Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 30 of 39
Found at i:5724598 original size:25 final size:25
Alignment explanation
Indices: 5724570--5724634 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 25
5724560 CACTAGTACA
5724570 ATTAATATTAGTATTTTTTATTTT-T
1 ATTAATATTA-TATTTTTTATTTTAT
*
5724595 ATTATTATATATATTTTTTATTTTAAT
1 ATTAATAT-TATATTTTTTATTTT-AT
5724622 ATTAAATATTATA
1 ATT-AATATTATA
5724635 ATAAAATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 20 0.59
26 2 0.06
27 8 0.24
28 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
ATTAATATTATATTTTTTATTTTAT
Found at i:5724618 original size:24 final size:25
Alignment explanation
Indices: 5724581--5724630 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
5724571 TTAATATTAG
* *
5724581 TATTTTTTATTTTTATTATTATATA
1 TATTTTTTATTTTTAATATTAAATA
5724606 TATTTTTTA-TTTTAATATTAAATA
1 TATTTTTTATTTTTAATATTAAATA
5724630 T
1 T
5724631 TATAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TATTTTTTATTTTTAATATTAAATA
Found at i:5726505 original size:19 final size:19
Alignment explanation
Indices: 5726481--5726520 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5726471 TAACAAACTC
5726481 CTAATTGCTGCTGACTCAG
1 CTAATTGCTGCTGACTCAG
* * *
5726500 CTAATTGTTGTTTACTCAG
1 CTAATTGCTGCTGACTCAG
5726519 CT
1 CT
5726521 TACATGCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (19 bp):
CTAATTGCTGCTGACTCAG
Found at i:5728218 original size:16 final size:17
Alignment explanation
Indices: 5728191--5728233 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
5728181 GATTCGTATC
*
5728191 ATATTTAAAAAAATTAG
1 ATATCTAAAAAAATTAG
* *
5728208 ATATC-AAAAAATTTGG
1 ATATCTAAAAAAATTAG
5728224 ATATCTAAAA
1 ATATCTAAAA
5728234 TTTCAGATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (17 bp):
ATATCTAAAAAAATTAG
Found at i:5728782 original size:154 final size:154
Alignment explanation
Indices: 5728609--5728917 Score: 591
Period size: 154 Copynumber: 2.0 Consensus size: 154
5728599 AATTGAGATC
5728609 TATACTGGAAATATTTTTGAAATAATTTTTATTAAAGGTTTCGAACTTTAATCGAGTCCAAAACT
1 TATACTGGAAATATTTTTGAAATAATTTTTATTAAAGGTTTCGAACTTTAATCGAGTCCAAAACT
*
5728674 CAATTTTAACTAAGTAGTACCGATACTGCTAAAGTAGTACCGATACTGTCCAAATTTTTTTCGAA
66 CAATTTTAACTAAGTAGTACCGATACTGCTAAAGCAGTACCGATACTGTCCAAATTTTTTTCGAA
5728739 TTTTCGGATAATTCGAAAATGATT
131 TTTTCGGATAATTCGAAAATGATT
* *
5728763 TATATTGGAAATATTTTTGAAATAATTTTTATTAAATGTTTCGAACTTTAATCGAGTCCAAAACT
1 TATACTGGAAATATTTTTGAAATAATTTTTATTAAAGGTTTCGAACTTTAATCGAGTCCAAAACT
5728828 CAATTTTAACTAAGTAGTACCGATACTGCTAAAGCAGTACCGATACTGTCCAAATTTTTTTCGAA
66 CAATTTTAACTAAGTAGTACCGATACTGCTAAAGCAGTACCGATACTGTCCAAATTTTTTTCGAA
5728893 TTTTCGGATAATTCGAAAATGATT
131 TTTTCGGATAATTCGAAAATGATT
5728917 T
1 T
5728918 TTTATCGATC
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
154 152 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (154 bp):
TATACTGGAAATATTTTTGAAATAATTTTTATTAAAGGTTTCGAACTTTAATCGAGTCCAAAACT
CAATTTTAACTAAGTAGTACCGATACTGCTAAAGCAGTACCGATACTGTCCAAATTTTTTTCGAA
TTTTCGGATAATTCGAAAATGATT
Found at i:5733909 original size:3 final size:3
Alignment explanation
Indices: 5733894--5733954 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
5733884 AATTTTAATT
* *
5733894 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TT- TTGT TTA TTAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TT-A TTA
5733940 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
5733955 ATTACATATT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.04
3 45 0.87
4 5 0.10
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5733941 original size:19 final size:19
Alignment explanation
Indices: 5733894--5733958 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
5733884 AATTTTAATT
*
5733894 TTATT-ATTGTTATTATTA
1 TTATTAATTATTATTATTA
*
5733912 TTATT-ATTATTATT-TTGT
1 TTATTAATTATTATTATT-A
5733930 TTATTAATTATTATTATTA
1 TTATTAATTATTATTATTA
5733949 TTATTAATTA
1 TTATTAATTA
5733959 CATATTACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
17 2 0.05
18 18 0.44
19 19 0.46
20 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTATTAATTATTATTATTA
Found at i:5738796 original size:22 final size:20
Alignment explanation
Indices: 5738734--5738779 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
5738724 ACATTCCCTC
5738734 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
5738754 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
5738774 TCTTTG
1 TCTTTG
5738780 TGTGGCCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (20 bp):
TCTTTGAGACCTTGAAACAT
Found at i:5740333 original size:22 final size:23
Alignment explanation
Indices: 5740282--5740336 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
5740272 TGAAAGGGGT
5740282 AATATTTTCAAAATCTTTGATTA
1 AATATTTTCAAAATCTTTGATTA
*
5740305 AACATTTT-AAAACTCTTTGA-TA
1 AATATTTTCAAAA-TCTTTGATTA
*
5740327 GATATTTTCA
1 AATATTTTCA
5740337 GACTTTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.45
Consensus pattern (23 bp):
AATATTTTCAAAATCTTTGATTA
Found at i:5740621 original size:4 final size:4
Alignment explanation
Indices: 5740612--5740732 Score: 174
Period size: 4 Copynumber: 30.8 Consensus size: 4
5740602 TCGAGAAAAG
* *
5740612 CATA CATA CATA CATA CATA CATA CATA CATA AATA CATA CATA TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
5740660 CATA TATA TATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
5740708 CAAA CATA TATA C--A CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
5740733 TATATATAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
2 2 0.02
4 103 0.98
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:5740840 original size:12 final size:12
Alignment explanation
Indices: 5740825--5740855 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
5740815 TTTCATCTTG
5740825 ACATCCATCATA
1 ACATCCATCATA
5740837 ACATCCATCATA
1 ACATCCATCATA
5740849 ACATCCA
1 ACATCCA
5740856 AGATAGTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (12 bp):
ACATCCATCATA
Found at i:5741144 original size:36 final size:36
Alignment explanation
Indices: 5741088--5741185 Score: 144
Period size: 36 Copynumber: 2.7 Consensus size: 36
5741078 TGAGAATTTT
* *
5741088 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTCT-C
1 AAAACAAA-TTTTGTCTCGCTTGAGAAAATTTCT-TGA
5741125 AAAACAAATTTTGTCTCGCTTGAGAAAATTTCTTGA
1 AAAACAAATTTTGTCTCGCTTGAGAAAATTTCTTGA
*
5741161 AAAACAAATTTCGTCTCGCTTGAGA
1 AAAACAAATTTTGTCTCGCTTGAGA
5741186 TACAAATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
35 1 0.02
36 48 0.84
37 8 0.14
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGAAAATTTCTTGA
Found at i:5741288 original size:37 final size:36
Alignment explanation
Indices: 5741240--5741322 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 36
5741230 TTGAGATCGT
* *
5741240 TTTCTCAAAAAAATAAACTT-TGTCTCGCTTGAGACAA
1 TTTCTCTAAAAAACAAA-TTCTGTCTCGCTTGAGAC-A
*
5741277 TTTCTCT-AAAAACAAATTCTTTCTCGCTTGAGACA
1 TTTCTCTAAAAAACAAATTCTGTCTCGCTTGAGACA
5741312 TTTCTCATAAA
1 TTTCTC-TAAA
5741323 TTTTGAGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
35 9 0.22
36 23 0.57
37 8 0.20
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAAACAAATTCTGTCTCGCTTGAGACA
Found at i:5741623 original size:35 final size:34
Alignment explanation
Indices: 5741577--5741685 Score: 121
Period size: 35 Copynumber: 3.1 Consensus size: 34
5741567 TTGATATCGT
*
5741577 TTTCTCAAAAACAAACTTTGTCTCTCTTGAGACAA
1 TTTCTCTAAAACAAA-TTTGTCTCTCTTGAGACAA
* *
5741612 TTTCTCTAAAACAATTTTTGTCTCGT-TTAAGACAA
1 TTTCTCTAAAACAA-ATTTGTCTC-TCTTGAGACAA
* *
5741647 TTTCTCTAAAAACAAATGTTGTCTCACTTGAGGCAA
1 TTTCTCT-AAAACAAAT-TTGTCTCTCTTGAGACAA
5741683 TTT
1 TTT
5741686 TCCAAATTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
35 37 0.60
36 25 0.40
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (34 bp):
TTTCTCTAAAACAAATTTGTCTCTCTTGAGACAA
Found at i:5741759 original size:30 final size:31
Alignment explanation
Indices: 5741723--5741781 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5741713 AACAAACATA
*
5741723 ATCTTTGAGTC-ATTTCTTTTGAAACAAAGG
1 ATCTTTGAGTCTATTTCATTTGAAACAAAGG
*
5741753 ATCTTTGAGTCTGTTTCATTTGAAACAAA
1 ATCTTTGAGTCTATTTCATTTGAAACAAA
5741782 ATGAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (31 bp):
ATCTTTGAGTCTATTTCATTTGAAACAAAGG
Found at i:5742286 original size:36 final size:35
Alignment explanation
