Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008032.1 Hibiscus syriacus cultivar Beakdansim tig00110514_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: 1200719
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:4650 original size:19 final size:20
Alignment explanation
Indices: 4604--4650 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
4594 TAATAATTAA
**
4604 TTTAAATTTTATAAATAATT
1 TTTAAATTTTATAAATAAGG
*
4624 TTTTAATTTT-TAAATAAGG
1 TTTAAATTTTATAAATAAGG
4643 TTTAAATT
1 TTTAAATT
4651 GAATTTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTAAATTTTATAAATAAGG
Found at i:14438 original size:16 final size:16
Alignment explanation
Indices: 14417--14450 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
14407 TAGAAGTTTG
14417 AATAAT-AAGTAAAATA
1 AATAATCAAGT-AAATA
14433 AATAATCAAGTAAATA
1 AATAATCAAGTAAATA
14449 AA
1 AA
14451 AGTATATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.24
Consensus pattern (16 bp):
AATAATCAAGTAAATA
Found at i:22050 original size:71 final size:71
Alignment explanation
Indices: 21925--22056 Score: 194
Period size: 71 Copynumber: 1.9 Consensus size: 71
21915 GCAGGTTTAA
* *
21925 CTTGATCAAACTGGTAATTCCTTATACAGGTTCATACCGATCGAATTGGTAATTTCTTACGGTAG
1 CTTGATCAAACTGGTAATTCCTTATACAGGTTCAGACCGATCGAATTGGCAATTTCTTACGGTAG
21990 GATCAG
66 GATCAG
* * * *
21996 CTTGGTCAAATTGGTAATTCCTTATATAGGTTCAGACTGATC-AAGTTGGCAATTTCTTACG
1 CTTGATCAAACTGGTAATTCCTTATACAGGTTCAGACCGATCGAA-TTGGCAATTTCTTACG
22057 TATCTAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
70 2 0.04
71 52 0.96
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (71 bp):
CTTGATCAAACTGGTAATTCCTTATACAGGTTCAGACCGATCGAATTGGCAATTTCTTACGGTAG
GATCAG
Found at i:36712 original size:15 final size:16
Alignment explanation
Indices: 36682--36714 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
36672 AAAATCTTTC
*
36682 TTTCCCGTTTTGGATT
1 TTTCCCGTTCTGGATT
36698 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
36713 TT
1 TT
36715 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.21, G:0.18, T:0.55
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:39859 original size:39 final size:39
Alignment explanation
Indices: 39802--39880 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
39792 AATGTTGTTG
**
39802 TGAGTTATATTATGATTAGAATTAATTATTAGTATTTTA
1 TGAGTTATATTACAATTAGAATTAATTATTAGTATTTTA
*
39841 TGAGTTATATTACAATTAGGATTAATTATTAGTATTTTA
1 TGAGTTATATTACAATTAGAATTAATTATTAGTATTTTA
39880 T
1 T
39881 TTTATTAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.51
Consensus pattern (39 bp):
TGAGTTATATTACAATTAGAATTAATTATTAGTATTTTA
Found at i:48058 original size:13 final size:14
Alignment explanation
Indices: 48042--48074 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
48032 AAAACCTCGC
48042 ATGAAATGAA-AAA
1 ATGAAATGAAGAAA
48055 ATG-AATGAAGAAA
1 ATGAAATGAAGAAA
48068 ATGAAAT
1 ATGAAAT
48075 TGTGAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.33
13 9 0.50
14 3 0.17
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (14 bp):
ATGAAATGAAGAAA
Found at i:48706 original size:20 final size:20
Alignment explanation
Indices: 48677--48715 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48667 AGAGCCCATA
*
48677 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
48697 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
48716 GCGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:49579 original size:21 final size:20
Alignment explanation
Indices: 49544--49582 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
49534 TAATGGATGA
49544 TTGTTTTTGTATGATGTTAT
1 TTGTTTTTGTATGATGTTAT
*
49564 TTGTTTTGTTTATGATGTT
1 TTGTTTT-TGTATGATGTT
49583 TAATGCCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.13, C:0.00, G:0.21, T:0.67
Consensus pattern (20 bp):
TTGTTTTTGTATGATGTTAT
Found at i:56634 original size:38 final size:38
Alignment explanation
Indices: 56589--56722 Score: 173
Period size: 38 Copynumber: 3.6 Consensus size: 38
56579 GATAATGCTC
*
56589 TATTATTTAAGGATTTATATTCAATTAAAATTCAAATA
1 TATTATTTAAGAATTTATATTCAATTAAAATTCAAATA
* * *
56627 TATTATTTACGAATTTATATTCAATTGAAATAT-GAATA
1 TATTATTTAAGAATTTATATTCAATTAAAAT-TCAAATA
* *
56665 TATTATTTATGAATTTATATTCAATTAAAATACAAATA
1 TATTATTTAAGAATTTATATTCAATTAAAATTCAAATA
* *
56703 TATTA-ATATGAATTTATATT
1 TATTATTTAAGAATTTATATT
56723 AGATTAGAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
37 14 0.16
38 70 0.82
39 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (38 bp):
TATTATTTAAGAATTTATATTCAATTAAAATTCAAATA
Found at i:64814 original size:23 final size:23
Alignment explanation
Indices: 64788--64831 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
64778 TAAAATAATT
64788 AAAACAA-CAAATATAAAAAACAG
1 AAAACAACCAAATA-AAAAAACAG
* *
64811 AAAATAACCACATAAAAAAAC
1 AAAACAACCAAATAAAAAAAC
64832 CTAAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.73, C:0.16, G:0.02, T:0.09
Consensus pattern (23 bp):
AAAACAACCAAATAAAAAAACAG
Found at i:66020 original size:26 final size:26
Alignment explanation
Indices: 65985--66038 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
65975 AAGGTAAAGT
*
65985 AAAACTGGAGA-AAAAGAAAGCAAAAA
1 AAAAATGGAGAGAAAA-AAAGCAAAAA
* *
66011 AAAAATGGAGAGCAAAAAATCAAAAA
1 AAAAATGGAGAGAAAAAAAGCAAAAA
66037 AA
1 AA
66039 TTCTTTTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.70, C:0.07, G:0.17, T:0.06
Consensus pattern (26 bp):
AAAAATGGAGAGAAAAAAAGCAAAAA
Found at i:66785 original size:54 final size:54
Alignment explanation
Indices: 66717--67041 Score: 424
Period size: 54 Copynumber: 6.0 Consensus size: 54
66707 ACGTAATGCG
* *
66717 ATACGGTCGTTCATCAACATATAATGAATTCCGTGGGTTGCACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCT
* * * * *
66771 ATACAGTCGTTCATCAACATATGATGAACTCCATTGGTTTCACACATAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCT
*** *
66825 ATACGG-CTGTTCATCAACATATGATGAATTTTTTGGGTTGCACACATAGTGCAT
1 ATACGGTC-GTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCT
* * *
66879 ATACGGTCGTTCATCAACATATGATGGATTCTGTGGGTTGCACACATAGTTCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCT
* * *
66933 ATACGGGT-GTTCATTAACATATGATGGATTCCGTGGGTTGCACACATAGTTCCT
1 ATAC-GGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCT
* *
66987 ATATGGTCGTTCATCAACATATGATGAATAT--GTGGTTTGCACACATAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAAT-TCCGTGGGTTGCACACATAGTGCCT
67040 AT
1 AT
67042 CGTTCATCAA
Statistics
Matches: 239, Mismatches: 27, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
53 26 0.11
54 208 0.87
55 5 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (54 bp):
ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCT
Found at i:68595 original size:117 final size:116
Alignment explanation
Indices: 68456--68665 Score: 321
Period size: 117 Copynumber: 1.8 Consensus size: 116
68446 TGATGGAATG
* *
68456 ACCAAGGTTGAACAAGTTCTTCTCAATATGAACTTGTTCTCCCTCATCGGATGAGTTCTTCTCAT
1 ACCAAGGTTGAACAAGTTCTTCTCAATATGAACTTCTTCTCCATCATCGGATGAGTTCTTCTCAT
* *
68521 TATGATCTCTTCACTCAAAATGTTGATCCACCTCCTTTTTTGATGGAGTTGA
66 TATGAACTCTCCACT-AAAATGTTGATCCACCTCCTTTTTTGATGGAGTTGA
* * ** *
68573 ACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTATTGTTGGATGAGTTCTTCTCAT
1 ACCAAGGTTGAACAAGTTCTTCTCAATATGAACTTCTTCTCCATCATCGGATGAGTTCTTCTCAT
*
68638 TATGAACTCTCCACTGAAATGTTGATCC
66 TATGAACTCTCCACTAAAATGTTGATCC
68666 CTCGAGTGAG
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
116 12 0.14
117 71 0.86
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (116 bp):
ACCAAGGTTGAACAAGTTCTTCTCAATATGAACTTCTTCTCCATCATCGGATGAGTTCTTCTCAT
TATGAACTCTCCACTAAAATGTTGATCCACCTCCTTTTTTGATGGAGTTGA
Found at i:68604 original size:20 final size:19
Alignment explanation
Indices: 68581--68644 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
68571 GAACCAAGGT
68581 TGAACAAGTTCTTCTCATTA
1 TGAAC-AGTTCTTCTCATTA
*
68601 TGAAC--TTCTTCTCTATTGT
1 TGAACAGTTCTTCTC-ATT-A
**
68620 TGGATGAGTTCTTCTCATTA
1 T-GAACAGTTCTTCTCATTA
68640 TGAAC
1 TGAAC
68645 TCTCCACTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 11
0.66 0.12 0.22
Matches are distributed among these distances:
17 8 0.24
18 3 0.09
19 3 0.09
20 8 0.24
21 3 0.09
22 8 0.24
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (19 bp):
TGAACAGTTCTTCTCATTA
Found at i:68830 original size:91 final size:91
Alignment explanation
Indices: 68714--69510 Score: 1071
Period size: 91 Copynumber: 8.8 Consensus size: 91
68704 GAATCAAACA
* * * * * * * *
68714 AAGGTTGAATACGTTATTCTTATTATAAATTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
* *
68779 GAACTCTCCATTGAAAATGTTGA-GT
66 GAACTCTCCACTGGAAATGTTGATGT
* * *
68804 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCATTGGATGAGTTCTTCTCATTA
1 -AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
* * *
68869 AGAACTATCCACTGGAAATGTTGA-GCC
65 TGAACTCTCCACTGGAAATGTTGATG-T
* * * * *
68896 AAGGTTGAATAAGTTATTCTCATTATAAACTTCTTATCCCTCGTTGGATGAGCTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
*
68961 GAACTCCCCACTGGAAATGTTGATGT
66 GAACTCTCCACTGGAAATGTTGATGT
*
68987 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
* *
69052 GAACTCCCCACTGGAAATGTTCATGT
66 GAACTCTCCACTGGAAATGTTGATGT
* *** * *
69078 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCGTCATATAAGTTCCTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
** *
69143 GAACTCTCTGCTGGAAATGTTGATGC
66 GAACTCTCCACTGGAAATGTTGATGT
* * *
69169 AAGGTTGAACAAGTTATTCTCATTATGAACTTATTCTCCCTCATTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
* *
69234 GAACTCTCCACTGGAAATTTTGATGC
66 GAACTCTCCACTGGAAATGTTGATGT
* * *
69260 AAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTCCCTCTTTGGATGAGTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
* *
69325 AAACTCCCCACTGGAAATGTTGATGT
66 GAACTCTCCACTGGAAATGTTGATGT
* * *
69351 AAGGTTGAACAAGTTCTTCCCATTATGAACTTCTTATCCCTCGTTGGATGAGTTCTTCTCATTAA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
*
69416 GAGCTC-CACACTGG-AATGTTGATGT
66 GAACTCTC-CACTGGAAATGTTGATGT
* * * *
69441 AAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCACTCGTCGGATGAATTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
69506 GAACT
66 GAACT
69511 TATTCTTACT
Statistics
Matches: 624, Mismatches: 79, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
90 74 0.12
91 549 0.88
92 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (91 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATGTTGATGT
Found at i:69479 original size:17 final size:17
Alignment explanation
Indices: 69457--69516 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 17
69447 GAACAAGTTC
69457 TTCTCATTATGAACTTA
1 TTCTCATTATGAACTTA
*
69474 TTCTCACTCGTCGGATGAA-TTC
1 TTCTCA-T--T---ATGAACTTA
69496 TTCTCATTATGAACTTA
1 TTCTCATTATGAACTTA
69513 TTCT
1 TTCT
69517 TACTCGTCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
16 5 0.15
17 12 0.35
18 1 0.03
19 1 0.03
20 1 0.03
21 1 0.03
22 8 0.24
23 5 0.15
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (17 bp):
