499 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
482521 CGGGAGTTATA
1 CAGGAGTTATA
482532 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:488266 original size:6 final size:6
Alignment explanation
Indices: 488255--488333 Score: 149
Period size: 6 Copynumber: 13.2 Consensus size: 6
488245 ACGGCTCGGC
*
488255 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
488303 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
488334 AATACGTGTC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.01, C:0.16, G:0.49, T:0.33
Consensus pattern (6 bp):
TCGTGG
Found at i:488633 original size:22 final size:22
Alignment explanation
Indices: 488608--488662 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
488598 TCAGGAGTTA
* *
488608 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
488630 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
488652 CGGGAGTTATA
1 CAGGAGTTATA
488663 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:495096 original size:24 final size:25
Alignment explanation
Indices: 495052--495100 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
495042 CTGAAATTAC
*
495052 ATTAAAAATCAACATATTAATTAAG
1 ATTAAAAATCAACATACTAATTAAG
495077 ATTAATAAAT-AAC-TACTAATTAAG
1 ATTAA-AAATCAACATACTAATTAAG
495101 CTTCATAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 8 0.36
26 4 0.18
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (25 bp):
ATTAAAAATCAACATACTAATTAAG
Found at i:501444 original size:96 final size:96
Alignment explanation
Indices: 501259--501462 Score: 273
Period size: 96 Copynumber: 2.1 Consensus size: 96
501249 TTCAAGTAGT
501259 AACCAGTTAAATTCCATGATCCATAAATCAAGAACAATCATATTTTCCAGTGAAAAAAGGAAACC
1 AACCAG-TAAATTCCATGATCCATAAATCAAGAACAATCATATTTTCCAGTGAAAAAAGGAAACC
* * *
501324 ATATAACATATTTCAGGTAACCATAATTCATA
65 AGAAAACATATATCAGGTAACCATAATTCATA
* * * * * * *
501356 AACCAGTAGATTCCATGATCCATAGATCATGAACTATTATATTTTCCAGTGAAAACAGGTAACCA
1 AACCAGTAAATTCCATGATCCATAAATCAAGAACAATCATATTTTCCAGTGAAAAAAGGAAACCA
* * *
501421 GAAAACATATATCATGTAGCCATAGTTCATA
66 GAAAACATATATCAGGTAACCATAATTCATA
*
501452 ACCCAGTAAAT
1 AACCAGTAAAT
501463 CAGTGATTTT
Statistics
Matches: 92, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
96 86 0.93
97 6 0.07
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (96 bp):
AACCAGTAAATTCCATGATCCATAAATCAAGAACAATCATATTTTCCAGTGAAAAAAGGAAACCA
GAAAACATATATCAGGTAACCATAATTCATA
Found at i:504996 original size:20 final size:20
Alignment explanation
Indices: 504951--505020 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
504941 ATGACCAACA
** *
504951 AATTCGCAACGCGAACTC-C
1 AATTCGCAACGCGATTTCTG
504970 AATTTCGCAACGCGATTTCTG
1 AA-TTCGCAACGCGATTTCTG
*
504991 AATTCGCAACTCGATTT-TCG
1 AATTCGCAACGCGATTTCT-G
505011 AATTCGCAAC
1 AATTCGCAAC
505021 ACGAATTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
19 3 0.07
20 39 0.89
21 2 0.05
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (20 bp):
AATTCGCAACGCGATTTCTG
Found at i:505036 original size:20 final size:19
Alignment explanation
Indices: 504973--505041 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
504963 GAACTCCAAT
*
504973 TTCGCAACGCGATTTCTGAA
1 TTCGCAACACGATTT-TGAA
*
504993 TTCGCAACTCGATTTTCGAA
1 TTCGCAACACGATTTT-GAA
505013 TTCGCAACACGAATTTT-AA
1 TTCGCAACACG-ATTTTGAA
505032 TTTCGCAACA
1 -TTCGCAACA
505042 GGTTTTAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.07
20 36 0.82
21 5 0.11
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGATTTTGAA
Found at i:505852 original size:12 final size:12
Alignment explanation
Indices: 505831--505869 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
505821 ACCACATTTC
*
505831 CAATACCAAACA
1 CAATATCAAACA
505843 CAATATCAAACA
1 CAATATCAAACA
*
505855 CAATCTCAAAACA
1 CAATATC-AAACA
505868 CA
1 CA
505870 CAACCTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.13
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:506043 original size:24 final size:24
Alignment explanation
Indices: 505985--506031 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
505975 AGTCAGTATT
*
505985 CGAAATTTGATCTTAGTCAATACC
1 CGAACTTTGATCTTAGTCAATACC
*
506009 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTAGTCAATAC
506032 TTGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTAGTCAATACC
Found at i:508324 original size:18 final size:18
Alignment explanation
Indices: 508301--508336 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
508291 AAGCAACAGG
508301 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
508319 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
508337 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:508610 original size:20 final size:20
Alignment explanation
Indices: 508585--508624 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
508575 TTGTTGCGAT
508585 TGTTGCGAAAGTCAAATTCG
1 TGTTGCGAAAGTCAAATTCG
508605 TGTTGCGAAAGTCAAATTCG
1 TGTTGCGAAAGTCAAATTCG
508625 AAACGCGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
TGTTGCGAAAGTCAAATTCG
Found at i:508632 original size:20 final size:20
Alignment explanation
Indices: 508589--508634 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
508579 TGCGATTGTT
****
508589 GCGAAAGTCAAATTCGTGTT
1 GCGAAAGTCAAATTCGAAAC
508609 GCGAAAGTCAAATTCGAAAC
1 GCGAAAGTCAAATTCGAAAC
508629 GCGAAA
1 GCGAAA
508635 TCGTAACGCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGAAAC
Found at i:510193 original size:21 final size:20
Alignment explanation
Indices: 510167--510237 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
510157 GTGAATCGGG
*
510167 CTCTTGAACGGTGGGAGAGAC
1 CTCTTGAACGGTGGGAG-GGC
* **
510188 CTCTTGAACGATGACAGGTGC
1 CTCTTGAACGGTGGGAGG-GC
*
510209 CTCTTGAATGGTGGGAGGGGC
1 CTCTTGAACGGTGGGA-GGGC
510230 CTCTTGAA
1 CTCTTGAA
510238 GGATGATAGG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.03
21 37 0.93
22 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.24
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGC
Found at i:510248 original size:21 final size:21
Alignment explanation
Indices: 510187--510249 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
510177 GTGGGAGAGA
* *
510187 CCTCTTGAACGATGACAGGTG
1 CCTCTTGAAGGATGACAGGGG
**
510208 CCTCTTGAATGG-TGGGAGGGG
1 CCTCTTGAA-GGATGACAGGGG
*
510229 CCTCTTGAAGGATGATAGGGG
1 CCTCTTGAAGGATGACAGGGG
510250 TCGCTTTAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.06
21 31 0.91
22 1 0.03
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.24
Consensus pattern (21 bp):
CCTCTTGAAGGATGACAGGGG
Found at i:510715 original size:21 final size:21
Alignment explanation
Indices: 510688--510740 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
510678 TACACCATTG
510688 TCATCACGTAAAGTACCGACC
1 TCATCACGTAAAGTACCGACC
* * **
510709 TCCTCACGCAAAGTATTGACC
1 TCATCACGTAAAGTACCGACC
510730 TCATCACGTAA
1 TCATCACGTAA
510741 CTCCCCTAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.32, G:0.13, T:0.23
Consensus pattern (21 bp):
