Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 51
Found at i:5186817 original size:15 final size:15
Alignment explanation
Indices: 5186774--5186821 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
5186764 AAAAAATTGA
*
5186774 AAAAAATGAAAAAATG
1 AAAAAATGAAGAAA-G
5186790 AAAAAA-GAAGAAAG
1 AAAAAATGAAGAAAG
*
5186804 AAAAAATGATGAAA-
1 AAAAAATGAAGAAAG
5186818 AAAA
1 AAAA
5186822 GAAAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 11 0.38
15 12 0.41
16 6 0.21
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (15 bp):
AAAAAATGAAGAAAG
Found at i:5186833 original size:7 final size:7
Alignment explanation
Indices: 5186582--5186837 Score: 104
Period size: 8 Copynumber: 33.9 Consensus size: 7
5186572 ATTTCGCTTG
5186582 AAGAAGAA
1 AAGAA-AA
5186590 AAGGAAAA
1 AA-GAAAA
**
5186598 ATTAAAA
1 AAGAAAA
5186605 AATGAAAA
1 AA-GAAAA
5186613 AATGAAAA
1 AA-GAAAA
*
5186621 ATGAAAA
1 AAGAAAA
*
5186628 ATGAAAA
1 AAGAAAA
*
5186635 ATGAAAA
1 AAGAAAA
*
5186642 ATGAAAA
1 AAGAAAA
5186649 AAGAAGAA
1 AAGAA-AA
5186657 AATGAAAA
1 AA-GAAAA
* *
5186665 ATGTAAAG
1 AAG-AAAA
*
5186673 AATAAAA
1 AAGAAAA
*
5186680 AAGGAAA
1 AAGAAAA
* *
5186687 AGGGAAA
1 AAGAAAA
*
5186694 AATAAAA
1 AAGAAAA
5186701 AAGGAAAA
1 AA-GAAAA
**
5186709 GGGAAAAA
1 AAG-AAAA
5186717 AATGAAAA
1 AA-GAAAA
5186725 AATGAAAA
1 AA-GAAAA
5186733 AA-AAAA
1 AAGAAAA
**
5186739 TTTGAAAAA
1 -AAG-AAAA
5186748 AATGAAAA
1 AA-GAAAA
5186756 AATGAAAA
1 AA-GAAAA
5186764 AA-AAAA
1 AAGAAAA
**
5186770 TTGAAAAA
1 AAG-AAAA
5186778 AATGAAAA
1 AA-GAAAA
5186786 AATGAAAA
1 AA-GAAAA
*
5186794 AAGAAGA
1 AAGAAAA
5186801 AAGAAAA
1 AAGAAAA
5186808 AATGATGAAA
1 AA-GA--AAA
*
5186818 AAAAGAAA
1 AAGA-AAA
5186826 AAG-AAA
1 AAGAAAA
5186832 AAGAAA
1 AAGAAA
5186838 TAAAAGGGGG
Statistics
Matches: 195, Mismatches: 34, Indels: 39
0.73 0.13 0.15
Matches are distributed among these distances:
6 14 0.07
7 71 0.36
8 91 0.47
9 14 0.07
10 5 0.03
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (7 bp):
AAGAAAA
Found at i:5186835 original size:31 final size:29
Alignment explanation
Indices: 5186711--5186842 Score: 158
Period size: 31 Copynumber: 4.3 Consensus size: 29
5186701 AAGGAAAAGG
5186711 GAAAAAAATGAAAAAATGAAAAAAAAAATTT
1 GAAAAAAATGAAAAAATGAAAAAAAAAA--T
5186742 GAAAAAAATGAAAAAATGAAAAAAAAAATT
1 GAAAAAAATGAAAAAATGAAAAAAAAAA-T
*
5186772 GAAAAAAATGAAAAAATGAAAAAAGAAGAAA
1 GAAAAAAATGAAAAAATGAAAAAA-AA-AAT
*
5186803 GAAAAAATGATGAAAAAAAGAAAAAGAAAAA-
1 GAAAAAA--ATGAAAAAATGAAAAA-AAAAAT
5186834 GAAATAAAA
1 GAAA-AAAA
5186843 GGGGGTTCAA
Statistics
Matches: 93, Mismatches: 2, Indels: 13
0.86 0.02 0.12
Matches are distributed among these distances:
30 27 0.29
31 41 0.44
32 7 0.08
33 17 0.18
34 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.11
Consensus pattern (29 bp):
GAAAAAAATGAAAAAATGAAAAAAAAAAT
Found at i:5186924 original size:45 final size:44
Alignment explanation
Indices: 5186840--5186924 Score: 107
Period size: 45 Copynumber: 1.9 Consensus size: 44
5186830 AAAAGAAATA
* * *
5186840 AAAGGGGGTTCAAGATGAAAACCCGAAAAGGGCGTCTTGAAACC
1 AAAGGAGGTTCAAGATGAAAACCCGAAAAGGGAGACTTGAAACC
* * *
5186884 AAAGGAGGTCTCAAGTTGAAAATCCGTAAAGGGAGACTTGA
1 AAAGGAGGT-TCAAGATGAAAACCCGAAAAGGGAGACTTGA
5186925 GTTTTAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 8 0.24
45 26 0.76
ACGTcount: A:0.39, C:0.15, G:0.29, T:0.16
Consensus pattern (44 bp):
AAAGGAGGTTCAAGATGAAAACCCGAAAAGGGAGACTTGAAACC
Found at i:5188185 original size:37 final size:36
Alignment explanation
Indices: 5188124--5188223 Score: 119
Period size: 37 Copynumber: 2.8 Consensus size: 36
5188114 TAGGTCAATT
* * * *
5188124 TTAAGCCTTCACGAAAAAACAGTGAAGCAATTCAAAC
1 TTAAGCCTTCACGGAAGAATAGTGAAGCAAATC-AAC
* *
5188161 TTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCATC
1 TTAAGCCTTCACGGAAGAATAGTGAAGCAAATCAAC
* *
5188197 ATAAGCCTTCACGGAAGATTAGTGAAG
1 TTAAGCCTTCACGGAAGAATAGTGAAG
5188224 GAAACTCATT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 27 0.49
37 28 0.51
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (36 bp):
TTAAGCCTTCACGGAAGAATAGTGAAGCAAATCAAC
Found at i:5188317 original size:55 final size:55
Alignment explanation
Indices: 5188243--5188579 Score: 439
Period size: 55 Copynumber: 6.1 Consensus size: 55
5188233 TTTATGAAGC
*
5188243 TCGAGTTCTATACTCTCTGATA-GAATAGGGAGCGGACTCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGA-ACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * *
5188298 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGTGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* *
5188353 TCGAGTCCTATACTCTCTGATA-GAATAGGGAGCGAACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGA-ACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* *
5188408 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAACGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGT
* * *
5188463 TCGAGTTTCTATACTCCCTGAACGAATAGGGAGCGGATCCGTTTATTGAAGATTGT
1 TCGAG-TTCTATACTCTCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * * * * * *
5188519 TTGAG-TCTTATACTCCCTGAACTAATAGGGAGCAGACACATTTGCTGAAGATTGT
1 TCGAGTTC-TATACTCTCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
5188574 TCGAGT
1 TCGAGT
5188580 CTTACATTCC
Statistics
Matches: 251, Mismatches: 23, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
54 5 0.02
55 196 0.78
56 49 0.20
57 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
Found at i:5188599 original size:166 final size:165
Alignment explanation
Indices: 5188243--5188608 Score: 456
Period size: 166 Copynumber: 2.2 Consensus size: 165
5188233 TTTATGAAGC
* * *
5188243 TCGAGTTCTATACTCTCTGATA-GAATAGGGAGCGGACTCGTTTGTTGAAGATTGTTCGAGTTCT
1 TCGAGTTCTATACTCCCT-AAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTCT
* * * * *
5188307 ATACTCTCTGAAGGAATAGAGAGTGGACCCGTTTGTTGAAGATTGTTCGAGTCCTATACTCTCTG
65 ATACTCCCTGAACGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTCGAGTCCTATACTCCCTG
* * *
5188372 ATAGAATAGGGAGCGAACCCGTTTGTTGAAGATTGT
130 ATAGAATAGGGAGCGAACACATTTGCTGAAGATTGT
* * *
5188408 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGTTCGAGTTTC
1 TCGAGTTCTATACTCCCTAAAGGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGTTCGAG-TTC
* * * *
5188472 TATACTCCCTGAACGAATAGGGAGCGGATCCGTTTATTGAAGATTGTTTGAGTCTTATACTCCCT
64 TATACTCCCTGAACGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTCGAGTCCTATACTCCCT
*
5188537 GA-ACTAATAGGGAGC-AGACACATTTGCTGAAGATTGT
129 GATA-GAATAGGGAGCGA-ACACATTTGCTGAAGATTGT
5188574 TCGAG-TCT-TACATTCCCTAAAGGAATAGGGAGCGG
1 TCGAGTTCTATAC--TCCCTAAAGGAATAGGGAGCGG
5188609 GCATGTCATT
Statistics
Matches: 174, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
164 5 0.03
165 57 0.33
166 112 0.64
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (165 bp):
TCGAGTTCTATACTCCCTAAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTCTA
TACTCCCTGAACGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTCGAGTCCTATACTCCCTGA
TAGAATAGGGAGCGAACACATTTGCTGAAGATTGT
Found at i:5190167 original size:28 final size:29
Alignment explanation
Indices: 5190109--5190177 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
5190099 CTCCATGTTT
* *
5190109 TATTTCATTTT-TGTATGTTTAATTTTAG
1 TATTTCATTTTATGTATATTTAATTTCAG
5190137 TATTTCATTTTATG-ATATTT-ATTTCATG
1 TATTTCATTTTATGTATATTTAATTTCA-G
*
5190165 TATTCCATATTTA
1 TATTTCAT-TTTA
5190178 AGCCTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 5 0.14
28 24 0.69
29 6 0.17
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.61
Consensus pattern (29 bp):
TATTTCATTTTATGTATATTTAATTTCAG
Found at i:5193395 original size:28 final size:30
Alignment explanation
Indices: 5193363--5193419 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
5193353 GTATTCTCCA
*
5193363 AAAT-AAAAAAT-GAGTGTCCTATTGGGCT
1 AAATAAAAAAATAGAGTGGCCTATTGGGCT
*
5193391 AAATAAAAAAATAGGGTGGCCTATTGGGC
1 AAATAAAAAAATAGAGTGGCCTATTGGGC
5193420 CAAAAAATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 7 0.28
30 14 0.56
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.25
Consensus pattern (30 bp):
AAATAAAAAAATAGAGTGGCCTATTGGGCT
Found at i:5193494 original size:19 final size:20
Alignment explanation
Indices: 5193470--5193509 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5193460 TTTATGTAAA
*
5193470 AATA-TTAAAAAATGTCAAC
1 AATATTTAAAAAATATCAAC
*
5193489 AATATTTTAAAAATATCAAC
1 AATATTTAAAAAATATCAAC
5193509 A
1 A
5193510 CTCAACAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (20 bp):
AATATTTAAAAAATATCAAC
Found at i:5205000 original size:20 final size:22
Alignment explanation
Indices: 5204952--5205007 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
5204942 GTACTTAGGA
*
5204952 AAGTATCAATACCATAGACCAG
1 AAGTATCAATACCATAGACAAG
5204974 AAGTATCAATACTCA-AGA-AAG
1 AAGTATCAATAC-CATAGACAAG
5204995 -AGTATCAATACCA
1 AAGTATCAATACCA
5205008 CCTATTTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 2 0.06
20 11 0.34
21 2 0.06
22 15 0.47
23 2 0.06
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (22 bp):
AAGTATCAATACCATAGACAAG
Found at i:5212505 original size:30 final size:30
Alignment explanation
Indices: 5212469--5212526 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
5212459 GTTTATAGAC
5212469 TATTTATGA-CCTCTATATTCATAAATAAGG
1 TATTTATGACCCT-TATATTCATAAATAAGG
*
5212499 TATTTATGACCCTTATATTCATACATAA
1 TATTTATGACCCTTATATTCATAAATAA
5212527 CTCTTTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (30 bp):
TATTTATGACCCTTATATTCATAAATAAGG
Found at i:5212764 original size:21 final size:21
Alignment explanation
Indices: 5212740--5212795 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
5212730 GTACTCAGAA
5212740 AAGTATCGATACCACAACAAG
1 AAGTATCGATACCACAACAAG
* *
5212761 AAGTATCGATA-CTCAAGAAG
1 AAGTATCGATACCACAACAAG
*
5212781 AAGCATCGATACCAC
1 AAGTATCGATACCAC
5212796 CCTTTTGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.16
Consensus pattern (21 bp):
AAGTATCGATACCACAACAAG
Found at i:5212783 original size:20 final size:20
Alignment explanation
Indices: 5212731--5212792 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
5212721 TTTGGTTCGG
5212731 TACTC-AGAA-AAGTATCGA
1 TACTCAAGAAGAAGTATCGA
* *
5212749 TACCACAACAAGAAGTATCGA
1 TA-CTCAAGAAGAAGTATCGA
*
5212770 TACTCAAGAAGAAGCATCGA
1 TACTCAAGAAGAAGTATCGA
5212790 TAC
1 TAC
5212793 CACCCTTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 21 0.58
21 11 0.31
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (20 bp):
TACTCAAGAAGAAGTATCGA
Found at i:5212869 original size:20 final size:20
Alignment explanation
Indices: 5212826--5212876 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5212816 ATAAGTTAAG
* **
5212826 AGTATCGATACCCAAAGGTT
1 AGTATCGATACCCAAAAGCC
5212846 AGTATCGATACCCAAAAGCC
1 AGTATCGATACCCAAAAGCC
*
5212866 AGTATCCATAC
1 AGTATCGATAC
5212877 TGAAGAGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (20 bp):
AGTATCGATACCCAAAAGCC
Found at i:5214075 original size:19 final size:20
Alignment explanation
Indices: 5214047--5214095 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
5214037 AAGTGTTGTA
5214047 GTATCGATACAGAA-GCTCG
1 GTATCGATACAGAATGCTCG
* * *
5214066 GTATCAATACATAATGGTCG
1 GTATCGATACAGAATGCTCG
5214086 GTATCGATAC
1 GTATCGATAC
5214096 CCCTGGTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (20 bp):
GTATCGATACAGAATGCTCG
Found at i:5217665 original size:21 final size:21
Alignment explanation
Indices: 5217636--5217687 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5217626 ATACCGCTGA
* *
5217636 TATCTATACCAGA-CAATTTGG
1 TATCCATACCAGATCAA-CTGG
*
5217657 TATCCATACCAGATGAACTGG
1 TATCCATACCAGATCAACTGG
5217678 TATCCATACC
1 TATCCATACC
5217688 GAAGGCTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (21 bp):
TATCCATACCAGATCAACTGG
Found at i:5218644 original size:20 final size:21