TTCTCATTATGAACTTA
Found at i:69500 original size:22 final size:23
Alignment explanation
Indices: 69465--69530 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
69455 TCTTCTCATT
69465 ATGAACTTATTCTCACTCGTCGG
1 ATGAACTTATTCTCACTCGTCGG
*
69488 ATGAA-TTCTTCTCA-T--T---
1 ATGAACTTATTCTCACTCGTCGG
*
69504 ATGAACTTATTCTTACTCGTCGG
1 ATGAACTTATTCTCACTCGTCGG
69527 ATGA
1 ATGA
69531 GTTCTTCTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 14
0.66 0.06 0.28
Matches are distributed among these distances:
16 5 0.15
17 7 0.21
18 1 0.03
19 1 0.03
20 1 0.03
21 1 0.03
22 8 0.24
23 9 0.27
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (23 bp):
ATGAACTTATTCTCACTCGTCGG
Found at i:69508 original size:39 final size:39
Alignment explanation
Indices: 69454--69546 Score: 168
Period size: 39 Copynumber: 2.4 Consensus size: 39
69444 GTTGAACAAG
69454 TTCTTCTCATTATGAACTTATTCTCACTCGTCGGATGAA
1 TTCTTCTCATTATGAACTTATTCTCACTCGTCGGATGAA
* *
69493 TTCTTCTCATTATGAACTTATTCTTACTCGTCGGATGAG
1 TTCTTCTCATTATGAACTTATTCTCACTCGTCGGATGAA
69532 TTCTTCTCATTATGA
1 TTCTTCTCATTATGA
69547 TCTCCCTGCT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.44
Consensus pattern (39 bp):
TTCTTCTCATTATGAACTTATTCTCACTCGTCGGATGAA
Found at i:69614 original size:130 final size:129
Alignment explanation
Indices: 69364--69640 Score: 376
Period size: 130 Copynumber: 2.1 Consensus size: 129
69354 GTTGAACAAG
* * * *
69364 TTCTTCCCATTATGAACTTCTTATCCCTCGTTGGATGAGTTCTTCTCATTAAGAGCTCCACACTG
1 TTCTTCTCATTATGAACTTATTATCACTCGTCGGATGAGTTCTTCTCATTAAGAGCTCCACACTG
** * *
69429 GAATGTTGATGTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCACTCGTCGGATGAA
66 GAATGTTGATACAAGGTTGAACAAGTTCTTCTAATTATAAACTTATTCTCACTCGTCGGATGAA
* * * * *
69493 TTCTTCTCATTATGAACTTATTCTTACTCGTCGGATGAGTTCTTCTCATTATGATCTCC-CTGCT
1 TTCTTCTCATTATGAACTTATTATCACTCGTCGGATGAGTTCTTCTCATTAAGAGCTCCAC-ACT
* * *
69557 GGAAATGTTGATACAAGGTTGAACAAGTTCTTCTAATTATAAACTTCTTCTCCCTCGTTGGATGA
65 GG-AATGTTGATACAAGGTTGAACAAGTTCTTCTAATTATAAACTTATTCTCACTCGTCGGATGA
*
69622 G
129 A
69623 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
69641 CTCCACTAGA
Statistics
Matches: 129, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
128 1 0.01
129 55 0.43
130 73 0.57
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.39
Consensus pattern (129 bp):
TTCTTCTCATTATGAACTTATTATCACTCGTCGGATGAGTTCTTCTCATTAAGAGCTCCACACTG
GAATGTTGATACAAGGTTGAACAAGTTCTTCTAATTATAAACTTATTCTCACTCGTCGGATGAA
Found at i:69653 original size:91 final size:92
Alignment explanation
Indices: 69493--69734 Score: 362
Period size: 91 Copynumber: 2.7 Consensus size: 92
69483 GTCGGATGAA
* ** * * *
69493 TTCTTCTCATTATGAACTTATTCTTACTCGTCGGATGAGTTCTTCTCATTATGATCTC-CCTGCT
1 TTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCTACT
* *
69557 GGAAATGTTGATACAAGGTTGAACAAG
66 AGAAATGTTGATACAAGATTGAACAAG
* *
69584 TTCTTCTAATTATAAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCC-ACT
1 TTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCTACT
*
69648 AGAAATGTTGATGCAAGATTGAACAAG
66 AGAAATGTTGATACAAGATTGAACAAG
*
69675 TTCTTCTCATTATGAACTTCTTCTCCATCGTTGGATGAGTTCTTCTCATTATGAACTCTC
1 TTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTC
69735 TATTTAAAAT
Statistics
Matches: 136, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
91 134 0.99
92 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (92 bp):
TTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCTACT
AGAAATGTTGATACAAGATTGAACAAG
Found at i:70687 original size:42 final size:42
Alignment explanation
Indices: 70605--70718 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
70595 TCCCAAAGGT
* * * * *
70605 CTTATGGATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAATCATCATGATCAAAAGA
*
70646 CTTATAGATGACCCGAAGGATTTAATCATCATGATCAAAAGA
1 CTTATAGATGACCCGAAGGACTTAATCATCATGATCAAAAGA
* * *
70688 CTTACTA-TTGTCCCGAAGGACTTACTCATCA
1 CTTA-TAGATGACCCGAAGGACTTAATCATCA
70719 AGAAACTCTT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 20 0.33
42 39 0.64
43 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGACTTAATCATCATGATCAAAAGA
Found at i:71006 original size:274 final size:273
Alignment explanation
Indices: 70477--71147 Score: 866
Period size: 274 Copynumber: 2.4 Consensus size: 273
70467 GATTCGTTTA
* * * * *
70477 TAGTTATCAAGAAACCCGTAAAATTA-GTTATAGCATTC-TTTAAAAATTCTTTGGAGATAATCA
1 TAGTTATCAAGGAACCCCTAAAATTAGGAT-TAGC-TTCTTTTAAAAAATCTTTGAAGATAATCA
* **
70540 TCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAA-T-ATTTTGAAAACAACATTCCCAAAG
64 TCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCA-TTTGAAAACATCAGGCCCAAAG
* * * *
70603 GTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGATT
128 GTCTTATGGATGGCCCAAAAGACTTATCATCTTGCTCGAAAGACTTATAAATGACCCAAAGGATT
** * * *
70668 TAATCATCATGATCAAAAGACTTACTATTGTCCCGAAGGACTTACTCATCAAGAAACTCTTGAAA
193 TAAGAATCATGATCAAAAGACTTACTATTGGCCAGAAGGACTTACTCATCAAGAAACACTTGAAA
*
70733 ATCAAGCTTAGTTTCT
258 ATCAAGCTTACTTTCT
* ** *
70749 TAGTTGTCAAGGAACCCCTAAAATTAGGATTAGCTTCCTTTTAAAACCTCTTTGTAGATAATCAT
1 TAGTTATCAAGGAACCCCTAAAATTAGGATTAGCTT-CTTTTAAAAAATCTTTGAAGATAATCAT
* * *
70814 CAAGAATCCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCATTTGAAAACATCCGGCCCGAAGGT
65 CAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCATTTGAAAACATCAGGCCCAAAGGT
*
70879 CTTATGGATGGCCCAAAAGACTTATCATCTTGCTCGAAAGACTTATAAATGACCCAAATGATTTA
130 CTTATGGATGGCCCAAAAGACTTATCATCTTGCTCGAAAGACTTATAAATGACCCAAAGGATTTA
* *
70944 AGAATCATGCTCGAAAGACTTACTGA-TGGCCAGAAGGACTTACTCATCAAGAAACACTTGAAAA
195 AGAATCATGATCAAAAGACTTACT-ATTGGCCAGAAGGACTTACTCATCAAGAAACACTTGAAAA
71008 TCAAGCTTACTTTCT
259 TCAAGCTTACTTTCT
* * * * *
71023 TAGCTGTCATCAAGGAACCCCTAAAAATTAGGATAAGCTTTTTTTAAAAAAAAATCATTAAAAAT
1 TAG-T-T-ATCAAGGAACCCCT-AAAATTAGGATTAGCTTCTTTT---AAAAAATCTTTGAAGAT
* * * *
71088 TATCATCAAGAAACCCTTGAAAATCAGGATTAGTTTTTAAAAACTCATTTGAAAACATCA
59 AATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCATTTGAAAACATCA
71148 AGAAACCCCT
Statistics
Matches: 345, Mismatches: 41, Indels: 18
0.85 0.10 0.04
Matches are distributed among these distances:
271 2 0.01
272 28 0.08
273 61 0.18
274 152 0.44
275 3 0.01
276 1 0.00
277 17 0.05
278 16 0.05
280 65 0.19
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.29
Consensus pattern (273 bp):
TAGTTATCAAGGAACCCCTAAAATTAGGATTAGCTTCTTTTAAAAAATCTTTGAAGATAATCATC
AAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCATTTGAAAACATCAGGCCCAAAGGTC
TTATGGATGGCCCAAAAGACTTATCATCTTGCTCGAAAGACTTATAAATGACCCAAAGGATTTAA
GAATCATGATCAAAAGACTTACTATTGGCCAGAAGGACTTACTCATCAAGAAACACTTGAAAATC
AAGCTTACTTTCT
Found at i:73179 original size:9 final size:9
Alignment explanation
Indices: 73165--73261 Score: 92
Period size: 9 Copynumber: 10.4 Consensus size: 9
73155 GATTTGTCTA
73165 TTTTCTTCT
1 TTTTCTTCT
73174 TTTTC-TCTT
1 TTTTCTTC-T
*
73183 TTTTTTTCT
1 TTTTCTTCT
*
73192 TTTGT-TTATT
1 TTT-TCTT-CT
73202 TTTTCTTTTCT
1 TTTTC--TTCT
73213 TTTTCTCTCT
1 TTTTCT-TCT
73223 TTTTCTTCT
1 TTTTCTTCT
*
73232 TTTT-TCCT
1 TTTTCTTCT
73240 TTTTCTTCT
1 TTTTCTTCT
73249 TTTTCTTCT
1 TTTTCTTCT
73258 TTTT
1 TTTT
73262 TCATTTTCTC
Statistics
Matches: 74, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
8 9 0.12
9 41 0.55
10 16 0.22
11 6 0.08
12 2 0.03
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.79
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:73226 original size:16 final size:17
Alignment explanation
Indices: 73207--73261 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
73197 TTATTTTTTC
73207 TTTTCTT-TTTCTCTCT
1 TTTTCTTCTTTCTCTCT
*
73223 TTTTCTTCTTT-TTTCCT
1 TTTTCTTCTTTCTCT-CT
*
73240 TTTTCTTCTTTTTCTTCT
1 TTTTCTTCTTTCTC-TCT
73258 TTTT
1 TTTT
73262 TCATTTTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 9 0.27
17 16 0.48
18 7 0.21
19 1 0.03
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCTTCTTTCTCTCT
Found at i:73233 original size:58 final size:59
Alignment explanation
Indices: 73165--73285 Score: 158
Period size: 57 Copynumber: 2.1 Consensus size: 59
73155 GATTTGTCTA
* * **
73165 TTTTCTTCTTTTTCTCTTTTTTTTTCTTTTGT-TTATTTTTTC-TTTTCT-TTTTCTCTCT
1 TTTTCTTCTTTTT-TCCTTTTTCTTCTTTT-TCTTATTTTTTCATTTTCTCTTTTCAATCT
*
73223 TTTTCTTCTTTTTTCCTTTTTCTTCTTTTTCTTCTTTTTTCATTTTCTCTTTTCAATCT
1 TTTTCTTCTTTTTTCCTTTTTCTTCTTTTTCTTATTTTTTCATTTTCTCTTTTCAATCT
73282 TTTT
1 TTTT
73286 TATGTTTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
56 1 0.02
57 23 0.42
58 19 0.35
59 12 0.22
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (59 bp):
TTTTCTTCTTTTTTCCTTTTTCTTCTTTTTCTTATTTTTTCATTTTCTCTTTTCAATCT
Found at i:73236 original size:26 final size:26
Alignment explanation
Indices: 73207--73272 Score: 107
Period size: 26 Copynumber: 2.5 Consensus size: 26
73197 TTATTTTTTC
73207 TTTTCTTTTTCTCTCTTTTTCTTCTT
1 TTTTCTTTTTCTCTCTTTTTCTTCTT
73233 TTTTCCTTTTTCT-TCTTTTTCTTCTT
1 TTTT-CTTTTTCTCTCTTTTTCTTCTT
*
73259 TTTTCATTTTCTCT
1 TTTTCTTTTTCTCT
73273 TTTCAATCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
25 7 0.19
26 22 0.59
27 8 0.22
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTCTTTTTCTCTCTTTTTCTTCTT
Found at i:73263 original size:10 final size:10
Alignment explanation
Indices: 73165--73263 Score: 88
Period size: 10 Copynumber: 10.5 Consensus size: 10
73155 GATTTGTCTA
73165 TTTTCTTC-T
1 TTTTCTTCTT
73174 TTTTC-TCTT
1 TTTTCTTCTT
*
73183 TTTTTTTCTT
1 TTTTCTTCTT
* *
73193 TTGT-TTATT
1 TTTTCTTCTT
*
73202 TTTTCTTTTCT
1 TTTTCTTCT-T
73213 TTTTC-TCTCT
1 TTTTCTTCT-T
73223 TTTTCTTCTT
1 TTTTCTTCTT
73233 TTTTC--C-T
1 TTTTCTTCTT
73240 TTTTCTTC-T
1 TTTTCTTCTT
73249 TTTTCTTCTT
1 TTTTCTTCTT
73259 TTTTC
1 TTTTC
73264 ATTTTCTCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 15
0.78 0.06 0.15
Matches are distributed among these distances:
7 6 0.08
8 3 0.04
9 27 0.36
10 31 0.41
11 9 0.12
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.79
Consensus pattern (10 bp):
TTTTCTTCTT
Found at i:73282 original size:24 final size:26
Alignment explanation
Indices: 73213--73286 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
73203 TTTCTTTTCT
* *
73213 TTTTCTCTCTTTTTCTTCTTTTTTCCT
1 TTTTCT-TCTTTTTCATCTTTTTTCCA
*
73240 TTTTCTTCTTTTTCTTCTTTTTT-CA
1 TTTTCTTCTTTTTCATCTTTTTTCCA
73265 TTTTC-TC-TTTTCAATCTTTTTT
1 TTTTCTTCTTTTTC-ATCTTTTTT
73287 ATGTTTTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
23 5 0.11
24 10 0.23
25 6 0.14
26 17 0.39
27 6 0.14
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (26 bp):
TTTTCTTCTTTTTCATCTTTTTTCCA
Found at i:74077 original size:55 final size:55
Alignment explanation
Indices: 73947--74228 Score: 343
Period size: 55 Copynumber: 5.1 Consensus size: 55
73937 AATGCATGAG
* * * * * *
73947 TAGTGCCTATACGGTAATTCATCTACTCATGATGAATTCCGTGG-TTTTCATACA
1 TAGTGCCTGTAAGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
* *
74001 TAGTGCCTGTACGGTTATTCATCAACTCATGATAAATTCCGTGGATTTGCACACA
1 TAGTGCCTGTAAGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
* * * * *
74056 TAGGGACTGTACA-GTTATTCATAAACTCATAATGAATTCCGTGGATTTACACACA
