Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001685.1 Hibiscus syriacus cultivar Beakdansim tig00003364_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: 81625
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2964 original size:85 final size:83
Alignment explanation
Indices: 2824--3324 Score: 615
Period size: 82 Copynumber: 6.1 Consensus size: 83
2814 AGAAGGTATA
* * * * *
2824 TGCCTATGAGCTGAATGAAATCGAACTCGAAGGTCTTTGATGACAGATAACCCTTCTCGCCTTGA
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGCCTTGA
* * *
2889 GCTATGCTGTAAATTTGATA
66 GTTATGCTGCAAA--TGATG
* ** *
2909 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGATCTTTGTTGATAGATAACCCTTCTCTCCTTGA
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGCCTTGA
*
2974 GCTATGCTGCAAATGATG
66 GTTATGCTGCAAATGATG
* *
2992 TGCC-TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCTCCTTGA
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGCCTTGA
3056 GTTATGCTGCAAATGATG
66 GTTATGCTGCAAATGATG
* ** * * * *
3074 TGCCTTGGAGCTGAGCAT-AGCGAACTTGAAGGTC----TT-GCAGATAACCCTTTTAGCCTTGA
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGCCTTGA
3133 GTTATGCTGCAAATGATG
66 GTTATGCTGCAAATGATG
* * * * *
3151 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGCCTTA
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGCCTTG
* *
3216 AGTTATGTTGTAAATGATG
65 AGTTATGCTGCAAATGATG
* * *
3235 TGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTC-TT-TTGGTAGATAACCCTTCTTGCCTTGA
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGCCTTGA
*
3298 GTTATGCTGTAAATGATG
66 GTTATGCTGCAAATGATG
3316 TGCCTTTGA
1 TGCCTTTGA
3325 TATCCTTGTC
Statistics
Matches: 366, Mismatches: 42, Indels: 20
0.86 0.10 0.05
Matches are distributed among these distances:
77 55 0.15
78 13 0.04
81 49 0.13
82 91 0.25
83 22 0.06
84 66 0.18
85 70 0.19
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (83 bp):
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGCCTTGA
GTTATGCTGCAAATGATG
Found at i:3827 original size:120 final size:120
Alignment explanation
Indices: 3609--3827 Score: 330
Period size: 120 Copynumber: 1.8 Consensus size: 120
3599 ATCTATTGGT
* * * * * *
3609 ACGATATCCTTTGTCGTGAAGTTGAAATCTTGGATGGCCCATCCGTCGTGAAGTTGAGCCTTGAC
1 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATCCATCGTGAAGTTGAACATTGAA
* *
3674 TTGAATATCCTTCGTCGTGAAGTTAAAATCCAAGCTTGTGCTGTTGCGGGTGGAC
66 TTGAATATCATTCGTCGTGAAGTTAAAACCCAAGCTTGTGCTGTTGCGGGTGGAC
* *
3729 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCATCGTGAAGTTGAACATTGAA
1 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATCCATCGTGAAGTTGAACATTGAA
* *
3794 TTGAATATTATTCGTCGTGAAGTTGAAACCCAAG
66 TTGAATATCATTCGTCGTGAAGTTAAAACCCAAG
3828 TTAGTTGCGT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
120 87 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (120 bp):
ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATCCATCGTGAAGTTGAACATTGAA
TTGAATATCATTCGTCGTGAAGTTAAAACCCAAGCTTGTGCTGTTGCGGGTGGAC
Found at i:4041 original size:43 final size:43
Alignment explanation
Indices: 3992--4144 Score: 207
Period size: 43 Copynumber: 3.6 Consensus size: 43
3982 CGATTCATTT
* ** * *
3992 CATCGTGAAGTTGAAACCGTGGATGTGTGGGCACGATATCCTC
1 CATCGTGAAGTTGAAATCGTGGATCCGTTGGTACGATATCCTC
* *
4035 CGTCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTC
1 CATCGTGAAGTTGAAATCGTGGATCCGTTGGTACGATATCCTC
* * * *
4078 TATCATGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTT
1 CATCGTGAAGTTGAAATCGTGGATCCGTTGGTACGATATCCTC
4121 CATCGTGAAGTTGAAATCGTGGAT
1 CATCGTGAAGTTGAAATCGTGGAT
4145 GGCCTCTTCG
Statistics
Matches: 96, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 96 1.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (43 bp):
CATCGTGAAGTTGAAATCGTGGATCCGTTGGTACGATATCCTC
Found at i:4422 original size:64 final size:64
Alignment explanation
Indices: 4342--4470 Score: 197
Period size: 64 Copynumber: 2.0 Consensus size: 64
4332 GAGCAAATTG
* * *
4342 TGAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAAAA-TTTTTTGT
1 TGAGTACAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAA-TGGAAAAGTTGTTTGT
* *
4406 TGAGTACAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTGTTTGT
1 TGAGTACAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAATGGAAAAGTTGTTTGT
4470 T
1 T
4471 AACAGACGCT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 6 0.10
64 53 0.90
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (64 bp):
TGAGTACAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAATGGAAAAGTTGTTTGT
Found at i:4495 original size:63 final size:63
Alignment explanation
Indices: 4352--4498 Score: 183
Period size: 64 Copynumber: 2.3 Consensus size: 63
4342 TGAGTTCAAT
* * *
4352 ATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAAAATTTTTTGTTGAGTACAAT
1 ATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAAAATTGTTTGTTGAG-ACAAG
* *
4416 ATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAA-TTGAAAAGTTGTTTGTT-A-ACAGAC
1 ATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAAAA-TTGTTTGTTGAGACA-A-
4478 G
63 G
*
4479 CTCCTTCGCTGTGAAGTTGA
1 ATCCTTCGCTGTGAAGTTGA
4499 GCATCCACCA
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
61 3 0.04
62 1 0.01
63 26 0.35
64 44 0.59
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (63 bp):
ATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAAAATTGTTTGTTGAGACAAG
Found at i:4799 original size:32 final size:32
Alignment explanation
Indices: 4728--4816 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 32
4718 TTGCATCAGG
* * *
4728 ATGTTGAACCCCCAAATATGCCCCAATATTCA
1 ATGTTGAATCTCCAAATATGCCCCAACATTCA
* **
4760 ATATTGAATCTCCAAATATGCCCCAACATTTG
1 ATGTTGAATCTCCAAATATGCCCCAACATTCA
* ** *
4792 CTGTTGAATCTTTAAAGATGCCCCA