Alignment explanation
Indices: 5218619--5218658 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5218609 TAGTCATTTT
5218619 AGTATCAATA-TCAAAGGTTG
1 AGTATCAATACTCAAAGGTTG
* *
5218639 AGTATCGATACTCAAGGGTT
1 AGTATCAATACTCAAAGGTT
5218659 AGTGATGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
AGTATCAATACTCAAAGGTTG
Found at i:5225512 original size:33 final size:33
Alignment explanation
Indices: 5225470--5225543 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
5225460 CCTCCAGGAT
*
5225470 GGGTCATATAACTCTATGACGGTGGAAGCGGCG
1 GGGTCATATAACTCTATGACGGTGGAAGCGGCA
*
5225503 GGGTCATATAACTCTGTGACGGTGGAAGCGGCA
1 GGGTCATATAACTCTATGACGGTGGAAGCGGCA
5225536 GGGTCATA
1 GGGTCATA
5225544 AAACCAAGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (33 bp):
GGGTCATATAACTCTATGACGGTGGAAGCGGCA
Found at i:5227343 original size:17 final size:16
Alignment explanation
Indices: 5227304--5227371 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 16
5227294 CTGTAAAAAA
*
5227304 ATTAATTAAA-TACAAT
1 ATTAAATAAATTA-AAT
*
5227320 ATTAAATAATTTAAAT
1 ATTAAATAAATTAAAT
5227336 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
* *
5227353 ATAAAATATAATAAAAT
1 ATTAAATA-AATTAAAT
5227370 AT
1 AT
5227372 ACCTTCAACA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
16 18 0.41
17 26 0.59
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:5227413 original size:24 final size:24
Alignment explanation
Indices: 5227384--5227429 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
5227374 CTTCAACAGA
5227384 TAATATAAAAGTATTTGAGAGAGG
1 TAATATAAAAGTATTTGAGAGAGG
5227408 TAATATAAAAGTATTTGAGAGA
1 TAATATAAAAGTATTTGAGAGA
5227430 AGTTGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (24 bp):
TAATATAAAAGTATTTGAGAGAGG
Found at i:5227726 original size:19 final size:19
Alignment explanation
Indices: 5227702--5227744 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
5227692 GTAAAACGCT
5227702 CTGCAGGGCGCACGTCTTA
1 CTGCAGGGCGCACGTCTTA
5227721 CTGCAGGGCGCACGTCTTA
1 CTGCAGGGCGCACGTCTTA
5227740 CTGCA
1 CTGCA
5227745 AAGGGTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.33, G:0.30, T:0.21
Consensus pattern (19 bp):
CTGCAGGGCGCACGTCTTA
Found at i:5241467 original size:96 final size:96
Alignment explanation
Indices: 5241342--5241541 Score: 278
Period size: 96 Copynumber: 2.1 Consensus size: 96
5241332 ATCACTGATT
* *
5241342 TACTGGTTTATGAACTATGGTTACTTGAAATATGTTCTCTGG-TTACATGT-TTTCACTATAAAA
1 TACTGGTTTATGAACTATGGTTACCTGAAATATGTTCTCTGGTTTAC-T-TCTTTCACTAGAAAA
* * *
5241405 TATGATTGTTCCTGATTTATAGATCATGGAATC
64 TATGATCGTTCCTGAATTATAGATCATGAAATC
* * *
5241438 TACTGGTTTATGAACTATGGTTACCTGAAATATGTTGTCTGGTTTTCTTCTTTCACTGGAAAATA
1 TACTGGTTTATGAACTATGGTTACCTGAAATATGTTCTCTGGTTTACTTCTTTCACTAGAAAATA
*
5241503 TGATCGTTCCTGAATTATGGATCATGAAATC
66 TGATCGTTCCTGAATTATAGATCATGAAATC
*
5241534 TATTGGTT
1 TACTGGTT
5241542 ACTACTTGAA
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
95 1 0.01
96 88 0.96
97 3 0.03
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (96 bp):
TACTGGTTTATGAACTATGGTTACCTGAAATATGTTCTCTGGTTTACTTCTTTCACTAGAAAATA
TGATCGTTCCTGAATTATAGATCATGAAATC
Found at i:5244053 original size:17 final size:18
Alignment explanation
Indices: 5244018--5244053 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5244008 TTAGGGCAAT
*
5244018 TAATAAACGCATGAATCA
1 TAATAAACACATGAATCA
5244036 TAATAAACACAT-AATCA
1 TAATAAACACATGAATCA
5244053 T
1 T
5244054 CTTGATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.25
Consensus pattern (18 bp):
TAATAAACACATGAATCA
Found at i:5252120 original size:19 final size:21
Alignment explanation
Indices: 5252096--5252155 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 21
5252086 TTTTGGTGCA
5252096 GAGGGAATCGA-TCCCCC-TT
1 GAGGGAATCGATTCCCCCTTT
*
5252115 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCTTT
5252136 GAAGGGGAATCGATTCCCCC
1 G-A-GGGAATCGATTCCCCC
5252156 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.29
20 6 0.17
21 3 0.09
22 1 0.03
23 15 0.43
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.20
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCTTT
Found at i:5252164 original size:21 final size:21
Alignment explanation
Indices: 5252138--5252177 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5252128 CCCCCTTTGA
*
5252138 AGGGGAATCGATTCCCCCCAC
1 AGGGGAATCGATACCCCCCAC
5252159 AGGGGAATCGATACCCCCC
1 AGGGGAATCGATACCCCCC
5252178 CTGGGGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGGGGAATCGATACCCCCCAC
Found at i:5254521 original size:13 final size:13
Alignment explanation
Indices: 5254503--5254546 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
5254493 AGGGGGAGTA
5254503 ATTTCAAAACTTG
1 ATTTCAAAACTTG
5254516 ATTTCAAAA----
1 ATTTCAAAACTTG
5254525 ATTTCAAAACTTG
1 ATTTCAAAACTTG
5254538 ATTTCAAAA
1 ATTTCAAAA
5254547 TCTTAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
9 9 0.33
13 18 0.67
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (13 bp):
ATTTCAAAACTTG
Found at i:5254530 original size:22 final size:22
Alignment explanation
Indices: 5254502--5254546 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5254492 AAGGGGGAGT
5254502 AATTTCAAAACTTGATTTCAAA
1 AATTTCAAAACTTGATTTCAAA
5254524 AATTTCAAAACTTGATTTCAAA
1 AATTTCAAAACTTGATTTCAAA
5254546 A
1 A
5254547 TCTTAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (22 bp):
AATTTCAAAACTTGATTTCAAA
Found at i:5261109 original size:357 final size:359
Alignment explanation
Indices: 5260423--5261111 Score: 1107
Period size: 357 Copynumber: 1.9 Consensus size: 359
5260413 TTACGGGAGG
* * *
5260423 GTACATGGATTAATTGATATGATGAAATATTTAAATCTTTCTTTGGTGTTGACCTTCCAATAATA
1 GTACATGGATTAATTGATAGGATGAAATATTTAAATCCTTCTTTGGTGTTGACCTTCCAATAAGA
*
5260488 TAGAATTCTCTTGAATATAAACTCTCTAATGGGGATAAGAGAAAAAACGAGATGATCTATTTATT
66 TAGAATTCTCTTGAATATAAACTCTCTAATGGGGATAAGAGAAAAAACGAGATGATCTATTTATC
* **
5260553 GGGACCATAACCCCTTTGTATAGTTGATTTAAGAATCAATTATTGTTTGTACTTATAACTCTACC
131 GGGACCATAACCCCTTTATATAAATGATTTAAGAATCAATTATTGTTTGTACTTATAACTCTACC
* * *
5260618 CCTCATCAAATTATAAATACAACTTTAATAGTATCTAAATTTTTATTTCCATGACACTTCTAATT
196 CCTCATCAAATTATAAATACAACTTTAATAGTATCAAAACTTTTATTTCCATAACACTTCTAATT
*
5260683 CCTTATGACTTTATAACATAATTGGTCACTTAATTTATATCATATTTTATGATAACAATATATAT
261 CCATATGACTTTATAACATAATTGGTCACTTAATTTATATCATATTTTATGATAACAATATATAT
5260748 TAAAAATATGTATAAACTATTTCTTTATAACAAT
326 TAAAAATATGTATAAACTATTTCTTTATAACAAT
* * *
5260782 GTACTTGGATTAATTGATAGGATGAAATCTTTAAATCCTTCTTTGGT-TGTGATCTTCCAATAAG
1 GTACATGGATTAATTGATAGGATGAAATATTTAAATCCTTCTTTGGTGT-TGACCTTCCAATAAG
* * * * *
5260846 ATAGGA-TCTCTTGAGTATAAACTCTCTTATGGGGATAAGAGAAAATACGAGATGATCTATTTCT
65 ATAGAATTCTCTTGAATATAAACTCTCTAATGGGGATAAGAGAAAAAACGAGATGATCTATTTAT
5260910 CGGGACCATAACCCCTTTATATAAATGATTTAAGAATCAATTATTGTTTGTACTTATAACTCTA-
130 CGGGACCATAACCCCTTTATATAAATGATTTAAGAATCAATTATTGTTTGTACTTATAACTCTAC
* * * *
5260974 CCCTTATCAAATTATAAATACATCTTTAATAGTATCAAAACTTTTATTTTCATAATACTTCTAA-
195 CCCTCATCAAATTATAAATACAACTTTAATAGTATCAAAACTTTTATTTCCATAACACTTCTAAT
* *
5261038 TCTCATATGACTTTATAACATAATTGGTCACTTAATTTATGTCATATTTTATGATAACAATATGT
260 TC-CATATGACTTTATAACATAATTGGTCACTTAATTTATATCATATTTTATGATAACAATATAT
5261103 ATTAAAAAT
324 ATTAAAAAT
5261112 GTGTGCCCGT
Statistics
Matches: 303, Mismatches: 25, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
356 2 0.01
357 125 0.41
358 115 0.38
359 61 0.20
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.40
Consensus pattern (359 bp):
GTACATGGATTAATTGATAGGATGAAATATTTAAATCCTTCTTTGGTGTTGACCTTCCAATAAGA
TAGAATTCTCTTGAATATAAACTCTCTAATGGGGATAAGAGAAAAAACGAGATGATCTATTTATC
GGGACCATAACCCCTTTATATAAATGATTTAAGAATCAATTATTGTTTGTACTTATAACTCTACC
CCTCATCAAATTATAAATACAACTTTAATAGTATCAAAACTTTTATTTCCATAACACTTCTAATT
CCATATGACTTTATAACATAATTGGTCACTTAATTTATATCATATTTTATGATAACAATATATAT
TAAAAATATGTATAAACTATTTCTTTATAACAAT
Found at i:5261830 original size:13 final size:13
Alignment explanation
Indices: 5261812--5261838 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5261802 TAATCTTCCG
5261812 CTTCAATTGAGCT
1 CTTCAATTGAGCT
5261825 CTTCAATTGAGCT
1 CTTCAATTGAGCT
5261838 C
1 C
5261839 AAATTTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CTTCAATTGAGCT
Found at i:5265489 original size:22 final size:23
Alignment explanation
Indices: 5265446--5265490 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5265436 AATAGGAATA
* *
5265446 TTTTATAAAATTAAGGTGATTTT
1 TTTTATAAAATTAAGCTAATTTT
5265469 TTTTATAAAATTAA-CTAATTTT
1 TTTTATAAAATTAAGCTAATTTT
5265491 ATTAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (23 bp):
TTTTATAAAATTAAGCTAATTTT
Found at i:5265490 original size:21 final size:23
Alignment explanation
Indices: 5265446--5265499 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
5265436 AATAGGAATA
* *
5265446 TTTTATAAAATTAAGGTGATTTT
1 TTTTATAAAATTAAGCTGAATTT
5265469 TTTTATAAAATTAA-CT-AATTT
1 TTTTATAAAATTAAGCTGAATTT
*
5265490 TATTA-AAAAT
1 TTTTATAAAAT
5265500 ATAATTTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 8 0.29
22 1 0.04
23 14 0.50
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.50
Consensus pattern (23 bp):
TTTTATAAAATTAAGCTGAATTT
Found at i:5266943 original size:31 final size:32
Alignment explanation
Indices: 5266907--5266977 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
5266897 CAAACTTGAC
*
5266907 CGACCCGACCTCACCCCT-AAAAAACCCGACT
1 CGACCCGACCTCACCCCTGAAAAAACACGACT
* * * * *
5266938 CGACCCCACCTCTCGCCTGAAAAAATATGACT
1 CGACCCGACCTCACCCCTGAAAAAACACGACT
5266970 CGACCCGA
1 CGACCCGA
5266978 ACCTAATTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
31 15 0.47
32 17 0.53
ACGTcount: A:0.31, C:0.44, G:0.13, T:0.13
Consensus pattern (32 bp):
CGACCCGACCTCACCCCTGAAAAAACACGACT
Found at i:5268010 original size:2 final size:2
Alignment explanation
Indices: 5267999--5268034 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5267989 ATTACAAGAG
5267999 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5268035 GGTTTCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5271637 original size:77 final size:77
Alignment explanation
Indices: 5271530--5271701 Score: 294
Period size: 77 Copynumber: 2.3 Consensus size: 77
5271520 TATGTTGAGT
*
5271530 GCCTGCGCC--TATATATATATACGACATCCCTCGTGGAATATAAGAATTAACAACCATTAGGCT
1 GCCTGCGCCTATATATATATATACGACATCCCTCATGGAATATAAGAATTAACAACCATTAGGCT
5271593 TTAACTTATTTA
66 TTAACTTATTTA
*
5271605 GCCTGCGCCTATATATATATATATGACATCCCTCATGGAATATAAGAATTAACAACCATTAGGCT
1 GCCTGCGCCTATATATATATATACGACATCCCTCATGGAATATAAGAATTAACAACCATTAGGCT
5271670 TTAACTTATTTA
66 TTAACTTATTTA
* *
5271682 GCCTGCACCTATAGATATAT
1 GCCTGCGCCTATATATATAT
5271702 GCCATGCCTA
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
75 9 0.10
77 82 0.90
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33
Consensus pattern (77 bp):
GCCTGCGCCTATATATATATATACGACATCCCTCATGGAATATAAGAATTAACAACCATTAGGCT
TTAACTTATTTA
Found at i:5275189 original size:20 final size:20
Alignment explanation
Indices: 5275164--5275217 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
5275154 CTTTACATAG
*
5275164 TAGTATCGATACTAAAGGCT
1 TAGTATCGATACCAAAGGCT
5275184 TAGTATCGATACCAAAGGCT
1 TAGTATCGATACCAAAGGCT
5275204 TAGTATCGATACCA
1 TAGTATCGATACCA
5275218 TCAGGCCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (20 bp):
TAGTATCGATACCAAAGGCT
Found at i:5278548 original size:36 final size:37
Alignment explanation
Indices: 5278508--5278588 Score: 103
Period size: 36 Copynumber: 2.2 Consensus size: 37
5278498 TTTAGAATTG
* * * *
5278508 AGCTCGACTT-GAAAGTTCACAAGTTTGAAATTGTTA
1 AGCTCGACTTCAAAAGTTCACAAGCTTAAAATTGTCA
5278544 AGCTCGA-TTCAAAAGTTCACAAGCTTAAAATTGTCA
1 AGCTCGACTTCAAAAGTTCACAAGCTTAAAATTGTCA
*
5278580 AGCTAGACT