1 TAGTGCCTGTA-AGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
* *
74111 TAGTGCCTGTAAGGTTATTCATCAATTCATGATGAATTCCGTGGATTTGCACATA
1 TAGTGCCTGTAAGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
** * * * *
74166 TAAAGCGTGTAAGGTTATTCATAAACTCATGATGAATTTCATGGATTTGCACACA
1 TAGTGCCTGTAAGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
*
74221 TAATGCCT
1 TAGTGCCT
74229 ATTTGGTAAT
Statistics
Matches: 195, Mismatches: 30, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
54 41 0.21
55 154 0.79
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (55 bp):
TAGTGCCTGTAAGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
Found at i:74581 original size:22 final size:22
Alignment explanation
Indices: 74539--74592 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
74529 TGGCTCCTCA
*
74539 GTATCGATAC--CCATACCATG
1 GTATCGATACTACCATACAATG
74559 GTATCGATACTACCATACAATG
1 GTATCGATACTACCATACAATG
*
74581 GTACCGATACTA
1 GTATCGATACTA
74593 TGCTATGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 10 0.33
22 20 0.67
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (22 bp):
GTATCGATACTACCATACAATG
Found at i:82455 original size:21 final size:20
Alignment explanation
Indices: 82426--82464 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
82416 TAAGGCATTA
*
82426 AACATCATAAACAAAACAAAT
1 AACAGCATAAA-AAAACAAAT
*
82447 AACAGCATACAAAAACAA
1 AACAGCATAAAAAAACAA
82465 CTATCCATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.67, C:0.21, G:0.03, T:0.10
Consensus pattern (20 bp):
AACAGCATAAAAAAACAAAT
Found at i:83323 original size:20 final size:20
Alignment explanation
Indices: 83295--83332 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
83285 TTCCACCACA
*
83295 TGCAACTATATGCTCCTAAT
1 TGCAACTATATGATCCTAAT
*
83315 TGCATCTATATGATCCTA
1 TGCAACTATATGATCCTA
83333 TATGATCTCT
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:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (20 bp):
TGCAACTATATGATCCTAAT
Found at i:85667 original size:29 final size:29
Alignment explanation
Indices: 85616--85702 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
85606 AATATCTTGT
*
85616 AGAATTAGGA-CGGGA-AGTAATCCCATGC
1 AGAATTAGGATAGGGATA-TAATCCCATGC
**
85644 AGAATTAGGATAGGGATATAATCCCATAT
1 AGAATTAGGATAGGGATATAATCCCATGC
* * *
85673 AGAATCA-GATTGGGGATATAATCTCATGC
1 AGAATTAGGA-TAGGGATATAATCCCATGC
85702 A
1 A
85703 AAATCGACAC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
28 12 0.25
29 35 0.73
30 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (29 bp):
AGAATTAGGATAGGGATATAATCCCATGC
Found at i:85707 original size:29 final size:28
Alignment explanation
Indices: 85656--85823 Score: 106
Period size: 29 Copynumber: 5.9 Consensus size: 28
85646 AATTAGGATA
* ** * *
85656 GGGATATAATCCCATATAGAATCAGATTG
1 GGGATATAATCTCATGCAAAATCAGA-CG
*
85685 GGGATATAATCTCATGCAAAATC-GACAC
1 GGGATATAATCTCATGCAAAATCAGAC-G
** *
85713 ATGATATAATCCCATGCAAAATCAGGACG
1 GGGATATAATCTCATGCAAAATCA-GACG
* *
85742 GTGATATAAT-TCCATCCAAAATCAGGACG
1 GGGATATAATCT-CATGCAAAATCA-GACG
** * * *
85771 ATGATATAATCTCATGTAGAATCAGAATG
1 GGGATATAATCTCATGCAAAATCAG-ACG
* *
85800 GGGATATAATCACATGTAAAATCA
1 GGGATATAATCTCATGCAAAATCA
85824 CAACAGGGAT
Statistics
Matches: 111, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
28 23 0.21
29 84 0.76
30 4 0.04
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (28 bp):
GGGATATAATCTCATGCAAAATCAGACG
Found at i:85821 original size:58 final size:57
Alignment explanation
Indices: 85658--85858 Score: 183
Period size: 58 Copynumber: 3.5 Consensus size: 57
85648 TTAGGATAGG
* *
85658 GATATAATCCCATATAGAATCAGATTGGGGATATAATCTCATGCAAAATC-GACACAT
1 GATATAATCCCATGTAGAATCAGAATGGGGATATAATC-CATGCAAAATCAGACACAT
* * * * * * *
85715 GATATAATCCCATGCAAAATCAGGACGGTGATATAATTCCATCCAAAATCAGGAC-GAT
1 GATATAATCCCATGTAGAATCAGAATGGGGATATAA-TCCATGCAAAATCA-GACACAT
* * * *
85773 GATATAATCTCATGTAGAATCAGAATGGGGATATAATCACATGTAAAATCACA-ACAGG
1 GATATAATCCCATGTAGAATCAGAATGGGGATATAATC-CATGCAAAATCAGACACA-T
* * *
85831 GATACAATCCTATATAGAATCAAGAATG
1 GATATAATCCCATGTAGAATC-AGAATG
85859 TATCAATATA
Statistics
Matches: 113, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
57 43 0.38
58 61 0.54
59 9 0.08
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (57 bp):
GATATAATCCCATGTAGAATCAGAATGGGGATATAATCCATGCAAAATCAGACACAT
Found at i:85832 original size:29 final size:29
Alignment explanation
Indices: 85773--85839 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
85763 TCAGGACGAT
* * * **
85773 GATATAATCTCATGTAGAATCAGAATGGG
1 GATATAATCACATGTAAAATCACAACAGG
85802 GATATAATCACATGTAAAATCACAACAGG
1 GATATAATCACATGTAAAATCACAACAGG
*
85831 GATACAATC
1 GATATAATC
85840 CTATATAGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (29 bp):
GATATAATCACATGTAAAATCACAACAGG
Found at i:102598 original size:19 final size:19
Alignment explanation
Indices: 102570--102611 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
102560 CAAAAACTAT
102570 GAATTATTCATGATTTATG
1 GAATTATTCATGATTTATG
*
102589 GAATTGTTCATGATTTATG
1 GAATTATTCATGATTTATG
102608 GAAT
1 GAAT
102612 CATGGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (19 bp):
GAATTATTCATGATTTATG
Found at i:136529 original size:19 final size:19
Alignment explanation
Indices: 136492--136531 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
136482 ATAAATGAAG
*
136492 AAAAATTAAGGAAAATAAA
1 AAAAATTAAGCAAAATAAA
* *
136511 AAAAATTAAGCTAACTAAA
1 AAAAATTAAGCAAAATAAA
136530 AA
1 AA
136532 GAAAATATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.17
Consensus pattern (19 bp):
AAAAATTAAGCAAAATAAA
Found at i:138756 original size:11 final size:11
Alignment explanation
Indices: 138740--138775 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
138730 AGGCAACTCA
138740 TTTCATTTTAT
1 TTTCATTTTAT
*
138751 TTTCATTTTAA
1 TTTCATTTTAT
138762 TTTCATTTTAT
1 TTTCATTTTAT
138773 TTT
1 TTT
138776 TAGAAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTCATTTTAT
Found at i:145789 original size:200 final size:196
Alignment explanation
Indices: 145407--145799 Score: 734
Period size: 200 Copynumber: 2.0 Consensus size: 196
145397 TTGCAGGTCA
145407 CTTCAGGCATAAGTGAGCTTACTCACAATGATTTTCCCTACGTCAATGGCATGCCCAAAAATAAT
1 CTTCAGGCATAAGTGAGCTTACTCACAATGATTTTCCCTACGTCAATGGCATGCCCAAAAATAAT
145472 TGAATGCAAGATAAGCATCGCTGACAGGAAACAGTAGGTTGTGGGAAGTGGTAGAAGCTTGTGCT
66 TGAATGCAAGATAAGCATCGCTGACAGGAAACAGTAGGTTGTGGGAAGTGGTAGAAGCTTGTGCT
145537 TCATAAAGTGATTCCACAACTGGCTTGCTGGCAGCAACCTTTCTCGGTCTAGCATCCTATGGCGG
131 TCATAAAGTGATTCCACAACTGGCTTGCTGGCAGCAACCTTTCTCGGTCTAGCATCCTATGGCGG
145602 T
196 T
145603 CTTCAGGCATAAGTGAGCTTACTCCACAATGATTTTCCCTACGTCAATGGCATGCCCAAAAATAA
1 CTTCAGGCATAAGTGAGCTTACT-CACAATGATTTTCCCTACGTCAATGGCATGCCCAAAAATAA
145668 TTGAATGCAAGATAAGCATCCGCTGACAGGAAACAGTAGTGTTGTGGGAAGTGGGTAGAAGCTTG
65 TTGAATGCAAGATAAGCAT-CGCTGACAGGAAACAGTAG-GTTGTGGGAAGT-GGTAGAAGCTTG
145733 TGCTTCATAAAGTGATTCCACAACTTGGCTTGC-GGCAGCAACCTTTCTCGGTCTAGCATCCTAT
127 TGCTTCATAAAGTGATTCCACAAC-TGGCTTGCTGGCAGCAACCTTTCTCGGTCTAGCATCCTAT
145797 GGC
191 GGC
145800 TCAGTTGCTA
Statistics
Matches: 192, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
196 23 0.12
197 60 0.31
198 19 0.10
199 12 0.06
200 70 0.36
201 8 0.04
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (196 bp):
CTTCAGGCATAAGTGAGCTTACTCACAATGATTTTCCCTACGTCAATGGCATGCCCAAAAATAAT
TGAATGCAAGATAAGCATCGCTGACAGGAAACAGTAGGTTGTGGGAAGTGGTAGAAGCTTGTGCT
TCATAAAGTGATTCCACAACTGGCTTGCTGGCAGCAACCTTTCTCGGTCTAGCATCCTATGGCGG
T
Found at i:150903 original size:13 final size:13
Alignment explanation
Indices: 150885--150920 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
150875 GATGGAGTTC
150885 GCATGGTCTTGCA
1 GCATGGTCTTGCA
150898 GCATGGTCTTGCA
1 GCATGGTCTTGCA
*
150911 GCATTGTCTT
1 GCATGGTCTT
150921 TATTGTTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.36
Consensus pattern (13 bp):
GCATGGTCTTGCA
Found at i:160924 original size:15 final size:15
Alignment explanation
Indices: 160904--160958 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
160894 CGTAGAGCAC
160904 TTTCACATA-AGGTAT
1 TTTCACATAGA-GTAT
*
160919 TTTCACGTAGAGTAT
1 TTTCACATAGAGTAT
* *
160934 TTTCACGTAGCA-CAT
1 TTTCACATAG-AGTAT
160949 TTTCACATAG
1 TTTCACATAG
160959 GACATTTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 33 0.94
16 2 0.06
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (15 bp):
TTTCACATAGAGTAT
Found at i:160963 original size:15 final size:15
Alignment explanation
Indices: 160932--160965 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
160922 CACGTAGAGT
*
160932 ATTTTCACGTAGCAC
1 ATTTTCACATAGCAC
*
160947 ATTTTCACATAGGAC
1 ATTTTCACATAGCAC
160962 ATTT
1 ATTT
160966 CCATATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (15 bp):
ATTTTCACATAGCAC
Found at i:161507 original size:21 final size:23
Alignment explanation
Indices: 161472--161514 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
161462 TTGGTATGGA
161472 TACTTCTACATCAGTACCGATAC
1 TACTTCTACATCAGTACCGATAC
*
161495 TACTTC-A-ATCAGTATCGATA
1 TACTTCTACATCAGTACCGATA
161515 ATGTTCATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 1 0.05
23 6 0.32
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.33
Consensus pattern (23 bp):
TACTTCTACATCAGTACCGATAC
Found at i:162061 original size:3 final size:3
Alignment explanation
Indices: 162053--162116 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
162043 CACTAGAAAG
162053 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
162101 AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA A
162117 AAGTGAACCA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:165420 original size:14 final size:13
Alignment explanation
Indices: 165383--165455 Score: 57
Period size: 14 Copynumber: 5.7 Consensus size: 13
165373 CGCTTCACCA
*
165383 TAAAATTAATATC
1 TAAAATTAATATT
*
165396 TATAATATAATATT
1 TAAAAT-TAATATT
165410 TAAAAATTAATA-T
1 T-AAAATTAATATT
165423 T-AAATT--TATT
1 TAAAATTAATATT
165433 TGAAAAATTAATA-T
1 T--AAAATTAATATT
165447 TAAAATTAA
1 TAAAATTAA
165456 AATCAAATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
9 2 0.04
10 2 0.04
11 5 0.10
12 8 0.16
13 12 0.24
14 14 0.29
15 6 0.12
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (13 bp):
TAAAATTAATATT
Found at i:165422 original size:19 final size:22
Alignment explanation
Indices: 165398--165446 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
165388 TTAATATCTA
165398 TAATAT-AA-TATTT-AAAAAT
1 TAATATAAATTATTTGAAAAAT
165417 TAATATTAAATTTATTTGAAAAAT
1 TAATA-TAAA-TTATTTGAAAAAT
165441 TAATAT
1 TAATAT
165447 TAAAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 5 0.20
20 1 0.04
21 2 0.08
23 6 0.24
24 11 0.44
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TAATATAAATTATTTGAAAAAT
Found at i:165422 original size:28 final size:24
Alignment explanation
Indices: 165406--165450 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
165396 TATAATATAA