Indices: 5742235--5742331 Score: 90
Period size: 36 Copynumber: 2.7 Consensus size: 35
5742225 TTTAAGAAAA
* * **
5742235 ATCTTTAAGTCTGTTT-CTTTGAAAACAAAATTAAT
1 ATCTTTGAGTCTGTTTCCCTTG-AAACAAAACAAAT
*
5742270 CATCTTTGAGTTTGTTTCCCTTGAAACAAAACAAAT
1 -ATCTTTGAGTCTGTTTCCCTTGAAACAAAACAAAT
**
5742306 ATCTTTGAGATC-ACTTCCCTTGAAAC
1 ATCTTTGAG-TCTGTTTCCCTTGAAAC
5742332 GAATTTTGTC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
35 21 0.41
36 26 0.51
37 4 0.08
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (35 bp):
ATCTTTGAGTCTGTTTCCCTTGAAACAAAACAAAT
Found at i:5742642 original size:43 final size:43
Alignment explanation
Indices: 5742422--5742655 Score: 151
Period size: 43 Copynumber: 5.5 Consensus size: 43
5742412 TGGCCAGTCT
* * ** *
5742422 TCCTCATCACGTAGGAACCGTGTCATCCCCTG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCAACCTTTGATAACCAGAAC
* * *
5742462 TTCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAG-TC
1 TCCTCATCACGTAGGAGCCGTGTCAACCTTTGATAACCAGAAC
* * * * *
5742504 GTCCTCATCACTTAGGAACCGTGTTATCACCTTTAGATGACCATAAC
1 -TCCTCATCACGTAGGAGCCGTGTCA--ACCTTT-GATAACCAGAAC
* * * * * * * * *
5742551 TCTTCATCAAGTATGAGTCGTGTC-ATCATCG---ACCTGATC
1 TCCTCATCACGTAGGAGCCGTGTCAACCTTTGATAACCAGAAC
*
5742590 TCCTCATCACGTGGGAGCCGTGTCAACCTTTGATAACCAGAAC
1 TCCTCATCACGTAGGAGCCGTGTCAACCTTTGATAACCAGAAC
* *
5742633 TCTTCATCACGTATGAGCCGTGT
1 TCCTCATCACGTAGGAGCCGTGT
5742656 TATCACCTTC
Statistics
Matches: 142, Mismatches: 40, Indels: 21
0.70 0.20 0.10
Matches are distributed among these distances:
39 24 0.17
40 30 0.21
42 3 0.02
43 55 0.39
45 5 0.04
46 24 0.17
47 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (43 bp):
TCCTCATCACGTAGGAGCCGTGTCAACCTTTGATAACCAGAAC
Found at i:5742647 original size:82 final size:84
Alignment explanation
Indices: 5742505--5742660 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 84
5742495 TAACCAGTCG
* * * * *
5742505 TCCTCATCACTTAGGAACCGTGTTATCACCTTTAGATGACCATAACTCTTCATCAAGTATGAGTC
1 TCCTCATCACGTAGGAACCGTGTCA-CACCTTTAGATAACCAGAACTCTTCATCAAGTATGAGCC
5742570 GTGTCATCATCGACCTGATC
65 GTGTCATCATCGACCTGATC
* * *
5742590 TCCTCATCACGTGGGAGCCGTGTCA-ACCTTT-GATAACCAGAACTCTTCATCACGTATGAGCCG
1 TCCTCATCACGTAGGAACCGTGTCACACCTTTAGATAACCAGAACTCTTCATCAAGTATGAGCCG
*
5742653 TGTTATCA
66 TGTCATCA
5742661 CCTTCGTAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
82 35 0.56
83 6 0.10
85 21 0.34
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (84 bp):
TCCTCATCACGTAGGAACCGTGTCACACCTTTAGATAACCAGAACTCTTCATCAAGTATGAGCCG
TGTCATCATCGACCTGATC
Found at i:5742766 original size:133 final size:130
Alignment explanation
Indices: 5742406--5742788 Score: 430
Period size: 133 Copynumber: 2.9 Consensus size: 130
5742396 CCATTATCCC
** * * ** *
5742406 TAAAGATGGCCAGTCTTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGATCTTCTCATCA
1 TAAAGATGGCCAGAATTCTTCATCACGTATGAGTCGTGTCATCCCC-GACCAGATCTCCTCATCA
* * * * *
5742471 CGTAGGAGCCGTGTCAACCTTAGATAACCAG-TCGTCCTCATCACTTAGGAACCGTGTTATCACC
65 CGTAGGAGCCGTGTCAACCTTAGATAACCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC
5742535 TT
129 TT
* * * * ** *
5742537 T--AGATGACCATAACTCTTCATCAAGTATGAGTCGTGTCATCATCGACCTGATCTCCTCATCAC
1 TAAAGATGGCCAGAATTCTTCATCACGTATGAGTCGTGTCATCCCCGACCAGATCTCCTCATCAC
* *
5742600 GTGGGAGCCGTGTCAACCTTTGATAACCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTT
66 GTAGGAGCCGTGTCAACCTTAGATAACCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTT
* *
5742665 CGTAAAGATGGCCAAGAATTCTTCATCACGTATGAGTAGTGTCATCCCCGACCAAATCTCCTCAT
1 --TAAAGATGGCC-AGAATTCTTCATCACGTATGAGTCGTGTCATCCCCGACCAGATCTCCTCAT
* * * ** * *
5742730 CACGTAGGAACCGAGTCACCCTTAGACGACCCGAACTCTTCATCACGTATGAGCAGTGT
63 CACGTAGGAGCCGTGTCAACCTTAGATAACCAGAACTCTTCATCACGTATGAGCCGTGT
5742789 CGTCCCCAAC
Statistics
Matches: 207, Mismatches: 39, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
128 73 0.35
129 32 0.15
130 1 0.00
131 1 0.00
132 7 0.03
133 93 0.45
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (130 bp):
TAAAGATGGCCAGAATTCTTCATCACGTATGAGTCGTGTCATCCCCGACCAGATCTCCTCATCAC
GTAGGAGCCGTGTCAACCTTAGATAACCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTT
Found at i:5742969 original size:3 final size:3
Alignment explanation
Indices: 5742954--5743038 Score: 109
Period size: 3 Copynumber: 28.0 Consensus size: 3
5742944 AATTTTAATT
* * *
5742954 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA ATG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5743002 TTA TT- TTGT TTA TTAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TT-A TTA TTA TTA TTA TTA TTA TTA
5743039 ATTACATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
2 2 0.03
3 65 0.90
4 5 0.07
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5743783 original size:9 final size:9
Alignment explanation
Indices: 5743769--5743793 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5743759 AAGAAAACAG
5743769 AGAGAGAGA
1 AGAGAGAGA
5743778 AGAGAGAGA
1 AGAGAGAGA
5743787 AGAGAGA
1 AGAGAGA
5743794 AAGCTTACCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
AGAGAGAGA
Found at i:5749613 original size:13 final size:13
Alignment explanation
Indices: 5749595--5749619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5749585 AAAGAAAATC
5749595 AAATTACAATAAA
1 AAATTACAATAAA
5749608 AAATTACAATAA
1 AAATTACAATAA
5749620 TAAGAAAAAA
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATTACAATAAA
Found at i:5756145 original size:21 final size:21
Alignment explanation
Indices: 5756103--5756145 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5756093 AATATGTAAA
*
5756103 TCGCATTGCGATTTTACGAAT
1 TCGCATTGCGATTTTACAAAT
* *
5756124 TCGCGTTGCGATTTTTCAAAT
1 TCGCATTGCGATTTTACAAAT
5756145 T
1 T
5756146 TGCAACATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:5756188 original size:20 final size:20
Alignment explanation
Indices: 5756165--5756211 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
5756155 ATTTTCAAAT
*
5756165 TCGCAATGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
5756185 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
5756205 TCGCAAC
1 TCGCAAC
5756212 ACAAAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:5756243 original size:20 final size:20
Alignment explanation
Indices: 5756220--5756312 Score: 107
Period size: 20 Copynumber: 4.6 Consensus size: 20
5756210 ACACAAAAGT
5756220 CAAATTCGCAACGCGATTTC
1 CAAATTCGCAACGCGATTTC
* *
5756240 CAAATTCGCAACGTGATTTA
1 CAAATTCGCAACGCGATTTC
*
5756260 CAAATTCGCAACACTGAATTT-
1 CAAATTCGCAACGC-G-ATTTC
*
5756281 CAAATTCGCAACTCGATTTC
1 CAAATTCGCAACGCGATTTC
**
5756301 TGAATTCGCAAC
1 CAAATTCGCAAC
5756313 TCAATTTTCG
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 4 0.06
20 41 0.65
21 14 0.22
22 4 0.06
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTC
Found at i:5756249 original size:60 final size:61
Alignment explanation
Indices: 5756159--5756312 Score: 152
Period size: 60 Copynumber: 2.5 Consensus size: 61
5756149 AACATGATTT
* * * **
5756159 TCAAATTCGCAATGCGAATATGTAAA-TCGCAACGCGAATCTGTAAA-TCGCAACAC-AAAAG
1 TCAAATTCGCAACGCG-ATTTCTAAATTCGCAACGCG-ATCTACAAATTCGCAACACTAAAAG
* * * * **
5756219 TCAAATTCGCAACGCGATTTCCAAATTCGCAACGTGATTTACAAATTCGCAACACTGAATT
1 TCAAATTCGCAACGCGATTTCTAAATTCGCAACGCGATCTACAAATTCGCAACACTAAAAG
* *
5756280 TCAAATTCGCAACTCGATTTCTGAATTCGCAAC
1 TCAAATTCGCAACGCGATTTCTAAATTCGCAAC
5756313 TCAATTTTCG
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
59 12 0.16
60 33 0.43
61 32 0.42
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.25
Consensus pattern (61 bp):
TCAAATTCGCAACGCGATTTCTAAATTCGCAACGCGATCTACAAATTCGCAACACTAAAAG
Found at i:5756298 original size:61 final size:60
Alignment explanation
Indices: 5756205--5756351 Score: 161
Period size: 61 Copynumber: 2.4 Consensus size: 60
5756195 AATCTGTAAA
* ** *
5756205 TCGCAACACAAAAGTCAAATTCGCAACGCGATTTCCAAATTCGCAACGT-GATTTACAAAT
1 TCGCAACACGAATTTCAAATTCGCAACGCGATTTCCAAATTCGCAAC-TCAATTTACAAAT
* ** * *
5756265 TCGCAACACTGAATTTCAAATTCGCAACTCGATTTCTGAATTCGCAACTCAATTTTCGAAT
1 TCGCAACAC-GAATTTCAAATTCGCAACGCGATTTCCAAATTCGCAACTCAATTTACAAAT
* * *
5756326 TCGTAACACGAATTTTAATTTCGCAA
1 TCGCAACACGAATTTCAAATTCGCAA
5756352 AAGGTTTTAT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
60 25 0.34
61 48 0.66
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (60 bp):
TCGCAACACGAATTTCAAATTCGCAACGCGATTTCCAAATTCGCAACTCAATTTACAAAT