TCATCACGTAAAGTACCGACC
Found at i:511860 original size:19 final size:20
Alignment explanation
Indices: 511836--511883 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
511826 CCTCATCACT
511836 GCGTTGCGATTTTCA-TTTC
1 GCGTTGCGATTTTCATTTTC
511855 GCGTTGCGATTTTCATTTTC
1 GCGTTGCGATTTTCATTTTC
*
511875 GTGTTGCGA
1 GCGTTGCGA
511884 ATTTAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (20 bp):
GCGTTGCGATTTTCATTTTC
Found at i:512242 original size:20 final size:21
Alignment explanation
Indices: 512217--512265 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
512207 TCTGAGAGAT
512217 GGAGAT-AGACGAATTTCGCC
1 GGAGATGAGACGAATTTCGCC
**
512237 GGAGATGGAGACGAATTTCGTT
1 GGAGAT-GAGACGAATTTCGCC
512259 GGAGATG
1 GGAGATG
512266 GGGACGGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 1 0.04
22 18 0.72
ACGTcount: A:0.29, C:0.12, G:0.37, T:0.22
Consensus pattern (21 bp):
GGAGATGAGACGAATTTCGCC
Found at i:512250 original size:22 final size:22
Alignment explanation
Indices: 512223--512281 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
512213 AGATGGAGAT
512223 AGACGAATTTCGCCGGAGATGG
1 AGACGAATTTCGCCGGAGATGG
**
512245 AGACGAATTTCGTTGGAGATGG
1 AGACGAATTTCGCCGGAGATGG
* * *
512267 GGACGGATGTCGCCG
1 AGACGAATTTCGCCG
512282 TAGAGAGTGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (22 bp):
AGACGAATTTCGCCGGAGATGG
Found at i:512457 original size:20 final size:20
Alignment explanation
Indices: 512429--512470 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
512419 TAAACGCGCT
*
512429 TTGCGAATTTGACTTCTGTG
1 TTGCAAATTTGACTTCTGTG
*
512449 TTGCAAATTTGACTTTTGTG
1 TTGCAAATTTGACTTCTGTG
512469 TT
1 TT
512471 ATGAATTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.12, G:0.21, T:0.50
Consensus pattern (20 bp):
TTGCAAATTTGACTTCTGTG
Found at i:512477 original size:20 final size:20
Alignment explanation
Indices: 512432--512477 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
512422 ACGCGCTTTG
*
512432 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTCTGTGTTA
* *
512452 CAAATTTGACTTTTGTGTTA
1 CGAATTTGACTTCTGTGTTA
*
512472 TGAATT
1 CGAATT
512478 ACAAATTTGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.22, C:0.11, G:0.20, T:0.48
Consensus pattern (20 bp):
CGAATTTGACTTCTGTGTTA
Found at i:520257 original size:36 final size:36
Alignment explanation
Indices: 520210--520291 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
520200 CACAGTCTGT
* *
520210 TACAAATGTAGGTCTC-CCAGGACCTGTT-TTACCTCC
1 TACAAACGTAGGTCTCTCC-GGACATGTTCTT-CCTCC
520246 TACAAACGTAGGTCTCTCCGGACATGTTCTTCCTCC
1 TACAAACGTAGGTCTCTCCGGACATGTTCTTCCTCC
520282 TACAAACGTA
1 TACAAACGTA
520292 AGACACAGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 38 0.90
37 4 0.10
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.29
Consensus pattern (36 bp):
TACAAACGTAGGTCTCTCCGGACATGTTCTTCCTCC
Found at i:529279 original size:29 final size:29
Alignment explanation
Indices: 529245--529329 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 29
529235 AATTAGTTAT
529245 TAAACTTTTGAACATTCTAATTTCATCCC
1 TAAACTTTTGAACATTCTAATTTCATCCC
* * * * *
529274 TAAAC-TATGACCTTTCTAAATTGATCCC
1 TAAACTTTTGAACATTCTAATTTCATCCC
* *
529302 CAAACTTTTGAATATTCTAATTTCATCC
1 TAAACTTTTGAACATTCTAATTTCATCC
529330 TTGCATTCAT
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
28 22 0.51
29 21 0.49
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.40
Consensus pattern (29 bp):
TAAACTTTTGAACATTCTAATTTCATCCC
Done.