1 ATGTTGAATCTCCAAATATGCCCCA
4817 TTGTTCCTCA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (32 bp):
ATGTTGAATCTCCAAATATGCCCCAACATTCA
Found at i:6659 original size:30 final size:30
Alignment explanation
Indices: 6623--6679 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
6613 GTTTAAAGGA
6623 TTAAGCAAACATGAAAGATCAAAACGCCCT
1 TTAAGCAAACATGAAAGATCAAAACGCCCT
6653 TTAAGCAAACATGAAAGATCAAAACGC
1 TTAAGCAAACATGAAAGATCAAAACGC
6680 GTTCAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.16
Consensus pattern (30 bp):
TTAAGCAAACATGAAAGATCAAAACGCCCT
Found at i:6693 original size:30 final size:30
Alignment explanation
Indices: 6628--6690 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
6618 AAGGATTAAG
* *
6628 CAAACATGAAAGATCAAAACGCCCTTTAAG
1 CAAACATGAAAGATCAAAACGCCCTTCAAA
*
6658 CAAACATGAAAGATCAAAACG-CGTTCAAA
1 CAAACATGAAAGATCAAAACGCCCTTCAAA
6687 CAAA
1 CAAA
6691 ACAATGCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.51, C:0.22, G:0.13, T:0.14
Consensus pattern (30 bp):
CAAACATGAAAGATCAAAACGCCCTTCAAA
Found at i:7804 original size:16 final size:15
Alignment explanation
Indices: 7783--7812 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
7773 TGATGAAAAT
7783 AAAATAAAAGAGAATA
1 AAAATAAAA-AGAATA
7799 AAAATAAAAAGAAT
1 AAAATAAAAAGAAT
7813 TAGTGAGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (15 bp):
AAAATAAAAAGAATA
Found at i:17964 original size:19 final size:19
Alignment explanation
Indices: 17940--17988 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
17930 GGTTTCTGGC
*
17940 ACCGGAACAGCATTCCGCT
1 ACCGGAACAGCATTCCCCT
17959 ACCGGAACAGCATTCCCCT
1 ACCGGAACAGCATTCCCCT
17978 ACCGGAACAGC
1 ACCGGAACAGC
17989 TCCGCCCCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.29, C:0.39, G:0.20, T:0.12
Consensus pattern (19 bp):
ACCGGAACAGCATTCCCCT
Found at i:18658 original size:60 final size:60
Alignment explanation
Indices: 18559--18723 Score: 199
Period size: 60 Copynumber: 2.8 Consensus size: 60
18549 GCACAATATG
* * * * **
18559 TCCCCAAACTATGATCCTCATTTTAAGTTAGT-CTCTAAACTTTTAAGCATTTTAATT-TCA
1 TCCCCAAACTATGATTCTCATTCTAAATTAGTCCT-TAAACTTTTAAACATTCCAATTCT-A
* * *
18619 TCCCTAAACTACGATTCTCATCCTAAATTAGTCCTTAAACTTTTAAACATTCCAATTCTA
1 TCCCCAAACTATGATTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCCAATTCTA
* *
18679 TCCCCAAACTATGAATATCATTCTAAATTAGTCCTTAAACTTTTA
1 TCCCCAAACTATGATTCTCATTCTAAATTAGTCCTTAAACTTTTA
18724 CATCTCCCAA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
60 86 0.97
61 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.39
Consensus pattern (60 bp):
TCCCCAAACTATGATTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCCAATTCTA
Found at i:18719 original size:31 final size:30
Alignment explanation
Indices: 18636--18719 Score: 73
Period size: 29 Copynumber: 2.8 Consensus size: 30
18626 ACTACGATTC
* * *
18636 TCATCCTAAATTAGTCCTTAAACTTTTAAA
1 TCATTCTAAATTAGTCCTTAAACTATGAAA
* * **
18666 -CATTCCAATTCTA-TCCCCAAACTATGAATA
1 TCATTCTAAAT-TAGTCCTTAAACTATGAA-A
18696 TCATTCTAAATTAGTCCTTAAACT
1 TCATTCTAAATTAGTCCTTAAACT
18720 TTTACATCTC
Statistics
Matches: 39, Mismatches: 11, Indels: 7
0.68 0.19 0.12
Matches are distributed among these distances:
29 18 0.46
30 5 0.13
31 16 0.41
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.37
Consensus pattern (30 bp):
TCATTCTAAATTAGTCCTTAAACTATGAAA
Found at i:18852 original size:59 final size:60
Alignment explanation
Indices: 18774--18922 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 60
18764 TCGGGGAATG
* *
18774 ATTTAGAATAAATAG-CATAGTTTGGGGATGATAA-TGAAATG-TTAAAAGTTT-GAGGACTA
1 ATTTAGAAT-GATAGTCATAGATTGGGGATGA-AAGTGAAATGTTTAAAAGTTTAG-GGACTA
* *
18833 ATTTAGAATGATAGTCATAGCTTGGGGATGAAAGTGAAATGTTTAAATGTTTAGGGACTA
1 ATTTAGAATGATAGTCATAGATTGGGGATGAAAGTGAAATGTTTAAAAGTTTAGGGACTA
*
18893 ACTTTA-AATGAGCA-TCATAGATTGGGGATG
1 A-TTTAGAATGA-TAGTCATAGATTGGGGATG
18923 TATGAATAGG
Statistics
Matches: 79, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
58 6 0.08
59 31 0.39
60 36 0.46
61 6 0.08
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (60 bp):
ATTTAGAATGATAGTCATAGATTGGGGATGAAAGTGAAATGTTTAAAAGTTTAGGGACTA
Found at i:20638 original size:60 final size:58
Alignment explanation
Indices: 20543--20706 Score: 204
Period size: 59 Copynumber: 2.8 Consensus size: 58
20533 GCATGATATG
* * * *
20543 TCCCCAAACTATTATCTTCATT-TAAAGTTAGTCCTTGAACTTTTAAGCATTCCAATTTCA
1 TCCCCAAACTATGATC-TCATTCTAAA-TTAGTCCTTAAACTTTTAA-AATTCCAATTCCA
* *
20603 TCCCCAAACTACGACTCTCATTCTAAATTAATCCTTAAACTTTTAAAATTCCAATTCCA
1 TCCCCAAACTATGA-TCTCATTCTAAATTAGTCCTTAAACTTTTAAAATTCCAATTCCA
* *
20662 TCCCCAAACTATGAATATCATTCTAAATTGGTCCTTAAACTTTTA
1 TCCCCAAACTATG-ATCTCATTCTAAATTAGTCCTTAAACTTTTA
20707 CATCTCCCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
59 50 0.55
60 35 0.38
61 6 0.07
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (58 bp):
TCCCCAAACTATGATCTCATTCTAAATTAGTCCTTAAACTTTTAAAATTCCAATTCCA
Found at i:24954 original size:116 final size:116
Alignment explanation
Indices: 24692--25033 Score: 359
Period size: 116 Copynumber: 2.9 Consensus size: 116
24682 AAACTCAAGA
* * * *
24692 AATCAGCTCAAATTCTTTCTGATTCATCATCCGTTTCTTCAGATTCAACATTCATAGTTACTTAC
1 AATCAGCTCAAATTCTTTTTAATTCATCATTCGTTTCTTCAGATTCAACATTAATAGTTACTTAC
* *
24757 AAGACATCATTAAACTTAATTATCGAACTGATATTAGATCAAAATTAAACG
66 AAGACATCATTAAACTTAATTATCGAACTGATATTAAATCAAAATTAAACC
* * * *
24808 AATCAGCTCAAATTCCTTTTAATTCCTCATTCGTTTCTTCAGATTTAACATTAATAGTTACTTGC
1 AATCAGCTCAAATTCTTTTTAATTCATCATTCGTTTCTTCAGATTCAACATTAATAGTTACTTAC
** * * **
24873 GTGACCTTATTAAACTTAAATT-TC-AACTGATATTAAATCCGAATT-AACTC
66 AAGACATCATTAAACTT-AATTATCGAACTGATATTAAATCAAAATTAAAC-C
* * * * ** * *
24923 AATCAGCTCAACTTCTTTTTTTATTCATCATTCATTCCTTCAGATTCAACATCCATAGTCAATTA