Found at i:5756299 original size:41 final size:39
Alignment explanation
Indices: 5756219--5756312 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 39
5756209 AACACAAAAG
*
5756219 TCAAATTCGCAACGCGATTTCCAAATTCGCAACGTGATT
1 TCAAATTCGCAACACGATTTCCAAATTCGCAACGTGATT
5756258 TACAAATTCGCAACACTGAATTT-CAAATTCGCAAC-TCGATT
1 T-CAAATTCGCAACAC-G-ATTTCCAAATTCGCAACGT-GATT
*
5756299 TCTGAATTCGCAAC
1 TC-AAATTCGCAAC
5756313 TCAATTTTCG
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
39 1 0.02
40 15 0.31
41 28 0.58
42 4 0.08
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.29
Consensus pattern (39 bp):
TCAAATTCGCAACACGATTTCCAAATTCGCAACGTGATT
Found at i:5756313 original size:20 final size:19
Alignment explanation
Indices: 5756219--5756351 Score: 106
Period size: 20 Copynumber: 6.6 Consensus size: 19
5756209 AACACAAAAG
*
5756219 TCAAATTCGCAACGCGATT
1 TCAAATTCGCAACTCGATT
5756238 TCCAAATTCGCAACGT-GATT
1 T-CAAATTCGCAAC-TCGATT
*
5756258 TACAAATTCGCAACACTGAATT
1 T-CAAATTCGCAACTC-G-ATT
5756280 TCAAATTCGCAACTCGATT
1 TCAAATTCGCAACTCGATT
* *
5756299 TCTGAATTCGCAACTCAATTT
1 TC-AAATTCGCAACTCGA-TT
* * *
5756320 TCGAATTCGTAACACGAATT
1 TCAAATTCGCAACTCG-ATT
* *
5756340 TTAATTTCGCAA
1 TCAAATTCGCAA
5756352 AAGGTTTTAT
Statistics
Matches: 93, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
19 6 0.06
20 64 0.69
21 19 0.20
22 4 0.04
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTCGATT
Found at i:5757161 original size:12 final size:12
Alignment explanation
Indices: 5757140--5757173 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5757130 ACCACATTTC
*
5757140 CAATACCAAACA
1 CAATATCAAACA
5757152 CAATATCAAACA
1 CAATATCAAACA
*
5757164 CAATCTCAAA
1 CAATATCAAA
5757174 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:5757326 original size:24 final size:24
Alignment explanation
Indices: 5757299--5757352 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
5757289 GTATTTGAAA
* *
5757299 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTCGTAAATACCCGGAC
* *
5757323 TTTGATCTTCGTAAATACTCGGAT
1 TTTGATCTTCGTAAATACCCGGAC
5757347 TTTGAT
1 TTTGAT
5757353 GATGTTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTCGTAAATACCCGGAC
Found at i:5759918 original size:25 final size:25
Alignment explanation
Indices: 5759882--5759929 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
5759872 ATCAATTAAA
*
5759882 CATTGTTGTGGGTACATTATTTGAT
1 CATTGTTATGGGTACATTATTTGAT
5759907 CATTGTTATGGGTACATTATTTG
1 CATTGTTATGGGTACATTATTTG
5759930 GAAAATAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.48
Consensus pattern (25 bp):
CATTGTTATGGGTACATTATTTGAT
Found at i:5760333 original size:18 final size:18
Alignment explanation
Indices: 5760312--5760348 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5760302 GTAATTGGAG
5760312 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
5760330 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
5760348 T
1 T
5760349 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:5760355 original size:24 final size:24
Alignment explanation
Indices: 5760304--5760356 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5760294 TTTCATATGT
* * *
5760304 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
5760328 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
5760352 AATTT
1 AATTT
5760357 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:5761946 original size:14 final size:14
Alignment explanation
Indices: 5761927--5761960 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
5761917 CATAAATTAA
5761927 ACAAATCAACTTTT
1 ACAAATCAACTTTT
5761941 ACAAATCAACTTTT
1 ACAAATCAACTTTT
5761955 ACAAAT
1 ACAAAT
5761961 ACATCAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5763356 original size:21 final size:21
Alignment explanation
Indices: 5763332--5763434 Score: 125
Period size: 21 Copynumber: 4.9 Consensus size: 21
5763322 GTGGGAGTGA
*
5763332 CCTCTTAAACGATGACAGGGG
1 CCTCTTGAACGATGACAGGGG
**
5763353 CCTCTTGAACGATGGGAGGGG
1 CCTCTTGAACGATGACAGGGG
* * *
5763374 CCTCTTGAATGATGATAAGGG
1 CCTCTTGAACGATGACAGGGG
* * *
5763395 CCTCTTGAACGATAAGAGAGG
1 CCTCTTGAACGATGACAGGGG
5763416 CCTCTTGAACGATGACAGG
1 CCTCTTGAACGATGACAGG
5763435 TGAATCGGGC
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.21
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:5763378 original size:42 final size:42
Alignment explanation
Indices: 5763312--5763434 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 42
5763302 GTGAATCGGG
* * * * *
5763312 CTCTCGAACGGTGGGAGTGACCTCTTAAACGATGACAGGGGC
1 CTCTTGAACGATGGGAGAGGCCTCTTGAACGATGACAGGGGC
* * * *
5763354 CTCTTGAACGATGGGAGGGGCCTCTTGAATGATGATAAGGGC
1 CTCTTGAACGATGGGAGAGGCCTCTTGAACGATGACAGGGGC
**
5763396 CTCTTGAACGATAAGAGAGGCCTCTTGAACGATGACAGG
1 CTCTTGAACGATGGGAGAGGCCTCTTGAACGATGACAGG
5763435 TGAATCGGGC
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGATGGGAGAGGCCTCTTGAACGATGACAGGGGC
Found at i:5765552 original size:20 final size:20
Alignment explanation
Indices: 5765529--5765593 Score: 98
Period size: 19 Copynumber: 3.4 Consensus size: 20
5765519 TCTGAAACTT
*
5765529 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
5765549 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
5765568 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
5765587 AAAATCG
1 AAAATCG
5765594 TGTTGCGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
19 26 0.62
20 16 0.38
ACGTcount: A:0.51, C:0.22, G:0.17, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:5765632 original size:20 final size:20
Alignment explanation
Indices: 5765591--5765632 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5765581 GAAACTAAAA
* * *
5765591 TCGTGTTGCGATTTTCATTT
1 TCGTGTTGCGAATTTAAGTT
5765611 TCGTGTTGCGAATTTAAGTT
1 TCGTGTTGCGAATTTAAGTT
5765631 TC
1 TC
5765633 AAATAGTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (20 bp):
TCGTGTTGCGAATTTAAGTT
Found at i:5765987 original size:22 final size:22
Alignment explanation
Indices: 5765953--5766017 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
5765943 TCTGAAAGAT
5765953 GGAGATA--GACGGATTTCGCC
1 GGAGATAGGGACGGATTTCGCC
* *
5765973 GGAGATGGGGACGGATTTCGTC
1 GGAGATAGGGACGGATTTCGCC
*
5765995 GGAGATAGGGACGGATGTCGCC
1 GGAGATAGGGACGGATTTCGCC
5766017 G
1 G
5766018 TAGAGAGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 6 0.16
22 32 0.84
ACGTcount: A:0.22, C:0.17, G:0.43, T:0.18
Consensus pattern (22 bp):
GGAGATAGGGACGGATTTCGCC
Found at i:5766208 original size:20 final size:20
Alignment explanation
Indices: 5766186--5766251 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
5766176 GACTTATGTG
*
5766186 TTGCGATTTACAGATTCGCG
1 TTGCGATTTACAGATTCGCA
5766206 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACAGATTCGCA
*
5766226 TTGCGATTTACATATTCGCA
1 TTGCGATTTACAGATTCGCA
5766246 TTGCGA
1 TTGCGA
5766252 ATTTGGAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCGATTTACAGATTCGCA
Found at i:5766303 original size:19 final size:19
Alignment explanation
Indices: 5766265--5766313 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
5766255 TGGAAACTAA
* *
5766265 GTTGCGAAATTGGAGTTCGC
1 GTTGCG-AATTCGAGATCGC
5766285 GTTGCGAATTCGAGATCGC
1 GTTGCGAATTCGAGATCGC
5766304 GTTGCGAATT
1 GTTGCGAATT
5766314 TGTTGGTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (19 bp):
GTTGCGAATTCGAGATCGC
Found at i:5767428 original size:75 final size:75
Alignment explanation
Indices: 5767342--5767524 Score: 181
Period size: 75 Copynumber: 2.4 Consensus size: 75
5767332 CTTAAACGGT
* * * * * *
5767342 TAAAATAAAATAAAC-ACTATCTATTATGTTGAACTACCTA-CTGATTTATTTGAAGGTTACTAA
1 TAAAATAAAATAAACGA-TATATATTACGTTAAAATACCTACCAG-TTTATTTAAAGGTTACTAA
5767405 TAATATAAAAAG
64 TAATATAAAAAG
** * * *
5767417 TAAAATAAAATAGGCGATATATATTACGTTAAAATGCGTACCAGTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAAACGATATATATTACGTTAAAATACCTACCAGTTTATTTAAAGGTTACTAATA
* *
5767482 ATGTAAAAGG
66 ATATAAAAAG
* * **
5767492 TAAAATAAAATAGACGGTACCTATTACGTTAAA
1 TAAAATAAAATAAACGATATATATTACGTTAAA
5767525 TAGACGCTAC
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
75 86 0.97
76 3 0.03
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (75 bp):
TAAAATAAAATAAACGATATATATTACGTTAAAATACCTACCAGTTTATTTAAAGGTTACTAATA
ATATAAAAAG
Found at i:5767528 original size:23 final size:23
Alignment explanation
