Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008584.1 Hibiscus syriacus cultivar Beakdansim tig00111519_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: 118284
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:391 original size:20 final size:20
Alignment explanation
Indices: 354--391 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
344 AAAATCTATT
**
354 TTCATTTATGTTCGTTTACG
1 TTCATTTATGTTAATTTACG
374 TTCATTTATGTTAATTTA
1 TTCATTTATGTTAATTTA
392 TTGTATTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.58
Consensus pattern (20 bp):
TTCATTTATGTTAATTTACG
Found at i:392 original size:10 final size:10
Alignment explanation
Indices: 354--392 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
344 AAAATCTATT
354 TTCATTTATG
1 TTCATTTATG
* *
364 TTCGTTTACG
1 TTCATTTATG
374 TTCATTTATG
1 TTCATTTATG
*
384 TTAATTTAT
1 TTCATTTAT
393 TGTATTTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (10 bp):
TTCATTTATG
Found at i:431 original size:22 final size:22
Alignment explanation
Indices: 406--449 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
396 ATTTGTTCAT
406 TTGTGTTC-GTTACGTTCGTTTA
1 TTGT-TTCTGTTACGTTCGTTTA
* *
428 TTGTTTCTTTTATGTTCGTTTA
1 TTGTTTCTGTTACGTTCGTTTA
450 CATCCGTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.09, C:0.11, G:0.18, T:0.61
Consensus pattern (22 bp):
TTGTTTCTGTTACGTTCGTTTA
Found at i:5499 original size:2 final size:2
Alignment explanation
Indices: 5492--5533 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
5482 TATGTCATAG
*
5492 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5534 CTTGGCTTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12317 original size:31 final size:31
Alignment explanation
Indices: 12279--12403 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
12269 AGGGTCGAGG
* * *
12279 GTTTACCTATGTTTTTTGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
12310 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
12341 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
12372 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
12403 G
1 G
12404 GTCCTTCGGA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
31 84 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:17169 original size:31 final size:31
Alignment explanation
Indices: 17131--17255 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
17121 AGGGTCGAGG
**
17131 GTTTACCTATGTTCTTCGGGACATATAAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
17162 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
17193 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
17224 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
17255 G
1 G
17256 GTCCTTCGGG
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:19534 original size:20 final size:20
Alignment explanation
Indices: 19509--19546 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
19499 TTCCCCTTGA
19509 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAT
19529 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
19547 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAT
Found at i:19562 original size:24 final size:20
Alignment explanation
Indices: 19509--19566 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
19499 TTCCCCTTGA
*
19509 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAC
19529 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
19552 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
19567 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:19632 original size:64 final size:65
Alignment explanation
Indices: 19555--19676 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 65
19545 CTTTAACATG
*
19555 TGCATCGATGCACTACC-CATGCATCGATACACCAATTACATTCGATGTT-TTTATTTTAAGGGG
1 TGCATCGATGCACT-CCTCATGCATCGATACACCAATTACAATCGATGTTATTTATTTTAAGGGG
19618 A
65 A
* * *
19619 TGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCAATCGATGTTCATTTATTT
1 TGCATCGATGCACTCCTCATGCATCGATACACCAATTACAATCGATGTT-ATTTATTT
19677 GAGAGTGCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
63 2 0.04
64 42 0.82
66 7 0.14
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (65 bp):
TGCATCGATGCACTCCTCATGCATCGATACACCAATTACAATCGATGTTATTTATTTTAAGGGGA