165406 TATTT-AAAAATTAATATTAAATT
1 TATTTGAAAAATTAATATTAAATT
165429 TATTTGAAAAATTAATATTAAA
1 TATTTGAAAAATTAATATTAAA
165451 ATTAAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TATTTGAAAAATTAATATTAAATT
Found at i:165453 original size:12 final size:12
Alignment explanation
Indices: 165383--165455 Score: 60
Period size: 13 Copynumber: 5.8 Consensus size: 12
165373 CGCTTCACCA
165383 TAAAATTAATAT
1 TAAAATTAATAT
*
165395 CTATAATATAATATT
1 -TAAAAT-TAATA-T
165410 TAAAAATTAATAT
1 T-AAAATTAATAT
*
165423 T-AAATTTAT-T
1 TAAAATTAATAT
165433 TGAAAAATTAATAT
1 T--AAAATTAATAT
165447 TAAAATTAA
1 TAAAATTAA
165456 AATCAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
10 2 0.04
11 7 0.14
12 8 0.16
13 14 0.29
14 13 0.27
15 5 0.10
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (12 bp):
TAAAATTAATAT
Found at i:168996 original size:508 final size:509
Alignment explanation
Indices: 168041--169057 Score: 2018
Period size: 508 Copynumber: 2.0 Consensus size: 509
168031 AAAAATGGGC
168041 AGTTTGCGTCTTTAAAGGAAAGTACCAGTACTTCAAGCTGGAATTCCTCGCAAACTGACCTTCAT
1 AGTTTGCGTCTTTAAAGGAAAGTACCAGTACTTCAAGCTGGAATTCCTCGCAAACTGACCTTCAT
168106 GATGGTACTCGTTGTCTAGAAACTGTGTGAGTTCCAAACTTGCATGTTGCCAGGTTATTTGGATA
66 GATGGTACTCGTTGTCTAGAAACTGTGTGAGTTCCAAACTTGCATGTTGCCAGGTTATTTGGATA
168171 TATGTTTCATGTTGAACCTTTTTAAGAATAATGTCTTCAATGTGTTTTAGTGTCCGGAGATGTCA
131 TATGTTTCATGTTGAACCTTTTTAAGAATAATGTCTTCAATGTGTTTTAGTGTCCGGAGATGTCA
168236 ACATTGTGGTGTTAGTGAAAATAATACTCCAGCAATGCGTCGTGGTCCTGCTGGTCCAAGGACTT
196 ACATTGTGGTGTTAGTGAAAATAATACTCCAGCAATGCGTCGTGGTCCTGCTGGTCCAAGGACTT
168301 TATGTAATGCGTGTGGGCTTATGTGGGCTAATAAGGTCTGCTTGTTCCGATAGTTTTTTTTTATT
261 TATGTAATGCGTGTGGGCTTATGTGGGCTAATAAGGTCTGCTTGTTCCGATAGTTTTTTTTTATT
168366 AAGCATCATCTTGTGTAGTTATACTTCAGCATAGTCTTTGGAATGTTGGTGATGATAATCTTCAA
326 AAGCATCATCTTGTGTAGTTATACTTCAGCATAGTCTTTGGAATGTTGGTGATGATAATCTTCAA
168431 ATATCCTTGTTGTGAATTGTGATTAGTGGTTTTCTGCAACTTTTTGTTGAATGTACAGGGAACAC
391 ATATCCTTGTTGTGAATTGTGATTAGTGGTTTTCTGCAACTTTTTGTTGAATGTACAGGGAACAC
168496 TTAGAGATCTTAGTAAAGGAGGAAGGAGTCTTTCCATGGACC-AACTGAGCCTG
456 TTAGAGATCTTAGTAAAGGAGGAAGGAGTCTTTCCATGGACCAAACTGAGCCTG
*
168549 AGTTTGCGTCTTTAAAGGAAAGTACCAGTACTTCAAGCTGGAATTCTTCGCAAACTGACCTTCAT
1 AGTTTGCGTCTTTAAAGGAAAGTACCAGTACTTCAAGCTGGAATTCCTCGCAAACTGACCTTCAT
168614 GATGGTACTCGTTGTCTAGAAACTGTGTGAGTTCCAAACTTGCATGTTGCCAGGTTATTTGGATA
66 GATGGTACTCGTTGTCTAGAAACTGTGTGAGTTCCAAACTTGCATGTTGCCAGGTTATTTGGATA
168679 TATGTTTCATGTTGAACCTTTTTAAGAATAATGTCTTCAATGTGTTTTAGTGTCCGGAGATGTCA
131 TATGTTTCATGTTGAACCTTTTTAAGAATAATGTCTTCAATGTGTTTTAGTGTCCGGAGATGTCA
168744 ACATTGTGGTGTTAGTGAAAATAATACTCCAGCAATGCGTCGTGGTCCTGCTGGTCCAAGGACTT
196 ACATTGTGGTGTTAGTGAAAATAATACTCCAGCAATGCGTCGTGGTCCTGCTGGTCCAAGGACTT
168809 TATGTAATGCGTGTGGGCTTATGTGGGCTAATAAGGTCTGCTTGTTCCGATAGTTTTTTTTTATT
261 TATGTAATGCGTGTGGGCTTATGTGGGCTAATAAGGTCTGCTTGTTCCGATAGTTTTTTTTTATT
168874 AAGCATCATCTTGTGTAGTTATACTTCAGCATAGTCTTTGGAATGTTGGTGATGATAATCTTCAA
326 AAGCATCATCTTGTGTAGTTATACTTCAGCATAGTCTTTGGAATGTTGGTGATGATAATCTTCAA
168939 ATATCCTTGTTGTGAATTGTGATTAGTGGTTTTCTGCAACTTTTTGTTGAATGTACAGGGAACAC
391 ATATCCTTGTTGTGAATTGTGATTAGTGGTTTTCTGCAACTTTTTGTTGAATGTACAGGGAACAC
169004 TTAGAGATCTTAGTAAAGGAGGAAGGAGTCTTTCCATGGACCAAACTGAGCCTG
456 TTAGAGATCTTAGTAAAGGAGGAAGGAGTCTTTCCATGGACCAAACTGAGCCTG
169058 TAAGTATCAT
Statistics
Matches: 507, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
508 496 0.98
509 11 0.02
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (509 bp):
AGTTTGCGTCTTTAAAGGAAAGTACCAGTACTTCAAGCTGGAATTCCTCGCAAACTGACCTTCAT
GATGGTACTCGTTGTCTAGAAACTGTGTGAGTTCCAAACTTGCATGTTGCCAGGTTATTTGGATA
TATGTTTCATGTTGAACCTTTTTAAGAATAATGTCTTCAATGTGTTTTAGTGTCCGGAGATGTCA
ACATTGTGGTGTTAGTGAAAATAATACTCCAGCAATGCGTCGTGGTCCTGCTGGTCCAAGGACTT
TATGTAATGCGTGTGGGCTTATGTGGGCTAATAAGGTCTGCTTGTTCCGATAGTTTTTTTTTATT
AAGCATCATCTTGTGTAGTTATACTTCAGCATAGTCTTTGGAATGTTGGTGATGATAATCTTCAA
ATATCCTTGTTGTGAATTGTGATTAGTGGTTTTCTGCAACTTTTTGTTGAATGTACAGGGAACAC
TTAGAGATCTTAGTAAAGGAGGAAGGAGTCTTTCCATGGACCAAACTGAGCCTG
Found at i:179419 original size:179 final size:178
Alignment explanation
Indices: 179015--179423 Score: 418
Period size: 178 Copynumber: 2.3 Consensus size: 178
179005 AAATTGAAGG
* * * * *
179015 CATATAGTGACAACTTTTGTAACTAGAAGTTTTAGTAACTATGAC-AAAAAAGTTGTCACAACAA
1 CATATAGTGACAAATTTTGTAACTATAAG-TTTAATAATTATTACAAAAAAAGTTGTCACAACAA
* * *** *
179079 ATAATGAGATTTAGATTTGTTGTGACAAATTTTGTTTGTAATTATATGTTTTAATTATAGTAACA
65 ATAATGAGATTAAGATTTGTTGTGAAAAACAATGTTTGTAATTATATGTTTTAATTATAATAACA
* *
179144 AAATGTATAGTCACAAATGATTATCTCCAATTTTTGGTAAAAACAAAAT
130 AAATATATAGTCACAAATGATTATCCCCAATTTTTGGTAAAAACAAAAT
* * * * * *
179193 CATATAGTGACATATTTTGTAACTATAAACTATAATTATTGTTACAAAAAAATTTGTCACAACAA
1 CATATAGTGACAAATTTTGTAACTAT-AAGTTTAATAATTATTACAAAAAAAGTTGTCACAACAA
* * ** *
179258 ATATTGAGATTCAAG-TTT-TTAGT-AAAAACAATGTTTTTCGTTATATGTTTTAATTATAATGA
65 ATAATGAGATT-AAGATTTGTT-GTGAAAAACAATGTTTGTAATTATATGTTTTAATTATAATAA
* * **
179320 CAAAATATATTGTCACAAA-GATTTTCCCCCATATTTTTTGCG-CCAAA-AAAAT
128 CAAAATATATAGTCACAAATGATTAT-CCCCA-A-TTTTTG-GTAAAAACAAAAT
* *
179372 TATATAATGACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAAA
1 CATATAGTGACAAATTTTGTAACTATAAGT-TTAATAATTATTACAAAAAAA
179424 CATTAACACA
Statistics
Matches: 187, Mismatches: 35, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
177 5 0.03
178 88 0.47
179 82 0.44
180 11 0.06
181 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (178 bp):
CATATAGTGACAAATTTTGTAACTATAAGTTTAATAATTATTACAAAAAAAGTTGTCACAACAAA
TAATGAGATTAAGATTTGTTGTGAAAAACAATGTTTGTAATTATATGTTTTAATTATAATAACAA
AATATATAGTCACAAATGATTATCCCCAATTTTTGGTAAAAACAAAAT
Found at i:180158 original size:27 final size:28
Alignment explanation
Indices: 180112--180177 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
180102 TTATACTATA
180112 AAAAAT-TTATCCCTATTTTTTGGTGCC
1 AAAAATGTTATCCCTATTTTTTGGTGCC
*
180139 AAAAATGTTATCCTTATTTTTTGGTGCC
1 AAAAATGTTATCCCTATTTTTTGGTGCC
180167 AAAAATGTTAT
1 AAAAATGTTAT
180178 ATAGTAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 6 0.16
28 31 0.84
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (28 bp):
AAAAATGTTATCCCTATTTTTTGGTGCC
Found at i:180827 original size:329 final size:333
Alignment explanation
Indices: 180420--181083 Score: 1282
Period size: 329 Copynumber: 2.0 Consensus size: 333
180410 ATATTACCAA
*
180420 AATGTTTTCATTTATTTTTTACGAAGCTAGTTTAAAATAAAAGATAATTAAAAAATATATTATCA
1 AATGTTTTCATTTATTTTTTACGAAGCTAGTTTAAAATAAAAGATAATAAAAAAATATATTATCA
180485 AAATAGTTAAAATGAAAATTAAATTTCTAAAAAATTGAACAAAATATATTAACCAAAGTAGGAGA
66 AAATAGTTAAAATGAAAATTAAATTTCTAAAAAATTGAACAAAATATATTAACCAAAGTAGGAGA
180550 AATTTCCTATTATTTTTTTACATTAAGTTTAGGTGAAGTTTACTTCCGTCAATCATGTTATATTC
131 AATTTCCTATTATTTTTTTACATTAAGTTTAGGTGAAGTTTACTTCCGTCAATCATGTTATATTC
180615 ACTACAAAGTTCTTCTTAGTTGTATAACTACTTTTTACAA-TTTT-TTAAACAGTTTCATAATGG
196 ACTACAAAGTTCTTCTTAGTTGTATAACTACTTTTTACAATTTTTATTAAACAGTTTCATAATGG
180678 TTAACGATAG-AATCATTGATTAAAGGGTC-TATTGAATGCAACAATAATTCGATGGCTAAATTG
261 TTAACGATAGAAATCATTGATTAAAGGGTCATATTGAATGCAACAATAATTCGATGGCTAAATTG
180741 ATATTTTC
326 ATATTTTC
180749 AATGTTTTCATTTATTTTTTACGAAGCTAGTTTAAAATAAAAGATAATAAAAAAATATATTATCA
1 AATGTTTTCATTTATTTTTTACGAAGCTAGTTTAAAATAAAAGATAATAAAAAAATATATTATCA
180814 AAATAGTTAAAATGAAAATTAAATTTCTAAAAAATTGAACAAAATATATTAACCAAAGTAGGAGA
66 AAATAGTTAAAATGAAAATTAAATTTCTAAAAAATTGAACAAAATATATTAACCAAAGTAGGAGA
180879 AATTTCCTATTATTTTTTTACATTAAGTTTAGGTGAAGTTTACTTCCGTCAATCATGTTATATTC
131 AATTTCCTATTATTTTTTTACATTAAGTTTAGGTGAAGTTTACTTCCGTCAATCATGTTATATTC
180944 ACTACAAAGTTCTTCTTAGTTGTATAACTACTTTTTACAATTTTTTATTAAACAGTTTCATAATG
196 ACTACAAAGTTCTTCTTAGTTGTATAACTACTTTTTACAA-TTTTTATTAAACAGTTTCATAATG
181009 GTTAACGATAGAAATCATTGATTAAAGGGTCATATTGAATGCAACAATAATTCGATGGCTAAATT
260 GTTAACGATAGAAATCATTGATTAAAGGGTCATATTGAATGCAACAATAATTCGATGGCTAAATT
181074 GATATTTTC
325 GATATTTTC
181083 A
1 A
181084 CAAAAGTACA
Statistics
Matches: 329, Mismatches: 1, Indels: 5
0.98 0.00 0.01
Matches are distributed among these distances:
329 234 0.71
331 4 0.01
332 29 0.09
333 19 0.06
334 43 0.13
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (333 bp):
AATGTTTTCATTTATTTTTTACGAAGCTAGTTTAAAATAAAAGATAATAAAAAAATATATTATCA
AAATAGTTAAAATGAAAATTAAATTTCTAAAAAATTGAACAAAATATATTAACCAAAGTAGGAGA
AATTTCCTATTATTTTTTTACATTAAGTTTAGGTGAAGTTTACTTCCGTCAATCATGTTATATTC
ACTACAAAGTTCTTCTTAGTTGTATAACTACTTTTTACAATTTTTATTAAACAGTTTCATAATGG
TTAACGATAGAAATCATTGATTAAAGGGTCATATTGAATGCAACAATAATTCGATGGCTAAATTG
ATATTTTC
Found at i:182494 original size:20 final size:21
Alignment explanation
Indices: 182469--182523 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 21
182459 ACTGACCTAC
182469 AATATTTTAAAAATATTA-TT
1 AATATTTTAAAAATATTATTT
182489 AATATTTT--AAAT-TTATTT
1 AATATTTTAAAAATATTATTT
*
182507 ATTATTTTAAAAATATT
1 AATATTTTAAAAATATT
182524 TCCTTCATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 3 0.10
18 13 0.43
20 12 0.40
21 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATATTTTAAAAATATTATTT
Found at i:183183 original size:19 final size:19
Alignment explanation
Indices: 183140--183177 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
183130 CTTAATCGCG
183140 AAAATTAAAAAATTAAATT
1 AAAATTAAAAAATTAAATT
* *
183159 AAAATTTAAAAATTCAATT
1 AAAATTAAAAAATTAAATT
183178 CGAATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTAAAAAATTAAATT
Found at i:183274 original size:3 final size:3
Alignment explanation
Indices: 183266--183300 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
183256 AGGAAAGAAA
*
183266 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
183301 CAAAAACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:183341 original size:9 final size:9
Alignment explanation
Indices: 183269--183347 Score: 65
Period size: 9 Copynumber: 9.0 Consensus size: 9
183259 AAAGAAAAAT
*
183269 AATAATAAT
1 AATAATAAA
*
183278 AATAATAAT
1 AATAATAAA
183287 AATAATAAA
1 AATAATAAA
*
183296 AATAACAAA
1 AATAATAAA
* *
183305 AACATTAAA
1 AATAATAAA
* *
183314 TA-AATCAGA
1 AATAAT-AAA
183323 AAT-A-AAA
1 AATAATAAA
183330 AATAATAAA
1 AATAATAAA
183339 AATAATAAA
1 AATAATAAA
183348 GGAAATGAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
7 5 0.09
8 3 0.05
9 48 0.86
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.23
Consensus pattern (9 bp):
AATAATAAA
Found at i:184769 original size:13 final size:13
Alignment explanation
Indices: 184751--184788 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
184741 ATAATAATTG
184751 TACAATATATATA
1 TACAATATATATA
184764 TACAATATAATATA
1 TACAATAT-ATATA
184778 TA-AATATATAT
1 TACAATATATAT
184789 GTTTATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 4 0.17
13 13 0.54
14 7 0.29
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (13 bp):
TACAATATATATA
Found at i:185730 original size:106 final size:106
Alignment explanation
Indices: 185546--186667 Score: 1745
Period size: 106 Copynumber: 10.6 Consensus size: 106
185536 GCATTGTTCC
* * * * * * *