Indices: 5767499--5767570 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
5767489 AGGTAAAATA
*
5767499 AAATAGACGGTACCTATTACGTT
1 AAATAGACGCTACCTATTACGTT
*
5767522 AAATAGACGCTACCTATTAGGTT
1 AAATAGACGCTACCTATTACGTT
* * *
5767545 AAATAAACGTTACCTATTATGTT
1 AAATAGACGCTACCTATTACGTT
5767568 AAA
1 AAA
5767571 ATAGCTATCG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (23 bp):
AAATAGACGCTACCTATTACGTT
Found at i:5767634 original size:75 final size:75
Alignment explanation
Indices: 5767555--5767720 Score: 235
Period size: 75 Copynumber: 2.2 Consensus size: 75
5767545 AAATAAACGT
*
5767555 TACCTATTATGTTAAAATAGCTA-TCGGTTTGTTTAAAGATTAATAATAATGTAAACGGTAAAAT
1 TACCTATTATGTTAAAATAGCTACT-GGTTTGTTTAAAGATTAATAATAACGTAAACGGTAAAAT
5767619 AAAATAGGCGC
65 AAAATAGGCGC
* * * * *
5767630 TACCTATTACGTTAAAATATCTACTGGTTTGTTTAAAGGTTACTAATAACGTAAATGGTAAAATA
1 TACCTATTATGTTAAAATAGCTACTGGTTTGTTTAAAGATTAATAATAACGTAAACGGTAAAATA
* *
5767695 AAATATGTGC
66 AAATAGGCGC
*
5767705 TATCTATTATGTTAAA
1 TACCTATTATGTTAAA
5767721 TATGCGTTAC
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
75 79 0.99
76 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (75 bp):
TACCTATTATGTTAAAATAGCTACTGGTTTGTTTAAAGATTAATAATAACGTAAACGGTAAAATA
AAATAGGCGC
Found at i:5767724 original size:23 final size:23
Alignment explanation
Indices: 5767695--5767789 Score: 109
Period size: 23 Copynumber: 4.1 Consensus size: 23
5767685 TGGTAAAATA
* * *
5767695 AAATATGTGCTATCTATTATGTT
1 AAATATGCGCTACCTATTACGTT
*
5767718 AAATATGCGTTACCTATTACGTT
1 AAATATGCGCTACCTATTACGTT
* *
5767741 AAATAGGTGCTACCTATTACGTT
1 AAATATGCGCTACCTATTACGTT
** *
5767764 AAATAAACGCTATCTATTACGTT
1 AAATATGCGCTACCTATTACGTT
5767787 AAA
1 AAA
5767790 CTAACTACCG
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (23 bp):
AAATATGCGCTACCTATTACGTT
Found at i:5767757 original size:196 final size:196
Alignment explanation
Indices: 5767402--5767766 Score: 484
Period size: 196 Copynumber: 1.9 Consensus size: 196
5767392 TGAAGGTTAC
*
5767402 TAATAATATAAAAAGTAAAATAAAATAGGCGATATATATTACGTTAAAATGCGTACCAGTTTGTT
1 TAATAATATAAAAAGTAAAATAAAATAGGCGATACATATTACGTTAAAATGCGTACCAGTTTGTT
* *
5767467 TAAAGGTTACTAATAATGTAAAAGGTAAAATAAAATAGACGGTACCTATTACGTTAAATAGACGC
66 TAAAGGTTACTAATAACGTAAAAGGTAAAATAAAATAGACGCTACCTATTACGTTAAATAGACGC
* * *
5767532 TACCTATTAGGTTAAATAAACGTTACCTATTATGTTAAAATAGCTATCGGTTTGTTTAAAGATTA
131 TACCTATTACGTTAAATAAACGCTACCTATTACGTTAAAATAGCTATCGGTTTGTTTAAAGATTA
5767597 A
196 A
* ** * * * **
5767598 TAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACGTTAAAATATC-TACTGGTTTGT
1 TAATAATATAAAAAGTAAAATAAAATAGGCGATACATATTACGTTAAAAT-GCGTACCAGTTTGT
* * * *
5767662 TTAAAGGTTACTAATAACGTAAATGGTAAAATAAAATATG-TGCTATCTATTATGTTAAATATG-
65 TTAAAGGTTACTAATAACGTAAAAGGTAAAATAAAATA-GACGCTACCTATTACGTTAAATA-GA
* ***
5767725 CGTTACCTATTACGTTAAATAGGTGCTACCTATTACGTTAAA
128 CGCTACCTATTACGTTAAATAAACGCTACCTATTACGTTAAA
5767767 TAAACGCTAT
Statistics
Matches: 144, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
196 141 0.98
197 3 0.02
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.34
Consensus pattern (196 bp):
TAATAATATAAAAAGTAAAATAAAATAGGCGATACATATTACGTTAAAATGCGTACCAGTTTGTT
TAAAGGTTACTAATAACGTAAAAGGTAAAATAAAATAGACGCTACCTATTACGTTAAATAGACGC
TACCTATTACGTTAAATAAACGCTACCTATTACGTTAAAATAGCTATCGGTTTGTTTAAAGATTA
A
Found at i:5767765 original size:46 final size:46
Alignment explanation
Indices: 5767695--5767789 Score: 127
Period size: 46 Copynumber: 2.1 Consensus size: 46
5767685 TGGTAAAATA
* * * ** *
5767695 AAATATGTGCTATCTATTATGTTAAATATGCGTTACCTATTACGTT
1 AAATAGGTGCTACCTATTACGTTAAATAAACGCTACCTATTACGTT
*
5767741 AAATAGGTGCTACCTATTACGTTAAATAAACGCTATCTATTACGTT
1 AAATAGGTGCTACCTATTACGTTAAATAAACGCTACCTATTACGTT
5767787 AAA
1 AAA
5767790 CTAACTACCG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (46 bp):
AAATAGGTGCTACCTATTACGTTAAATAAACGCTACCTATTACGTT
Found at i:5768279 original size:15 final size:15
Alignment explanation
Indices: 5768259--5768288 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5768249 GTGATTAATT
5768259 CAACAATAATAATAA
1 CAACAATAATAATAA
5768274 CAACAATAATAATAA
1 CAACAATAATAATAA
5768289 TGTATCCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (15 bp):
CAACAATAATAATAA
Found at i:5768301 original size:17 final size:17
Alignment explanation
Indices: 5768279--5768332 Score: 108
Period size: 17 Copynumber: 3.2 Consensus size: 17
5768269 AATAACAACA
5768279 ATAATAATAATGTATCC
1 ATAATAATAATGTATCC
5768296 ATAATAATAATGTATCC
1 ATAATAATAATGTATCC
5768313 ATAATAATAATGTATCC
1 ATAATAATAATGTATCC
5768330 ATA
1 ATA
5768333 CTTATTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (17 bp):
ATAATAATAATGTATCC
Found at i:5768662 original size:108 final size:106
Alignment explanation
Indices: 5768540--5768820 Score: 341
Period size: 107 Copynumber: 2.6 Consensus size: 106
5768530 TGTTAATATT
* * * *
5768540 TATTTATAACAAAATAAGAAATTAACATATTTTGTTCTCGTGAGATTTCGAAGATCCCACCAGCT
1 TATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGTGA-ATTTCGAAG-TCCCACCAACT
* *
5768605 TAAACTTTGATAACATTTTAGGCGCT-ACATAATATGTTGATAA
64 TAAACTTTGATAACATTTTAGGCGATAAC-TAATATGTTGAAAA
* * *
5768648 TATTAATAACAAAATAAGTAATTAACTTATTTTGTTATCGTCGAATTTCTAAG-CACCATCAACT
1 TATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGT-GAATTTCGAAGTC-CCACCAACT
*
5768712 TAAACTTTGATAATATTTTAGGCGATAACTAATATGTTGAAAA
64 TAAACTTTGATAACATTTTAGGCGATAACTAATATGTTGAAAA
* * * * * *
5768755 TATTGATAACAAATTAGGTAATTAACATATTTTATTATCGTCATATTTCGAAGGTCCCATCAACT
1 TATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGTGA-ATTTCGAA-GTCCCACCAACT
5768820 T
64 T
5768821 TAAAAATGTG
Statistics
Matches: 150, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
106 2 0.01
107 87 0.58
108 58 0.39
109 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (106 bp):
TATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGTGAATTTCGAAGTCCCACCAACTTA
AACTTTGATAACATTTTAGGCGATAACTAATATGTTGAAAA
Found at i:5769099 original size:223 final size:223
Alignment explanation
Indices: 5768682--5769120 Score: 535
Period size: 223 Copynumber: 2.0 Consensus size: 223
5768672 ACTTATTTTG
**
5768682 TTATCGTCGAATTTCTAAGCACCATCAACTTAAACTTTGATAATATTTTAGGCGATAACTAATAT
1 TTATCGTCGAATTTCTAAGCACCATCAACTTAAACTTTGATAATATTTTAAACGATAACTAATAT
* * * ** *
5768747 GTTGAAAATATTGATAACAAATTAGGTAATTAACATATTTTATTATCGTCATATTTCGAAGGTCC
66 ATTGAAAATATTGACAACAAATCAAATAATTAACATATTTTATTATCGTCATATTTCGAAGGACC
* * * * *
5768812 CATCAACTTTAAAAATGTGTTACCTATTACATTAAATAAATGTTAATTGTTATGTTAGTATGATT
131 CATCAACTTTAAAAAAGCGCTACCTATTACATTAAATAAACGCTAATTGTTATGTTAGTATGATT
5768877 AATAATATTTCCAATAATTAACATATTA
196 AATAATATTTCCAATAATTAACATATTA
* * * * * * *
5768905 TTATTGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAATATTTTAAATGCT-ACTTAAT
1 TTATCGTCGAATTTCTAA-GCACCATCAACTTAAACTTTGATAATATTTTAAACGATAAC-TAAT
* * *
5768969 ATATT-AATAATATTGACAACAAATCAAATAATTAACCTATTTTGTTATCGTCGA-ATTTCTAA-
64 ATATTGAA-AATATTGACAACAAATCAAATAATTAACATATTTTATTATCGTC-ATATTTCGAAG
* * * * *
5769031 GACCCATCAACTTTAAAAAAGCGCTACCTATTACGTTACATAAGCGCTACTTGTTATGTTATTAT
127 GACCCATCAACTTTAAAAAAGCGCTACCTATTACATTAAATAAACGCTAATTGTTATGTTAGTAT
* * *
5769096 GATTGATAATGTTTTCAATAATTAA
192 GATTAATAATATTTCCAATAATTAA
5769121 TCGGTTATGT
Statistics
Matches: 181, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
223 96 0.53
224 84 0.46
225 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (223 bp):
TTATCGTCGAATTTCTAAGCACCATCAACTTAAACTTTGATAATATTTTAAACGATAACTAATAT
ATTGAAAATATTGACAACAAATCAAATAATTAACATATTTTATTATCGTCATATTTCGAAGGACC
CATCAACTTTAAAAAAGCGCTACCTATTACATTAAATAAACGCTAATTGTTATGTTAGTATGATT
AATAATATTTCCAATAATTAACATATTA
Found at i:5774719 original size:22 final size:22
Alignment explanation
Indices: 5774694--5774744 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
5774684 GGTTTTTCGG
*
5774694 TGCAAGTTGTTGCA-CAGAAAGT
1 TGCAAGCTGTTGCACCA-AAAGT
5774716 TGCAAGCTGTTGCACCAAAAGT
1 TGCAAGCTGTTGCACCAAAAGT
5774738 TGCAAGC
1 TGCAAGC
5774745 ACCTCTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (22 bp):
TGCAAGCTGTTGCACCAAAAGT
Found at i:5784246 original size:34 final size:34
Alignment explanation
Indices: 5784186--5784253 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
5784176 TTTCTTGAGA
*
5784186 ATTGTTTTCTTCTTTTTATCAAGAGAGAA-TTGTC
1 ATTGTTTTCTTCTTTTGATC-AGAGAGAAGTTGTC
5784220 ATTGTTTTCTTCTTGTTAGATC-GAGAGAAGTTGT