1 AGCTCGACT
5278589 CGAACTCGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
35 2 0.05
36 35 0.92
37 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (37 bp):
AGCTCGACTTCAAAAGTTCACAAGCTTAAAATTGTCA
Found at i:5282793 original size:3 final size:3
Alignment explanation
Indices: 5282785--5282824 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5282775 TACATAAATA
5282785 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5282825 CCAAAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5282872 original size:12 final size:13
Alignment explanation
Indices: 5282840--5282864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5282830 ATAAAGTTAC
5282840 AAATAAAAATTTG
1 AAATAAAAATTTG
5282853 AAATAAAAATTT
1 AAATAAAAATTT
5282865 AACTAAAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATAAAAATTTG
Found at i:5284518 original size:24 final size:24
Alignment explanation
Indices: 5284491--5284552 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
5284481 CGTTCGTGAA
*
5284491 CGTTCGGTTATGTTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
* *
5284515 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
*
5284539 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
5284553 TAACCTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.13, C:0.11, G:0.23, T:0.53
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:5286081 original size:16 final size:16
Alignment explanation
Indices: 5286060--5286126 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
5286050 GTCTCCAACG
5286060 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
**
5286076 TTTATGTTCGTGTTTG
1 TTTATGTTCGTGTTCA
* *
5286092 TTTATGTTTGTGTTCG
1 TTTATGTTCGTGTTCA
5286108 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
5286122 TTTAT
1 TTTAT
5286127 TAAATGAACG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 38 0.84
ACGTcount: A:0.10, C:0.07, G:0.19, T:0.63
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:5295200 original size:19 final size:20
Alignment explanation
Indices: 5295155--5295202 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5295145 TCATATTTTT
* *
5295155 TTTTCAAAATTTCATTTTAC
1 TTTTCAAAATCTAATTTTAC
*
5295175 TTTTCAAAATCTAATTTTGC
1 TTTTCAAAATCTAATTTTAC
5295195 -TTTCAAAA
1 TTTTCAAAA
5295203 GAAAGTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.33, C:0.15, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATCTAATTTTAC
Found at i:5297111 original size:21 final size:21
Alignment explanation
Indices: 5297087--5297152 Score: 51
Period size: 23 Copynumber: 3.0 Consensus size: 21
5297077 ACACCAAAAT
5297087 ACCATATATTTGTCCCGAATA
1 ACCATATATTTGTCCCGAATA
* * **
5297108 ACCACATAGTTTTGTCTCGAACG
1 ACCATATA--TTTGTCCCGAATA
*
5297131 ACCATATAGAATTGTCCCGAAT
1 ACCATAT--ATTTGTCCCGAAT
5297153 GTCCACATAG
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
21 7 0.21
23 25 0.76
25 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (21 bp):
ACCATATATTTGTCCCGAATA
Found at i:5297121 original size:23 final size:23
Alignment explanation
Indices: 5297095--5297185 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
5297085 ATACCATATA
*
5297095 TTTGTCCCGAATAACCACATAGT
1 TTTGTCCCGAATGACCACATAGT
* * * *
5297118 TTTGTCTCGAACGACCATATAGA
1 TTTGTCCCGAATGACCACATAGT
* *
5297141 ATTGTCCCGAATGTCCACATAGGT
1 TTTGTCCCGAATGACCACATA-GT
*
5297165 TTT-TCACGAATGACCACATAG
1 TTTGTCCCGAATGACCACATAG
5297186 AACCCTCGAC
Statistics
Matches: 53, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
22 1 0.02
23 49 0.92
24 3 0.06
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (23 bp):
TTTGTCCCGAATGACCACATAGT
Found at i:5297149 original size:46 final size:46
Alignment explanation
Indices: 5297096--5297187 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
5297086 TACCATATAT
* *
5297096 TTGTCCCGAATAACCACATA-GTTTTGTCTCGAACGACCATATAGAA
1 TTGTCCCGAATAACCACATAGGTTTT-TCACGAACGACCACATAGAA
** *
5297142 TTGTCCCGAATGTCCACATAGGTTTTTCACGAATGACCACATAGAA
1 TTGTCCCGAATAACCACATAGGTTTTTCACGAACGACCACATAGAA
5297188 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 35 0.88
47 5 0.12
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (46 bp):
TTGTCCCGAATAACCACATAGGTTTTTCACGAACGACCACATAGAA
Found at i:5303251 original size:21 final size:21
Alignment explanation
Indices: 5303225--5303278 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
5303215 TTTGGGCAGA
5303225 GTGTATCGATACTCTACGTAT
1 GTGTATCGATACTCTACGTAT
*
5303246 GTGTATCGGTACTCTACGTAT
1 GTGTATCGATACTCTACGTAT
5303267 GTGTATCGATAC
1 GTGTATCGATAC
5303279 CCCCTTGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (21 bp):
GTGTATCGATACTCTACGTAT
Found at i:5303833 original size:23 final size:23
Alignment explanation
Indices: 5303800--5303843 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5303790 GAGTAGAGGG
5303800 TCTACGCGGTCCTTCAGGACAAT
1 TCTACGCGGTCCTTCAGGACAAT
* * *
5303823 TCTACGTGGTCTTTCGGGACA
1 TCTACGCGGTCCTTCAGGACA
5303844 TATATATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (23 bp):
TCTACGCGGTCCTTCAGGACAAT
Found at i:5305998 original size:612 final size:612
Alignment explanation
Indices: 5304825--5306043 Score: 1956
Period size: 612 Copynumber: 2.0 Consensus size: 612
5304815 TCAGAGCTAC
* *
5304825 AGTTTAACCGATTCTAGGCATAAACCATAGTCTAGAGTATCTTTATATGTGTACATGCTAACATA
1 AGTTTAACCGATTCTAGGCATAAACCAGAGTCTAGAGTATCTTTATATGTGTACATGCCAACATA
5304890 TAGTGAGAACTTCTGATCTGGTATAGTAATGAGTATGTTGTTTTGCTAATAGAACGATATGTGAA
66 TAGTGAGAACTTCTGATCTGGTATAGTAATGAGTATGTTGTTTTGCTAATAGAACGATATGTGAA
* * *
5304955 TTCTTATTAGATGTCCGAACATGATAGTTCTCGAAGTGAAGCGGGAGATGATCGGCCCGCTGAAA
131 TTCTTATTAGATGTCCGAACATGATAGTTCTCAAAGTGAAGCGGAAGATGATCGACCCGCTGAAA
* *
5305020 GTAGTAATTCACCTGCCCTTGCCAGGCAAGGTGAAGAATAGACACCTTTTGGAGTATCTATAGCT
196 GTAGTAATTCACCTGCCCTGGCCAGGCAAGGTGAAGAACAGACACCTTTTGGAGTATCTATAGCT
* * *
5305085 GATCAATATATGTTCTTTAGAACGTTAGATATGGTATTAACGCGTTTCTAACCTCCTGCTCCATC
261 GATCAAGATATGTTCTTTAGAACATTAGATATGGTATTAACGCGTTTCCAACCTCCTGCTCCATC
*
5305150 AACTCCCAGAGTAAATGTAGCAAAGGAGTAGAGACGATTAGGAGCTCCCGAATTAAAGGGAGAAT
326 AACTCCCAGAGTAAATGTAGCAAAGGAGTAGAGACGATTAGGAGCTCCCGAATTAAAGGGAGAAA
* *
5305215 CCGAAAAAGGTCTGATTGCAGCGGATCTTTGGTTAAATGATTTCAAAATTATGTTAGATGGTCTC
391 CCGAAAAAGGTCTGATTGCAGCGGATCTTTGGTTAAAGGATTTCAAAATCATGTTAGATGGTCTC
* *
5305280 CACTGTTCTGAAGTGGAGAAGCTGGATGGAGCTGTGTCATTACTTAGAGGACAAGCTAGAATATG
456 CACTATTCTGAAGTGGAGAAGATGGATGGAGCTGTGTCATTACTTAGAGGACAAGCTAGAATATG
* * *
5305345 ATAGACGAATGTCACTATGAGGATGTCAAGTGATCAAGTAACTTGGTATATGTTGTTAGAAGAGT
521 ATAGACGAATGCCACTATGAGGATGTCAAGTGATAAAGTAACTTGGTATATGTTCTTAGAAGAGT
* *
5305410 TTAAGCACAAATATATTTGAGAGTTAT
586 TTAAGCAAAAATATATTGGAGAGTTAT
* * *
5305437 AGTTTAGCCGATTCTAGGCGTAAACCAGAGTCTAGAGTGTCTTTATATGTGTACATGCCAACATA
1 AGTTTAACCGATTCTAGGCATAAACCAGAGTCTAGAGTATCTTTATATGTGTACATGCCAACATA
* **
5305502 TAGTGAGAACTTCTGATCTGGTATAGTAATGAGTATGTTGTTTTGCTAATAGAATGATATGTTTA
66 TAGTGAGAACTTCTGATCTGGTATAGTAATGAGTATGTTGTTTTGCTAATAGAACGATATGTGAA
*
5305567 TTCTTATTAGATGTCCGGACATGATAGTTCTCAAAGTGAAGCGGAAGATGATCGACCCGCTGAAA
131 TTCTTATTAGATGTCCGAACATGATAGTTCTCAAAGTGAAGCGGAAGATGATCGACCCGCTGAAA
* * *
5305632 TTAGTAATTCACCTGCTCTGGCCAGGCAAGGTGAAGAACATG-CA-CTTTCTGGAGTGTCTATAG
196 GTAGTAATTCACCTGCCCTGGCCAGGCAAGGTGAAGAACA-GACACCTTT-TGGAGTATCTATAG
* * * * *
5305695 CTGATCAAGATGTGTTCTTTAGAACATTAGATATGGTATTGATGCGTTTCCAACTTCTTGCTCCA
259 CTGATCAAGATATGTTCTTTAGAACATTAGATATGGTATTAACGCGTTTCCAACCTCCTGCTCCA
* * *
5305760 TCAACTCCCAGAGTAAATGTAGCAAAGGAGTTGAGAGGATTAGGAGCTCCCGAATTTAAGGGAGA
324 TCAACTCCCAGAGTAAATGTAGCAAAGGAGTAGAGACGATTAGGAGCTCCCGAATTAAAGGGAGA
* * * * *
5305825 AACTGAAGAAGGTCTGGTTGCAGCGGATCTTTGGTTAAAGGATTTGAAAATCATTTTAGATGGTC
389 AACCGAAAAAGGTCTGATTGCAGCGGATCTTTGGTTAAAGGATTTCAAAATCATGTTAGATGGTC
5305890 TCCACTATTCTGAAGTGGAGAAGATGGATGGAGCTGTGTCATTACTTAGAGGACAAGCTAGAATA
454 TCCACTATTCTGAAGTGGAGAAGATGGATGGAGCTGTGTCATTACTTAGAGGACAAGCTAGAATA
* * * * * *
5305955 TGGTAGATGGATGCCACTATGAGGATGTCAAGTGATAAAGTAACTTGGTCTCTGTTCTTGGAAGA
519 TGATAGACGAATGCCACTATGAGGATGTCAAGTGATAAAGTAACTTGGTATATGTTCTTAGAAGA
*
5306020 GTTTAAGTAAAAATATATTGGAGA
584 GTTTAAGCAAAAATATATTGGAGA
5306044 TCAATTCATC
Statistics
Matches: 555, Mismatches: 50, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
611 4 0.01
612 550 0.99
613 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (612 bp):
AGTTTAACCGATTCTAGGCATAAACCAGAGTCTAGAGTATCTTTATATGTGTACATGCCAACATA
TAGTGAGAACTTCTGATCTGGTATAGTAATGAGTATGTTGTTTTGCTAATAGAACGATATGTGAA
TTCTTATTAGATGTCCGAACATGATAGTTCTCAAAGTGAAGCGGAAGATGATCGACCCGCTGAAA
GTAGTAATTCACCTGCCCTGGCCAGGCAAGGTGAAGAACAGACACCTTTTGGAGTATCTATAGCT
GATCAAGATATGTTCTTTAGAACATTAGATATGGTATTAACGCGTTTCCAACCTCCTGCTCCATC
AACTCCCAGAGTAAATGTAGCAAAGGAGTAGAGACGATTAGGAGCTCCCGAATTAAAGGGAGAAA
CCGAAAAAGGTCTGATTGCAGCGGATCTTTGGTTAAAGGATTTCAAAATCATGTTAGATGGTCTC
CACTATTCTGAAGTGGAGAAGATGGATGGAGCTGTGTCATTACTTAGAGGACAAGCTAGAATATG
ATAGACGAATGCCACTATGAGGATGTCAAGTGATAAAGTAACTTGGTATATGTTCTTAGAAGAGT
TTAAGCAAAAATATATTGGAGAGTTAT
Found at i:5311480 original size:23 final size:23
Alignment explanation
Indices: 5311447--5311498 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
5311437 GTTTATGCGG
*
5311447 TCCTTCGGGACAATTCTACGTGA
1 TCCTTCAGGACAATTCTACGTGA
*
5311470 TCCTTCAGGACAATTCTACGTGG
1 TCCTTCAGGACAATTCTACGTGA
5311493 TCCTTC
1 TCCTTC
5311499 GGAACATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (23 bp):
TCCTTCAGGACAATTCTACGTGA
Found at i:5315004 original size:14 final size:14
Alignment explanation
Indices: 5314985--5315051 Score: 50
Period size: 14 Copynumber: 4.7 Consensus size: 14
5314975 AACTCTAGAA
5314985 TTTATTTTTTCTAG
1 TTTATTTTTTCTAG
5314999 TTTATTTTTTTCT--
1 TTTA-TTTTTTCTAG
**
5315012 TTTA-TTTTTGAAG
1 TTTATTTTTTCTAG
*
5315025 AAATTTATTTTTTCTAT
1 ---TTTATTTTTTCTAG
5315042 TTTATTTTTT
1 TTTATTTTTT
5315052 TCTCAAGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
11 5 0.12
13 4 0.10
14 14 0.34
15 8 0.20
16 4 0.10
17 6 0.15
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (14 bp):
TTTATTTTTTCTAG
Found at i:5315015 original size:13 final size:14
Alignment explanation
Indices: 5314984--5315020 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
5314974 CAACTCTAGA
5314984 ATTTA-TTTTTTCT
1 ATTTATTTTTTTCT
5314997 AGTTTATTTTTTTCT
1 A-TTTATTTTTTTCT
5315012 -TTTATTTTT
1 ATTTATTTTT
5315021 GAAGAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 4 0.18
15 8 0.36
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (14 bp):
ATTTATTTTTTTCT
Found at i:5316464 original size:14 final size:14
Alignment explanation
Indices: 5316447--5316475 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5316437 ATTCAAATGT
5316447 TAAATTCATTTTAA
1 TAAATTCATTTTAA
5316461 TAAATTCATTTTAA
1 TAAATTCATTTTAA
5316475 T
1 T
5316476 TTGCAAGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TAAATTCATTTTAA
Found at i:5316884 original size:26 final size:25
Alignment explanation
Indices: 5316835--5316882 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
5316825 GCACTTTTAA
* *
5316835 ACAACACTTTTAAAAGTTATTTTCC
1 ACAACACTTTTAAAAATCATTTTCC
5316860 ACAACACTTTTAAAAATCATTTT
1 ACAACACTTTTAAAAATCATTTT
5316883 TCAAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.40
Consensus pattern (25 bp):
ACAACACTTTTAAAAATCATTTTCC
Found at i:5329923 original size:18 final size:18
Alignment explanation
Indices: 5329900--5329935 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5329890 TTAAAAATCA
* *
5329900 ATATTTTATAATTATTTT
1 ATATTTTAAAAATATTTT
5329918 ATATTTTAAAAATATTTT
1 ATATTTTAAAAATATTTT
5329936 TAAATTAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTTAAAAATATTTT
Found at i:5329941 original size:29 final size:31
Alignment explanation
Indices: 5329864--5329942 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 31