Found at i:23119 original size:23 final size:23
Alignment explanation
Indices: 23101--23161 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
23091 CTCGTATAAA
*
23101 TACACCGAAGTGCTACGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
* *
23124 TGCACCGAAGTGCCGCGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
23147 TACACCGAAGTGCCA
1 TACACCGAAGTGCCA
23162 TATAAAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (23 bp):
TACACCGAAGTGCCACGTAGAAT
Found at i:28027 original size:38 final size:38
Alignment explanation
Indices: 27976--28052 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
27966 ACAGCATTTG
*
27976 AAGCCCCAGTTTTGGCATAAGGTATTACGCACTCGTAT
1 AAGCCCCAGTTTTGGCATAAGGTATTACGCACTCATAT
28014 AAGCCCCAGTTTTGGCATAAGGTATTACGCACTCATAT
1 AAGCCCCAGTTTTGGCATAAGGTATTACGCACTCATAT
28052 A
1 A
28053 TATATCGGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (38 bp):
AAGCCCCAGTTTTGGCATAAGGTATTACGCACTCATAT
Found at i:28289 original size:18 final size:18
Alignment explanation
Indices: 28265--28307 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28255 TTCGTATATA
28265 TTATTAATTTTACA-ATTT
1 TTATTAATTTTA-ATATTT
*
28283 TTTTTAATTTTAATATTT
1 TTATTAATTTTAATATTT
28301 TTATTAA
1 TTATTAA
28308 AAAAATATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTAATTTTAATATTT
Found at i:33402 original size:229 final size:226
Alignment explanation
Indices: 32998--33445 Score: 772
Period size: 229 Copynumber: 2.0 Consensus size: 226
32988 GTAAATTATC
* * *
32998 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
33063 TAATATTGTTAAATTTAAAATCTAAATAATATTTATAAAATATCAAAACAATCAAATAATTTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTATAAAATATCAAAACAATCAAATAATATTTT
33128 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
131 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
33193 AACATAAATTACATAACTTTCAAAAAAGTATA
196 AACATAAATTACATAACTTT-AAAAAAGTATA
* *
33225 TATCATTTTTATAAAAGTGTTCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
33290 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAAT
65 TTAATATTGTTAAATTTAAAATCTAAATAATA-TTTATAAAATATCAAAACAATCAAATAAT-AT
* *
33354 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
128 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
33419 TGAAACATAAATTACATAACTTTAAAA
193 TGAAACATAAATTACATAACTTTAAAA
33446 GCAGTTTTAA
Statistics
Matches: 209, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
227 35 0.17
228 61 0.29
229 113 0.54
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTATAAAATATCAAAACAATCAAATAATATTTT
GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAAGTATA
Found at i:33699 original size:20 final size:19
Alignment explanation
Indices: 33676--33722 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
33666 CGATATAACA
33676 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
33696 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
33716 GGTAAAA
1 GGTAAAA
33723 TGATACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:33724 original size:17 final size:18
Alignment explanation
Indices: 33680--33727 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
33670 ATAACAGGTA
33680 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
33699 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
33719 -AAAATGATA
1 AAAAATGATA
33728 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:35993 original size:21 final size:21
Alignment explanation
Indices: 35946--36010 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
35936 AAGACAATCA
* *
35946 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
35968 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
35988 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
36009 AG
1 AG
36011 GAATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:36086 original size:33 final size:33
Alignment explanation
Indices: 36044--36109 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
36034 AAATAGATGG
*
36044 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
36077 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
36110 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:37918 original size:19 final size:19
Alignment explanation