1 ATTGTTTTCTTCTT-TT-GATCAGAGAGAAGTTGT
5784254 AATTCCTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 21 0.70
35 6 0.20
36 3 0.10
ACGTcount: A:0.22, C:0.10, G:0.19, T:0.49
Consensus pattern (34 bp):
ATTGTTTTCTTCTTTTGATCAGAGAGAAGTTGTC
Found at i:5791170 original size:15 final size:15
Alignment explanation
Indices: 5791150--5791181 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5791140 AAAATCTTTC
*
5791150 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
5791165 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
5791180 TT
1 TT
5791182 CGATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:5797163 original size:20 final size:20
Alignment explanation
Indices: 5797107--5797163 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
5797097 TCTTATTCCC
*
5797107 TGGTAATCTTACATTCCCAT
1 TGGTAATCTTACATTCTCAT
* *
5797127 TGGTGATCTTATATTCTCAT
1 TGGTAATCTTACATTCTCAT
5797147 TGGTAATCTTACATTCT
1 TGGTAATCTTACATTCT
5797164 GTGAACCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (20 bp):
TGGTAATCTTACATTCTCAT
Found at i:5802446 original size:21 final size:21
Alignment explanation
Indices: 5802399--5802447 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
5802389 TGACTATCGT
*
5802399 AATGCGATTTTCCAATTTCGC
1 AATGCGATTTTCCAATTTCAC
**
5802420 GTTGCGATTTTCCCAATTT-AC
1 AATGCGATTTT-CCAATTTCAC
5802441 AATGCGA
1 AATGCGA
5802448 ATAAGTAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (21 bp):
AATGCGATTTTCCAATTTCAC
Found at i:5802480 original size:21 final size:21
Alignment explanation
Indices: 5802454--5802551 Score: 187
Period size: 21 Copynumber: 4.7 Consensus size: 21
5802444 GCGAATAAGT
5802454 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
5802475 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
5802496 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
5802517 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
*
5802538 AAATCGCAACGCGA
1 AAATCGCAATGCGA
5802552 TACTGACTAT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.21
Consensus pattern (21 bp):
AAATCGCAATGCGAATTTGGA
Found at i:5802565 original size:20 final size:20
Alignment explanation
Indices: 5802540--5802654 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
5802530 AATTTGGAAA
5802540 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
5802560 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
5802581 ATCACAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
5802601 TTCGCAACGCGATACTTAAT
1 ATCGCAACGCGATACTGACT
* *
5802621 TTCGCAACGCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
5802641 TTCGCAACGAGATA
1 ATCGCAACGCGATA
5802655 ATACATAATC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.03
20 60 0.77
21 14 0.18
22 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:5802582 original size:41 final size:41
Alignment explanation
Indices: 5802537--5802674 Score: 179
Period size: 41 Copynumber: 3.4 Consensus size: 41
5802527 GCGAATTTGG
*
5802537 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
5802578 AAAATCACAACGCGATACTGACTTTCGCAACGCGATACT-T
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
** * *
5802618 AATTTCGCAACGCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
5802659 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
5802675 TTTCAAAGCG
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 33 0.41
41 47 0.59
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:5802869 original size:22 final size:22
Alignment explanation
Indices: 5802841--5802884 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5802831 CACTCTCTCA
5802841 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
5802863 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
5802885 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:5803196 original size:20 final size:20
Alignment explanation
Indices: 5803147--5803205 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
5803137 TTTATTCTCT
* **
5803147 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
5803167 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
5803187 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
5803206 AGAAATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:5803396 original size:25 final size:24
Alignment explanation
Indices: 5803342--5803396 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
5803332 TGTTTATTAT
* *
5803342 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
5803366 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
5803392 TGTTT
1 TGTTT
5803397 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:5804546 original size:18 final size:18
Alignment explanation
Indices: 5804525--5804572 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
5804515 TCCACTTCGG
*
5804525 GAGCCATCTCCTCACCCA
1 GAGCCATCACCTCACCCA
*
5804543 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
5804561 GAGCCATCACCT
1 GAGCCATCACCT
5804573 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.25, C:0.46, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:5805162 original size:19 final size:19
Alignment explanation
Indices: 5805140--5805236 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
5805130 GGAAATGGCT
5805140 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
5805159 ATCGTAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
5805173 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5805192 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
5805206 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5805225 ATCGCAATGCGA
1 ATCGCAATGCGA
5805237 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.49
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5805182 original size:33 final size:33
Alignment explanation
Indices: 5805140--5805231 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
5805130 GGAAATGGCT
*
5805140 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
5805173 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
5805206 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
5805232 TGCGATTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:5805208 original size:14 final size:14
Alignment explanation
Indices: 5805156--5805214 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
5805146 ATGCGAAATG
*
5805156 AAAATCGTAACGAC
1 AAAATCGCAACGAC
*
5805170 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
5805189 AAAATCGCAACGAC
1 AAAATCGCAACGAC
5805203 AAAATCGCAACG
1 AAAATCGCAACG
5805215 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:5805308 original size:20 final size:19
Alignment explanation
Indices: 5805274--5805348 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
5805264 TTGCGATTTT
*
5805274 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
5805293 CATTTCTGCGTTGCGATAGC
1 CATTTC-GCGTTGCGATAGC
*
5805313 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
5805333 CATTTTCACGTTGCGA
1 CA-TTTCGCGTTGCGA
5805349 AAGTAAGTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.12
20 40 0.80
21 4 0.08
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:5805359 original size:20 final size:20
Alignment explanation
Indices: 5805321--5805359 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5805311 GCCATTTCCG
* * *
5805321 CGTTGCGATAGTCATTTTCA
1 CGTTGCGAAAGTAAGTTTCA
5805341 CGTTGCGAAAGTAAGTTTC
1 CGTTGCGAAAGTAAGTTTC
5805360 GTGTAGCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGAAAGTAAGTTTCA
Found at i:5805749 original size:21 final size:20
Alignment explanation
Indices: 5805723--5805791 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
5805713 CTGTCATCCC
5805723 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
5805744 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
5805765 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
5805785 TCAAGAG
1 TCAAGAG
5805792 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:5805803 original size:41 final size:42
Alignment explanation
Indices: 5805713--5805803 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
5805703 CCCGACTCAC
* *
5805713 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
5805755 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
5805796 CTGTCATC
1 CTGTCATC
5805804 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:5807246 original size:14 final size:14
Alignment explanation