5329854 TACTTAAATT
* *
5329864 AATAACATTTTATTATTATTTTTAATTTAAA
1 AATAATATTTTATAATTATTTTTAATTTAAA
*
5329895 AATCAATATTTTATAATTATTTTATATTTTAAA
1 AAT-AATATTTTATAATTATTTT-TAATTTAAA
5329928 AAT-AT-TTTTA-AATTA
1 AATAATATTTTATAATTA
5329943 ACAATAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
29 5 0.12
30 5 0.12
31 5 0.12
32 17 0.40
33 11 0.26
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (31 bp):
AATAATATTTTATAATTATTTTTAATTTAAA
Found at i:5329962 original size:25 final size:24
Alignment explanation
Indices: 5329924--5329992 Score: 95
Period size: 25 Copynumber: 2.9 Consensus size: 24
5329914 TTTTATATTT
5329924 TAAAA-ATATTTTTAAATTAACAA
1 TAAAATATATTTTTAAATTAACAA
* *
5329947 TAAAATATTATTTTTAAAATAAGAA
1 TAAAATA-TATTTTTAAATTAACAA
*
5329972 TAAAATATATTTCTAAATTAA
1 TAAAATATATTTTTAAATTAA
5329993 ACTAAGATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.12
24 13 0.32
25 22 0.55
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (24 bp):
TAAAATATATTTTTAAATTAACAA
Found at i:5330021 original size:32 final size:30
Alignment explanation
Indices: 5329964--5330076 Score: 99
Period size: 30 Copynumber: 3.7 Consensus size: 30
5329954 TTATTTTTAA
* *
5329964 AATAAGAATAAAATATATTTCTAAATTAAACT
1 AATAAAAATAAAATATA-TT-TAAATTAAAAT
*
5329996 AAGATAAAAATAATATATATTTAAATTAAAAT
1 -A-ATAAAAATAAAATATATTTAAATTAAAAT
* *
5330028 AATAATAATAAAATAT-TATTAAATT-AAGT
1 AATAAAAATAAAATATAT-TTAAATTAAAAT
*
5330057 --TAATAATAAAATATATTTAA
1 AATAAAAATAAAATATATTTAA
5330077 TGAGTTAAGA
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
27 18 0.25
28 1 0.01
29 4 0.06
30 20 0.28
31 1 0.01
32 10 0.14
33 3 0.04
34 14 0.20
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (30 bp):
AATAAAAATAAAATATATTTAAATTAAAAT
Found at i:5330029 original size:27 final size:27
Alignment explanation
Indices: 5329929--5330076 Score: 79
Period size: 27 Copynumber: 5.4 Consensus size: 27
5329919 TATTTTAAAA
*
5329929 ATATTTTTAAATTAACAAT-AAAAT-AT
1 ATATATTTAAATTAA-AATAAAAATAAT
* *
5329955 -TATTTTTAAAATAAGAAT-AAAATATAT
1 ATATATTTAAATTAA-AATAAAAATA-AT
* * * * *
5329982 TTCTAAATTAAACTAAGATAAAAATAAT
1 ATAT-ATTTAAATTAAAATAAAAATAAT
*
5330010 ATATATTTAAATTAAAATAATAATAAT
1 ATATATTTAAATTAAAATAAAAATAAT
* ** * *
5330037 AAAATATTATTAAATTAAGTTAATAATAAA
1 -ATATA-T-TTAAATTAAAATAAAAATAAT
5330067 ATATATTTAA
1 ATATATTTAA
5330077 TGAGTTAAGA
Statistics
Matches: 96, Mismatches: 18, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
25 21 0.22
27 25 0.26
28 13 0.14
29 19 0.20
30 18 0.19
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATATTTAAATTAAAATAAAAATAAT
Found at i:5330050 original size:30 final size:29
Alignment explanation
Indices: 5329948--5330073 Score: 98
Period size: 30 Copynumber: 4.3 Consensus size: 29
5329938 AATTAACAAT
* *
5329948 AAAATATTATT--TTTAAAATAAGAATAA
1 AAAATATTATTAAATTAAAATAATAATAA
* *
5329975 AATATATT-TCTAAATTAAACTAAGATAA-AA
1 AAAATATTAT-TAAATTAAAAT-A-ATAATAA
*
5330005 ATAATATATATTTAAATTAAAATAATAATAA
1 AAAATAT-TA-TTAAATTAAAATAATAATAA
**
5330036 TAAAATATTATTAAATTAAGTTAATAATAA
1 -AAAATATTATTAAATTAAAATAATAATAA
*
5330066 AATATATT
1 AAAATATT
5330074 TAATGAGTTA
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
26 1 0.01
27 8 0.10
29 13 0.17
30 30 0.38
31 9 0.12
32 16 0.21
33 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATATTATTAAATTAAAATAATAATAA
Found at i:5330085 original size:30 final size:29
Alignment explanation
Indices: 5329988--5330101 Score: 96
Period size: 30 Copynumber: 4.0 Consensus size: 29
5329978 ATATTTCTAA
* * *
5329988 ATTAAACTAAGA-TAAAAATAATATATAT
1 ATTAAATTAAGATTAATAATAAAATATAT
*
5330016 -TTAAATTAAAATAATAATAATAAAATAT-T
1 ATTAAATTAAGAT--TAATAATAAAATATAT
5330045 ATTAAATTAAG-TTAATAATAAAATATAT
1 ATTAAATTAAGATTAATAATAAAATATAT
*
5330073 -TTAATGAGTTAAGATCAA-AATAAAATATA
1 ATTAA--A-TTAAGATTAATAATAAAATATA
5330102 CTTTCAAAGT
Statistics
Matches: 71, Mismatches: 6, Indels: 16
0.76 0.06 0.17
Matches are distributed among these distances:
27 27 0.38
28 1 0.01
29 3 0.04
30 37 0.52
31 3 0.04
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (29 bp):
ATTAAATTAAGATTAATAATAAAATATAT
Found at i:5331170 original size:20 final size:20
Alignment explanation
Indices: 5331130--5331170 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5331120 TTAGTTGTTT
* * *
5331130 TCTATTATTTTTATTATAAA
1 TCTAATATTTTTATAACAAA
5331150 TCTAATATTTTTATAACAAA
1 TCTAATATTTTTATAACAAA
5331170 T
1 T
5331171 AAGATAAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (20 bp):
TCTAATATTTTTATAACAAA
Found at i:5331416 original size:32 final size:31
Alignment explanation
Indices: 5331378--5331467 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 31
5331368 ATTTGGTTCG
* *
5331378 GGTTGCTTTTGGATCTGGTTAATTTCGATTCA
1 GGTTGCTTTTGGTTC-GGTTAATTTCGATCCA
* *
5331410 GTTTGCTTTAT-GTTCGGGTTATTTTCGATCCA
1 GGTTGCTTT-TGGTTC-GGTTAATTTCGATCCA
5331442 GGTTGCTTTTGGTTCGTGTTAATTTC
1 GGTTGCTTTTGGTTCG-GTTAATTTC
5331468 AATTTCGACT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
31 2 0.04
32 45 0.94
33 1 0.02
ACGTcount: A:0.12, C:0.13, G:0.24, T:0.50
Consensus pattern (31 bp):
GGTTGCTTTTGGTTCGGTTAATTTCGATCCA
Found at i:5332830 original size:183 final size:182
Alignment explanation
Indices: 5332540--5333562 Score: 1452
Period size: 182 Copynumber: 5.6 Consensus size: 182
5332530 ATACAAATGA
* * * * * * * *
5332540 AAAATGGATCGACCCATAGCAATATTACAGGTACAAATATGACAAAACCGGTCCCAAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAATGACAA
5332605 AA-CATGTAAAACGTTACCGGATATGTGTCG--AGTGTCGATAATTTAATATAAGTATCGAAACT
66 AACCA-GTAAAACGTTACCGGATATGT-T-GAAAGTGTCGATAATTTAATATAAGTATCGAAACT
* * * *
5332667 TTTTGAATTTAAAAGAGAAGAAGTTATTGTGCCTAAAATGTGTCGACACTTTATG
128 TTCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATG
*
5332722 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACATGTCTCAAAATTGACA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAA-TGACA
* * * *
5332787 AAACCAGTAAAACGCTACCAGATATATTGAAAGTGTCGATAATTTAATATAAGTATCAAAACTTT
65 AAACCAGTAAAACGTTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTT
* * * *
5332852 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTAGATAC-TTA-A
130 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATG
** * *
5332903 AAAAAATATCGATCCACAATAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTC-AAAATGACA
* * * * * *
5332968 AAACCTG-AAAAAGTTACTGGATATGTTAAAAGTGTCAATAATTTAATATAAGTATCGACACTTT
65 AAACCAGTAAAACGTTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTT
*
5333032 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGAGTCGACACTTTATG
130 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATG
*
5333085 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACATGTCTCAAAATTGACA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAA-TGACA
* * *
5333150 AAACCAGTAAAACGCTACCGGATATATTGAAAGTGTCGATAATTTAATATTAA-TATCGACACTT
65 AAACCAGTAAAACGTTACCGGATATGTTGAAAGTGTCGATAATTTAATA-TAAGTATCGAAACTT
5333214 TCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATG
129 TCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATG
* * *
5333268 AAAATGTATCGATCCTTACCAATATAACAGGTAAAAATATGATAAAATAGGTCTCAAAAATGACA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTC-AAAATGACA
* *
5333333 AAACC-GGAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTT
65 AAACCAGTAAAACGTTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTT
* * *
5333397 TTGAATTTAAAAGAGAAGAAGTTATAGTGCTTAAAAAGTGTCGACACTTTATG
130 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATG
* * *
5333450 AAAATGTATCGATCCAGAACAATATAACAGTTAAAAATATGATAAAACCGGTCTCAAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAATGACAA
* * *
5333515 AACCGGTAAATA-GATACCGGATATGTTGAAAGTGTCGATACTTTAATA
66 AACCAGTAAA-ACGTTACCGGATATGTTGAAAGTGTCGATAATTTAATA
5333563 AGTACGAGTA
Statistics
Matches: 752, Mismatches: 75, Indels: 28
0.88 0.09 0.03
Matches are distributed among these distances:
180 91 0.12
181 86 0.11
182 306 0.41
183 260 0.35
184 9 0.01
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAATGACAA
AACCAGTAAAACGTTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTC
TGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATG
Found at i:5333231 original size:363 final size:364
Alignment explanation
Indices: 5332559--5333562 Score: 1543
Period size: 363 Copynumber: 2.8 Consensus size: 364
5332549 CGACCCATAG
* * * * * * *
5332559 CAATATTACAGGTACAAATATGACAAAACCGGTC-CCAAAATGACAAAACATGTAAAACGTTACC
1 CAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCTG-AAAAAGTTACC
**
5332623 GGATATGTGTCGAGTGTCGATAATTTAATATAAGTATCGAAACTTTTTGAATTTAAAAGAGAAGA
65 GGATATGT-TAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTTTGAATTTAAAAGAGAAGA
* *
5332688 AGTTATTGTGCCTAAAATGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGG
129 AGTTATAGTGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGG
*
5332753 TAAAAATATGATAAAACATGTCTCAAAATTGACAAAACCAGTAAAACGCTACCAGATATATTGAA
194 TAAAAATATGATAAAACATGTCTCAAAATTGACAAAACCAGTAAAACGCTACCGGATATATTGAA
5332818 AGTGTCGATAATTTAATATAAGTATCAAAACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCC
259 AGTGTCGATAATTTAATATAAGTATCAAAACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCC
* *
5332883 TATAAAGTGTAGATAC-TTA-AAAAAAATATCGATCCACAA
324 TAAAAAGTGTAGACACTTTATAAAAAAATATCGATCCACAA
* *
5332922 TAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCTGAAAAAGTTACTG
1 CAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCTGAAAAAGTTACCG
* * *
5332987 GATATGTTAAAAGTGTCAATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAA
66 GATATGTT-AAAGTGTCGATAATTTAATATAAGTATCGAAACTTTTTGAATTTAAAAGAGAAGAA
* *
5333052 GTTATAGCGCCTAAAAAGAGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGT
130 GTTATAGTGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGT
5333117 AAAAATATGATAAAACATGTCTCAAAATTGACAAAACCAGTAAAACGCTACCGGATATATTGAAA
195 AAAAATATGATAAAACATGTCTCAAAATTGACAAAACCAGTAAAACGCTACCGGATATATTGAAA
* *
5333182 GTGTCGATAATTTAATATTAA-TATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCC
260 GTGTCGATAATTTAATA-TAAGTATCAAAACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCC
* * ** ** *
5333246 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCTTAC
324 TAAAAAGTGTAGACACTTTATAAAAAAATATCGATCCACAA
* *
5333287 CAATATAACAGGTAAAAATATGATAAAATAGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCG
1 CAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCTGAAAAAGTTACCG
5333352 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTTTGAATTTAAAAGAGAAGAA
66 GATATGTT-AAAGTGTCGATAATTTAATATAAGTATCGAAACTTTTTGAATTTAAAAGAGAAGAA
* * *
5333417 GTTATAGTGCTTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCAGAACAATATAACAGTT
130 GTTATAGTGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGT
** * * *
5333482 AAAAATATGATAAAACCGGTCTCAAAA-TGACAAAACCGGTAAATA-GATACCGGATATGTTGAA
195 AAAAATATGATAAAACATGTCTCAAAATTGACAAAACCAGTAAA-ACGCTACCGGATATATTGAA
*
5333545 AGTGTCGATACTTTAATA
259 AGTGTCGATAATTTAATA
5333563 AGTACGAGTA
Statistics
Matches: 586, Mismatches: 49, Indels: 11
0.91 0.08 0.02
Matches are distributed among these distances:
362 1 0.00
363 293 0.50
364 70 0.12
365 222 0.38
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (364 bp):
CAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCTGAAAAAGTTACCG
GATATGTTAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTTTGAATTTAAAAGAGAAGAAG
TTATAGTGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTA
AAAATATGATAAAACATGTCTCAAAATTGACAAAACCAGTAAAACGCTACCGGATATATTGAAAG
TGTCGATAATTTAATATAAGTATCAAAACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTA
AAAAGTGTAGACACTTTATAAAAAAATATCGATCCACAA
Found at i:5333972 original size:18 final size:19
Alignment explanation