Indices: 37894--37942 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
37884 AATGTCGAGT
37894 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
37913 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
37932 TATTTTTGTAT
1 TAATTTTGTAT
37943 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:38575 original size:197 final size:199
Alignment explanation
Indices: 38061--39423 Score: 2602
Period size: 197 Copynumber: 6.9 Consensus size: 199
38051 CAATATGGCC
* *
38061 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
38126 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
38191 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
38256 TGGAA
195 TGGAA
38261 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
38326 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
38390 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATAC-TTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
38454 GGAA
196 GGAA
*
38458 AACAAGGTGCACCCATAAAGTGTCGATCTATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
38522 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
38587 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTATGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
38652 GG-A
196 GGAA
38655 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
38720 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
38784 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
38849 GG-A
196 GGAA
38852 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
38917 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
38982 AATATGTCTAAATAATGTGTCGACA-TAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
39046 GGAA
196 GGAA
39050 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
39115 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
39180 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATAC-TTTTT-CCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
39243 GGAA
196 GGAA
*
39247 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
39312 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
39376 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
39424 AATTTAAATA
Statistics
Matches: 1149, Mismatches: 7, Indels: 17
0.98 0.01 0.01
Matches are distributed among these distances:
196 91 0.08
197 565 0.49
198 408 0.36
199 51 0.04
200 34 0.03
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (199 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGAA
Found at i:38838 original size:395 final size:397
Alignment explanation
Indices: 38061--39423 Score: 2607
Period size: 395 Copynumber: 3.4 Consensus size: 397
38051 CAATATGGCC
* *
38061 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
38126 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
38191 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
38256 TGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
195 TGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
38321 GAACCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
260 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
38385 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTCCCAGAAT
325 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTCCCAGAAT
38450 GAATGGAA
390 GAATGGAA
*
38458 AACAAGGTGCACCCATAAAGTGTCGATCTATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
38522 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
38587 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTATGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
38652 GG-AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
38716 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
38780 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATAC-TTTTTCCCAGAAT
38845 GAATGG-A
390 GAATGGAA
38852 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
38917 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
38982 AATATGTCTAAATAATGTGTCGACA-TAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
39046 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
39111 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
39176 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTT-CCAGAATG