1 AATCAGCTCAAATTC-TTTTTAATTCATCATTCGTTTCTTCAGATTCAACATTAATAGTTACTTA
** * **
24988 TGAGACATCATTAAACTTAAATT-CCGAACTGATATTGGATCAAAAT
65 CAAGACATCATTAAACTT-AATTATCGAACTGATATTAAATCAAAAT
25034 CAACTAAACC
Statistics
Matches: 185, Mismatches: 37, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
114 3 0.02
115 32 0.17
116 130 0.70
117 20 0.11
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.37
Consensus pattern (116 bp):
AATCAGCTCAAATTCTTTTTAATTCATCATTCGTTTCTTCAGATTCAACATTAATAGTTACTTAC
AAGACATCATTAAACTTAATTATCGAACTGATATTAAATCAAAATTAAACC
Found at i:25685 original size:31 final size:30
Alignment explanation
Indices: 25614--25701 Score: 108
Period size: 31 Copynumber: 3.0 Consensus size: 30
25604 AAATATTATT
*
25614 TTGGTCATTAAATTT-TCAAAAGTTATAAA
1 TTGGTCATTAAATTTATCAAAAGTTACAAA
* * *
25643 ATGATCATTAAATTTATCAAATTGTTACAAA
1 TTGGTCATTAAATTTATCAAA-AGTTACAAA
*
25674 TTGGTCATTAAATTTAT-AAAAGGTACAA
1 TTGGTCATTAAATTTATCAAAAGTTACAA
25702 TTATTATAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 19 0.39
30 8 0.16
31 22 0.45
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (30 bp):
TTGGTCATTAAATTTATCAAAAGTTACAAA
Found at i:31161 original size:31 final size:31
Alignment explanation
Indices: 31121--31185 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
31111 GTTTTGGTCT
* *
31121 CTTATGTTATCGTTTTATTAAGTTCTGGTAA
1 CTTACGTTATCGTTTCATTAAGTTCTGGTAA
* * *
31152 CTTACGTTATTGTTTCATTAAGTTTTGGTCA
1 CTTACGTTATCGTTTCATTAAGTTCTGGTAA
31183 CTT
1 CTT
31186 GGACATTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.52
Consensus pattern (31 bp):
CTTACGTTATCGTTTCATTAAGTTCTGGTAA
Found at i:34386 original size:27 final size:27
Alignment explanation
Indices: 34349--34520 Score: 113
Period size: 27 Copynumber: 6.4 Consensus size: 27
34339 TTAAATCGGT
*
34349 TTTTGAAAACATATATATATTATATAG
1 TTTTGAAAACATATATATAATATATAG
34376 TTTTGAAAACATATATATAATATATAG
1 TTTTGAAAACATATATATAATATATAG
* * * * * *
34403 TTTTTAAAAAACAT-TTTGAAAACAT-G
1 TTTTGAAAACATATATAT-AATATATAG
* * * * * * * *
34429 TATAT-AATATATAGTTTTTAAAAAACA-
1 T-TTTGAAAACATA-TATATAATATATAG
* *
34456 TTTTGAAAATATATGTATAATATATAG
1 TTTTGAAAACATATATATAATATATAG
34483 TTTTTGAAAACATATATAT--TATATAG
1 -TTTTGAAAACATATATATAATATATAG
34509 TTTTGAAAACAT
1 TTTTGAAAACAT
34521 TTTGAAAACA
Statistics
Matches: 115, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
25 12 0.10
26 26 0.23
27 58 0.50
28 19 0.17
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (27 bp):
TTTTGAAAACATATATATAATATATAG
Found at i:34422 original size:40 final size:40
Alignment explanation
Indices: 34376--34492 Score: 198
Period size: 40 Copynumber: 2.9 Consensus size: 40
34366 TATTATATAG
34376 TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
*
34416 TTTTGAAAACATGTATATAATATATAGTTTTTAAAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
* * *
34456 TTTTGAAAATATATGTATAATATATAGTTTTTGAAAA
1 TTTTGAAAACATATATATAATATATAGTTTTTAAAAA
34493 CATATATATT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (40 bp):
TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
Found at i:34507 original size:26 final size:26
Alignment explanation
Indices: 34456--34520 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
34446 TTAAAAAACA
*
34456 TTTTGAAAATATATGTATAATATATAG
1 TTTTGAAAACATA-GTATAATATATAG
*
34483 TTTTTGAAAACATA-TATATTATATAG
1 -TTTTGAAAACATAGTATAATATATAG
34509 TTTTGAAAACAT
1 TTTTGAAAACAT
34521 TTTGAAAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 12 0.34
26 11 0.31
28 12 0.34
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (26 bp):
TTTTGAAAACATAGTATAATATATAG
Found at i:34531 original size:36 final size:36
Alignment explanation
Indices: 34484--34775 Score: 176
Period size: 36 Copynumber: 7.9 Consensus size: 36
34474 AATATATAGT
*
34484 TTTTGAAAACATATATATTATATAGTTTTGAAAACA
1 TTTTGAAAACATATATATTATATAGTTTTAAAAACA
*
34520 TTTTGAAAACATATATA-TATA-ATTTTTAAAAACA
1 TTTTGAAAACATATATATTATATAGTTTTAAAAACA
* * * *
34554 TTTTGAAAATATATATATATATATA-TATATATATATATA
1 TTTTGAAAACATATATAT-TATATAGT-T-T-TAAAAACA
* * * *
34593 TATAT-ATATATATATATATATATATATTTTTTAAAAACA
1 T-TTTGA-AAACATATATAT-TATATA-GTTTTAAAAACA
* *
34632 TTTTGAATACATATATAATATATAGTTTTTAAAAA-A
1 TTTTGAAAACATATATATTATATAG-TTTTAAAAACA
* * * *
34668 TGTTTTAAAA-ATATATATAATATATAGTTTTGGACAATA
1 T-TTTGAAAACATATATAT--TATATAGTTTT-AAAAACA
34707 TTTTTG--AA-A-ATATATTATATAGTTTTAAAAACAA
1 -TTTTGAAAACATATATATTATATAGTTTTAAAAAC-A
* *
34741 TGTTTTTG-AAA-ATATATAATATATAATTTTAAAAA
1 ---TTTTGAAAACATATATATTATATAGTTTTAAAAA
34776 AGATTTTTTT
Statistics
Matches: 207, Mismatches: 26, Indels: 44
0.75 0.09 0.16
Matches are distributed among these distances:
33 3 0.01
34 39 0.19
35 4 0.02
36 43 0.21
37 33 0.16
38 43 0.21
39 18 0.09
40 22 0.11
41 1 0.00
42 1 0.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (36 bp):
TTTTGAAAACATATATATTATATAGTTTTAAAAACA
Found at i:34569 original size:2 final size:2
Alignment explanation
Indices: 34562--34619 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
34552 CATTTTGAAA
34562 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34604 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
34620 TTTTTAAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34572 original size:38 final size:38
Alignment explanation
Indices: 34484--34727 Score: 168
Period size: 38 Copynumber: 6.6 Consensus size: 38
34474 AATATATAGT
* * *
34484 TTTTGAAAACATATATAT-TATAT-AGTTTTGAAAACA
1 TTTTGAAAATATATATATATATATAATTTTTAAAAACA
*
34520 TTTTG--AA-A-ACATATATATATAATTTTTAAAAACA
1 TTTTGAAAATATATATATATATATAATTTTTAAAAACA
* * * * *
34554 TTTTGAAAATATATATATATATATATATATATATATATA
1 TTTTGAAAATATATATATATATATA-ATTTTTAAAAACA
* * *
34593 TATAT-ATATATATATATATATATATATTTTTTAAAAACA