Indices: 5807212--5807250 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5807202 TGGATTGTTT
5807212 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
5807226 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
5807240 TGTTGATTTGT
1 AATTGATTTGT
5807251 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:5808421 original size:23 final size:23
Alignment explanation
Indices: 5808395--5808439 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5808385 CACCACAGCT
*
5808395 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
5808418 CGTAGAATTGTACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
5808440 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:5808582 original size:25 final size:25
Alignment explanation
Indices: 5808554--5808622 Score: 129
Period size: 25 Copynumber: 2.8 Consensus size: 25
5808544 TATATATATA
5808554 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
5808579 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
*
5808604 TCCCGAATGACCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
5808623 CCCTCTACTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.19
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:5810312 original size:21 final size:21
Alignment explanation
Indices: 5810288--5810332 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5810278 TGTTGTTCGT
* *
5810288 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5810309 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5810330 TTG
1 TTG
5810333 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5813800 original size:25 final size:25
Alignment explanation
Indices: 5813765--5813840 Score: 134
Period size: 25 Copynumber: 3.0 Consensus size: 25
5813755 AAGAATATAT
5813765 ATATATATCCCGAAGGACCGCGTAGA
1 ATAT-TATCCCGAAGGACCGCGTAGA
5813791 ATATTATCCCGAAGGACCGCGTAGA
1 ATATTATCCCGAAGGACCGCGTAGA
*
5813816 ATATTGTCCCGAAGGACCGCGTAGA
1 ATATTATCCCGAAGGACCGCGTAGA
5813841 CCCTCTACTC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 45 0.92
26 4 0.08
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.20
Consensus pattern (25 bp):
ATATTATCCCGAAGGACCGCGTAGA
Found at i:5815530 original size:21 final size:21
Alignment explanation
Indices: 5815506--5815550 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5815496 TGTTGTTCGT
* *
5815506 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5815527 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5815548 TTG
1 TTG
5815551 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5817644 original size:19 final size:18
Alignment explanation
Indices: 5817622--5817719 Score: 77
Period size: 19 Copynumber: 5.7 Consensus size: 18
5817612 GGAAATTACT
5817622 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
5817641 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
5817655 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
5817674 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
5817688 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
5817707 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
5817720 TTTAGTTTCG
Statistics
Matches: 62, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
14 17 0.27
15 4 0.06
16 4 0.06
17 4 0.06
18 4 0.06
19 29 0.47
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:5817664 original size:33 final size:33
Alignment explanation
Indices: 5817622--5817715 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
5817612 GGAAATTACT
5817622 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
5817655 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
5817688 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
5817716 CGAATTTAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:5819348 original size:20 final size:19
Alignment explanation
Indices: 5819321--5819409 Score: 80
Period size: 20 Copynumber: 4.8 Consensus size: 19
5819311 TCTTTTGGTT
5819321 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
5819340 GATAATGAAAATCACAACGCG
1 GA-AATGAAAATCGCAACG-A
**
5819361 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
5819380 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
5819394 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
5819410 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 2 0.04
19 11 0.20
20 28 0.51
21 2 0.04
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:5819462 original size:19 final size:20
Alignment explanation
Indices: 5819440--5819490 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
5819430 GCGATTATCT
5819440 CGTTGCGATTTTTATTT-CG
1 CGTTGCGATTTTTATTTCCG
**
5819459 CGTTGCGATAGTTATTTCCG
1 CGTTGCGATTTTTATTTCCG
5819479 CGTTGCGATTTT
1 CGTTGCGATTTT
5819491 CATTCTCGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (20 bp):
CGTTGCGATTTTTATTTCCG
Found at i:5820050 original size:20 final size:20
Alignment explanation
Indices: 5820025--5820113 Score: 124
Period size: 20 Copynumber: 4.4 Consensus size: 20
5820015 ATGTAAATCA
5820025 CATTGCGATTTACGTATTCG
1 CATTGCGATTTACGTATTCG
* *
5820045 CATTGCGATTTTCCTAATTCG
1 CATTGCGATTTACGT-ATTCG
* *
5820066 CATTGCGATTTACTTAATCG
1 CATTGCGATTTACGTATTCG
*
5820086 CGTTGCGATTTACGTATTCG
1 CATTGCGATTTACGTATTCG
5820106 CATTGCGA
1 CATTGCGA
5820114 ATTATGAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 41 0.69
21 18 0.31
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (20 bp):
CATTGCGATTTACGTATTCG
Found at i:5820092 original size:41 final size:40
Alignment explanation
Indices: 5820025--5820113 Score: 124
Period size: 41 Copynumber: 2.2 Consensus size: 40
5820015 ATGTAAATCA
* *
5820025 CATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCG
1 CATTGCGATTTACGTAATCGCATTGCGATTTACCT-ATTCG
* * *
5820066 CATTGCGATTTACTTAATCGCGTTGCGATTTACGTATTCG
1 CATTGCGATTTACGTAATCGCATTGCGATTTACCTATTCG
5820106 CATTGCGA
1 CATTGCGA
5820114 ATTATGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 13 0.30
41 30 0.70
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (40 bp):
CATTGCGATTTACGTAATCGCATTGCGATTTACCTATTCG
Found at i:5820126 original size:41 final size:42
Alignment explanation
Indices: 5820042--5820172 Score: 126
Period size: 41 Copynumber: 3.2 Consensus size: 42
5820032 ATTTACGTAT
* * * *
5820042 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACT--TAA
1 TCGCATTGCGATTTACGTAATTCGCATTGCGAATTA-TGAAAA
*
5820083 TCGCGTTGCGATTTACGT-ATTCGCATTGCGAATTATGAAAA
1 TCGCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAA
* * * * * *
5820124 TCGCAATGCGA-ATATGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAA
5820165 TCGCATTG
1 TCGCATTG
5820173 TGATAGTCAT
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.01
40 20 0.27
41 53 0.72
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (42 bp):
TCGCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAA
Found at i:5820133 original size:21 final size:21
Alignment explanation
Indices: 5820103--5820169 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
5820093 ATTTACGTAT
*
5820103 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTATGAAAA
*
5820124 TCGCAATGCGAA-TATGTAAA
1 TCGCAATGCGAATTATGAAAA
*
5820144 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTATGAAAA
5820165 TCGCA
1 TCGCA
5820170 TTGTGATAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 19 0.46
21 22 0.54
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAATTATGAAAA
Found at i:5820146 original size:61 final size:62
Alignment explanation
Indices: 5820014--5820154 Score: 155
Period size: 61 Copynumber: 2.3 Consensus size: 62
5820004 CGAATGGCGC
* * * * * *
5820014 TATGTAAATCACATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATT
1 TATGTAAATCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAATGCGATA
* *
5820076 TACT-T-AATCGCGTTGCGATTTACGTATTCGCATTGCGAATTAT-GAAAATCGCAATGCGA-A
1 TA-TGTAAATCGCATTGCGATTTACGTATTCGCATTGCG-ATTATCCAAAATCGCAATGCGATA
*
5820136 TATGTAAATCGCAATGCGA
1 TATGTAAATCGCATTGCGA
5820155 ATTAGGAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
59 1 0.02
60 3 0.05
61 53 0.82
62 7 0.11
63 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (62 bp):
TATGTAAATCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAATGCGATA
Found at i:5823548 original size:33 final size:32
Alignment explanation
Indices: 5823504--5823594 Score: 132
Period size: 33 Copynumber: 2.9 Consensus size: 32
5823494 CATGAGTCTC
5823504 GTGCACCTGAACAACCTGTAGCTGAGCCAGTT