185546 GAGTTCAATATCCTCCG-TCGTGAAGTTGAAATTGACTCTGGAACTG-GAAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTATTGAC
* * * *
185609 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
185652 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGACGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
185717 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
185758 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
185823 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
185864 GAGTCCAATATCTTTCACTGTGAAGTTGAAATTGCCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
185929 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
185970 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
186035 CCAACGGTCCCTTCGTCGTGAAGTTTAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
186076 GAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
186141 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTT--G-CGTTGTCTG
*
186185 GAGTCCAATATCCTTCGTTGTGAAGTTG----TGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
186246 CCAGCGGTCCCTTCGTCGTGAAGTCGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
186287 GAGTCCAATATCCTT-GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
186351 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
186392 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
186457 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
186498 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTATGGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
186563 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
186604 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACA
186668 GACAACTTTT
Statistics
Matches: 944, Mismatches: 62, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
101 12 0.01
102 23 0.02
103 1 0.00
105 147 0.16
106 723 0.77
107 2 0.00
108 1 0.00
109 35 0.04
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:190419 original size:19 final size:19
Alignment explanation
Indices: 190376--190413 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
190366 CTTAATCGCG
190376 AAAATTAAAAAATTAAATT
1 AAAATTAAAAAATTAAATT
* *
190395 AAAATTTAAAAATTCAATT
1 AAAATTAAAAAATTAAATT
190414 CGAATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTAAAAAATTAAATT
Found at i:190509 original size:3 final size:3
Alignment explanation
Indices: 190501--190569 Score: 115
Period size: 3 Copynumber: 23.7 Consensus size: 3
190491 AAGAAAAGAA
190501 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
190549 AAT AA- AAT AA- AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
190570 CAAAATAACA
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 4 0.06
3 58 0.94
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:190618 original size:9 final size:9
Alignment explanation
Indices: 190499--190624 Score: 98
Period size: 9 Copynumber: 14.2 Consensus size: 9
190489 AAAAGAAAAG
190499 AAAATAATA
1 AAAATAATA
*
190508 ATAATAATA
1 AAAATAATA
*
190517 ATAATAATA
1 AAAATAATA
*
190526 ATAATAATA
1 AAAATAATA
*
190535 ATAATAATA
1 AAAATAATA
*
190544 ATAATAATA
1 AAAATAATA
*
190553 AAATAAAATA
1 AAA-ATAATA
*
190563 AAAATAA-C
1 AAAATAATA
*
190571 AAAATAACA
1 AAAATAATA
* *
190580 AAAACATTA
1 AAAATAATA
*
190589 AATA-AATCA
1 AAAATAAT-A
*
190598 GAAAT-A-A
1 AAAATAATA
190605 AAAATAATA
1 AAAATAATA
190614 AAAATAATA
1 AAAATAATA
190623 AA
1 AA
190625 GGAAATGAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
7 5 0.05
8 10 0.10
9 74 0.76
10 8 0.08
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (9 bp):
AAAATAATA
Found at i:192119 original size:16 final size:16
Alignment explanation
Indices: 192098--192130 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
192088 TGTGTGTACA
192098 ATTAGTTAGTTATATT
1 ATTAGTTAGTTATATT
*
192114 ATTAGTTATTTATATT
1 ATTAGTTAGTTATATT
192130 A
1 A
192131 ATTATGTGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (16 bp):
ATTAGTTAGTTATATT
Found at i:195163 original size:42 final size:45
Alignment explanation
Indices: 195081--195172 Score: 109
Period size: 42 Copynumber: 2.1 Consensus size: 45
195071 TTTAATTTTG
* * * *
195081 TTTTTCGAGTAAATGTATGCGAACTAGAGATCATGTGGTTA-GGT
1 TTTTTCGAATAAATGTATACGAACTAGAGATCATGCGGTTATGAT
* *
195125 TTTTTCGAAT-AA-GTATACGAATTAGATATCATGCGGTTATGAT
1 TTTTTCGAATAAATGTATACGAACTAGAGATCATGCGGTTATGAT
195168 TTTTT
1 TTTTT
195173 GTGAATAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 23 0.56
43 9 0.22
44 9 0.22
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (45 bp):
TTTTTCGAATAAATGTATACGAACTAGAGATCATGCGGTTATGAT
Found at i:200673 original size:45 final size:45
Alignment explanation
Indices: 200558--201190 Score: 640
Period size: 45 Copynumber: 14.0 Consensus size: 45
200548 GAAACTTAAA
* * * *
200558 CTTGACTTTCTCGTGGAGAGGATTTAATCTTTTAGTGTTTATCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG-TTGTCATT
* * * *
200604 CTTGACTTTCTCGCGAGGAGGAGTCAATCTTTTAGTGTTTTCCTT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATT
* * *
200649 CTTGACTTTCTCGTGAAGATGAGTCAATCTTTCAGTGTTGTCACT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATT
* * * *
200694 CTTGAGC-TTCTCGTGAGGAGGAGTTAATCTTTTAGTGTTATCCTT
1 CTTGA-CTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATT
* * *
200739 CTTGATTTTCTCGTAAAGAGGAGTCAATCTTTTAGTGTTGTTATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATT
* * * *
200784 CTTGACTTTCTC-TCGAGGATGAGTCAATCTTTTAGTGTTATCCTT
1 CTTGACTTTCTCGT-GAAGAGGAGTCAATCTTTTAGTGTTGTCATT
* * * *
200829 CTTGACTTTCTCGTGAAAAGGAGTCAATATTTCAATGTTGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATT
* * * * *
200874 CTTGAATTTCTCCTGACGAGGAGTCAATCTTTCAGTGTTGTTATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATT
* *
200919 CTTGACTTTCTCGTGATGAGGAGTCAATCTTTTAGTGTTGTCCTT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATT
* * * * *
200964 CTGGACTTTCTCATGAAGAGGAGTTAATCTTTCAGTGTTTTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATT
* * * *
201009 CTTGACTTTCTCGCGAGGAGGAGTTAATCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATT
* * * * * *
201054 TTTAACTTTCTCGCGAAGAAGAGTCAACCTTTTAGTGTTGTAATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATT
* ** * * * * *
201099 CTTAACTTTCTCACGAAAATGAGTCTACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATT
* * * ** * * * *
201144 ATTAACTTTCTCGAGAAGAACAATAAACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATT
201189 CT
1 CT
201191 CAACTTGACT
Statistics
Matches: 488, Mismatches: 95, Indels: 9
0.82 0.16 0.02
Matches are distributed among these distances:
44 1 0.00
45 453 0.93
46 34 0.07
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (45 bp):
CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATT
Found at i:202163 original size:133 final size:133
Alignment explanation
Indices: 201988--202392 Score: 379
Period size: 133 Copynumber: 3.1 Consensus size: 133
201978 TACCCTAAAA
* * * * * *
201988 AGTGGAACAACTTATTCTTCTTTTAGATTTGGTCTTCTTATAGAGAAACGAAGAAAATCA-ATTC
1 AGTGGAGCAAATTCTTCTTCTTTCAGATTTGGTATTCCTATAGAGAAACGAAGAAAATCACATT-
* * * * * * ** *
202052 CGATTTAATCTTCCTTGAAGAGCAGCAAAGTGGATCAAATTAATATGTGCCTGGTCTCCCCTAAA
65 CGATTCAATATTCCCTGAAGAACAACAAAGTGGATCAAAATAATACATGCCTGATCTCCCCTAAA
202117 GAGT
130 GAGT
* * * *
202121 AGTGGAGCAAATTCTTCTTCTTCCAGATTTGGTTTTCCTATAGTGCAAA-GAAGAAAATCACGTT
1 AGTGGAGCAAATTCTTCTTCTTTCAGATTTGGTATTCCTATAGAG-AAACGAAGAAAATCACATT
** * **
202185 CGATTCAATATTCCCTGAAGAACAATGAAGTGGATCAAAATATTACATGTTTGATCTCCCCTAAA
65 CGATTCAATATTCCCTGAAGAACAACAAAGTGGATCAAAATAATACATGCCTGATCTCCCCTAAA
202250 GAGT
130 GAGT
** * * * * *
202254 AGTGGAGCATTTTCTTCTTCTTTCAGATTTGGTATTCCTGTAGAGAAGCGAAGCATATCACGTAT
1 AGTGGAGCAAATTCTTCTTCTTTCAGATTTGGTATTCCTATAGAGAAACGAAGAAAATCACAT-T
* *** * * ** *
202319 -GATTCAATATTCCCTGAAGAGCAGTGAAGTGCATCAAAAT-TTACGA-GTATGACCTCCCCTAA
65 CGATTCAATATTCCCTGAAGAACAACAAAGTGGATCAAAATAATAC-ATGCCTGATCTCCCCTAA
202381 AGAGT
129 AGAGT
202386 AGTGGAG
1 AGTGGAG
202393 TAGACCCACA
Statistics
Matches: 230, Mismatches: 37, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
132 32 0.14
133 192 0.83
134 6 0.03
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (133 bp):
AGTGGAGCAAATTCTTCTTCTTTCAGATTTGGTATTCCTATAGAGAAACGAAGAAAATCACATTC
GATTCAATATTCCCTGAAGAACAACAAAGTGGATCAAAATAATACATGCCTGATCTCCCCTAAAG
AGT
Found at i:202440 original size:132 final size:133
Alignment explanation
Indices: 202107--202465 Score: 345
Period size: 133 Copynumber: 2.7 Consensus size: 133
202097 TGTGCCTGGT
* * ** * * *
202107 CTCCCCTAAAGAGTAGTGGAGCA-AATTCTTCTTCTTCCAGATTTGGTTTTCCT-ATAGTGCAA-
1 CTCCCCTAAAGAGTAGTGGAGCATGA-CCCACTTCTTTCAGATTTGGTATTCCTGA-AGAG-AAG
* * *
202169 AGAAGAAAATCACGTTCGATTCAATATTCCCTGAAGAACAATGAAGTGGATCAAAATATTACATG
63 CGAAGCAAATCACGTTCGATTCAATATTCCCTGAAGAACAATGAAGTGCATCAAAATATTACATG
* *
202234 TTTGAT
128 TATGAC
*** ** *
202240 CTCCCCTAAAGAGTAGTGGAGCATTTTCTTCTTCTTTCAGATTTGGTATTCCTGTAGAGAAGCGA
1 CTCCCCTAAAGAGTAGTGGAGCATGACCCACTTCTTTCAGATTTGGTATTCCTGAAGAGAAGCGA
* * *
202305 AGCATATCACGTAT-GATTCAATATTCCCTGAAGAGCAGTGAAGTGCATCAAAAT-TTACGA-GT
66 AGCAAATCACGT-TCGATTCAATATTCCCTGAAGAACAATGAAGTGCATCAAAATATTAC-ATGT
202367 ATGAC
129 ATGAC
* * * * * *
202372 CTCCCCTAAAGAGTAGTGGAGTA-GACCCACATTCTTTCATATTTGGTCTTTCTGAAGAGCAGTG
1 CTCCCCTAAAGAGTAGTGGAGCATGACCCAC-TTCTTTCAGATTTGGTATTCCTGAAGAGAAGCG
* * *
202436 AAGCAAATCAAGTTCGATTTAATCTTCCCT
65 AAGCAAATCACGTTCGATTCAATATTCCCT
202466 AAATAGTAGC
Statistics
Matches: 189, Mismatches: 30, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
131 3 0.02
132 84 0.44
133 101 0.53
134 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (133 bp):
CTCCCCTAAAGAGTAGTGGAGCATGACCCACTTCTTTCAGATTTGGTATTCCTGAAGAGAAGCGA
AGCAAATCACGTTCGATTCAATATTCCCTGAAGAACAATGAAGTGCATCAAAATATTACATGTAT
GAC
Found at i:206221 original size:14 final size:13
Alignment explanation
Indices: 206204--206233 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
206194 ACATATTAAT
206204 AATATATAGAAATA
1 AATATATA-AAATA
206218 AATATATAAAATA
1 AATATATAAAATA
206231 AAT
1 AAT
206234 GCGTAAAGTC
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:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AATATATAAAATA
Found at i:206276 original size:9 final size:8
Alignment explanation
Indices: 206261--206377 Score: 87
Period size: 8 Copynumber: 14.0 Consensus size: 8
206251 AGATATAAAT
206261 ATAATATA
1 ATAATATA
206269 ATTAATATA
1 A-TAATATA
*
206278 ATAATAGA
1 ATAATATA
*
206286 AAAATATA
1 ATAATATA
*
206294 GAT-GTATTA
1 -ATAATA-TA
206303 ATAATATA
1 ATAATATA
*
206311 AAAATATA
1 ATAATATA
206319 AT-ATATA
1 ATAATATA
206326 TATATATATA
1 -ATA-ATATA
206336 ATGAATA-A
1 AT-AATATA
* *
206344 AAAATTTA
1 ATAATATA
206352 TATAATATAA
1 -ATAATAT-A
206362 ATAATATA
1 ATAATATA
206370 ATAATATA
1 ATAATATA
206378 TTACATAAGA
Statistics
Matches: 86, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
7 8 0.09
8 41 0.48
9 30 0.35
10 7 0.08
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (8 bp):
ATAATATA
Found at i:206291 original size:25 final size:25