Indices: 5333949--5333993 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
5333939 TAGTTAATAT
5333949 TTATAGGTA-AAAATGATA
1 TTATAGGTAGAAAATGATA
5333967 TTATAGGTAGAAAATGATA
1 TTATAGGTAGAAAATGATA
*
5333986 TTTTAGGT
1 TTATAGGT
5333994 TGTATAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (19 bp):
TTATAGGTAGAAAATGATA
Found at i:5334263 original size:17 final size:19
Alignment explanation
Indices: 5334238--5334276 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
5334228 TTAAAATGGT
5334238 AATTGGATTA-AAACTTTA
1 AATTGGATTACAAACTTTA
*
5334256 AATT-GATTACAAATTTTA
1 AATTGGATTACAAACTTTA
5334274 AAT
1 AAT
5334277 GTTGACAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
AATTGGATTACAAACTTTA
Found at i:5335288 original size:22 final size:22
Alignment explanation
Indices: 5335237--5335292 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
5335227 AATGTTTTTG
*
5335237 TTTTTTTATATAAAATGATAGTA
1 TTTTATTATATAAAATGATAG-A
*
5335260 TAGTTATTATATAAAATGATA-A
1 T-TTTATTATATAAAATGATAGA
5335282 CTTTTATTATA
1 -TTTTATTATA
5335293 AATGCAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 2 0.07
24 17 0.61
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTTATTATATAAAATGATAGA
Found at i:5336011 original size:22 final size:18
Alignment explanation
Indices: 5335962--5336000 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5335952 AAAAAAATTT
*
5335962 GAAGAAGAGAAGATGGAG
1 GAAGAAGAAAAGATGGAG
5335980 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
5335998 GAA
1 GAA
5336001 ATGAGGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:5337494 original size:19 final size:19
Alignment explanation
Indices: 5337468--5337516 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
5337458 AAATGCATGG
5337468 TTAA-TTTGTATAAGATTT
1 TTAATTTTGTATAAGATTT
*
5337486 TTAATTTTGTATACGATTT
1 TTAATTTTGTATAAGATTT
*
5337505 ATAATTTTGTAT
1 TTAATTTTGTAT
5337517 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TTAATTTTGTATAAGATTT
Found at i:5338207 original size:199 final size:199
Alignment explanation
Indices: 5337860--5339552 Score: 2711
Period size: 199 Copynumber: 8.5 Consensus size: 199
5337850 GTAAACTTAT
* * * * *
5337860 GTGTCGATACATTTATAACAAGTATTGATCCCAAAAACATCAAAAACCATAATTATAATGTAAT-
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
* * * *
5337924 GGTAAATTAGCAATATAACCGGTCTAAATATACCGATTTTTGAGAAAACATGTGTAAAAAAATTA
66 GGTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
* *
5337989 TCGACACAAATCGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACTA
5338054 AAAA
196 AAAA
*
5338058 GTGTTGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
* *
5338123 GGTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTTAGAAAACATGTGTAAAAAAAGTA
66 GGTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
* *
5338188 TCTG-CTCAAATCAAACAAGTGTCGATACTTTTGGTCCATAATGTATTTCAAAACCAAGTGCACT
131 TC-GACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACT
5338252 AAAAA
195 AAAAA
5338257 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
* * *
5338322 GGTAGGTTAGCAATATAACCGGTCTAAATATATCGGTTTTTGAGAAAACATGTGTAAAAAAAGTA
66 GGTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
*
5338387 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCCCTA
131 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACTA
5338452 AAAA
196 AAAA
*
5338456 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCAAAAACTATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
* * *
5338521 GGTAGATTAGCAATATAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGT-ACAACAGTA
66 GGTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
* *
5338585 TCGACACAAAT-AGAACAAGTGTCGATACTTTTGGTCCATAATGTATTTCAGAACCAAGTGCAC-
131 TCGACACAAATCA-AACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACT
*
5338648 ATAAAT
195 A-AAAA
** * *
5338654 GTGTCGATACATTTAAAACAAATGTCGATCCCGAAAACATCGAAAAAC-ATAATTATAATGTAAT
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCG-AAAACTATAATTATAATGTAAT
* * * * * * *
5338718 AGGTAAATTATTC-ATGTAAACGGTCTAAATATACTGGTTTTTTAGAAAACAGGTGTAAAAAAGG
65 AGGTAGATTA-GCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAG
* *
5338782 TATCGACACAAAAT-AAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCATGTGCA
129 TATCGACAC-AAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCA
5338846 CTAAAAA
193 CTAAAAA
*
5338853 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAATATCGAAAACTATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
* * * *
5338918 GGTATATTAGCAATATAATCGGTCTAAATATATCAGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
66 GGTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
*
5338983 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCCCTA
131 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACTA
5339048 AAAA
196 AAAA
*
5339052 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATAGAAAACTATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
* * * *
5339117 GGTAGATTAGCAATATAACCGGTCTAAATATACTGATTTTTGAAAAAACATGTGTAAAAAAAGTA
66 GGTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
5339182 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTC-AAACCAAGTGCACTA
131 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACTA
5339246 AAAA
196 AAAA
5339250 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
* * *
5339315 GGTAGATTAGCAATATAATCGGTCTAAATATAGCGATTTTTGAGAAAACAGGTGTAAAAAAAGTA
66 GGTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
* *
5339380 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCTAAAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACTA
5339445 AAAA
196 AAAA
* * *
5339449 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCAAAAACCATAATTGTAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
* * *
5339514 GGTAAATTAGCAATATAACCAGTCTAAATATATCGGTTT
66 GGTAGATTAGCAATATAACCGGTCTAAATATACCGGTTT
5339553 AAATTGAAAA
Statistics
Matches: 1387, Mismatches: 94, Indels: 27
0.92 0.06 0.02
Matches are distributed among these distances:
197 2 0.00
198 426 0.31
199 952 0.69
200 7 0.01
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (199 bp):
GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
GGTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACTA
AAAA
Found at i:5338642 original size:596 final size:595
Alignment explanation
Indices: 5337860--5339552 Score: 2792
Period size: 596 Copynumber: 2.8 Consensus size: 595
5337850 GTAAACTTAT
* * * *
5337860 GTGTCGATACATTTATAACAAGTATTGATCCCAAAAACATCAAAAACCATAATTATAATGTAAT-
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCAAAAACTATAATTATAATGTAATA
* *
5337924 GGTAAATTAGCAATATAACCGGTCTAAATATACCGATTTTTGAGAAAACATGTGTAAAAAAATTA
66 GGTAGATTAGCAATATAACCGGTCTAAATATACCGATTTTTGAGAAAACATGTGTAAAAAAAGTA
* *
5337989 TCGACACAAATCGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTC-AAACCAAGTGCACTA
*
5338054 AAAAGTGTTGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGT
195 AAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGT
* *
5338119 AATAGGTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTTAGAAAACATGTGTAAAAAA
260 AATAGGTAGATTAGCAATATAAACGGTCTAAATATACCGGTTTTTTAGAAAACAGGTGTAAAAAA
* *
5338184 AGTATCTG-CTCAAATCAAACAAGTGTCGATACTTTTGGTCCATAATGTATTTCAAAACCAAGTG
325 AGTATC-GACACAAAT-AAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTG
5338248 CACTAAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTAT
388 CACTAAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTAT
** *
5338313 AATGTAATAGGTAGGTTAGCAATATAACCGGTCTAAATATATCGGTTTTTGAGAAAACATGTGTA
453 AATGTAATAGGTAAATTAGCAATATAACCGGTCTAAATATATCGGTTTTTGAGAAAACAGGTGTA
5338378 AAAAAAGTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCA
518 AAAAAAGTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCA
5338443 AGTGCCCTAAAAA
583 AGTGCCCTAAAAA
5338456 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCAAAAACTATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCAAAAACTATAATTATAATGTAATA
* * *
5338521 GGTAGATTAGCAATATAACCGGTCTAAATATACC-AGTTTTTGAGAAAACAGGTGT-ACAACAGT
66 GGTAGATTAGCAATATAACCGGTCTAAATATACCGA-TTTTTGAGAAAACATGTGTAAAAAAAGT
*
5338584 ATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCATAATGTATTTCAGAACCAAGTGCAC-
130 ATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCA-AACCAAGTGCACT
* ** * *
5338648 ATAAATGTGTCGATACATTTAAAACAAATGTCGATCCCGAAAACATCGAAAAAC-ATAATTATAA
194 A-AAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCG-AAAACTATAATTATAA
* * * *
5338712 TGTAATAGGTAAATTATTC-ATGTAAACGGTCTAAATATACTGGTTTTTTAGAAAACAGGTGTAA
257 TGTAATAGGTAGATTA-GCAATATAAACGGTCTAAATATACCGGTTTTTTAGAAAACAGGTGTAA
* * *
5338776 AAAAGGTATCGACACAAAATAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAT
321 AAAAAGTATCGACAC-AAATAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAA
*
5338841 GTGCACTAAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAATATCGAAAACTATAAT
385 GTGCACTAAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAAT
* * *
5338906 TATAATGTAATAGGTATATTAGCAATATAATCGGTCTAAATATATCAGTTTTTGAGAAAACAGGT
450 TATAATGTAATAGGTAAATTAGCAATATAACCGGTCTAAATATATCGGTTTTTGAGAAAACAGGT
5338971 GTAAAAAAAGTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAA
515 GTAAAAAAAGTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAA
5339036 CCAAGTGCCCTAAAAA
580 CCAAGTGCCCTAAAAA
5339052 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACAT-AGAAAACTATAATTATAATGTAAT
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCA-AAAACTATAATTATAATGTAAT
* *
5339116 AGGTAGATTAGCAATATAACCGGTCTAAATATACTGATTTTTGAAAAAACATGTGTAAAAAAAGT
65 AGGTAGATTAGCAATATAACCGGTCTAAATATACCGATTTTTGAGAAAACATGTGTAAAAAAAGT
5339181 ATCGACACAAATCA-AACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAACCAAGTGCACT
130 ATCGACACAAAT-AGAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAACCAAGTGCACT
5339245 AAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATG
194 AAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATG
* * * *
5339310 TAATAGGTAGATTAGCAATATAATCGGTCTAAATATAGCGATTTTTGAGAAAACAGGTGTAAAAA
259 TAATAGGTAGATTAGCAATATAAACGGTCTAAATATACCGGTTTTTTAGAAAACAGGTGTAAAAA
*
5339375 AAGTATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCTAAAATGTATTTCAAAACCAAGTG
324 AAGTATCGACACAAAT-AAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTG
* * *
5339440 CACTAAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCAAAAACCATAATTGT
388 CACTAAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTAT
*
5339505 AATGTAATAGGTAAATTAGCAATATAACCAGTCTAAATATATCGGTTT
453 AATGTAATAGGTAAATTAGCAATATAACCGGTCTAAATATATCGGTTT
5339553 AAATTGAAAA
Statistics
Matches: 1017, Mismatches: 64, Indels: 32
0.91 0.06 0.03
Matches are distributed among these distances:
595 14 0.01
596 885 0.87
597 117 0.12
598 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (595 bp):
GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCAAAAACTATAATTATAATGTAATA
GGTAGATTAGCAATATAACCGGTCTAAATATACCGATTTTTGAGAAAACATGTGTAAAAAAAGTA
TCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAACCAAGTGCACTAA
AAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTA
ATAGGTAGATTAGCAATATAAACGGTCTAAATATACCGGTTTTTTAGAAAACAGGTGTAAAAAAA
GTATCGACACAAATAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCAC
TAAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAAT
GTAATAGGTAAATTAGCAATATAACCGGTCTAAATATATCGGTTTTTGAGAAAACAGGTGTAAAA
AAAGTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGT
GCCCTAAAAA
Found at i:5338802 original size:397 final size:398
Alignment explanation
Indices: 5337860--5339545 Score: 2725
Period size: 397 Copynumber: 4.2 Consensus size: 398
5337850 GTAAACTTAT
* * *
5337860 GTGTCGATACATTTATAACAAGTATTGATCCCAAAAACATC-AAAAACCATAATTATAATGTAAT
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAAA-CATAATTATAATGTAAT