1 GTGCACCTGAACAACCTGTAGCTGAGCCAGTT
* *
5823536 GTGGCACCTGAACAACCTGTAGCTGAACCGGTT
1 GT-GCACCTGAACAACCTGTAGCTGAGCCAGTT
*
5823569 GT--ACCTGAACAGCCTGTAGCTGAGCC
1 GTGCACCTGAACAACCTGTAGCTGAGCC
5823595 GATTATGGTG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
30 22 0.41
32 2 0.04
33 30 0.56
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.21
Consensus pattern (32 bp):
GTGCACCTGAACAACCTGTAGCTGAGCCAGTT
Found at i:5823563 original size:15 final size:15
Alignment explanation
Indices: 5823543--5823591 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
5823533 GTTGTGGCAC
*
5823543 CTGAACAACCTGTAG
1 CTGAACAGCCTGTAG
* ** *
5823558 CTGAACCGGTTGTAC
1 CTGAACAGCCTGTAG
5823573 CTGAACAGCCTGTAG
1 CTGAACAGCCTGTAG
5823588 CTGA
1 CTGA
5823592 GCCGATTATG
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (15 bp):
CTGAACAGCCTGTAG
Found at i:5825859 original size:24 final size:23
Alignment explanation
Indices: 5825830--5825875 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
5825820 ATCATAAGGA
5825830 ATATGCCACAAGAGCAGAAGAAAT
1 ATATGCCACAAGAGCAG-AGAAAT
5825854 ATATGCCACAAGAGCAGAGAAA
1 ATATGCCACAAGAGCAGAGAAA
5825876 AGCGTGCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.50, C:0.17, G:0.22, T:0.11
Consensus pattern (23 bp):
ATATGCCACAAGAGCAGAGAAAT
Found at i:5826476 original size:2 final size:2
Alignment explanation
Indices: 5826460--5826521 Score: 108
Period size: 2 Copynumber: 31.0 Consensus size: 2
5826450 TCTTTAACAT
5826460 TA TA -A TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5826502 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
5826522 ACTAATTGGT
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 55 0.95
3 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5831703 original size:35 final size:35
Alignment explanation
Indices: 5831657--5831726 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
5831647 TGATGCGTAT
5831657 TGGCATGAATTGATAAAATGTTAGAAAATGGAGGG
1 TGGCATGAATTGATAAAATGTTAGAAAATGGAGGG
5831692 TGGCATGAATTGATAAAATGTTAGAAAATGGAGGG
1 TGGCATGAATTGATAAAATGTTAGAAAATGGAGGG
5831727 GATGGGAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.03, G:0.31, T:0.26
Consensus pattern (35 bp):
TGGCATGAATTGATAAAATGTTAGAAAATGGAGGG
Found at i:5832407 original size:22 final size:22
Alignment explanation
Indices: 5832373--5832417 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5832363 AATTTGCACA
* * *
5832373 GAACTCCATACAACTTAACCAC
1 GAACCCCAGACAACCTAACCAC
5832395 GAACCCCAGACAACCTAACCAC
1 GAACCCCAGACAACCTAACCAC
5832417 G
1 G
5832418 CCCTGCCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.09, T:0.11
Consensus pattern (22 bp):
GAACCCCAGACAACCTAACCAC
Found at i:5834997 original size:2 final size:2
Alignment explanation
Indices: 5834990--5835015 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5834980 AGTTGTCGAC
5834990 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
5835016 TACCTCCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5838305 original size:44 final size:44
Alignment explanation
Indices: 5838255--5838345 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
5838245 AAGTTCAAAG
5838255 AATATACAACTTCTAATTCTGATCATGGCAGAACCAAATCAATA
1 AATATACAACTTCTAATTCTGATCATGGCAGAACCAAATCAATA
5838299 AATATACAACTTCTAATTCTGATCATGGCAGAACCAAATCAATA
1 AATATACAACTTCTAATTCTGATCATGGCAGAACCAAATCAATA
5838343 AAT
1 AAT
5838346 GTACCATTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (44 bp):
AATATACAACTTCTAATTCTGATCATGGCAGAACCAAATCAATA
Found at i:5842661 original size:23 final size:23
Alignment explanation
Indices: 5842630--5842721 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
5842620 CACCACAGCT
* * *
5842630 CGTATAAATGCACCAAAGTGTCA
1 CGTAGAAATGCACCGAAGTGCCA
*
5842653 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
5842676 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
5842699 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
5842722 TATAATGCAC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:5847542 original size:18 final size:18
Alignment explanation
Indices: 5847519--5847555 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5847509 TAATAATTTA
*
5847519 TTTTTATACTTTAAGCCT
1 TTTTTATACTTCAAGCCT
5847537 TTTTTATACTTCAAGCCT
1 TTTTTATACTTCAAGCCT
5847555 T
1 T
5847556 ATTATCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTTTATACTTCAAGCCT
Found at i:5848091 original size:2 final size:2
Alignment explanation
Indices: 5848084--5848158 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
5848074 CAACTCCACT
5848084 TA TA TA TA -A 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
5848125 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
5848159 AACTCAATTC
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 71 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5848696 original size:2 final size:2
Alignment explanation
Indices: 5848689--5848713 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5848679 GTGAAAAATA
5848689 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 A
5848714 CCAATCAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5849723 original size:27 final size:29
Alignment explanation
Indices: 5849663--5849723 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 29
5849653 GCCGAATTAA
* **
5849663 TAAAAGCATAAATATTGAAAGTTATTTTC
1 TAAAAGCATAAATATTGAAAGTTAATGCC
*
5849692 AAAAAG-A-AAATATTGAAAGTTAATGCC
1 TAAAAGCATAAATATTGAAAGTTAATGCC
5849719 TAAAA
1 TAAAA
5849724 AGAGAAAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 21 0.78
28 1 0.04
29 5 0.19
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (29 bp):
TAAAAGCATAAATATTGAAAGTTAATGCC
Found at i:5850442 original size:28 final size:24
Alignment explanation
Indices: 5850390--5850444 Score: 65
Period size: 28 Copynumber: 2.1 Consensus size: 24
5850380 CTATTATATA
*
5850390 AAATTAATAAAATTATTTAAATGT
1 AAATTAATAAAATTATTAAAATGT
5850414 AAATTAGATAAAACATTATTAATAATGT
1 AAATTA-AT-AAA-ATTATTAA-AATGT
5850442 AAA
1 AAA
5850445 GGAAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 6 0.23
25 2 0.08
26 3 0.12
27 7 0.27
28 8 0.31
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.36
Consensus pattern (24 bp):
AAATTAATAAAATTATTAAAATGT
Found at i:5850489 original size:22 final size:24
Alignment explanation
Indices: 5850448--5850496 Score: 84
Period size: 22 Copynumber: 2.1 Consensus size: 24
5850438 ATGTAAAGGA
5850448 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
5850472 AAATT-ATATAG-TTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
5850494 AAA
1 AAA
5850497 GACAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 14 0.56
23 6 0.24
24 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:5853856 original size:102 final size:102
Alignment explanation
Indices: 5853615--5853926 Score: 506
Period size: 102 Copynumber: 3.1 Consensus size: 102
5853605 AATAAACAAC
* *
5853615 CAACAGTAGCTACAAATTAAACAATTTATTTAAACTGTAAAT-AAAGACATCTAACAACCTTATA
1 CAACAGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAAG-CAGCTAACAACCTTATA
* **
5853679 AAAGTAATCCAAATGAACAA-C--CAACACAAACAAAT
65 AAAGCAATCTGAATGAACAACCAACAACACAAACAAAT
* *
5853714 CAACAGTAACTACAAATTAAAAAGTTTATTTAAACTGTAAATAAAAGCAGCTAACAACCTTATAA
1 CAACAGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAAGCAGCTAACAACCTTATAA
*
5853779 AAACAATCTGAATGAACAACCAACAACACAAACAAAT
66 AAGCAATCTGAATGAACAACCAACAACACAAACAAAT
*
5853816 CAACAGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
1 CAACAGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAAGCAGCTAACAACCTTATAA
5853881 AAGCAATCTGAATGAACAACCAACAACACAAACAAAT
66 AAGCAATCTGAATGAACAACCAACAACACAAACAAAT
5853918 CAACAGTAG
1 CAACAGTAG
5853927 AAACAAATCA
Statistics
Matches: 197, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
99 71 0.36
100 5 0.03
102 121 0.61
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (102 bp):
CAACAGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAAGCAGCTAACAACCTTATAA
AAGCAATCTGAATGAACAACCAACAACACAAACAAAT
Found at i:5853930 original size:17 final size:17
Alignment explanation
Indices: 5853910--5853942 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5853900 CCAACAACAC
5853910 AAACAAATCAACAGTAG
1 AAACAAATCAACAGTAG
5853927 AAACAAATCAACAGTA
1 AAACAAATCAACAGTA
5853943 TCTAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.12
Consensus pattern (17 bp):