Alignment explanation
Indices: 206263--206377 Score: 75
Period size: 25 Copynumber: 4.6 Consensus size: 25
206253 ATATAAATAT
206263 AATATAATTAATATAATAATAGAAA
1 AATATAATTAATATAATAATAGAAA
*
206288 AATATAGATGT-AT-TAATAATATAAA
1 AATATA-AT-TAATATAATAATAGAAA
206313 AATATAA-TATATATATATATATAATGAATA
1 AATATAATTA-ATATA-ATA-AT-A-GAA-A
* *
206343 AA-A-AATTTATATAAT-ATA-AAT
1 AATATAATTAATATAATAATAGAAA
206364 AATATAA-TAATATA
1 AATATAATTAATATA
206378 TTACATAAGA
Statistics
Matches: 72, Mismatches: 5, Indels: 29
0.68 0.05 0.27
Matches are distributed among these distances:
21 2 0.03
22 10 0.14
23 2 0.03
24 4 0.06
25 27 0.38
26 7 0.10
27 5 0.07
28 8 0.11
29 4 0.06
30 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (25 bp):
AATATAATTAATATAATAATAGAAA
Found at i:206291 original size:30 final size:29
Alignment explanation
Indices: 206257--206375 Score: 95
Period size: 30 Copynumber: 3.9 Consensus size: 29
206247 GTATAGATAT
206257 AAATATAATATAATTAATATAATAATAGAA
1 AAATATAATATAATTAATATAATAATA-AA
*
206287 AAATATAGATGT-ATT-A-ATAAT-AT-AA
1 AAATATA-ATATAATTAATATAATAATAAA
206312 AAATATAATATATATATATATATAATGAATAAAA
1 AAATATAATATA-AT-TA-ATATAAT-AAT-AAA
*
206346 AATTTATATAATATAAATAATATAATAATA
1 AA---ATATAATATAATTAATATAATAATA
206376 TATTACATAA
Statistics
Matches: 72, Mismatches: 3, Indels: 26
0.71 0.03 0.26
Matches are distributed among these distances:
24 3 0.04
25 9 0.12
26 2 0.03
27 3 0.04
28 5 0.07
29 2 0.03
30 15 0.21
31 3 0.04
32 3 0.04
33 3 0.04
34 11 0.15
35 2 0.03
36 1 0.01
37 10 0.14
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
AAATATAATATAATTAATATAATAATAAA
Found at i:207765 original size:135 final size:131
Alignment explanation
Indices: 207523--208263 Score: 366
Period size: 135 Copynumber: 5.5 Consensus size: 131
207513 TCCCTTTTAC
* * * * * * * * *
207523 GAGTTAAGTCAAATCTGGATGCTCTTCGAGTCTAATATTCTTCATCATG-AAGTTCAAATTTGAG
1 GAGTTAAGT-AATTTTGGATGTTCTTCGAGCCCAATATCCTTCTTC--GCAAGTTGAAATTTGAC
* * ** * * *
207587 TCAAAAACT-TTGACTGGAAAATAGCTCATCACTATTAAGTTAAGCTAAATTGCACTTGACTCTT
63 T-AAAAAATATTGACTGGAAAATAGTTCATCGTTGTTGAGTTAAGCTAAATTGCA-ATGA-TCTT
207651 CCATTAT
125 CCATTAT
* *
207658 GAGTTAAGTAGATTTTGGGTGTTCTTTGAGCCCAATATCCTTCTTCGTCAAGTTGAAATTTGACT
1 GAGTTAAGTA-ATTTTGGATGTTCTTCGAGCCCAATATCCTTCTTCG-CAAGTTGAAATTTGACT
* * *
207723 AAAAAATATTGACTGGAAAATAGTTCCTCGTTGTTGAGTTAAGCTAGATTACAAATGA-C-T-C-
64 AAAAAATATTGACTGGAAAATAGTTCATCGTTGTTGAGTTAAGCTAAATTGC-AATGATCTTCCA
*
207784 TTGT
128 TTAT
* * * * * * * *
207788 GAATTAAGTCGATTTTGGATGTGCCTTCGAACCCAATATCCTTCAATACG-AAGTTAAAATTGGT
1 GAGTTAAGT-AATTTTGGATGT-TCTTCGAGCCCAATATCCTTC--TTCGCAAGTTGAAATTTGA
* * * * * * * * *
207852 CTTTAAAAA-CTTGACTGGAAAATAGCTCATCGTTTTTTAGTTAAGCTAGACTGAAGATGAGTCC
62 C-TAAAAAATATTGACTGGAAAATAGTTCATCGTTGTTGAGTTAAGCTAAATTGCA-ATGA-TCT
207916 TCCA--AT
124 TCCATTAT
* * *** * *
207922 GAGATTTAAGTTAATTTTGGGTGTTC-ACTGAGTTGAATATCCTTCATCGCGAAGTTGAAATTTA
1 GAG--TTAAG-TAATTTTGGATGTTCTTC-GAGCCCAATATCCTTCTTCGC-AAGTTGAAATTTG
** * * * * *
207986 ACTAAAAAACCTTGACTGAAAAATAAATT-TTTGTTGTTGAGTTAAGCTAAATTGC-AGGAATCT
61 ACTAAAAAATATTGACTGGAAAAT-AGTTCATCGTTGTTGAGTTAAGCTAAATTGCAATG-ATCT
*
208049 TCTATTAT
124 TCCATTAT
** * *
208057 GAGTTAAGTCAATTTTTGGATGTTCTTCGAGTTCAATATCCTTTTTCATG-AAATTGAAATTTGA
1 GAGTTAAGT-AA-TTTTGGATGTTCTTCGAGCCCAATATCCTTCTTC--GCAAGTTGAAATTTGA
* * * ** *
208121 CTAGAAAATATTGGCTAGAAAATA-TCTCATTC-TTGTTGAGTTAAGAAAAATTGTAAATGAATC
62 CTAAAAAATATTGACTGGAAAATAGT-TCA-TCGTTGTTGAGTTAAGCTAAATTG-CAATG-ATC
* * *
208184 CTCTATTGT
123 TTCCATTAT
* * ** * * * *
208193 GAGTTAAGTCGATTTT-AACATTCTTCGAGTCTAATATTCTTCGTCATG-AAGTTGAAATTTGAC
1 GAGTTAAGT-AATTTTGGATGTTCTTCGAGCCCAATATCCTTCTTC--GCAAGTTGAAATTTGAC
*
208256 TCAAAAAT
63 TAAAAAAT
208264 TGGAAATTTT
Statistics
Matches: 465, Mismatches: 104, Indels: 75
0.72 0.16 0.12
Matches are distributed among these distances:
130 22 0.05
131 72 0.15
132 9 0.02
133 24 0.05
134 138 0.30
135 156 0.34
136 43 0.09
137 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (131 bp):
GAGTTAAGTAATTTTGGATGTTCTTCGAGCCCAATATCCTTCTTCGCAAGTTGAAATTTGACTAA
AAAATATTGACTGGAAAATAGTTCATCGTTGTTGAGTTAAGCTAAATTGCAATGATCTTCCATTA
T
Found at i:208143 original size:134 final size:133
Alignment explanation
Indices: 208005--208256 Score: 283
Period size: 134 Copynumber: 1.9 Consensus size: 133
207995 CCTTGACTGA
** * ** * *
208005 AAAATAAATTTTTGTTGTTGAGTTAAGCTAAATTG-CAGGAATCTTCTATTATGAGTTAAGTCAA
1 AAAATAAATCATTCTTGTTGAGTTAAGAAAAATTGAAAGGAATCCTCTATTATGAGTTAAGTCAA
* ** **
208069 TTTTTGGATGTTCTTCGAGT-TCAATATCCTTTTTCATGAAATTGAAATTTGACTAGAAAATATT
66 -TTTT-AACATTCTTCGAGTCT-AATATCCTTCGTCATGAAATTGAAATTTGACTAGAAAATATT
208133 GGCTAG
128 GGCTAG
** * * *
208139 AAAATATCTCATTCTTGTTGAGTTAAGAAAAATTGTAAATGAATCCTCTATTGTGAGTTAAGTCG
1 AAAATAAATCATTCTTGTTGAGTTAAGAAAAATTG-AAAGGAATCCTCTATTATGAGTTAAGTCA
* *
208204 ATTTTAACATTCTTCGAGTCTAATATTCTTCGTCATGAAGTTGAAATTTGACT
65 ATTTTAACATTCTTCGAGTCTAATATCCTTCGTCATGAAATTGAAATTTGACT
208257 CAAAAATTGG
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
134 67 0.70
135 5 0.05
136 24 0.25
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (133 bp):
AAAATAAATCATTCTTGTTGAGTTAAGAAAAATTGAAAGGAATCCTCTATTATGAGTTAAGTCAA
TTTTAACATTCTTCGAGTCTAATATCCTTCGTCATGAAATTGAAATTTGACTAGAAAATATTGGC
TAG
Found at i:235417 original size:2 final size:2
Alignment explanation
Indices: 235405--235444 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
235395 TGGTTTTCTG
*
235405 AT AT AT GT 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 AT AT
235445 CTTATGAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:248103 original size:24 final size:24
Alignment explanation
Indices: 248076--248131 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
248066 CTATTTTTTC
248076 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
248100 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
248124 GCTTCAAT
1 GCTTCAAT
248132 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:248390 original size:30 final size:30
Alignment explanation
Indices: 248354--248419 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
248344 AGTGAACCGG
* *
248354 CGGTTCAAACCGGTTTTGCCGGTTTTCAGC
1 CGGTTCAAACCAGTTTTCCCGGTTTTCAGC
** *
248384 CGGTTCACCCCAGTTTTCCCGGTTTTCAGT
1 CGGTTCAAACCAGTTTTCCCGGTTTTCAGC
248414 CGGTTC
1 CGGTTC
248420 TTCCGGTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.11, C:0.30, G:0.24, T:0.35
Consensus pattern (30 bp):
CGGTTCAAACCAGTTTTCCCGGTTTTCAGC
Found at i:254753 original size:17 final size:18
Alignment explanation
Indices: 254731--254769 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
254721 AATTTAAAAA
*
254731 TTTAATATTTCCT-TTAT
1 TTTAATATTTACTCTTAT
*
254748 TTTAATTTTTACTCTTAT
1 TTTAATATTTACTCTTAT
254766 TTTA
1 TTTA
254770 TTTTATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTAATATTTACTCTTAT
Found at i:255960 original size:64 final size:65
Alignment explanation
Indices: 255824--255984 Score: 172
Period size: 64 Copynumber: 2.5 Consensus size: 65
255814 ATTATTCAGT
*
255824 GTGTATCGATGCACAGGAAGTGTATCGATGCA-CCCATTAAAAATGGAAACATCGAATGCAGTTA
1 GTGTATCGATGCATAGGAAGTGTATCGATGCACCCCATTAAAAATGGAAACATCGAATGCAGTTA
* * *
255888 ATGCATCGATGCATAAGG-AGTGTATCGATGCACCCCCTT-AAAAT-GAAAGCATCGAAGGTG-A
1 GTGTATCGATGCAT-AGGAAGTGTATCGATGCACCCCATTAAAAATGGAAA-CATCGAA--TGCA
*
255949 -TTG
62 GTTA
* * *
255952 GTGTATCGATGCATTGGTAGTGCATCGATGCAC
1 GTGTATCGATGCATAGGAAGTGTATCGATGCAC
255985 ATGTTAAAGA
Statistics
Matches: 82, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
63 6 0.07
64 65 0.79
65 9 0.11
66 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (65 bp):
GTGTATCGATGCATAGGAAGTGTATCGATGCACCCCATTAAAAATGGAAACATCGAATGCAGTTA
Found at i:256017 original size:20 final size:20
Alignment explanation
Indices: 255992--256029 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
255982 CACATGTTAA
255992 AGAATGCATCGATGCACTCT
1 AGAATGCATCGATGCACTCT
*
256012 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
256030 TCAAGAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTCT
Found at i:256672 original size:22 final size:21
Alignment explanation
Indices: 256629--256673 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
256619 TGTGAACATG
* **
256629 TGAATTATATGAAAAGTGATA
1 TGAATTACATGAAAAGCCATA
256650 TGAATTACATGAAAAAGCCATA
1 TGAATTACATG-AAAAGCCATA
256672 TG
1 TG
256674 TCTACATGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.29
Consensus pattern (21 bp):
TGAATTACATGAAAAGCCATA
Found at i:256747 original size:25 final size:27
Alignment explanation
Indices: 256706--256757 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
256696 GCTATGAGCT
*
256706 TATATGAACATGTGAT-A-TGAAAATG
1 TATATGAACATGAGATAAGTGAAAATG
256731 TATAGTGAA-ATGAGATAAGTGAAAATG
1 TATA-TGAACATGAGATAAGTGAAAATG
256758 CCTATGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 10 0.43
26 5 0.22
27 8 0.35
ACGTcount: A:0.46, C:0.02, G:0.23, T:0.29
Consensus pattern (27 bp):
TATATGAACATGAGATAAGTGAAAATG
Found at i:257779 original size:28 final size:27
Alignment explanation
Indices: 257741--257834 Score: 125
Period size: 27 Copynumber: 3.4 Consensus size: 27
257731 ACTCCCTTTT
* *
257741 TTTTTTACTTTTTACATTTCTATTTCA
1 TTTTTAACTTTTTACATTTCTCTTTCA
* *
257768 TTTTTAACCTTTTCCATTTCTCTTTCA
1 TTTTTAACTTTTTACATTTCTCTTTCA
*
257795 TTTTTAACTTTTTCTCATTTCTCTTTCA
1 TTTTTAACTTTTT-ACATTTCTCTTTCA
*
257823 TTTGTAACTTTT
1 TTTTTAACTTTT
257835 ACTTTTCCTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
27 35 0.59
28 24 0.41
ACGTcount: A:0.16, C:0.19, G:0.01, T:0.64
Consensus pattern (27 bp):
TTTTTAACTTTTTACATTTCTCTTTCA
Found at i:268599 original size:13 final size:12
Alignment explanation
Indices: 268542--268600 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 12
268532 ATTCTTCATT
268542 ATTCATTTTATTAC
1 ATTCA-TTT-TTAC
268556 TATTCATTCTTTAC
1 -ATTCATT-TTTAC
*
268570 ATTC-TTTTTTC
1 ATTCATTTTTAC
268581 -TTCATTGTTTAC
1 ATTCATT-TTTAC
268593 ATTCATTT
1 ATTCATTT
268601 ATAAATTTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 3 0.08
11 6 0.16
12 7 0.18
13 10 0.26
14 6 0.16
15 6 0.16
ACGTcount: A:0.20, C:0.17, G:0.02, T:0.61
Consensus pattern (12 bp):
ATTCATTTTTAC
Found at i:272632 original size:19 final size:20
Alignment explanation
Indices: 272584--272637 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 20
272574 TTTGTATCAT
*
272584 ATTTCTAT-ATTTT-TAT-A
1 ATTTCTATAATTTTCCATGA
*
272601 ATTTCTATGA-TTTCCATGA
1 ATTTCTATAATTTTCCATGA
*
272620 ATTTTTATAATTTTCCAT
1 ATTTCTATAATTTTCCAT
272638 ATTTCATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 11 0.37
18 3 0.10
19 9 0.30
20 7 0.23
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.57
Consensus pattern (20 bp):
ATTTCTATAATTTTCCATGA
Found at i:273580 original size:44 final size:44
Alignment explanation
Indices: 273476--273583 Score: 128
Period size: 44 Copynumber: 2.5 Consensus size: 44
273466 CTTTATTCTT
*
273476 GATTTCATCACATAAGGAGCTAGATCAACATTACCAATTAGCTC
1 GATTCCATCACATAAGGAGCTAGATCAACATTACCAATTAGCTC