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTCCCAGAATG
39240 AATGGAA
391 AATGGAA
*
39247 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
39312 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
39376 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
39424 AATTTAAATA
Statistics
Matches: 952, Mismatches: 7, Indels: 16
0.98 0.01 0.02
Matches are distributed among these distances:
394 255 0.27
395 603 0.63
396 61 0.06
397 33 0.03
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (397 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTCCCAGAATG
AATGGAA
Found at i:40901 original size:3 final size:3
Alignment explanation
Indices: 40893--40967 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
40883 TGAAGCTGAC
* * * ** * *
40893 GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
40941 GAT GAT GAT GAT GAT GAA GAT GCT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
40968 CCAAACAAGT
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.07, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:42545 original size:183 final size:182
Alignment explanation
Indices: 42159--42669 Score: 882
Period size: 183 Copynumber: 2.8 Consensus size: 182
42149 CAAAGTTTTC
* * *
42159 ACACTTT-TAATATTGTGTCTGTACTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
** *
42223 AAAAAAGTGTCGA-ATGAAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
66 AAAAAAGTGTCGACAT---TTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
*
42287 TATAACCGGTATAAATATACGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAAAATACGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
42342 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
42407 AAAAAAGTGTCGACATTTACACATTGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
*
42472 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
131 AACCGGTATAAAAATA-CGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
42525 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
42590 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
42655 AACCGGTATAAAAAT
131 AACCGGTATAAAAAT
42670 GTGTCGATAC
Statistics
Matches: 314, Mismatches: 11, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
182 60 0.19
183 185 0.59
184 67 0.21
185 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (182 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAAAATACGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:45852 original size:21 final size:23
Alignment explanation
Indices: 45802--45863 Score: 83
Period size: 21 Copynumber: 2.8 Consensus size: 23
45792 ATAGGTAAAC
*
45802 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* *
45825 ATATAATGTAATAGGTA-TCGTT
1 ATATAATGTAATAGGTAGCCCTT
45847 -TATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
45864 TGGTTATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 16 0.46
22 3 0.09
23 16 0.46
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:45870 original size:21 final size:21
Alignment explanation
Indices: 45826--45877 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
45816 GTAGCCCTTA
*
45826 TATAATGTAATAGGTATCGTT
1 TATAATGTAATAGGTATCGGT
45847 TATAATGTAATAGGTAGT-GGT
1 TATAATGTAATAGGTA-TCGGT
*
45868 TATATTGTAA
1 TATAATGTAA
45878 AGTGTCTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (21 bp):
TATAATGTAATAGGTATCGGT
Found at i:45911 original size:18 final size:19
Alignment explanation
Indices: 45876--45912 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
45866 GTTATATTGT
* *
45876 AAAGTGTCTATCCTTTTTA
1 AAAGTGTCCATACTTTTTA
45895 AAAGTGTCCATACTTTTT
1 AAAGTGTCCATACTTTTT
45913 CACTGTGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (19 bp):
AAAGTGTCCATACTTTTTA
Found at i:46251 original size:23 final size:23
Alignment explanation
Indices: 46220--46283 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
46210 ATAGGTAAAC
*
46220 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
46243 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
46266 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
46284 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:46290 original size:23 final size:23
Alignment explanation
Indices: 46220--46292 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