* *
5337924 -GGTAAATTAGCAATATAACCGGTCTAAATATACCGATTTTTGAGAAAACATGTGTAAAAAAATT
65 AGGTAAATTAGCAATATAACCGGTCTAAATATACTGATTTTTGAGAAAACATGTGTAAAAAAAGT
* *
5337988 ATCGACACAAATCGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACT
130 ATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACT
*
5338053 AAAAAGTGTTGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATG
195 AAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATG
* * *
5338118 TAATAGGTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTTAGAAAACATGTGTAAAAA
260 TAATAGGTAGATTAGCAATATAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTAAAAA
* *
5338183 AAGTATCTG-CTCAAATCAAACAAGTGTCGATACTTTTGGTCCATAATGTATTTCAAAACCAAGT
325 AAGTATC-GACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGT
5338247 GCACTAAAAA
389 GCACTAAAAA
5338257 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCG-AAAACTATAATTATAATGTAAT
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAAAC-ATAATTATAATGTAAT
** *
5338321 AGGTAGGTTAGCAATATAACCGGTCTAAATATA-TCGGTTTTTGAGAAAACATGTGTAAAAAAAG
65 AGGTAAATTAGCAATATAACCGGTCTAAATATACT-GATTTTTGAGAAAACATGTGTAAAAAAAG
*
5338385 TATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCCC
129 TATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCAC
*
5338450 TAAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCAAAAACTATAATTATAAT
194 TAAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAAT
*
5338515 GTAATAGGTAGATTAGCAATATAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGT-ACA
259 GTAATAGGTAGATTAGCAATATAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTAAAA
* * *
5338579 ACAGTATCGACACAAAT-AGAACAAGTGTCGATACTTTTGGTCCATAATGTATTTCAGAACCAAG
324 AAAGTATCGACACAAATCA-AACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAG
*
5338643 TGCAC-ATAAAT
388 TGCACTA-AAAA
** * *
5338654 GTGTCGATACATTTAAAACAAATGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAATA
* * * * * * *
5338719 GGTAAATTATTC-ATGTAAACGGTCTAAATATACTGGTTTTTTAGAAAACAGGTGTAAAAAAGGT
66 GGTAAATTA-GCAATATAACCGGTCTAAATATACTGATTTTTGAGAAAACATGTGTAAAAAAAGT
* *
5338783 ATCGACACAAAAT-AAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCATGTGCAC
130 ATCGACAC-AAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCAC
*
5338847 TAAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAATATCGAAAACTATAATTATAAT
194 TAAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAAT
* * *
5338912 GTAATAGGTATATTAGCAATATAATCGGTCTAAATATATCAGTTTTTGAGAAAACAGGTGTAAAA
259 GTAATAGGTAGATTAGCAATATAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTAAAA
5338977 AAAGTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGT
324 AAAGTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGT
*
5339042 GCCCTAAAAA
389 GCACTAAAAA
*
5339052 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATAG-AAAACTATAATTATAATGTAAT
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAAAC-ATAATTATAATGTAAT
* *
5339116 AGGTAGATTAGCAATATAACCGGTCTAAATATACTGATTTTTGAAAAAACATGTGTAAAAAAAGT
65 AGGTAAATTAGCAATATAACCGGTCTAAATATACTGATTTTTGAGAAAACATGTGTAAAAAAAGT
5339181 ATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTC-AAACCAAGTGCACT
130 ATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACT
5339245 AAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATG
195 AAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATG
* *
5339310 TAATAGGTAGATTAGCAATATAATCGGTCTAAATATAGC-GATTTTTGAGAAAACAGGTGTAAAA
260 TAATAGGTAGATTAGCAATATAACCGGTCTAAATATACCAG-TTTTTGAGAAAACAGGTGTAAAA
* *
5339374 AAAGTATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCTAAAATGTATTTCAAAACCAAGT
324 AAAGTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGT
5339439 GCACTAAAAA
389 GCACTAAAAA
*
5339449 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATC-AAAAACCATAATTGTAATGTAAT
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAAA-CATAATTATAATGTAAT
*
5339513 AGGTAAATTAGCAATATAACCAGTCTAAATATA
65 AGGTAAATTAGCAATATAACCGGTCTAAATATA
5339546 TCGGTTTAAA
Statistics
Matches: 1196, Mismatches: 73, Indels: 40
0.91 0.06 0.03
Matches are distributed among these distances:
396 5 0.00
397 718 0.60
398 471 0.39
399 2 0.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (398 bp):
GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAATA
GGTAAATTAGCAATATAACCGGTCTAAATATACTGATTTTTGAGAAAACATGTGTAAAAAAAGTA
TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACTA
AAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGT
AATAGGTAGATTAGCAATATAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTAAAAAA
AGTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGC
ACTAAAAA
Found at i:5341329 original size:17 final size:17
Alignment explanation
Indices: 5341309--5341344 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5341299 ATTTTGCTTA
5341309 CAGAATTTTTTTGTTGC
1 CAGAATTTTTTTGTTGC
5341326 CAGAATTTTTTTGTTGC
1 CAGAATTTTTTTGTTGC
5341343 CA
1 CA
5341345 TTTGGTCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (17 bp):
CAGAATTTTTTTGTTGC
Found at i:5342845 original size:199 final size:199
Alignment explanation
Indices: 5342500--5343545 Score: 1489
Period size: 199 Copynumber: 5.3 Consensus size: 199
5342490 CAAATAAAAC
* ** * *
5342500 AAGTTTCGATACATTTAAAACAAAAGTCGATCCCGAAAACATCAAAAAACATAATTATAATGTAA
1 AAGTGTCGATACATTTAAAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAA
* *
5342565 TAGGTAAATTATTCATGTAAACGGTCTAAATATACCGGTTTTTGAGAAAAACAGGTGT-AAAACA
66 TAGGTAAATTATTCATGTAAACGGTCTAAATATACCGATTTTTGAG-AAAACAGGTGTAAAAAAA
*
5342629 GTATCGACACAAATCAAACAAGTGTTGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCA
130 GTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCA
5342694 CATAA
195 CATAA
*
5342699 AAGTGTCGATACATTTAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAA
1 AAGTGTCGATACATTTAAAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAA
5342764 TAGGTAAATTATTCATGTAAACGGTCTAAATATACCGATTTTTGAGAAAACAGGTGTAAAAAAAG
66 TAGGTAAATTATTCATGTAAACGGTCTAAATATACCGATTTTTGAGAAAACAGGTGTAAAAAAAG
5342829 TATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCAC
131 TATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCAC
5342894 -TAAA
196 AT-AA
* * *
5342898 AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATTGAAAACCATAATTATAATGTAA
1 AAGTGTCGATACATTTAAAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAA
*** * * * *
5342963 TAGGTAAATTAGAAATATAATCGGTCTAAATATACCAGTTTTTTGAGAAAACAGGTGTACAAACA
66 TAGGTAAATTATTCATGTAAACGGTCTAAATATACC-GATTTTTGAGAAAACAGGTGTA-AAAAA
* * *
5343028 A-TATCGACACAAAT-AGAACAAGTGTTGATACTTTTGGTCCAGAATGTATTTCAGAACCAAGTG
129 AGTATCGACACAAATCA-AACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTG
5343091 CACATAA
193 CACATAA
*
5343098 AAGTGTCGATACATTTAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAA
1 AAGTGTCGATACATTTAAAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAA
*
5343163 TAGGTAAATTATTCATGTAAACGGTCT-AA-AT----A----TGAGAAAACATGTGTAAAAAAAG
66 TAGGTAAATTATTCATGTAAACGGTCTAAATATACCGATTTTTGAGAAAACAGGTGTAAAAAAAG
5343218 TATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCAC
131 TATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCAC
5343283 -TAAA
196 AT-AA
* * *
5343287 AACG-GTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAAACCATAATTATAATGTA
1 AA-GTGTCGATACATTTAAAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTA
*** * * * * *
5343351 ATAGGTAAATTAGAAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTACAAAAA
65 ATAGGTAAATTATTCATGTAAACGGTCTAAATATACCGATTTTTGAGAAAACAGGTGTAAAAAAA
* * * * * *
5343416 GTATCGACACAAAT-AGAATAAGTGTCAATACTTTTTGTCCAGAATGTATTTTAGAACCAAGTGC
130 GTATCGACACAAATCA-AACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGC
5343480 ACA-ACA
194 ACATA-A
* * *
5343486 AAGTTTCGATACATTTATAACAATTGTCGATCCCAAAAACATCGAAAAACATAATTATAA
1 AAGTGTCGATACATTTAAAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAA
5343546 CCAAATGTCT
Statistics
Matches: 766, Mismatches: 57, Indels: 48
0.88 0.07 0.06
Matches are distributed among these distances:
188 6 0.01
189 158 0.21
190 4 0.01
191 2 0.00
198 17 0.02
199 407 0.53
200 166 0.22
201 6 0.01
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.27
Consensus pattern (199 bp):
AAGTGTCGATACATTTAAAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAA
TAGGTAAATTATTCATGTAAACGGTCTAAATATACCGATTTTTGAGAAAACAGGTGTAAAAAAAG
TATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCAC
ATAA
Found at i:5346699 original size:162 final size:162
Alignment explanation
Indices: 5346427--5346761 Score: 571
Period size: 162 Copynumber: 2.1 Consensus size: 162
5346417 ACCAGTCTAT
* * *
5346427 AAATGACAAAACAGGTAAAGCGCTACCAGATATGTTGATAGTGTCGATATTTTATTATAAATATC
1 AAATGACAAAACAGGTAAAGAGATACCAGATATATTGATAGTGTCGATATTTTATTATAAATATC
* *
5346492 GACACTTTTGGAATTTAAAAGAGAATAAGTTATAGCGCTAATAAAGTGTCGATACTTTATAAAAA
66 GACACTTTTGGAATTTAAAAGAAAATAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAA
* *
5346557 TGTATCGATTCATAACAATATAACATGTAAAA
131 TGTATCGATCCATAACAATATAACAGGTAAAA
* * *
5346589 AAATGACAAAACCGGTAAAGAGATGCCAGATATATTGATAGTGTCGATATTTTATTATAAGTATC
1 AAATGACAAAACAGGTAAAGAGATACCAGATATATTGATAGTGTCGATATTTTATTATAAATATC
5346654 GACACTTTTGGAATTTAAAAGAAAATAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAA
66 GACACTTTTGGAATTTAAAAGAAAATAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAA
5346719 TGTATCGATCCATAACAATATAACAGGTAAAA
131 TGTATCGATCCATAACAATATAACAGGTAAAA
*
5346751 ATATGACAAAA
1 AAATGACAAAA
5346762 TCGATCTCGA
Statistics
Matches: 162, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 162 1.00
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.30
Consensus pattern (162 bp):
AAATGACAAAACAGGTAAAGAGATACCAGATATATTGATAGTGTCGATATTTTATTATAAATATC
GACACTTTTGGAATTTAAAAGAAAATAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAA
TGTATCGATCCATAACAATATAACAGGTAAAA
Found at i:5347168 original size:20 final size:20
Alignment explanation
Indices: 5347140--5347178 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5347130 AAATCGATAA
*
5347140 TTATTATGTAACAGGTAAAT
1 TTATAATGTAACAGGTAAAT
*
5347160 TTATAATGTAACCGGTAAA
1 TTATAATGTAACAGGTAAA
5347179 AATATACTGG
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:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (20 bp):
TTATAATGTAACAGGTAAAT
Found at i:5347184 original size:20 final size:20
Alignment explanation
Indices: 5347145--5347184 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5347135 GATAATTATT
**
5347145 ATGTAACAGGTAAATTTATA
1 ATGTAACAGGTAAAAATATA
*
5347165 ATGTAACCGGTAAAAATATA
1 ATGTAACAGGTAAAAATATA
5347185 CTGGTTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGTAACAGGTAAAAATATA
Found at i:5347436 original size:23 final size:23
Alignment explanation
Indices: 5347407--5347454 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5347397 AAATAGGTCA
* *
5347407 ATATAAGTGCTACCTATTATATT
1 ATATAAGCGCTACCTAATATATT
5347430 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATATATT
5347453 AT
1 AT
5347455 TGTACTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATATATT
Found at i:5349701 original size:36 final size:36
Alignment explanation
Indices: 5349654--5349761 Score: 162
Period size: 36 Copynumber: 3.0 Consensus size: 36
5349644 AGGAGCAACC
* *
5349654 CAATCAAGAAAGAGGCAAACGTGATCAGCATTTGCA
1 CAATCAAGAAAGAGGCAGACATGATCAGCATTTGCA
* *
5349690 CAATCAAGAAAGAGGCAGGCATGACCAGCATTTGCA
1 CAATCAAGAAAGAGGCAGACATGATCAGCATTTGCA
* *
5349726 CAGTCAAGAAAGACGCAGACATGATCAGCATTTGCA
1 CAATCAAGAAAGAGGCAGACATGATCAGCATTTGCA
5349762 GTCTCAATCA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (36 bp):
CAATCAAGAAAGAGGCAGACATGATCAGCATTTGCA
Found at i:5357905 original size:2 final size:2
Alignment explanation
Indices: 5357898--5357986 Score: 57