1 T-TTTGA-AAATATATATATATATATAATTTTTAAAAACA
* * *
34632 TTTTGAATACATATATA-ATATATAGTTTTTAAAAA-A
1 TTTTGAAAATATATATATATATATAATTTTTAAAAACA
* * ** * *
34668 TGTTTTAAAA-ATATATATAATATATAGTTTTGGACAATA
1 T-TTTGAAAATATATATAT-ATATATAATTTTTAAAAACA
34707 TTTTTGAAAATATAT-TATATA
1 -TTTTGAAAATATATATATATA
34728 GTTTTAAAAA
Statistics
Matches: 166, Mismatches: 26, Indels: 30
0.75 0.12 0.14
Matches are distributed among these distances:
32 5 0.03
33 6 0.04
34 18 0.11
36 16 0.10
37 24 0.14
38 42 0.25
39 30 0.18
40 25 0.15
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (38 bp):
TTTTGAAAATATATATATATATATAATTTTTAAAAACA
Found at i:34783 original size:36 final size:37
Alignment explanation
Indices: 34604--34783 Score: 149
Period size: 38 Copynumber: 4.9 Consensus size: 37
34594 ATATATATAT
* * *
34604 ATATATATATATATATTTTTTAAAAACA-TTTTGAATAC
1 ATATATA-ATATATAGTTTTAAAAAAGATTTTTGAA-AC
** *
34642 ATATATAATATATAGTTTTTAAAAAATG-TTTTAAAAAT
1 ATATATAATATATAG-TTTTAAAAAA-GATTTTTGAAAC
** * *
34680 ATATATAATATATAGTTTTGGACAATATTTTTGAAA-
1 ATATATAATATATAGTTTTAAAAAAGATTTTTGAAAC
34716 ATATAT--TATATAGTTTTAAAAACA-ATGTTTTTGAAA-
1 ATATATAATATATAGTTTTAAAAA-AGA--TTTTTGAAAC
*
34752 ATATATAATATATAATTTTAAAAAAGATTTTT
1 ATATATAATATATAGTTTTAAAAAAGATTTTT
34784 TTTCTTTTAT
Statistics
Matches: 116, Mismatches: 16, Indels: 22
0.75 0.10 0.14
Matches are distributed among these distances:
34 14 0.12
35 1 0.01
36 26 0.22
37 22 0.19
38 48 0.41
39 5 0.04
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (37 bp):
ATATATAATATATAGTTTTAAAAAAGATTTTTGAAAC
Found at i:34785 original size:38 final size:38
Alignment explanation
Indices: 34632--34785 Score: 156
Period size: 38 Copynumber: 4.1 Consensus size: 38
34622 TTTAAAAACA
*
34632 TTTTGAATACATATATAATATATAGTTTTTAAAAAATGT
1 TTTTGAA-ACATATATAATATATAGTTTTAAAAAAATGT
** * ** * *
34671 TTTAAAAATATATATAATATATAGTTTT-GGACAATAT
1 TTTTGAAACATATATAATATATAGTTTTAAAAAAATGT
34708 TTTTGAAA-ATATAT--TATATAGTTTTAAAAACAATGT
1 TTTTGAAACATATATAATATATAGTTTTAAAAA-AATGT
* *
34744 TTTTGAAA-ATATATAATATATAATTTTAAAAAAGATTT
1 TTTTGAAACATATATAATATATAGTTTTAAAAAA-ATGT
34782 TTTT
1 TTTT
34786 TCTTTTATAT
Statistics
Matches: 95, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
34 11 0.12
35 1 0.01
36 24 0.25
37 12 0.13
38 42 0.44
39 5 0.05
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (38 bp):
TTTTGAAACATATATAATATATAGTTTTAAAAAAATGT
Found at i:34826 original size:25 final size:23
Alignment explanation
Indices: 34789--34835 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
34779 TTTTTTTTCT
34789 TTTATATTATATTAATATTATTTA
1 TTTATATTATATTAATA-TATTTA
*
34813 TTTATTATTTTATTAATATATTT
1 TTTA-TATTATATTAATATATTT
34836 TTCTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATATTATATTAATATATTTA
Found at i:34890 original size:13 final size:13
Alignment explanation
Indices: 34872--34904 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
34862 TTCTTTTTTT
34872 AGGGTCCGAATAA
1 AGGGTCCGAATAA
34885 AGGGTCCGAATAA
1 AGGGTCCGAATAA
*
34898 AAGGTCC
1 AGGGTCC
34905 AAATTCATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.18, G:0.30, T:0.15
Consensus pattern (13 bp):
AGGGTCCGAATAA
Found at i:36052 original size:5 final size:5
Alignment explanation
Indices: 36042--36138 Score: 56
Period size: 5 Copynumber: 18.4 Consensus size: 5
36032 TTTTTCCTTT
* * **
36042 TTTTA TTTTA TTTTA CTTCA TTTTCA TTATTA TTTTA TTATCCC TTTTAA
1 TTTTA TTTTA TTTTA TTTTA TTTT-A TT-TTA TTTTA TT-T-TA TTTT-A
*
36092 TATTA -TTT- TTTTA -TTTA TTTTA TTTTTTA TTTTA TTTTA TTATTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA --TTTTA TTTTA TTTTA TT-TTA
36137 TT
1 TT
36139 CTTTCTGTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 21
0.70 0.10 0.21
Matches are distributed among these distances:
4 9 0.13
5 37 0.52
6 16 0.23
7 9 0.13
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:36098 original size:3 final size:3
Alignment explanation
Indices: 36092--36186 Score: 55
Period size: 3 Copynumber: 33.7 Consensus size: 3
36082 TCCCTTTTAA
*
36092 TAT TAT T-T TTT TATT TAT T-T TAT T-T T-T TAT T-T TAT T-T TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
36132 TAT TAT TCT T-T CTGT TAA TAT GAT T-T TACT TAT T-T TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
36176 TAT TAT TAT TA
1 TAT TAT TAT TA
36187 ACCCTTTTTC
Statistics
Matches: 74, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
2 17 0.23
3 50 0.68
4 7 0.09
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:36116 original size:17 final size:18
Alignment explanation
Indices: 36039--36132 Score: 68
Period size: 17 Copynumber: 5.1 Consensus size: 18
36029 CATTTTTTCC
36039 TTTTTTTATTTTATTTTA
1 TTTTTTTATTTTATTTTA
*
36057 CTTCATTTTCATTATTATTTTA
1 -TT--TTTTTATT-TTATTTTA
*** * *
36079 TTATCCCT-TTTAATATTA
1 TT-TTTTTATTTTATTTTA
36097 TTTTTTTA-TTTATTTTA
1 TTTTTTTATTTTATTTTA
36114 -TTTTTTATTTTATTTTA
1 TTTTTTTATTTTATTTTA
36131 TT
1 TT
36133 ATTATTCTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 13
0.70 0.15 0.16
Matches are distributed among these distances:
16 7 0.12
17 18 0.32
18 9 0.16
19 4 0.07
20 2 0.04
21 9 0.16
22 8 0.14
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTTATTTTATTTTA
Found at i:36150 original size:58 final size:60
Alignment explanation
Indices: 36039--36185 Score: 149
Period size: 58 Copynumber: 2.4 Consensus size: 60
36029 CATTTTTTCC
* *
36039 TTTT-TTTATTTTATTTTACTTCATTTTCATTATTATTTTATTATCCCTTTTAATATTATTT
1 TTTTATTTATTTTATTTTA-TT-ATTTTCATTATTATTTTATTATCCCTGTTAATATGATTT
* **
36100 TTTTATTTATTTTATTTT-TTATTTT-ATT-TTATTATTATTCTTTCTGTTAATATGATTT
1 TTTTATTTATTTTATTTTATTATTTTCATTATTATT-TTATTATCCCTGTTAATATGATTT
*
36158 TACTTATTTTATTATTATTATTATTATT
1 T-TTTA-TTTATT-TTATT-TTATTATT