46210 ATAGGTAAAC
* **
46220 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
46243 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
46266 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
46289 ATAT
1 ATAT
46293 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:46525 original size:427 final size:416
Alignment explanation
Indices: 45706--46526 Score: 1475
Period size: 427 Copynumber: 1.9 Consensus size: 416
45696 AATTCGCAGT
45706 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
1 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
45771 AAAGTATGGACACTTTCAATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAA
66 AAAGTATGGACACTTTCAATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAA
45836 TAGGTATCGTTTATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAAAAGTG
131 TAGGTATCGTTTATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAAAAGTG
45901 TCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTGAGTGAGTTTAAGATTAATT
196 TCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTGAGTGAGTTTAAGATTAATT
* *
45966 TAGTAATTATAGGCGTCTAATGATTTATTTTACGTTACGGTATATATTATTATTAAATTAAAAAT
261 TAGTAATTATAGGCGTATAATGATTTATTTTACGTTACGATATATATTATTATTAAATTAAAAAT
46031 TCTAAATAATATTTTATAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAA
326 TCTAAATAATATTTTATAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAA
46096 TCAATATTGTAGGTGGAAAACATGAA
391 TCAATATTGTAGGTGGAAAACATGAA
46122 ACACTGTTAAAAAAATTGAAA-ATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
46186 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
65 AAAAGTATGGACACTTTC-A-ATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
46251 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTATA
128 TAATAGGTATCG-TT-TATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTT-TA
46316 AAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
190 AAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATC-TTTGAGTGAG-TTTAA
46381 GATATTAATTTAGTAATTATAGGCGTATAATGATTTATTTTTTACGTTACGATATATATTATTAT
253 G--ATTAATTTAGTAATTATAGGCGTATAATGATTTA--TTTTACGTTACGATATATATTATTAT
* *
46446 TAAATT-AAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAA
314 TAAATTAAAAATTCTAAATAATATTTTAT-AAATATAAAAACAATCAAATAATTTTTTGTGCAAA
46510 TGAAATTATTAAATCAA
378 TGAAATTATTAAATCAA
46527 ATAATTCAAA
Statistics
Matches: 388, Mismatches: 4, Indels: 15
0.95 0.01 0.04
Matches are distributed among these distances:
416 69 0.18
417 13 0.03
418 56 0.14
419 2 0.01
420 46 0.12
421 50 0.13
422 10 0.03
423 6 0.02
425 33 0.09
426 21 0.05
427 82 0.21
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (416 bp):
ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
AAAGTATGGACACTTTCAATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAA
TAGGTATCGTTTATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAAAAGTG
TCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTGAGTGAGTTTAAGATTAATT
TAGTAATTATAGGCGTATAATGATTTATTTTACGTTACGATATATATTATTATTAAATTAAAAAT
TCTAAATAATATTTTATAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAA
TCAATATTGTAGGTGGAAAACATGAA
Found at i:46592 original size:25 final size:25
Alignment explanation
Indices: 46558--46608 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
46548 ACAACAAATC
*
46558 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
46583 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
46608 A
1 A
46609 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:46878 original size:18 final size:18
Alignment explanation
Indices: 46857--46893 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
46847 GTAATTGGAG
46857 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
46875 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
46893 T
1 T
46894 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:46901 original size:24 final size:24
Alignment explanation
Indices: 46849--46895 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
46839 TTTCATATGT
* *
46849 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
46873 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
46896 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:47236 original size:39 final size:38