* * * * *
273520 GATTCCATTACGTAAGGAG-TTGAATCAACATTACCACTTCGCTC
1 GATTCCATCACATAAGGAGCTAG-ATCAACATTACCAATTAGCTC
* *
273564 GGTTCCATCGCATAAGGAGC
1 GATTCCATCACATAAGGAGC
273584 ATTTCACTCG
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
43 2 0.04
44 50 0.96
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (44 bp):
GATTCCATCACATAAGGAGCTAGATCAACATTACCAATTAGCTC
Found at i:273852 original size:24 final size:23
Alignment explanation
Indices: 273781--273900 Score: 88
Period size: 24 Copynumber: 5.2 Consensus size: 23
273771 TATACCTAGC
*
273781 ATATTATATATAGTTTGAAATTATGT
1 ATATTATATA-ATTTTGAAA-TA-GT
**
273807 -TA-TATATTTTTTTGAAA-A-T
1 ATATTATATAATTTTGAAATAGT
273826 ATA-TATTATAATTTTGAAAGTAGT
1 ATATTA-TATAATTTTGAAA-TAGT
* * *
273850 ATATTATATAGTTTTGAAAAATT
1 ATATTATATAATTTTGAAATAGT
*
273873 ATATTCTATAATTTTGAAAATAGT
1 ATATTATATAATTTTG-AAATAGT
273897 ATAT
1 ATAT
273901 AGGTTTGGAA
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
19 1 0.01
20 4 0.05
21 12 0.16
23 24 0.32
24 30 0.40
25 4 0.05
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (23 bp):
ATATTATATAATTTTGAAATAGT
Found at i:273857 original size:47 final size:47
Alignment explanation
Indices: 273816--273965 Score: 134
Period size: 47 Copynumber: 3.2 Consensus size: 47
273806 TTATATATTT
*
273816 TTTTG-AAAA-TATATAT-TATAATTTTGAAAGTAGTATATTATATAG
1 TTTTGAAAAATTATAT-TCTATAATTTTGAAAATAGTATATTATATAG
*
273861 TTTTGAAAAATTATATTCTATAATTTTGAAAATAG--TA-TATA-GG
1 TTTTGAAAAATTATATTCTATAATTTTGAAAATAGTATATTATATAG
* * * *
273904 TTTGGAAGTATATATATATATATTTATAATTTTTAAAATAGTATATTATATAT
1 TTTTGAA--A-A-AT-TATAT-TCTATAATTTTGAAAATAGTATATTATATAG
273957 TTTTGAAAA
1 TTTTGAAAA
273966 CATATTATAG
Statistics
Matches: 84, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
43 7 0.08
44 4 0.05
45 8 0.10
46 6 0.07
47 23 0.27
48 5 0.06
49 17 0.20
50 1 0.01
51 3 0.04
52 4 0.05
53 6 0.07
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (47 bp):
TTTTGAAAAATTATATTCTATAATTTTGAAAATAGTATATTATATAG
Found at i:274071 original size:3 final size:3
Alignment explanation
Indices: 274063--274106 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
274053 TAATATCGTT
*
274063 TTA TTA TTA TTA TTA TTA TTA TT- CTA TT- TTA TT- TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
274107 TTTAATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 5 0.14
3 31 0.86
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:275141 original size:3 final size:3
Alignment explanation
Indices: 275122--275172 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
275112 TCACCCGGAC
* * * *
275122 ATT AAT ATT AAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
275170 ATT
1 ATT
275173 TTTGTTTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:277137 original size:19 final size:20
Alignment explanation
Indices: 277113--277158 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
277103 AATTAATCGT
277113 ATTTTTA-TATATGTTTGTA
1 ATTTTTATTATATGTTTGTA
* *
277132 ATTTTTATTTTATTTTTGTA
1 ATTTTTATTATATGTTTGTA
*
277152 TTTTTTA
1 ATTTTTA
277159 ATGGGATCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.72
Consensus pattern (20 bp):
ATTTTTATTATATGTTTGTA
Found at i:277321 original size:23 final size:22
Alignment explanation
Indices: 277295--277338 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
277285 TAAAAAATAA
277295 TTAAATACTTCATTTCTTCCTCC
1 TTAAATACTTCATTT-TTCCTCC
*
277318 TTAAATATTTCATTTTTCCTC
1 TTAAATACTTCATTTTTCCTC
277339 GTGAAATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAATACTTCATTTTTCCTCC
Found at i:277345 original size:22 final size:23
Alignment explanation
Indices: 277297--277345 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
277287 AAAAATAATT
*
277297 AAATACTTCATTTCTTCCTCCTT
1 AAATACTTCATTTCTTCCTCCTG
* *
277320 AAATATTTCATTT-TTCCTCGTG
1 AAATACTTCATTTCTTCCTCCTG
277342 AAAT
1 AAAT
277346 GCAAAGAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (23 bp):
AAATACTTCATTTCTTCCTCCTG
Found at i:288339 original size:15 final size:15
Alignment explanation
Indices: 288288--288349 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
288278 AATAATAATG
*
288288 AAAATGAAAAAAGAA
1 AAAATGAAAAATGAA
* *
288303 GAAA-GAAAACT-AA
1 AAAATGAAAAATGAA
288316 AAAGA-GAAAAGA-GAA
1 AAA-ATGAAAA-ATGAA
288331 AAAATGAAAAATGAA
1 AAAATGAAAAATGAA
288346 AAAA
1 AAAA
288350 GGACAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
13 4 0.11
14 13 0.35
15 20 0.54
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.06
Consensus pattern (15 bp):
AAAATGAAAAATGAA
Found at i:288364 original size:7 final size:7
Alignment explanation
Indices: 288288--288366 Score: 52
Period size: 7 Copynumber: 10.7 Consensus size: 7
288278 AATAATAATG
*
288288 AAAATGA
1 AAAAAGA
288295 AAAAAGA
1 AAAAAGA
*
288302 AGAAAGA
1 AAAAAGA
*
288309 AAACTA-A
1 AAA-AAGA
*
288316 AAAGAGA
1 AAAAAGA
*
288323 AAAGAGA
1 AAAAAGA
288330 AAAAATGA
1 AAAAA-GA
*
288338 AAAATGA
1 AAAAAGA
288345 AAAAAGGACA
1 AAAAA-G--A
288355 AAAAAGA
1 AAAAAGA
288362 AAAAA
1 AAAAA
288367 AAGTAAATAA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
6 1 0.02
7 42 0.72
8 8 0.14
9 1 0.02
10 6 0.10
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (7 bp):
AAAAAGA
Found at i:289987 original size:132 final size:132
Alignment explanation
Indices: 289709--290239 Score: 668
Period size: 132 Copynumber: 4.0 Consensus size: 132
289699 CAATCTTCCT
* * * * *
289709 TGAAGAGCAGTGGAATGAATCAATGTTTCCAGATTTAATCTCCCCTGAAGAGCAGCGGAGCAGAT
1 TGAAGAGTAGTGGAATGAATCAATGTTTCCAGATCTGATCTCCCCTGAAGAGCAACAGAGCAGAT
* * * * *
289774 CCCTCT-TTTCAGACTTGATCTTCCTTGAAGCGCAGTGGAACAAATCTTCCTTGATTCAATATTC
66 CCCTCTCTTTCAGATTTGATCTTCCTTGAGGAGCAGTGGAACAAATCTTCCTTAATTCAATATAC
289838 CC
131 CC
* * * * ***
289840 TGAAGAGTAGTGGAATGAATCAATATTTCCATATCTGATATCCCCTGAAGAGTAGTGGAGCAGAT
1 TGAAGAGTAGTGGAATGAATCAATGTTTCCAGATCTGATCTCCCCTGAAGAGCAACAGAGCAGAT
* * * * *
289905 CCTTCTCTTTCAGATTTGATCTTCCCTGAGGAGCAGTAGAACAAATATTCCTTAATCCAATATAC
66 CCCTCTCTTTCAGATTTGATCTTCCTTGAGGAGCAGTGGAACAAATCTTCCTTAATTCAATATAC
289970 CC
131 CC
* * * * * *
289972 TGAAGTGTAGCGGAATGGATCAATGTTTCCAGATCTGATCTCCCCTGAAGAGCAATAGATCATAT
1 TGAAGAGTAGTGGAATGAATCAATGTTTCCAGATCTGATCTCCCCTGAAGAGCAACAGAGCAGAT
** * * * * * *
290037 CATTCTCTTTCATATTTGACCTTTCTTGAGGAGCAGTGGAACGAATTTTCCTTAATTCAATCTAC
66 CCCTCTCTTTCAGATTTGATCTTCCTTGAGGAGCAGTGGAACAAATCTTCCTTAATTCAATATAC
290102 CC
131 CC
* ** * *
290104 TGAAGAGCAGTGGAATGAATCAATGTTTTAATATCTGATCTCCCCTAAAGAGCAACAGAGCAGAT
1 TGAAGAGTAGTGGAATGAATCAATGTTTCCAGATCTGATCTCCCCTGAAGAGCAACAGAGCAGAT
* *
290169 CCCTCTCTTTCAGATTTGATCTTCCTTGAGGAGCAGTGGAACAAATCTGCCTTAATTCAATCTAC
66 CCCTCTCTTTCAGATTTGATCTTCCTTGAGGAGCAGTGGAACAAATCTTCCTTAATTCAATATAC
290234 CC
131 CC
290236 TGAA
1 TGAA
290240 AAGCAACGGA
Statistics
Matches: 341, Mismatches: 58, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
131 62 0.18
132 279 0.82
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (132 bp):
TGAAGAGTAGTGGAATGAATCAATGTTTCCAGATCTGATCTCCCCTGAAGAGCAACAGAGCAGAT
CCCTCTCTTTCAGATTTGATCTTCCTTGAGGAGCAGTGGAACAAATCTTCCTTAATTCAATATAC
CC
Found at i:290482 original size:13 final size:14
Alignment explanation
Indices: 290464--290493 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
290454 ATTATTATTA
290464 TTTTATTT-TTTAT
1 TTTTATTTCTTTAT
290477 TTTTATTTCTTTAT
1 TTTTATTTCTTTAT
290491 TTT
1 TTT
290494 GCAGGCCGAA
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:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTATTTCTTTAT
Found at i:290482 original size:21 final size:21
Alignment explanation
Indices: 290452--290493 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
290442 TCGGAAATTA
290452 TTATTATTATTAT-TTTATTTT
1 TTATTATTATT-TCTTTATTTT
*
290473 TTATTTTTATTTCTTTATTTT
1 TTATTATTATTTCTTTATTTT
290494 GCAGGCCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (21 bp):
TTATTATTATTTCTTTATTTT
Found at i:290977 original size:18 final size:17
Alignment explanation
Indices: 290938--290977 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
290928 AAATAGAGAG
*
290938 AAAAATTAAAAGATAAA
1 AAAAATTAAAAGAAAAA
290955 AAAAATTAAAAGGAAAAA
1 AAAAATTAAAA-GAAAAA
290973 AAAAA
1 AAAAA
290978 GATATACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (17 bp):
AAAAATTAAAAGAAAAA
Found at i:291694 original size:13 final size:13
Alignment explanation
Indices: 291678--291706 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
291668 TATTAGTATG
291678 CTTAGTCCTTATT
1 CTTAGTCCTTATT
291691 CTTAGTCCTTATT
1 CTTAGTCCTTATT
291704 CTT
1 CTT
291707 TTCCATGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.24, G:0.07, T:0.55
Consensus pattern (13 bp):
CTTAGTCCTTATT
Found at i:295273 original size:24 final size:25
Alignment explanation
Indices: 295240--295288 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
295230 TGATTTATGG
* * *
295240 TTTTCGTAAATCCAAATTTTTTATT
1 TTTTCGTAAAACAAAATGTTTTATT
295265 TTTTC-TAAAACAAAATGTTTTATT
1 TTTTCGTAAAACAAAATGTTTTATT
295289 AAAACCACCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.53
Consensus pattern (25 bp):
TTTTCGTAAAACAAAATGTTTTATT
Found at i:298233 original size:17 final size:17
Alignment explanation
Indices: 298211--298254 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
298201 TAGCAATTAG
298211 TCTTCGTATGAATTTAT
1 TCTTCGTATGAATTTAT
*
298228 TCTTCGTAGGAATTTAT
1 TCTTCGTATGAATTTAT
*
298245 TCCTCGTATG
1 TCTTCGTATG
298255 GACATAGGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (17 bp):
TCTTCGTATGAATTTAT
Found at i:303766 original size:88 final size:87
Alignment explanation
Indices: 303569--303766 Score: 202
Period size: 88 Copynumber: 2.2 Consensus size: 87
303559 TTCACATGCC
* * *
303569 TTAAACCATGAAGGTGAGTCATACGAAGAATATTTCACCTGACTTAAACTCACGAATAGGAGTCG
1 TTAAACCATG-AGGTGAGTCATACGAAGAACATTTCACCTGACTTAAACTAACGAATAGGAGTCA
* *
303634 TCCAAAAAAATATTTCACCCAGA
65 TCCAAAAAAACATTTAACCCAGA
* * * * * * *
303657 TTAAACCCACGAGGGGAGTCATCCGCAGAACATTTCACTTGATTTAAACTAATGAA-AGAGAGTC
1 TTAAA-CCATGAGGTGAGTCATACGAAGAACATTTCACCTGACTTAAACTAACGAATAG-GAGTC
** *
303721 ATCCAAAAGTACATTTAACCCATA
64 ATCCAAAAAAACATTTAACCCAGA
303745 TTAAACTCATGTAGGTG-GTCAT
1 TTAAAC-CATG-AGGTGAGTCAT
303767 TCAGAAAAAA
Statistics
Matches: 89, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
87 3 0.03
88 78 0.88
89 8 0.09
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (87 bp):
TTAAACCATGAGGTGAGTCATACGAAGAACATTTCACCTGACTTAAACTAACGAATAGGAGTCAT
CCAAAAAAACATTTAACCCAGA
Found at i:303826 original size:44 final size:44
Alignment explanation
Indices: 303778--303899 Score: 120
Period size: 44 Copynumber: 2.8 Consensus size: 44
303768 CAGAAAAAAA
* *
303778 TTCACCTGGTTTAAA-CTCGCAAAGGGGAATCATTCGAAGAATAC
1 TTCACCTGGCTTAAATC-CGCAAAGGGGAATCATCCGAAGAATAC
* * * *
303822 TTCACCTGGCTTAAATCCGCGAAGGGGAGTCATCCGAAGAACAT
1 TTCACCTGGCTTAAATCCGCAAAGGGGAATCATCCGAAGAATAC
** * * * *
303866 TTCATATGGCTTAAACCCACAAAAGGGATTCATC
1 TTCACCTGGCTTAAATCCGCAAAGGGGAATCATC