Period size: 2 Copynumber: 48.0 Consensus size: 2
5357888 AATAATTATT
* * *
5357898 TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA AA TT TA -A TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
5357936 AA T- TA TA TA TA TA TA TA TA TA -A TA TT TA TA TA TT TA -A TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5357975 TA AA TA TA TA TA
1 TA TA TA TA TA TA
5357987 CTCGGTCCTA
Statistics
Matches: 64, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
1 7 0.11
2 57 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5357954 original size:41 final size:41
Alignment explanation
Indices: 5357897--5357986 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
5357887 AAATAATTAT
5357897 TTATATATATATATATATAATATTAATAAATTTAATTTAAA
1 TTATATATATATATATATAATATTAATAAATTTAATTTAAA
* *
5357938 TTATATATATATATATATAATATTTATATATTTAATTTAAA
1 TTATATATATATATATATAATATTAATAAATTTAATTTAAA
5357979 -TATATATA
1 TTATATATA
5357987 CTCGGTCCTA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 8 0.17
41 39 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (41 bp):
TTATATATATATATATATAATATTAATAAATTTAATTTAAA
Found at i:5359527 original size:28 final size:28
Alignment explanation
Indices: 5359468--5359528 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
5359458 TTTTTTAATA
* * *
5359468 AAAAATATTAAAGAAGCCCAAAATTTTC
1 AAAAATATTAAAAAAGCCAAAAACTTTC
5359496 AAAAATATTAAAAAAGCCAAAAAACTTT-
1 AAAAATATTAAAAAAGCC-AAAAACTTTC
5359524 AAAAA
1 AAAAA
5359529 CCATAATTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.62, C:0.11, G:0.05, T:0.21
Consensus pattern (28 bp):
AAAAATATTAAAAAAGCCAAAAACTTTC
Found at i:5359915 original size:21 final size:21
Alignment explanation
Indices: 5359868--5359915 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
5359858 AAGATTTTGG
*
5359868 AAATTTTGGATTTTTTAAAATA
1 AAATTTT-GATTTTTTAAAAAA
*
5359890 CAATTTT-ATTTTTCTAAAAAA
1 AAATTTTGATTTTT-TAAAAAA
5359911 AAATT
1 AAATT
5359916 CAAAATTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 10 0.45
22 6 0.27
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (21 bp):
AAATTTTGATTTTTTAAAAAA
Found at i:5361088 original size:50 final size:50
Alignment explanation
Indices: 5361034--5361136 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
5361024 AATTGTCGAA
5361034 TACTATTTTTTAAATTTTATCAATTTAACACCCTTTATAATAAGACATGT
1 TACTATTTTTTAAATTTTATCAATTTAACACCCTTTATAATAAGACATGT
5361084 TACTATTTTTTAAATTTTATCAATTTAACACCCTTTATAATAAGACATGT
1 TACTATTTTTTAAATTTTATCAATTTAACACCCTTTATAATAAGACATGT
5361134 TAC
1 TAC
5361137 ATAAAACGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.46
Consensus pattern (50 bp):
TACTATTTTTTAAATTTTATCAATTTAACACCCTTTATAATAAGACATGT
Found at i:5362613 original size:51 final size:51
Alignment explanation
Indices: 5362536--5362660 Score: 153
Period size: 51 Copynumber: 2.5 Consensus size: 51
5362526 AGAAAGGTGT
* * *
5362536 GGCCCATGCACCGCGCCTTACACTGATGT-GTCGCCACGTGGGGTAAAGCGC
1 GGCCCATGCACCGCGCCTTACGCTGATATGGT-GCCACGTAGGGTAAAGCGC
* * * * *
5362587 GGCCCATGCACCGCTCCTTACGCTGATATGGTGCCACGTATGGTAAGGTGT
1 GGCCCATGCACCGCGCCTTACGCTGATATGGTGCCACGTAGGGTAAAGCGC
*
5362638 GGTCCATGCACCGCGCCTTACGC
1 GGCCCATGCACCGCGCCTTACGC
5362661 CAGCTGGAGC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 61 0.97
52 2 0.03
ACGTcount: A:0.17, C:0.33, G:0.30, T:0.21
Consensus pattern (51 bp):
GGCCCATGCACCGCGCCTTACGCTGATATGGTGCCACGTAGGGTAAAGCGC
Found at i:5362880 original size:29 final size:30
Alignment explanation
Indices: 5362818--5362897 Score: 126
Period size: 29 Copynumber: 2.7 Consensus size: 30
5362808 AAATGTTACG
*
5362818 CTCTCAACTTGTAAACATTCACACAACAATC
1 CTCTCAACCTGTAAACA-TCACACAACAATC
5362849 CTCTCAACCTGTAAACAT-ACACAACAATC
1 CTCTCAACCTGTAAACATCACACAACAATC
*
5362878 CTCTCAACCCGTAAACATCA
1 CTCTCAACCTGTAAACATCA
5362898 TTCGACAATC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 28 0.61
30 2 0.04
31 16 0.35
ACGTcount: A:0.39, C:0.35, G:0.04, T:0.23
Consensus pattern (30 bp):
CTCTCAACCTGTAAACATCACACAACAATC
Found at i:5366808 original size:9 final size:9
Alignment explanation
Indices: 5366782--5366823 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
5366772 ACTCCTCACT
5366782 GTCATCATC
1 GTCATCATC
* *
5366791 ATCACCATC
1 GTCATCATC
*
5366800 GTCGTCATC
1 GTCATCATC
5366809 GTCATCATC
1 GTCATCATC
5366818 GTCATC
1 GTCATC
5366824 GTCATCAGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.21, C:0.36, G:0.12, T:0.31
Consensus pattern (9 bp):
GTCATCATC
Found at i:5366824 original size:15 final size:15
Alignment explanation
Indices: 5366796--5366830 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5366786 TCATCATCAC
*
5366796 CATCGTCGTCATCGT
1 CATCATCGTCATCGT
5366811 CATCATCGTCATCGT
1 CATCATCGTCATCGT
5366826 CATCA
1 CATCA
5366831 GGAGCAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.34, G:0.14, T:0.31
Consensus pattern (15 bp):
CATCATCGTCATCGT
Found at i:5366944 original size:9 final size:9
Alignment explanation
Indices: 5366930--5366961 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
5366920 ACCGTTCATA
5366930 GAAAACTGG
1 GAAAACTGG
5366939 GAAAACTGG
1 GAAAACTGG
*
5366948 GAAAACTGA
1 GAAAACTGG
5366957 GAAAA
1 GAAAA
5366962 TACAGACATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.53, C:0.09, G:0.28, T:0.09
Consensus pattern (9 bp):
GAAAACTGG
Found at i:5373415 original size:24 final size:22
Alignment explanation
Indices: 5373341--5373421 Score: 76
Period size: 24 Copynumber: 3.6 Consensus size: 22
5373331 CATATCCCCG
*
5373341 TGCATCGATGCACATTCGAGGCA
1 TGCATCGATGCACATTC-AGGGA
* *
5373364 TGCATCGGTGCATCA-TCA-TGA
1 TGCATCGATGCA-CATTCAGGGA
*
5373385 TGAATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC--AGGGA
5373409 TGCATCGATGCAC
1 TGCATCGATGCAC
5373422 TGTTAAGTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 2 0.04
21 13 0.28
22 1 0.02
23 14 0.30
24 16 0.35
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (22 bp):
TGCATCGATGCACATTCAGGGA
Found at i:5380373 original size:46 final size:46
Alignment explanation
Indices: 5380306--5380399 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
5380296 GAATGAATTA
5380306 TGGGGTCCTTATGAGAATATATATATATTACGTAGAGTTAAGATGT
1 TGGGGTCCTTATGAGAATATATATATATTACGTAGAGTTAAGATGT
5380352 TGGGGTCCTTATGAGAATATATATATATTACGTAGAGTTAAGATGT
1 TGGGGTCCTTATGAGAATATATATATATTACGTAGAGTTAAGATGT
5380398 TG
1 TG
5380400 AACCATGTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (46 bp):
TGGGGTCCTTATGAGAATATATATATATTACGTAGAGTTAAGATGT
Found at i:5382267 original size:18 final size:17
Alignment explanation
Indices: 5382244--5382279 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5382234 AGATTTCAAA
5382244 AGAAGAAGGAGGAAGAAG
1 AGAAGAAGGAGG-AGAAG
*
5382262 AGAAGAAGGTGGAGAAG
1 AGAAGAAGGAGGAGAAG
5382279 A
1 A
5382280 AAACTGTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (17 bp):
AGAAGAAGGAGGAGAAG
Found at i:5384392 original size:43 final size:42
Alignment explanation
Indices: 5384337--5384585 Score: 202
Period size: 43 Copynumber: 5.9 Consensus size: 42
5384327 TGTGAAATAA
5384337 AAACACCGCAAAAAGTCAAGATCTATAGCGGCGTTTTTGAAAC
1 AAACACCGCAAAAAGTC-AGATCTATAGCGGCGTTTTTGAAAC
* **
5384380 AAACACCGCAAAAGGTCGAGATCTATAGCGGAATTTTCT-AAAC
1 AAACACCGCAAAAAGTC-AGATCTATAGCGGCGTTTT-TGAAAC
** * * *
5384423 --ACGTCGCAAAAAGTCAGATCTATAGCGGCTTTTTTTATAC
1 AAACACCGCAAAAAGTCAGATCTATAGCGGCGTTTTTGAAAC
* ** *
5384463 AAACTA-CGTAAAATA-TCGAGATCTATAGCGGTATTTTTGGAAC
1 AAAC-ACCGCAAAA-AGTC-AGATCTATAGCGGCGTTTTTGAAAC
*** * * *
5384506 AAATGTCGCAAAAGGTCAGATCTATAGCGGTGTTTTTAGATAC
1 AAACACCGCAAAAAGTCAGATCTATAGCGGCGTTTTT-GAAAC
* * * *
5384549 AAACGCAGCAAAAAGTCATATTTATAGCGGCGTTTTT
1 AAACACCGCAAAAAGTCAGATCTATAGCGGCGTTTTT
5384586 ATATACAAAC
Statistics
Matches: 165, Mismatches: 31, Indels: 20
0.76 0.14 0.09
Matches are distributed among these distances:
39 1 0.01
40 20 0.12
41 12 0.07
42 29 0.18
43 102 0.62
44 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (42 bp):
AAACACCGCAAAAAGTCAGATCTATAGCGGCGTTTTTGAAAC
Found at i:5384482 original size:83 final size:84
Alignment explanation
Indices: 5384343--5384561 Score: 248
Period size: 83 Copynumber: 2.6 Consensus size: 84
5384333 ATAAAAACAC
* * *
5384343 CGCAAAAAGTCAAGATCTATAGCGGCGTTTTTGAAACAAACACCGCAAAAGGTCGAGATCTATAG
1 CGCAAAAAGTC-AGATCTATAGCGGCTTTTTTGATACAAACACCGCAAAAGATCGAGATCTATAG
*
5384408 CGGAATTTTCT-AA-ACACGT
65 CGGAATTTT-TGAACAAACGT
* * *
5384427 CGCAAAAAGTCAGATCTATAGCGGCTTTTTTTATACAAACTA-CGTAAAATATCGAGATCTATAG
1 CGCAAAAAGTCAGATCTATAGCGGCTTTTTTGATACAAAC-ACCGCAAAAGATCGAGATCTATAG
* *
5384491 CGGTATTTTTGGAACAAATGT
65 CGGAATTTTT-GAACAAACGT
* * *
5384512 CGCAAAAGGTCAGATCTATAGCGG-TGTTTTTAGATACAAACGCAGCAAAA
1 CGCAAAAAGTCAGATCTATAGCGGCT-TTTTT-GATACAAACACCGCAAAA
5384562 AGTCATATTT
Statistics
Matches: 114, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
82 1 0.01
83 53 0.46
84 15 0.13
85 32 0.28
86 13 0.11
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26
Consensus pattern (84 bp):
CGCAAAAAGTCAGATCTATAGCGGCTTTTTTGATACAAACACCGCAAAAGATCGAGATCTATAGC
GGAATTTTTGAACAAACGT
Found at i:5384575 original size:85 final size:82
Alignment explanation
Indices: 5384334--5384578 Score: 237
Period size: 83 Copynumber: 2.9 Consensus size: 82
5384324 GTTTGTGAAA
** * * * *
5384334 TAAAAACACCGCAAAAAGTCAAGATCTATAGCGGCGTTTTTGAAACAAACACCGCAAAAGGTCGA
1 TAAAAACGTCGCAAAAAGTC-AGATCTATAGCGGTGTTTTTGATACAAAC-CAGCAAAAAGTCGA
5384399 GATCTATAGCGGAATTTTC
64 GATCTATAGCGGAATTTTC
* * * *
5384418 TAAACACGTCGCAAAAAGTCAGATCTATAGCGGCT-TTTTTTATACAAACTACGTAAAATA-TCG
1 TAAAAACGTCGCAAAAAGTCAGATCTATAGCGG-TGTTTTTGATACAAACCA-GCAAAA-AGTCG
*
5384481 AGATCTATAGCGGTATTTT-
63 AGATCTATAGCGGAATTTTC
* *
5384500 TGGAACAAATGTCGCAAAAGGTCAGATCTATAGCGGTGTTTTTAGATACAAACGCAGCAAAAAGT
1 T--AA-AAACGTCGCAAAAAGTCAGATCTATAGCGGTGTTTTT-GATACAAAC-CAGCAAAAAGT
* *
5384565 C-ATATTTATAGCGG
61 CGAGATCTATAGCGG
5384579 CGTTTTTATA
Statistics
Matches: 132, Mismatches: 19, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
82 1 0.01
83 51 0.39
84 20 0.15
85 44 0.33
86 15 0.11
87 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (82 bp):
TAAAAACGTCGCAAAAAGTCAGATCTATAGCGGTGTTTTTGATACAAACCAGCAAAAAGTCGAGA
TCTATAGCGGAATTTTC
Found at i:5388578 original size:23 final size:23
Alignment explanation
Indices: 5388551--5388616 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
5388541 ATGAACGAAC
*
5388551 ATAAATGAACATAAGCAAACACA
1 ATAAATGAACATAAACAAACACA
* *
5388574 ATAAATGAACATAAACGAACATA
1 ATAAATGAACATAAACAAACACA
*
5388597 ATAAATAAACATAAACAAAC
1 ATAAATGAACATAAACAAAC
5388617 CTGCACAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.64, C:0.15, G:0.06, T:0.15
Consensus pattern (23 bp):
ATAAATGAACATAAACAAACACA
Found at i:5388611 original size:33 final size:33
Alignment explanation
Indices: 5388547--5388611 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
5388537 ACAAATGAAC
* * *
5388547 GAACATAAATGAACATAAGCAAACACAATAAAT
1 GAACATAAACGAACATAAGAAAAAACAATAAAT
*
5388580 GAACATAAACGAACATAATAAATAAAC-ATAAA
1 GAACATAAACGAACATAAGAAA-AAACAATAAA
5388612 CAAACCTGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 24 0.89
34 3 0.11
ACGTcount: A:0.63, C:0.14, G:0.08, T:0.15
Consensus pattern (33 bp):
GAACATAAACGAACATAAGAAAAAACAATAAAT
Found at i:5388917 original size:24 final size:24
Alignment explanation
Indices: 5388890--5388989 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
5388880 AGACATAAAA
5388890 GAACATATATAAACATAAATGAAC
1 GAACATATATAAACATAAATGAAC
* *
5388914 GAACATATACAGACATAAATGAA-
1 GAACATATATAAACATAAATGAAC
* *
5388937 TAA-ATATAAACGAACATAAATGAAC
1 GAACATATATA--AACATAAATGAAC
* * * * *
5388962 TAATATAAATAGACATAAATAAAC
1 GAACATATATAAACATAAATGAAC
5388986 GAAC
1 GAAC
5388990 GGATTATCGA