36186 AACCCTTTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
57 5 0.07
58 23 0.32
59 8 0.11
60 8 0.11
61 9 0.12
62 15 0.21
63 5 0.07
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.70
Consensus pattern (60 bp):
TTTTATTTATTTTATTTTATTATTTTCATTATTATTTTATTATCCCTGTTAATATGATTT
Found at i:36183 original size:12 final size:11
Alignment explanation
Indices: 36042--36186 Score: 77
Period size: 12 Copynumber: 13.0 Consensus size: 11
36032 TTTTTCCTTT
36042 TTTTATT-TTA
1 TTTTATTATTA
* *
36052 TTTTACT-TCA
1 TTTTATTATTA
36062 TTTTCATTATTA
1 TTTT-ATTATTA
**
36074 TTTTATTATCCC
1 TTTTATTAT-TA
*
36086 TTTTAATATTA
1 TTTTATTATTA
*
36097 TTTTTTTATTTA
1 TTTTATTA-TTA
*
36109 TTTTATTTTTTA
1 TTTTA-TTATTA
36121 TTTTATT-TTA
1 TTTTATTATTA
*
36131 TTATTATTCTT-
1 TT-TTATTATTA
* *
36142 TCTGTTAATATGA
1 T-T-TTATTATTA
*
36155 TTTTA--CTTA
1 TTTTATTATTA
36164 TTTTATTATTA
1 TTTTATTATTA
36175 TTATTATTATTA
1 TT-TTATTATTA
36187 ACCCTTTTTC
Statistics
Matches: 103, Mismatches: 20, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
9 7 0.07
10 17 0.17
11 29 0.28
12 47 0.46
13 3 0.03
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.69
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:41483 original size:15 final size:15
Alignment explanation
Indices: 41463--41491 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41453 ATATGTCAAG
41463 ACTAAATCTACTATA
1 ACTAAATCTACTATA
41478 ACTAAATCTACTAT
1 ACTAAATCTACTAT
41492 CTGATATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (15 bp):
ACTAAATCTACTATA
Found at i:42729 original size:12 final size:13
Alignment explanation
Indices: 42708--42736 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
42698 TATTTTTAAT
42708 TTTAAGAATTATC
1 TTTAAGAATTATC
42721 TTTAA-AATTATC
1 TTTAAGAATTATC
42733 TTTA
1 TTTA
42737 TGTAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (13 bp):
TTTAAGAATTATC
Found at i:42867 original size:11 final size:12
Alignment explanation
Indices: 42844--42899 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
42834 TTTTATAAAG
42844 TTTTACTTTTTC
1 TTTTACTTTTTC
42856 TTTTACTTTTCTTTC
1 TTTTAC--TT-TTTC
42871 TTTTA-TTTTTC
1 TTTTACTTTTTC
* *
42882 TTTAAATGTTTTC
1 TTTTACT-TTTTC
42895 TTTTA
1 TTTTA
42900 AAAATGCTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
11 8 0.22
12 9 0.24
13 9 0.24
14 2 0.05
15 9 0.24
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.73
Consensus pattern (12 bp):
TTTTACTTTTTC
Found at i:42872 original size:15 final size:15
Alignment explanation
Indices: 42852--42884 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
42842 AGTTTTACTT
42852 TTTCTTTTACTTTTC
1 TTTCTTTTACTTTTC
*
42867 TTTCTTTTATTTTTC
1 TTTCTTTTACTTTTC
42882 TTT
1 TTT
42885 AAATGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTTTACTTTTC
Found at i:44140 original size:53 final size:53
Alignment explanation
Indices: 44045--44145 Score: 130
Period size: 53 Copynumber: 1.9 Consensus size: 53
44035 GAAATCCAAA
* * * * *
44045 TTTTCTTTGATTAGTTATTTATTTTACTGATGGTACCCACCTTGAAATCTGAG
1 TTTTCTTCGATTAGTTACTTATTTTACAGACGGTACCCACCTTAAAATCTGAG
** *
44098 TTTTCTTCGATTAGTTACTTATTTTACAGACGGTGTCTACCTTAAAAT
1 TTTTCTTCGATTAGTTACTTATTTTACAGACGGTACCCACCTTAAAAT
44146 TTTATTTGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
53 40 1.00
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.47
Consensus pattern (53 bp):
TTTTCTTCGATTAGTTACTTATTTTACAGACGGTACCCACCTTAAAATCTGAG
Found at i:45059 original size:19 final size:19
Alignment explanation
Indices: 45014--45052 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
45004 ATATTATTAA
*
45014 TTATTTTAAAATATTAAAT
1 TTATTTTAAAATATAAAAT
45033 TTAATTTTAAAATATAAAAT
1 TT-ATTTTAAAATATAAAAT
45053 ATTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATTTTAAAATATAAAAT
Found at i:46070 original size:20 final size:23
Alignment explanation
Indices: 46027--46070 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
46017 ATAAATTGAG
*
46027 AAAATAATAATAAAAATATTAAA
1 AAAATAATAATAAAAATATGAAA
46050 AAAATAA-AA-AAAAATA-GAAA
1 AAAATAATAATAAAAATATGAAA
46070 A
1 A
46071 TATTCAGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 7 0.35
22 2 0.10
23 7 0.35
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAATAATAATAAAAATATGAAA
Found at i:46190 original size:38 final size:40
Alignment explanation
Indices: 46147--46227 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 40
46137 AACAATATTT
46147 TTAAAAG-AACAAAATAA-AAATATAAAA-ATATAT-TAATA
1 TTAAAAGTAACAAAA-AATAAAT-TAAAACATATATATAATA
*
46185 TTAAAAGTAATAAAAAATAAATTAAAAGCATATATATAATA
1 TTAAAAGTAACAAAAAATAAATTAAAA-CATATATATAATA
46226 TT
1 TT
46228 TTGTTCTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
38 14 0.38
39 10 0.27
40 6 0.16
41 7 0.19
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (40 bp):
TTAAAAGTAACAAAAAATAAATTAAAACATATATATAATA
Found at i:47732 original size:18 final size:18
Alignment explanation
Indices: 47691--47733 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 18
47681 AAAAAACAAA
47691 AAAAGAAAATATAATAAT
1 AAAAGAAAATATAATAAT
47709 --AA-AAAATATAATAAT
1 AAAAGAAAATATAATAAT
47724 AAAAGAAAAT
1 AAAAGAAAAT
47734 TGTTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 13 0.59
16 2 0.09
17 2 0.09
18 5 0.23
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAAGAAAATATAATAAT
Found at i:47802 original size:22 final size:22
Alignment explanation
Indices: 47760--47803 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
47750 AATAATACGA
*
47760 AAAAATAGTTTAAAAATGAAAAG
1 AAAAATAG-TTAAAAAGGAAAAG
47783 AAAAATA-TTAAAATAGGAAAA
1 AAAAATAGTTAAAA-AGGAAAA
47804 CCAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAAATAGTTAAAAAGGAAAAG
Found at i:49886 original size:84 final size:81