Alignment explanation
Indices: 47151--47274 Score: 221
Period size: 38 Copynumber: 3.2 Consensus size: 38
47141 TCCGATGCTC
* *
47151 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAGGAA
47189 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGC-AAAGGAA
47228 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAGGAA
47266 ATCAAAATC
1 ATCAAAATC
47275 TACAACTTGA
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
38 45 0.54
39 38 0.46
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.18
Consensus pattern (38 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAGGAA
Found at i:47706 original size:23 final size:23
Alignment explanation
Indices: 47675--47738 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
47665 ATAGGTAAAC
*
47675 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
47698 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
47721 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
47739 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:47745 original size:23 final size:23
Alignment explanation
Indices: 47675--47747 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
47665 ATAGGTAAAC
* **
47675 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
47698 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
47721 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
47744 ATAT
1 ATAT
47748 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:68240 original size:27 final size:27
Alignment explanation
Indices: 68210--68267 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
68200 TTTTATGTTG
*
68210 AGGGCCAACTTGAATTTATAAAATTTT
1 AGGGCCAACTTAAATTTATAAAATTTT
** *
68237 AGGGGTGAATTTAAATTTATAAAATTTT
1 A-GGGCCAACTTAAATTTATAAAATTTT
68265 AGG
1 AGG
68268 AGGCGAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (27 bp):
AGGGCCAACTTAAATTTATAAAATTTT
Found at i:70150 original size:58 final size:58
Alignment explanation
Indices: 70060--70176 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 58
70050 GTGGACCCTA
*
70060 AGTATATGCAATCCAAAGCATGTGTTGTAATTTTTAAGACAAATTTAGATTTACTTTT
1 AGTATATGCAATCCAAAGCATATGTTGTAATTTTTAAGACAAATTTAGATTTACTTTT
* * *
70118 AGTATATGCAGTCCAAAGCATATGTTGTAATTTTTGAGACGAATTTAGATTTACTTTT
1 AGTATATGCAATCCAAAGCATATGTTGTAATTTTTAAGACAAATTTAGATTTACTTTT
70176 A
1 A
70177 ATATCTTTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (58 bp):
AGTATATGCAATCCAAAGCATATGTTGTAATTTTTAAGACAAATTTAGATTTACTTTT
Found at i:71069 original size:20 final size:21
Alignment explanation
Indices: 71029--71085 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
71019 AATAGCAAAG
* *
71029 GAAAATTGAAGAACAACGAAA
1 GAAAATAGAAGAACAAAGAAA
71050 GAAAATAGAA-AACAAAGAAA
1 GAAAATAGAAGAACAAAGAAA
*
71070 GAAACTA-AAGAACAAA
1 GAAAATAGAAGAACAAA
71086 AGTAGAACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.06
20 21 0.66
21 9 0.28
ACGTcount: A:0.68, C:0.09, G:0.16, T:0.07
Consensus pattern (21 bp):
GAAAATAGAAGAACAAAGAAA
Found at i:73482 original size:21 final size:20
Alignment explanation
Indices: 73452--73491 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
73442 TCGAAAATAT
73452 TAAAAAAATAATATTTTAAG
1 TAAAAAAATAATATTTTAAG
73472 TAAAAATAATAATATTTTAA
1 TAAAAA-AATAATATTTTAA
73492 ATAATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TAAAAAAATAATATTTTAAG
Found at i:74867 original size:16 final size:16
Alignment explanation
Indices: 74842--74877 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
74832 GATTTTTATG
74842 TTGGTCGTCATTCTCA
1 TTGGTCGTCATTCTCA
*
74858 TTGGTGGTCATTCTCA
1 TTGGTCGTCATTCTCA
74874 TTGG
1 TTGG
74878 AATGTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.44
Consensus pattern (16 bp):
TTGGTCGTCATTCTCA
Found at i:75783 original size:21 final size:22
Alignment explanation
Indices: 75745--75786 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
75735 TATCTTCTTC
* *
75745 TTTTTCTTTCTTTCCATATTTT
1 TTTTTATTTCTTTACATATTTT
75767 TTTTTATTT-TTTACATATTT
1 TTTTTATTTCTTTACATATTT
75787 GAATTTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTATTTCTTTACATATTTT
Found at i:77460 original size:42 final size:41
Alignment explanation
Indices: 77394--77474 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 41