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
22 6 0.10
23 2 0.03
24 45 0.74
25 3 0.05
26 5 0.08
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.20
Consensus pattern (24 bp):
GAACATATATAAACATAAATGAAC
Found at i:5392120 original size:11 final size:11
Alignment explanation
Indices: 5392104--5392129 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5392094 TTAAAAATGG
5392104 TTTTTTAGTAT
1 TTTTTTAGTAT
5392115 TTTTTTAGTAT
1 TTTTTTAGTAT
5392126 TTTT
1 TTTT
5392130 AATGAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTTTAGTAT
Found at i:5394940 original size:17 final size:16
Alignment explanation
Indices: 5394902--5394937 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
5394892 CGAGTTAACA
5394902 TTTTATTTTATATATG
1 TTTTATTTTATATATG
5394918 TTTTATTTTAGTA-ATG
1 TTTTATTTTA-TATATG
5394934 TTTT
1 TTTT
5394938 TATACAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.89
17 2 0.11
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (16 bp):
TTTTATTTTATATATG
Found at i:5396682 original size:20 final size:21
Alignment explanation
Indices: 5396648--5396686 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5396638 GCGAGACTTC
5396648 AAAATAAGGAGGAAGAAGAGA
1 AAAATAAGGAGGAAGAAGAGA
*
5396669 AAAATATGGA-GAAGAAGA
1 AAAATAAGGAGGAAGAAGA
5396687 AAGTTGGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.08
Consensus pattern (21 bp):
AAAATAAGGAGGAAGAAGAGA
Found at i:5401148 original size:41 final size:42
Alignment explanation
Indices: 5401090--5401175 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 42
5401080 CCATTTCATG
* *
5401090 TATTTAGTATTGATATTGCTAATACAGTATCAATATTATTTT
1 TATTTAGTATTGATATTGCTAATACAATATCAATATTATTCT
* * * * *
5401132 TATTTGGT-TTGATATTGTTCATTCAATATCGATATTATTCT
1 TATTTAGTATTGATATTGCTAATACAATATCAATATTATTCT
5401173 TAT
1 TAT
5401176 AGTATCTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 30 0.81
42 7 0.19
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.52
Consensus pattern (42 bp):
TATTTAGTATTGATATTGCTAATACAATATCAATATTATTCT
Found at i:5401810 original size:25 final size:25
Alignment explanation
Indices: 5401768--5401822 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 25
5401758 TTTTGTTTAC
*
5401768 ATAATTTTTTTGTATATACT-TATAT
1 ATAATTTTTTTATATATA-TATATAT
5401793 ATAATTTTTTTAATTATATATATATAT
1 ATAATTTTTTT-A-TATATATATATAT
5401820 ATA
1 ATA
5401823 TATACACACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 11 0.42
26 1 0.04
27 14 0.54
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
ATAATTTTTTTATATATATATATAT
Found at i:5403569 original size:2 final size:2
Alignment explanation
Indices: 5403562--5403644 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
5403552 AGTTTCTATT
5403562 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5403604 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5403645 TAACTTTATT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5405890 original size:19 final size:20
Alignment explanation
Indices: 5405866--5405908 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
5405856 GTCTAGAAGA
5405866 AGTTAAGCTGATGGATGA-T
1 AGTTAAGCTGATGGATGACT
5405885 AGTTAAGCTGATGGATGACT
1 AGTTAAGCTGATGGATGACT
5405905 AGTT
1 AGTT
5405909 TTGGTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (20 bp):
AGTTAAGCTGATGGATGACT
Found at i:5406085 original size:20 final size:20
Alignment explanation
Indices: 5406060--5406098 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5406050 ATCATTTTAT
5406060 AACTTTTAATAATCGATGAG
1 AACTTTTAATAATCGATGAG
*
5406080 AACTTTTAATAGTCGATGA
1 AACTTTTAATAATCGATGA
5406099 ATTGAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (20 bp):
AACTTTTAATAATCGATGAG
Found at i:5406253 original size:2 final size:2
Alignment explanation
Indices: 5406246--5406282 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5406236 CGACTAGTAT
5406246 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5406283 GATAAACTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5406640 original size:20 final size:20
Alignment explanation
Indices: 5406617--5406661 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
5406607 AAATCGCAAC
5406617 GCGATTTTCCATTTCGCGTT
1 GCGATTTTCCATTTCGCGTT
5406637 GCGATTTTCCATTTCGCGTT
1 GCGATTTTCCATTTCGCGTT
5406657 GCGAT
1 GCGAT
5406662 AGTTGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.42
Consensus pattern (20 bp):
GCGATTTTCCATTTCGCGTT
Found at i:5406655 original size:61 final size:61
Alignment explanation
Indices: 5406585--5406702 Score: 218
Period size: 61 Copynumber: 1.9 Consensus size: 61
5406575 ATTCGCGTTG
5406585 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCATTTCGCGTTGCGATTTTC
* *
5406646 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCTATTTTCCATTTCGCTTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCATTTCGCGTTGCGAT
5406703 AGTTGAAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (61 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCATTTCGCGTTGCGATTTTC
Found at i:5406685 original size:41 final size:41
Alignment explanation
Indices: 5406637--5406746 Score: 184
Period size: 41 Copynumber: 2.7 Consensus size: 41
5406627 ATTTCGCGTT
**
5406637 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAAC
1 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATAACAAC
* *
5406678 GCTATTTTCCATTTCGCTTTGCGATAGTTGAAAATAACAAC
1 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATAACAAC
5406719 GCGATTTTCCATTTCGCGTTGCGATAGT
1 GCGATTTTCCATTTCGCGTTGCGATAGT
5406747 CTACAGTTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (41 bp):
GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATAACAAC
Found at i:5406761 original size:22 final size:22
Alignment explanation
Indices: 5406735--5406809 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
5406725 TTCCATTTCG
5406735 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
5406757 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
5406776 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
5406798 TGTTGCGATAGT
1 CGTTGCGATAGT
5406810 TAAAAAAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 10 0.24
20 5 0.12
21 5 0.12
22 21 0.51
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:5406799 original size:19 final size:20
Alignment explanation
Indices: 5406735--5406799 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 20
5406725 TTCCATTTCG
5406735 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAG-T-T
** * *
5406757 CGTTGCGATTTTCCA-AATT
1 CGTTGCGATAGTCTACAGTT
5406776 CGTTGCGATAGTCTACAGTT
1 CGTTGCGATAGTCTACAGTT
5406796 -GTTG
1 CGTTG
5406800 TTGCGATAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
19 17 0.50
20 4 0.12
21 1 0.03
22 12 0.35
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCTACAGTT
Found at i:5407574 original size:22 final size:22
Alignment explanation
Indices: 5407518--5407592 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
5407508 AATTTGAAAA
* *
5407518 ATCGCAACGACAACCGTAAACT
1 ATCGCAACGACAACTGTAGACT
** *
5407540 ATCATAACTACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
5407562 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
5407584 ATCGCAACG
1 ATCGCAACG
5407593 CGAAATGGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.39, C:0.28, G:0.15, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:5407612 original size:20 final size:20
Alignment explanation
Indices: 5407584--5407798 Score: 115
Period size: 20 Copynumber: 10.6 Consensus size: 20
5407574 ACTGTAGACT
5407584 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* *
5407604 ATCGTAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
5407624 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
5407645 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
**** ** ** *
5407665 ATCGCGTTACGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
5407686 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
* *** ** ** *
5407706 ATCTCTTTGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
* *
5407727 ATCGCAACGCAAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
* *
5407747 ATCGTAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
*
5407767 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
5407787 ATCGCAACGCGA
1 ATCGCAACGCGA
5407799 TTTTCAACTA
Statistics
Matches: 137, Mismatches: 55, Indels: 6
0.69 0.28 0.03
Matches are distributed among these distances:
20 102 0.74
21 35 0.26
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:5407656 original size:41 final size:41
Alignment explanation
Indices: 5407604--5407810 Score: 254
Period size: 41 Copynumber: 5.1 Consensus size: 41
5407594 GAAATGGAAA
*
5407604 ATCGTAACGCGAAATGAAAAATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGAAATGAAAAATCGCAATGCGATTTTCAACT
* ** *
5407645 ATCGCAACGCGAAATGGAAAATCGCGTTACGATTTTCAACT
1 ATCGCAACGCGAAATGAAAAATCGCAATGCGATTTTCAACT
* **
5407686 ATCGCAACGCGAAATGAAAAATCTCTTTGCGATTTTCAACT
1 ATCGCAACGCGAAATGAAAAATCGCAATGCGATTTTCAACT
* * * ** * **
5407727 ATCGCAACGCAAAATGAAAAATCGTAACGCGA-AATGAAAA
1 ATCGCAACGCGAAATGAAAAATCGCAATGCGATTTTCAACT
*
5407767 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGAAAAATCGCAATGCGATTTTCAACT
5407808 ATC
1 ATC
5407811 ACAATTCGAA
Statistics
Matches: 138, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
40 33 0.24
41 105 0.76
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGAAATGAAAAATCGCAATGCGATTTTCAACT
Found at i:5407832 original size:12 final size:12
Alignment explanation
Indices: 5407812--5407844 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5407802 TCAACTATCA
*
5407812 CAATTCGAAATG
1 CAATGCGAAATG
5407824 CAATGCGAAATG
1 CAATGCGAAATG
5407836 CAATGCGAA
1 CAATGCGAA
5407845 TTTACGATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.18
Consensus pattern (12 bp):
CAATGCGAAATG
Found at i:5408902 original size:18 final size:18
Alignment explanation
Indices: 5408879--5408928 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
5408869 TAACATTCAT
5408879 TGTTTATGGGTAAATTGG
1 TGTTTATGGGTAAATTGG
5408897 TGTTTATGGGTAAATTGG
1 TGTTTATGGGTAAATTGG
5408915 TGTTTATGGGTAAA
1 TGTTTATGGGTAAA
5408929 AGAAAACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (18 bp):
TGTTTATGGGTAAATTGG
Found at i:5413148 original size:19 final size:19
Alignment explanation
Indices: 5413124--5413179 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 19
5413114 AATTACATAT
5413124 TTATAACTAATTGAAAATA
1 TTATAACTAATTGAAAATA
*
5413143 TTATAA--AA--G-AAATG
1 TTATAACTAATTGAAAATA
5413157 TTAT--CTAATTGAAAATA
1 TTATAACTAATTGAAAATA
5413174 TTATAA
1 TTATAA
5413180 AAAGAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
14 10 0.36
15 1 0.04
16 1 0.04
17 10 0.36
19 6 0.21
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.38
Consensus pattern (19 bp):
TTATAACTAATTGAAAATA
Found at i:5413233 original size:44 final size:43
Alignment explanation
Indices: 5413185--5413276 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 43
5413175 TATAAAAAGA
* *
5413185 AATTATCA-GTTTTTAATTCCATATTTATGACTAATTATAATTAT
1 AATTATCATATTTTTAATTCCATATTGAT-A-TAATTATAATTAT
*
5413229 AATTA-CATATTTTTATTTCCATATTGATATAATTATAATTAT
1 AATTATCATATTTTTAATTCCATATTGATATAATTATAATTAT
5413271 AATTAT
1 AATTAT
5413277 AATTCTATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 18 0.42
43 3 0.07
44 22 0.51
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (43 bp):
AATTATCATATTTTTAATTCCATATTGATATAATTATAATTAT
Found at i:5413265 original size:6 final size:6
Alignment explanation
Indices: 5413256--5413280 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5413246 TCCATATTGA
5413256 TATAAT TATAAT TATAAT TATAAT T
1 TATAAT TATAAT TATAAT TATAAT T
5413281 CTATATTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATAAT
Done.