Alignment explanation
Indices: 49591--50221 Score: 651
Period size: 84 Copynumber: 7.7 Consensus size: 81
49581 CAAACTCGGG
* * * *
49591 GGTCTTTG-GCAGATAACTCTTCTCGACTTAAGTTATACTGCCAATGATGTGCCTGAGAGCTGAG
1 GGTCTTTGTGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTAGAGCTGAG
*
49655 CGTAGTCGAACTCAAA
66 CGTAGTCGAACTCGAA
* * * * ** ** *
49671 GGTCTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATATTGTGAATGATGTGCCCTCCA-AGC
1 GGTCTTT-GTG-CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCT-TAGAGC
* * * *
49735 TGAGAGTAATTGAACTCGAG
62 TGAGCGTAGTCGAACTCGAA
* * *
49755 GGTCTTTG-GCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAG
1 GGTCTTTGTGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTAGAGCTGAG
49819 CGTAGTCGAACTCGAA
66 CGTAGTCGAACTCGAA
* * * * * * *
49835 GGTCTTTTAGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGC
1 GGTC-TTT-GT-GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTAG-AGC
* *
49900 TGAGTGTAATCGAACTCGAA
62 TGAGCGTAGTCGAACTCGAA
* * *
49920 GGTCTTTG-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAG
1 GGTCTTTGTGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTAGAGCTGAG
*
49984 CGTAGTCGAACTCAAA
66 CGTAGTCGAACTCGAA
**
50000 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGGAGC
1 GGTCTTT-G-T-GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTAGAGC
* *
50065 TGAGTGTAATCGAACTCGAA
62 TGAGCGTAGTCGAACTCGAA
* * * * *
50085 GGTCTTTG-GCAGATAGCCCTTCTCGGCTTAAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAG
1 GGTCTTTGTGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTAGAGCTGAG
*
50149 CGTAGTCGAACTCAAA
66 CGTAGTCGAACTCGAA
* * * * *
50165 GGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCC
1 GGTC-TTT-GT-GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
50222 CTCGAAGCTG
Statistics
Matches: 457, Mismatches: 74, Indels: 36
0.81 0.13 0.06
Matches are distributed among these distances:
79 1 0.00
80 89 0.19
81 120 0.26
82 4 0.01
83 36 0.08
84 149 0.33
85 58 0.13
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (81 bp):
GGTCTTTGTGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTAGAGCTGAG
CGTAGTCGAACTCGAA
Found at i:49933 original size:165 final size:164
Alignment explanation
Indices: 49522--50231 Score: 1042
Period size: 165 Copynumber: 4.3 Consensus size: 164
49512 TTATTGACAA
* * * * * * * *
49522 ATAACCCTTCTTGCCTTGAGCTATGTTGTAAACGATATGACCTCGAAGTTGAGTGTAATCAAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
** * * * * *
49587 CGGGGGTCTTTGGCAGATAACTCTTCTCGACTTAAGTTATACTGCCAATGATGTGCCTGAGAGCT
66 CGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCT
*
49652 GAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAG
131 GAGCGTAGTCGAACTCAAAGGTCTTTGGTCACAG
* ** * * * *
49686 ATAACCCTTATAGCCTTGAGTTATATTGTGAATGATGTGCCCTCCAAGCTGAGAGTAATTGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
*
49751 CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCT
66 CGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCT
* *
49816 GAGCGTAGTCGAACTCGAAGGTCTTTTAGTCACAG
131 GAGCGTAGTCGAACTCAAAGGTC-TTTGGTCACAG
49851 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
* *
49916 CGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
66 CGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCT
**
49981 GAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAG
131 GAGCGTAGTCGAACTCAAAGGTCTTTGG-TCACAG
* * * * *
50016 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGGAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
* ** *
50081 CGAAGGTCTTTGGCAGATAGCCCTTCTCGGCTTAAGCTATGTTGCAAATGATGTGCCTTGGAGCT
66 CGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCT
50146 GAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAG
131 GAGCGTAGTCGAACTCAAAGGTC-TTTGGTCACAG
50181 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTG
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTG
50232 GTCTGGGAAA
Statistics
Matches: 493, Mismatches: 50, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
164 137 0.28
165 351 0.71
166 5 0.01
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (164 bp):
ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
CGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCT
GAGCGTAGTCGAACTCAAAGGTCTTTGGTCACAG
Found at i:55028 original size:14 final size:13
Alignment explanation
Indices: 54994--55036 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
54984 AGAAAATAAT
**
54994 AATAAAAATATTA
1 AATAAAAATAGAA
55007 AA-AAAAATAAGAA
1 AATAAAAAT-AGAA
55020 AATAAAAATAGAA
1 AATAAAAATAGAA
55033 AATA
1 AATA
55037 TTCAGTCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 6 0.23
13 14 0.54
14 6 0.23
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (13 bp):
AATAAAAATAGAA
Found at i:55151 original size:21 final size:20
Alignment explanation
Indices: 55127--55174 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
55117 AAGAACAAAA
55127 TAAAA-AATAAAAATATTAAAT
1 TAAAAGAATAAAAA-A-TAAAT
55148 TAAAAGTAATAAAAAATAAAT
1 TAAAAG-AATAAAAAATAAAT
55169 TAAAAG
1 TAAAAG
55175 CATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 16 0.64
22 1 0.04
23 8 0.32
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (20 bp):
TAAAAGAATAAAAAATAAAT
Found at i:56229 original size:2 final size:2
Alignment explanation
Indices: 56222--56273 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
56212 ATAATACATG
*
56222 TA TA TA TA -A TA TA TA T- TA TA CT- TA TA -A TA TA TA AA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
56260 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
56274 AGTTTATATG
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
1 5 0.12
2 36 0.86
3 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:56230 original size:23 final size:24