77384 TGTTGAACAA
* * *
77394 ACGCCGCAATAGGTTCTGATATTTAGTGGCATTTGTTTTAAT
1 ACGCCGCAATAGGTTCTGAGATTTAGCGACATTT-TTTTAAT
* *
77436 ACGCTGCAATAGGTTTTGAGATTTAGCGACATTTTTTTA
1 ACGCCGCAATAGGTTCTGAGATTTAGCGACATTTTTTTA
77475 TACAAACGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 5 0.15
42 29 0.85
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.41
Consensus pattern (41 bp):
ACGCCGCAATAGGTTCTGAGATTTAGCGACATTTTTTTAAT
Found at i:77536 original size:44 final size:44
Alignment explanation
Indices: 77474--77679 Score: 261
Period size: 44 Copynumber: 4.7 Consensus size: 44
77464 ACATTTTTTT
* *
77474 ATACAAACGTCGCCAAATGTCTGGTATATAGCGGTGTTTTTAGG
1 ATACAAACGTCGCTAAATGTCTGGTATATAGCGGCGTTTTTAGG
** **
77518 ATACAAACACCGCTAAATGTCTGGTATATATTGGCGTTTTTAGG
1 ATACAAACGTCGCTAAATGTCTGGTATATAGCGGCGTTTTTAGG
* * * *
77562 ATACAAACGCCACTAAATGTCTGGTATATAGCGACGTTTTTATG
1 ATACAAACGTCGCTAAATGTCTGGTATATAGCGGCGTTTTTAGG
* * * *
77606 ATACAAACGTCGCTAAAAGTATGGTATATAGCAGCGTTTTTAGT
1 ATACAAACGTCGCTAAATGTCTGGTATATAGCGGCGTTTTTAGG
* *
77650 ATACAAACGTCGCTAAAGGT-TGATATATAG
1 ATACAAACGTCGCTAAATGTCTGGTATATAG
77680 TGGTGTTTGT
Statistics
Matches: 140, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
43 9 0.06
44 131 0.94
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (44 bp):
ATACAAACGTCGCTAAATGTCTGGTATATAGCGGCGTTTTTAGG
Found at i:83790 original size:64 final size:64
Alignment explanation
Indices: 83721--83877 Score: 153
Period size: 64 Copynumber: 2.5 Consensus size: 64
83711 TTGAAGGTGT
** *
83721 ATCGATGCACTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAAGATCGAATGCA-ATTAGT
1 ATCGATGCACTGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATATTA-T
83783 GC
63 GC
* * *
83785 ATCGATGCA-TAAGGCA-TGTATCGATGCATCCCATTAATAATAAAACATCGAATGCATTTTATG
1 ATCGATGCACT--GGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATG
83848 C
64 C
* **
83849 ACCGATGCACAAGTAGTGCATCGATGCAT
1 ATCGATGCACTGGTAGTGCATCGATGCAT
83878 ACCTTTATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
63 3 0.04
64 62 0.83
65 10 0.13
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCACTGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:84294 original size:29 final size:29
Alignment explanation
Indices: 84261--84361 Score: 177
Period size: 29 Copynumber: 3.5 Consensus size: 29
84251 TATGAGAACG
84261 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
*
84290 TGACATGAGCTATATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
*
84319 TGACATGAACTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
84348 TGACATGAG-TACAT
1 TGACATGAGCTACAT
84362 TAACATATGA
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
28 5 0.07
29 63 0.93
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.20
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:91237 original size:29 final size:29
Alignment explanation
Indices: 91204--91304 Score: 177
Period size: 29 Copynumber: 3.5 Consensus size: 29
91194 TATGAGAACG
91204 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
*
91233 TGACATGAGCTACATCATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
*
91262 TGACATGAACTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
91291 TGACATGAG-TACAT
1 TGACATGAGCTACAT
91305 TAACATATGA
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
28 5 0.07
29 63 0.93
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:92691 original size:18 final size:18
Alignment explanation
Indices: 92668--92702 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
92658 ATAAGCACAC
*
92668 ATAATTTAATTTCACATA
1 ATAATTTAAATTCACATA
92686 ATAATTTAAATTCACAT
1 ATAATTTAAATTCACAT
92703 TTATTTGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATTTAAATTCACATA
Found at i:92886 original size:24 final size:25
Alignment explanation
Indices: 92854--92924 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
92844 AATAAGTTTA
**
92854 TCTCTTAAAACATTACTTC-ATTTG
1 TCTCTTAAAACAACACTTCTATTTG
92878 TCTCTTAAAACAACACTTCATTATTTG
1 TCTCTTAAAACAACACTTC--TATTTG
92905 TCTCTTAAAAACAACACTTC
1 TCTCTT-AAAACAACACTTC
92925 ATGCATCCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.41
27 11 0.27
28 13 0.32
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (25 bp):