303900 TGATAACACT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 63 0.98
45 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (44 bp):
TTCACCTGGCTTAAATCCGCAAAGGGGAATCATCCGAAGAATAC
Found at i:305344 original size:15 final size:15
Alignment explanation
Indices: 305320--305349 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
305310 TCTTTCACAA
*
305320 TTTTATTTTAATTTT
1 TTTTAATTTAATTTT
305335 TTTTAATTTAATTTT
1 TTTTAATTTAATTTT
305350 CCACTTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTAATTTAATTTT
Found at i:305516 original size:7 final size:7
Alignment explanation
Indices: 305504--305547 Score: 52
Period size: 7 Copynumber: 5.7 Consensus size: 7
305494 TCTCTTTCTC
305504 TTTTTTA
1 TTTTTTA
305511 TTTTTTA
1 TTTTTTA
305518 TTTTCATTA
1 TTTT--TTA
305527 TTTTTTA
1 TTTTTTA
305534 TTTTACTTA
1 TTTT--TTA
305543 TTTTT
1 TTTTT
305548 AGATTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 19 0.58
9 14 0.42
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTA
Found at i:305548 original size:15 final size:16
Alignment explanation
Indices: 305508--305547 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
305498 TTTCTCTTTT
305508 TTATTTTTTATTTTCA
1 TTATTTTTTATTTTCA
305524 TTATTTTTTATTTT-A
1 TTATTTTTTATTTTCA
305539 CTTATTTTT
1 -TTATTTTT
305548 AGATTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (16 bp):
TTATTTTTTATTTTCA
Found at i:312550 original size:3 final size:3
Alignment explanation
Indices: 312529--312586 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
312519 TTTTTGTTAT
* *
312529 TTA TTA TTT TTA TTT TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
312575 TTA TTA TTA TTA
1 TTA TTA TTA TTA
312587 AATAATAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 4 0.08
3 45 0.92
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:312564 original size:14 final size:14
Alignment explanation
Indices: 312525--312586 Score: 81
Period size: 14 Copynumber: 4.4 Consensus size: 14
312515 CCCTTTTTTG
*
312525 TTATT-TATTATTT
1 TTATTATATTATTA
*
312538 TTATTTTTATTATTA
1 TTA-TTATATTATTA
312553 TTATTATATTATTA
1 TTATTATATTATTA
*
312567 TTATTATTTTATTA
1 TTATTATATTATTA
312581 TTATTA
1 TTATTA
312587 AATAATAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
13 3 0.07
14 31 0.70
15 10 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTATATTATTA
Found at i:317564 original size:10 final size:10
Alignment explanation
Indices: 317549--317580 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
317539 TTCAAATAGC
317549 AAAAAGAAAA
1 AAAAAGAAAA
317559 AAAAAGAAAA
1 AAAAAGAAAA
317569 AAAAAGAAAA
1 AAAAAGAAAA
317579 AA
1 AA
317581 GAAAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:317578 original size:17 final size:17
Alignment explanation
Indices: 317549--317593 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
317539 TTCAAATAGC
317549 AAAAAGAAA-AAAAAAG
1 AAAAAGAAAGAAAAAAG
*
317565 AAAAAAAAAGAAAAAAG
1 AAAAAGAAAGAAAAAAG
317582 AAAAAGAAAGAA
1 AAAAAGAAAGAA
317594 TAGAAAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAAG
Found at i:317591 original size:10 final size:9
Alignment explanation
Indices: 317549--317593 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
317539 TTCAAATAGC
317549 AAAAAGAAAA
1 AAAAAG-AAA
317559 AAAAAGAAA
1 AAAAAGAAA
*
317568 AAAAA-AGA
1 AAAAAGAAA
317576 AAAAAGAAA
1 AAAAAGAAA
317585 AAGAAAGAA
1 AA-AAAGAA
317594 TAGAAAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 7 0.23
9 12 0.39
10 12 0.39
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:320101 original size:42 final size:41
Alignment explanation
Indices: 320042--320143 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 41
320032 TCTTGATTCG
* * * * **
320042 TAAATCTTTCGGGTCATCTGTAAGTCTTTTGAGCATGATGTT
1 TAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGAT-AA
320084 TAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATAA
1 TAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATAA
320125 TAAGA-CCTTCGGGTCATCT
1 TAA-ATCCTTCGGGTCATCT
320144 ATAAAACCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 17 0.32
42 36 0.68
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (41 bp):
TAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATAA
Found at i:320783 original size:3 final size:3
Alignment explanation
Indices: 320770--320854 Score: 127
Period size: 3 Copynumber: 28.0 Consensus size: 3
320760 TGTCCCTTTT
*
320770 TTA TTA TTTA TTA TTT TTA TTA TTA TTA TATA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
*
320817 TTA TTA TT- TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
320855 AATAATAATA
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
2 2 0.03
3 67 0.89
4 6 0.08
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:322259 original size:2 final size:2
Alignment explanation
Indices: 322252--322279 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
322242 TACTTTAATC
322252 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
322280 TTTAATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:326036 original size:2 final size:2
Alignment explanation
Indices: 326031--326062 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
326021 TACAAAGTTA
326031 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
326063 GGAAAGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:328067 original size:16 final size:15
Alignment explanation
Indices: 328023--328058 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
328013 TTTATTAATA
328023 TATTAACAAATATATT
1 TATTAA-AAATATATT
328039 TATTAAACAATATATT
1 TATTAAA-AATATATT
328055 TATT
1 TATT
328059 TAGAAATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAAAAATATATT
Found at i:328394 original size:35 final size:35
Alignment explanation
Indices: 328317--328400 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 35
328307 ATAGGATTTT
* * *
328317 CATAAATAAATAAAT-TTATTTATATATATATTTA
1 CATAACTAAATAAATATTAGTTATATATATATTGA
*
328351 TA-AGACTAAATAAATATTAGTTATATATATATTGA
1 CATA-ACTAAATAAATATTAGTTATATATATATTGA
328386 CATAACT-AATAAATA
1 CATAACTAAATAAATA
328401 ATAATAGTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
33 1 0.02
34 19 0.45
35 21 0.50
36 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (35 bp):
CATAACTAAATAAATATTAGTTATATATATATTGA
Found at i:329746 original size:3 final size:3
Alignment explanation
Indices: 329738--329803 Score: 66
Period size: 3 Copynumber: 22.7 Consensus size: 3
329728 TATTTTTATT
* * *
329738 TAA TAA TAA TAA T-A TAA TATA GAA TAA TAA TAA T-A TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
329782 TAA T-A TAA TAA TAA AAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
329804 GAAAAAAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 6 0.12
3 43 0.84
4 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:329795 original size:14 final size:14
Alignment explanation
Indices: 329738--329803 Score: 68
Period size: 14 Copynumber: 4.9 Consensus size: 14
329728 TATTTTTATT
329738 TAATAATAATAAT-A
1 TAATAAT-ATAATAA
*
329752 TAAT-ATAGAATAA
1 TAATAATATAATAA
* *
329765 TAATAATATATTTA
1 TAATAATATAATAA
329779 TAATAATATAATAA
1 TAATAATATAATAA
329793 TAA-AA-ATAATA
1 TAATAATATAATA
329804 GAAAAAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
12 10 0.23
13 9 0.20
14 25 0.57
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
TAATAATATAATAA
Found at i:329974 original size:45 final size:45
Alignment explanation
Indices: 329910--331303 Score: 2127
Period size: 45 Copynumber: 31.3 Consensus size: 45
329900 CTTTGAAATG
*
329910 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
329955 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGA-CCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
329999 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCAAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
*
330045 TTGAAAACATCAAGCACTGAAGGGCTTATAGATGACCCGAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
*
330091 TTGAAAACATCAAG--CTGAAGGGCTTACAGATGACTCGAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
330135 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
330181 TTGAAAACATC-A--ACTGAAGGGCTTACAGATGACCCGAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
*
330224 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACTCG--GGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
330268 TTGAAAACATCAAGCACTGAAGGGC-TACAGATGACCCG-AGGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
*
330312 TTGAAAACATCAAGCA-TGAAGAGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
330356 TTGAAAAACATCAAGCACTGAAGGGCTTATAGATGACCCGAAGGTT
1 TTG-AAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
330402 TTGAAAACATCAAGCACTAAAGGGCTTACAAATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
330447 TTGAAAA-ATC-TGCACTGAAGGGCTTACAGATGA-CCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* * * *
330489 TT----CCA-CATGCACTGAAGGACTTACAGATGACCTG-AGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
330528 TTGAAAAACATCAAGCACTGAAGGGCTTACAGATGACTCAAAGGTTT
1 TTG-AAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
*
330575 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCAAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
330620 TTGAAAACATCAAGCACTG-AGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
330664 TTGAAAACAT-AAGCA-TGAAGGGCTTACAGATGACCCGAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
*
330708 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCTGAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
330754 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
330799 TTGAAAACATCAAGCACTGAAGGGCTTACAAATGA-CCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
330843 TTGAAAACATCAAGCATTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
330888 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
330933 TTGAAAACATCATGCACTGAAGGGCTTACGGATGA-CCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
330977 TT-AAAAAATCAAGCATTGAAGGGCTTACAGATGACCCGAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
331022 TTG-AAACATCAAGCACTGAAGGGCTTACA-ATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
331065 TTGAAAACATCAAGCATTGAAGGGCTTACAGATGACCCGAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
331111 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
331156 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
331201 TTGAAAACATCATGCACTGAAGGGCTTAC--A-GACCCGAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
*
331244 TTAAGAAAACATCAAGCACT-AA--ACTTACAGATGACCCGAAGGTTT
1 TT--GAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
331289 CATTGAAAACATCAA
1 --TTGAAAACATCAA
331304 AATAAAGATA
Statistics
Matches: 1259, Mismatches: 48, Indels: 84
0.91 0.03 0.06
Matches are distributed among these distances:
38 1 0.00
39 30 0.02
40 2 0.00
42 28 0.02
43 147 0.12
44 307 0.24
45 429 0.34
46 308 0.24
47 7 0.01
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (45 bp):
TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
Done.