Alignment explanation
Indices: 56182--56233 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
56172 AGGTGTCTAC
*
56182 AATATGTATGATAAATGTTATGAT
1 AATATGTATAATAAATGTTATGAT
*
56206 AATATG-ATAATACATGTATAT-AT
1 AATATGTATAATAAATGT-TATGAT
56229 AATAT
1 AATAT
56234 ATATTATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (24 bp):
AATATGTATAATAAATGTTATGAT
Found at i:56324 original size:16 final size:17
Alignment explanation
Indices: 56287--56324 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
56277 TTATATGTAT
56287 GTTTATATAACTATACAA
1 GTTTATATAACTATAC-A
56305 GTTTATATAACTATAC-
1 GTTTATATAACTATACA
56321 GTTT
1 GTTT
56325 TACTTATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.20
18 16 0.80
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (17 bp):
GTTTATATAACTATACA
Found at i:56352 original size:32 final size:32
Alignment explanation
Indices: 56309--56372 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
56299 ATACAAGTTT
* * *
56309 ATATAACTATACGTTTTACTTATAAGTATATA
1 ATATAACTATACATTATACTTATAAATATATA
*
56341 ATATAAGTATACATTATACTTATAAATATATA
1 ATATAACTATACATTATACTTATAAATATATA
56373 TAAGTTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (32 bp):
ATATAACTATACATTATACTTATAAATATATA
Found at i:56559 original size:2 final size:2
Alignment explanation
Indices: 56552--56589 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
56542 GAAAAATTAA
56552 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56590 ATACGTATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56641 original size:4 final size:4
Alignment explanation
Indices: 56632--56662 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
56622 TATGCATAAG
56632 TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TAT
56663 ATATTTGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:57695 original size:20 final size:20
Alignment explanation
Indices: 57666--57703 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
57656 TTTCAAGGTG
57666 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
57686 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
57704 TAAGTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:58724 original size:2 final size:2
Alignment explanation
Indices: 58719--58877 Score: 140
Period size: 2 Copynumber: 82.5 Consensus size: 2
58709 TAAAAAATTA
58719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
58761 AT AT AT AT AT AT AT AT -T AT A- AT AT GT AT GAT AA AT GT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
* * *
58801 GAT A- AT AT GAT A- AT AC AT GT AT AT AT A- AT AT AC AT -T AT ACT
1 -AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* *
58842 -T AT A- AT AT AA AA AT AT A- AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58878 AAAGTTTATA
Statistics
Matches: 130, Mismatches: 13, Indels: 28
0.76 0.08 0.16
Matches are distributed among these distances:
1 10 0.08
2 113 0.87
3 7 0.05
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:58913 original size:30 final size:29
Alignment explanation
Indices: 58866--58937 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 29
58856 ATAATATATA
* *
58866 TATATATA-TATAAAAGTTTATATGTATGTT
1 TATATA-ACTATACAAGTTTATATATATG-T
58896 TATATAACTATACAAGTTTATATATATGT
1 TATATAACTATACAAGTTTATATATATGT
58925 T-TATAACTATACA
1 TATATAACTATACA
58938 TTATACTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 12 0.31
29 3 0.08
30 24 0.62
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.46
Consensus pattern (29 bp):
TATATAACTATACAAGTTTATATATATGT
Found at i:58968 original size:32 final size:31
Alignment explanation
Indices: 58926--58987 Score: 97
Period size: 32 Copynumber: 2.0 Consensus size: 31
58916 TATATATGTT
*
58926 TATAACTATACATTATACTTATAAGTATATAA
1 TATAACTATACATTATAC-TATAAATATATAA
*
58958 TATAAGTATACATTATACTATAAATATATA
1 TATAACTATACATTATACTATAAATATATA
58988 TAAGTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.40
Consensus pattern (31 bp):
TATAACTATACATTATACTATAAATATATAA
Found at i:59175 original size:2 final size:2
Alignment explanation
Indices: 59170--59208 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
59160 AAATTAAAAA
59170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59209 ATACGTATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59328 original size:14 final size:14
Alignment explanation
Indices: 59309--59339 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
59299 ACACACACAC
59309 ATATAAGTATCTAT
1 ATATAAGTATCTAT
*
59323 ATATAAGTATGTAT
1 ATATAAGTATCTAT
59337 ATA
1 ATA
59340 CGTATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (14 bp):
ATATAAGTATCTAT
Found at i:59337 original size:10 final size:10
Alignment explanation
Indices: 59320--59362 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
59310 TATAAGTATC
59320 TATATATAAG
1 TATATATAAG
*
59330 TATGTATATACG
1 TA--TATATAAG
*
59342 TATATATAAA
1 TATATATAAG
59352 TATATATAAG
1 TATATATAAG
59362 T
1 T
59363 GTTGAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 18 0.67
12 9 0.33
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (10 bp):
TATATATAAG
Found at i:59337 original size:12 final size:12
Alignment explanation
Indices: 59309--59359 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
59299 ACACACACAC
59309 ATATAAGTATCTAT
1 ATATAAGTA--TAT
*
59323 ATATAAGTATGT
1 ATATAAGTATAT
*
59335 ATATACGTATAT
1 ATATAAGTATAT
59347 ATA-AA-TATAT
1 ATATAAGTATAT
59357 ATA
1 ATA
59360 AGTGTTGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
12 15 0.45
14 9 0.27
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (12 bp):
ATATAAGTATAT
Found at i:59644 original size:21 final size:19
Alignment explanation