TCTCTTAAAACAACACTTCTATTTG
Found at i:92903 original size:27 final size:28
Alignment explanation
Indices: 92873--92926 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
92863 ACATTACTTC
92873 ATTTGTCTCTT-AAAACAACACTTCATT
1 ATTTGTCTCTTAAAAACAACACTTCATT
92900 ATTTGTCTCTTAAAAACAACACTTCAT
1 ATTTGTCTCTTAAAAACAACACTTCAT
92927 GCATCCTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (28 bp):
ATTTGTCTCTTAAAAACAACACTTCATT
Found at i:96298 original size:22 final size:22
Alignment explanation
Indices: 96271--96319 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
96261 CACGTTTTGA
96271 AAAGCTATTATTATCATATTCG
1 AAAGCTATTATTATCATATTCG
* **
96293 AAAGCTATTATTTTTGTATTCG
1 AAAGCTATTATTATCATATTCG
96315 AAAGC
1 AAAGC
96320 AGAAAAACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (22 bp):
AAAGCTATTATTATCATATTCG
Found at i:97674 original size:157 final size:154
Alignment explanation
Indices: 97388--97819 Score: 457
Period size: 155 Copynumber: 2.8 Consensus size: 154
97378 CGATTTAGTC
* * * * *
97388 CATGATTTCATTATTTCTTCAATTCCTCCTTCATTTTAAGTCTATTTTTTTTACCAAATTTGAAC
1 CATGATTTCATTATTTCTTCAATTCGTCATTTATTTTAAGTC-AATTTTTTTATCAAATTTGAAC
* * *
97453 CACATACTCCTAAACCATATTAGAATACATGTGTATTTTCAATTCT-TTTTTATAACAAAATTTT
65 CACATGCTCCTAAACCATAATAGAATACATGTGTACTTTCAATTCTATTTTTATAAC--AATTTT
97517 TATTTTTCAATTTAGTCATTCAATTTTT
128 TATTTTT-AATTTAGTCATTCAATTTTT
* *
97545 CATGATTTCATTATTTCTTCAATTCGTCATTTATTTTAAGTCCA-TTTTTTATCAAATTTGAGCC
1 CATGATTTCATTATTTCTTCAATTCGTCATTTATTTTAAGTCAATTTTTTTATCAAATTTGAACC
* * *
97609 ACTTGCTCCTAAACCATAGTAGAATACACGTGTACTTTCAATTCCTATTTTTGATAACAA---TT
66 ACATGCTCCTAAACCATAATAGAATACATGTGTACTTTCAATT-CTATTTTT-ATAACAATTTTT
*
97671 -TTTTTAATTTAGTCCTTCAATTTTT
129 ATTTTTAATTTAGTCATTCAATTTTT
* * * ** * * *
97696 CATAATCTC-CTCGTTCTTTCAATTTGTGATTTATTTTAAATCAATTTTTTTTTATCAAATTTGA
1 CATGATTTCATTATTTC-TTCAATTCGTCATTTATTTTAAGTCAA--TTTTTTTATCAAATTTGA
* * * * * *
97760 ATCACATGCTCATATACCACAATAGAATACATATGTAACTTT-AATTGCTATTTTTTTAAC
63 ACCACATGCTCCTAAACCATAATAGAATACATGTGT-ACTTTCAATT-CTATTTTTATAAC
97820 TATCTTTTTA
Statistics
Matches: 234, Mismatches: 33, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
150 4 0.02
151 49 0.21
152 5 0.02
153 6 0.03
154 56 0.24
155 61 0.26
156 4 0.02
157 44 0.19
158 5 0.02
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.47
Consensus pattern (154 bp):
CATGATTTCATTATTTCTTCAATTCGTCATTTATTTTAAGTCAATTTTTTTATCAAATTTGAACC
ACATGCTCCTAAACCATAATAGAATACATGTGTACTTTCAATTCTATTTTTATAACAATTTTTAT
TTTTAATTTAGTCATTCAATTTTT
Found at i:98047 original size:2 final size:2
Alignment explanation
Indices: 98040--98071 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
98030 TGAAAGAATA
98040 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
98072 AAAATCAAAA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:113260 original size:14 final size:13
Alignment explanation
Indices: 113233--113262 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
113223 AAAATAAATG
113233 ATAAATATTATTA
1 ATAAATATTATTA
113246 ATAAATATCTATTA
1 ATAAATAT-TATTA
113260 ATA
1 ATA
113263 TAAACTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (13 bp):
ATAAATATTATTA
Found at i:114496 original size:41 final size:40
Alignment explanation
Indices: 114449--114531 Score: 130
Period size: 40 Copynumber: 2.0 Consensus size: 40
114439 CAGATGATAT
*
114449 TTAAATTTCACAAAAAACTATCATATTCTTGTTTATTTATA
1 TTAAATTTCAC-AAAAACTATCATAGTCTTGTTTATTTATA
**
114490 TTAAATTTTGCAAAAACTATCATAGTCTTGTTTATTTATA
1 TTAAATTTCACAAAAACTATCATAGTCTTGTTTATTTATA
114530 TT
1 TT
114532 CTTTTAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 30 0.77
41 9 0.23
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (40 bp):
TTAAATTTCACAAAAACTATCATAGTCTTGTTTATTTATA
Found at i:117052 original size:24 final size:23
Alignment explanation
Indices: 117025--117070 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
117015 AACTATTAGC
*
117025 TGTAACTGTTTCTGGTTAAGTTGT
1 TGTAACTGTTCCTGGTT-AGTTGT
117049 TGTAACTGTTCCTGGTTAGTTG
1 TGTAACTGTTCCTGGTTAGTTG
117071 GGCCGTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.15, C:0.11, G:0.26, T:0.48
Consensus pattern (23 bp):
TGTAACTGTTCCTGGTTAGTTGT
Done.