Indices: 59602--59674 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
59592 TACGGTTCAT
* *
59602 AGTTTGGAAACTTTGAAAG
1 AGTTTTGAAACTTTTAAAG
59621 AGTTTTGAAACTTTTATTAAG
1 AGTTTTGAAACTTTTA--AAG
*
59642 AGTTTTGAAA-TTTTACAAA
1 AGTTTTGAAACTTTTA-AAG
*
59661 AGTTTCGAAA-TTTT
1 AGTTTTGAAACTTTT
59675 GCACTCATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 29 0.62
20 5 0.11
21 13 0.28
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.42
Consensus pattern (19 bp):
AGTTTTGAAACTTTTAAAG
Found at i:60883 original size:58 final size:58
Alignment explanation
Indices: 60819--61001 Score: 357
Period size: 58 Copynumber: 3.2 Consensus size: 58
60809 GAATTTATAT
*
60819 ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGAATATTTAC
1 ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGTATATTTAC
60877 ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGTATATTTAC
1 ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGTATATTTAC
60935 ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGTATATTTAC
1 ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGTATATTTAC
60993 ATATGTATA
1 ATATGTATA
61002 TCATCATAAC
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 124 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (58 bp):
ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGTATATTTAC
Found at i:61038 original size:58 final size:57
Alignment explanation
Indices: 60819--61038 Score: 212
Period size: 58 Copynumber: 3.8 Consensus size: 57
60809 GAATTTATAT
* * * * * *
60819 ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGAATATTTAC
1 ATATGTATACATGCATAAAAAAAAAAAAAGAATACA-TTAATATATATGTATATTTAC
* * * * *
60877 ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGTATATTTAC
1 ATATGTATACATGCATAAAAAAAAAAAAAGAATACA-TTAATATATATGTATATTTAC
* * * * *
60935 ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGTATATTTAC
1 ATATGTATACATGCATAAAAAAAAAAAAAGAATACA-TTAATATATATGTATATTTAC
60993 ATATGTATATCAT-CATAACAAAAAAGAAAAAGAA-AGCA-TAATATAT
1 ATATGTATA-CATGCATAA-AAAAAA-AAAAAGAATA-CATTAATATAT
61039 GGTGCGATAG
Statistics
Matches: 152, Mismatches: 6, Indels: 8
0.92 0.04 0.05
Matches are distributed among these distances:
58 135 0.89
59 8 0.05
60 9 0.06
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (57 bp):
ATATGTATACATGCATAAAAAAAAAAAAAGAATACATTAATATATATGTATATTTAC
Found at i:61038 original size:116 final size:115
Alignment explanation
Indices: 60819--61038 Score: 320
Period size: 116 Copynumber: 1.9 Consensus size: 115
60809 GAATTTATAT
60819 ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGAATATTTACATATGTA
1 ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGAATATTTACATATGTA
* * * * *
60884 TACATGCATTAATACAAACAAAGAATACATTTATTATATATGTATATTTAC
66 TACATGCATAAAAAAAAAAAAAGAATACA-TTAATATATATGTATATTTAC
*
60935 ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGTATATTTACATATGTA
1 ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGAATATTTACATATGTA
61000 TATCAT-CATAACAAAAAAGAAAAAGAA-AGCA-TAATATAT
66 TA-CATGCATAA-AAAAAA-AAAAAGAATA-CATTAATATAT
61039 GGTGCGATAG
Statistics
Matches: 94, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
116 77 0.82
117 8 0.09
118 9 0.10
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (115 bp):
ATATGTATACATGCATTAATACAAACAAAGAATACATTTATTATATATGAATATTTACATATGTA
TACATGCATAAAAAAAAAAAAAGAATACATTAATATATATGTATATTTAC
Found at i:61078 original size:2 final size:2
Alignment explanation
Indices: 61073--61113 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
61063 ATATGAAAGC
61073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61114 CACGAAAGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:64504 original size:17 final size:16
Alignment explanation
Indices: 64482--64526 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
64472 GTAAAAGGAG
*
64482 GAAGAACAAAAATAAGA
1 GAAGAA-AAAAAAAAGA
64499 GAAGAAAAAAGAAAAGA
1 GAAGAAAAAA-AAAAGA
*
64516 AAAGAAAAAAA
1 GAAGAAAAAAA
64527 GTGTTACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (16 bp):
GAAGAAAAAAAAAAGA
Found at i:66585 original size:20 final size:20
Alignment explanation
Indices: 66560--66611 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
66550 TACTTTCACT
66560 AAGTTTCGAAACTTTC-TCAA
1 AAGTTTCGAAACTTTCTTC-A
* *
66580 AAGTTTCAAAATTTTCTTCA
1 AAGTTTCGAAACTTTCTTCA
66600 AAGTTTCGAAAC
1 AAGTTTCGAAAC
66612 CGCATGTGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (20 bp):
AAGTTTCGAAACTTTCTTCA
Found at i:74906 original size:23 final size:22
Alignment explanation
Indices: 74865--74988 Score: 75
Period size: 23 Copynumber: 5.8 Consensus size: 22
74855 AACACGGATG
* *
74865 TAAACGAACATAAAAGAACACAA
1 TAAACGAACAT-AATGAACAAAA
74888 TAAACGAACATAGATGAACAAAA
1 TAAACGAACATA-ATGAACAAAA
* * *
74911 CAAAAGAATATAATGAACATAAA
1 TAAACGAACATAATGAACA-AAA
* *
74934 T-CAC-AACATAAT-AATC-ACA
1 TAAACGAACATAATGAA-CAAAA
74953 T-AAC-AA-A-AATGAACAAAA
1 TAAACGAACATAATGAACAAAA
*
74971 AAAACGAACATAAATGAA
1 TAAACGAACAT-AATGAA
74989 TTTATTTTAT
Statistics
Matches: 78, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
17 4 0.05
18 5 0.06
19 10 0.13
20 4 0.05
21 9 0.12
22 9 0.12
23 37 0.47
ACGTcount: A:0.64, C:0.15, G:0.08, T:0.14
Consensus pattern (22 bp):
TAAACGAACATAATGAACAAAA
Found at i:76775 original size:29 final size:30
Alignment explanation
Indices: 76728--76786 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
76718 AAAATGATTC
76728 AAATTGTAAAGTTCAGTGAACAAAATAGAA
1 AAATTGTAAAGTTCAGTGAACAAAATAGAA
**
76758 AAATTG-AAAG-TCAGGTGAGGAAAATAGAA
1 AAATTGTAAAGTTCA-GTGAACAAAATAGAA
76787 GAGAGTATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 17 0.65
30 6 0.23
ACGTcount: A:0.53, C:0.05, G:0.22, T:0.20
Consensus pattern (30 bp):
AAATTGTAAAGTTCAGTGAACAAAATAGAA
Done.