AAACAAATCAACAGTAG
Found at i:5854215 original size:18 final size:18
Alignment explanation
Indices: 5854188--5854228 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5854178 AGGGTTTTTT
* *
5854188 AGGTTTGGGTTTGAATTC
1 AGGTTAGGGTTAGAATTC
*
5854206 AGGTTAGGGTTAGAGTTC
1 AGGTTAGGGTTAGAATTC
5854224 AGGTT
1 AGGTT
5854229 TTGGGTTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.05, G:0.37, T:0.39
Consensus pattern (18 bp):
AGGTTAGGGTTAGAATTC
Found at i:5854285 original size:6 final size:6
Alignment explanation
Indices: 5854276--5854345 Score: 86
Period size: 6 Copynumber: 11.5 Consensus size: 6
5854266 TGGGTTCAGA
* * * * *
5854276 TTTGGG TTTGGG CTCGGG TTAGGG TTTGGG TTCGGG TTTGAG TTTGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
5854324 TTTGGG TTTAGGG TTTGGG TTT
1 TTTGGG TTT-GGG TTTGGG TTT
5854346 AAATTAAGGT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
6 48 0.89
7 6 0.11
ACGTcount: A:0.04, C:0.04, G:0.46, T:0.46
Consensus pattern (6 bp):
TTTGGG
Found at i:5854285 original size:24 final size:23
Alignment explanation
Indices: 5854228--5854286 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
5854218 GAGTTCAGGT
5854228 TTTGGGTTTGGATTTGGATCCAG
1 TTTGGGTTTGGATTTGGATCCAG
* * * *
5854251 GTTGAGTTTTGGATTTGGGTTCAG
1 TTTG-GGTTTGGATTTGGATCCAG
5854275 ATTTGGGTTTGG
1 -TTTGGGTTTGG
5854287 GCTCGGGTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 3 0.11
24 22 0.79
25 3 0.11
ACGTcount: A:0.12, C:0.05, G:0.37, T:0.46
Consensus pattern (23 bp):
TTTGGGTTTGGATTTGGATCCAG
Found at i:5854300 original size:18 final size:18
Alignment explanation
Indices: 5854264--5854344 Score: 90
Period size: 18 Copynumber: 4.4 Consensus size: 18
5854254 GAGTTTTGGA
* * *
5854264 TTTGGGTTCAGATTTGGG
1 TTTGGGTTCGGGTTAGGG
*
5854282 TTTGGGCTCGGGTTAGGG
1 TTTGGGTTCGGGTTAGGG
* *
5854300 TTTGGGTTCGGGTTTGAG
1 TTTGGGTTCGGGTTAGGG
*
5854318 TTTGGGTTTGGGTTTAGGG
1 TTTGGGTTCGGG-TTAGGG
5854337 TTTGGGTT
1 TTTGGGTT
5854345 TAAATTAAGG
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
18 40 0.77
19 12 0.23
ACGTcount: A:0.06, C:0.05, G:0.44, T:0.44
Consensus pattern (18 bp):
TTTGGGTTCGGGTTAGGG
Found at i:5855076 original size:28 final size:28
Alignment explanation
Indices: 5855044--5855140 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 28
5855034 AATTAACTAT
5855044 TTATAATTAATATTATAATAATTATATA
1 TTATAATTAATATTATAATAATTATATA
*
5855072 TTATAATTAATATTAATATTAACTTATATTA
1 TTATAATTAATATT-ATAATAA-TTATA-TA
* *
5855103 ATATAATATAGT-TTATAAT--TTATA-A
1 TTATAAT-TAATATTATAATAATTATATA
5855128 TTA-ATATTAATAT
1 TTATA-ATTAATAT
5855141 AAAATATAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
24 4 0.07
25 6 0.11
27 5 0.09
28 14 0.25
29 6 0.11
30 9 0.16
31 10 0.18
32 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (28 bp):
TTATAATTAATATTATAATAATTATATA
Found at i:5855106 original size:50 final size:51
Alignment explanation
Indices: 5855044--5855140 Score: 137
Period size: 50 Copynumber: 1.9 Consensus size: 51
5855034 AATTAACTAT
*
5855044 TTATAATTAATATTATAATAA-TTAT-ATATTATAATTAATATTAATATTAAC
1 TTATAATTAATATAAT-ATAATTTATAAT-TTATAATTAATATTAATATTAAC
*
5855095 TTAT-ATTAATATAATATAGTTTATAATTTATAATTAATATTAATAT
1 TTATAATTAATATAATATAATTTATAATTTATAATTAATATTAATAT
5855141 AAAATATAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
49 3 0.07
50 33 0.79
51 6 0.14
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (51 bp):
TTATAATTAATATAATATAATTTATAATTTATAATTAATATTAATATTAAC
Found at i:5855178 original size:24 final size:25
Alignment explanation
Indices: 5855133--5855179 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
5855123 TATAATTAAT
**
5855133 ATTAATATAAAATATAGTCTATAAC
1 ATTAATATAAAATATAAACTATAAC
*
5855158 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
5855180 TTTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAC
Found at i:5855206 original size:14 final size:14
Alignment explanation
Indices: 5855189--5855250 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
5855179 ATTTTATAAA
*
5855189 TTATATAGTATAGT
1 TTATATAATATAGT
5855203 TTATA-AACTATAGT
1 TTATATAA-TATAGT
*
5855217 TAATATAATTAATA-T
1 TTATATAA-T-ATAGT
*
5855232 TAATATAATATAGT
1 TTATATAATATAGT
5855246 TTATA
1 TTATA
5855251 AACTATATAC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 4 0.10
14 21 0.52
15 12 0.30
16 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (14 bp):
TTATATAATATAGT
Found at i:5855206 original size:81 final size:77
Alignment explanation
Indices: 5855042--5855208 Score: 187
Period size: 81 Copynumber: 2.1 Consensus size: 77
5855032 TTAATTAACT
* * *
5855042 ATTTATAATTAATATTATAATAATTATATATTATAATTAATATTAATATTAACTTATATTAATAT
1 ATTTATAATTAATATTATAATAATAATATATTATAATTAATATTAATATAAACTTATATTAAAAT
5855107 AATATAGTTTATA
66 AATATAG-TTATA
*
5855120 ATTTATAATTAATATTA-ATATAA-AATATAGTCTATAACATTAATATTAATATAAACTATATTT
1 ATTTATAATTAATATTATA-ATAATAATATA-T-TAT-A-ATTAATATTAATATAAACT-TATAT
*
5855183 TATAAATTATATAG-TATA
60 TA-AAATAATATAGTTATA
*
5855201 GTTTATAA
1 ATTTATAA
5855209 ACTATAGTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
77 6 0.08
78 22 0.29
79 3 0.04
80 1 0.01
81 29 0.38
82 6 0.08
83 9 0.12
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (77 bp):
ATTTATAATTAATATTATAATAATAATATATTATAATTAATATTAATATAAACTTATATTAAAAT
AATATAGTTATA
Found at i:5855290 original size:65 final size:64
Alignment explanation
Indices: 5855097--5855303 Score: 224
Period size: 65 Copynumber: 3.2 Consensus size: 64
5855087 ATATTAACTT
* * *
5855097 ATATTAATATAATATAGTTTATAATTTATA-ATTAATATTAATATAAAATATAGTCTATAA-CAT
1 ATATTAATATAATATAGTTTATAAATTATATACT-ATATTAATATAAAATATAGT-TA-AATAAT
5855160 TA
63 TA
* * *
5855162 ATATTAATATAAACTATATTTTATAAATTATATAGTATAGTT--TATAAACTATAGTTAATATAA
1 ATATTAATAT-AA-TATAGTTTATAAATTATATACTATA-TTAATATAAAATATAGTTAA-ATAA
5855225 TTA
62 TTA
* *
5855228 ATATTAATATAATATAGTTTATAAACTATATACTATATTAATATAAATTATAGTTAAGATAATTA
1 ATATTAATATAATATAGTTTATAAATTATATACTATATTAATATAAAATATAGTTAA-ATAATTA
* *
5855293 ACAATAATATA
1 ATATTAATATA
5855304 TACTATATAG
Statistics
Matches: 122, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
63 2 0.02
64 23 0.19
65 46 0.38
66 28 0.23
67 19 0.16
68 4 0.03
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (64 bp):
ATATTAATATAATATAGTTTATAAATTATATACTATATTAATATAAAATATAGTTAAATAATTA
Found at i:5855351 original size:21 final size:21
Alignment explanation
Indices: 5855169--5855374 Score: 96
Period size: 21 Copynumber: 9.5 Consensus size: 21
5855159 TTAATATTAA
* *
5855169 TATAAACTATATTTTATAAAT
1 TATATACTATAATTTATAAAT
* * *
5855190 TATATAGTATAGTTTATAAAC
1 TATATACTATAATTTATAAAT
* *
5855211 TATAGTTAATATAA-TTA-ATAT
1 TATA--TACTATAATTTATAAAT
* * *
5855232 TAATATAATATAGTTTATAAAC
1 T-ATATACTATAATTTATAAAT
5855254 TATATACTAT-ATTAATATAAAT
1 TATATACTATAATT--TATAAAT
** * * *
5855276 TATAGTTAAGATAATTAACAATAA
1 TATA--TACTATAATTTATAA-AT
**
5855300 TATATACTATATAGTACATAAA-
1 TATATACTATA-A-TTTATAAAT
*
5855322 TATAAACTATAATTTATAAAT
1 TATATACTATAATTTATAAAT
** *
5855343 TATATACTATAGGTTATAAAG
1 TATATACTATAATTTATAAAT
*
5855364 TATAAACTATA
1 TATATACTATA
5855375 TAGTACACTA
Statistics
Matches: 139, Mismatches: 32, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
20 15 0.11
21 63 0.45
22 34 0.24
23 11 0.08
24 13 0.09
25 3 0.02
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
TATATACTATAATTTATAAAT
Found at i:5855444 original size:20 final size:21
Alignment explanation
Indices: 5855414--5855518 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 21
5855404 AATTATAGGT
5855414 TACATAT--ATAGTTTATATA
1 TACATATACATAGTTTATATA
*
5855433 -ACATATAAATAGATTGTATATA
1 TACATATACATAG-TT-TATATA
*
5855455 TACATATACTATAG-GT-TATA
1 TACATATAC-ATAGTTTATATA
5855475 T--ATATACATAGTTTATATA
1 TACATATACATAGTTTATATA
*
5855494 TAC-TATACATAGTTTATACA
1 TACATATACATAGTTTATATA
5855514 TACAT
1 TACAT
5855519 GTACTATAAG
Statistics
Matches: 71, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
17 4 0.06
18 13 0.18
19 5 0.07
20 28 0.39
21 4 0.06
22 6 0.08
23 7 0.10
24 4 0.06
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.42
Consensus pattern (21 bp):
TACATATACATAGTTTATATA
Found at i:5855456 original size:24 final size:24
Alignment explanation
Indices: 5855427--5855484 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
5855417 ATATATAGTT
*
5855427 TATATA-ACATATA-AATAGATTG
1 TATATATACATATACAATAGATTA
* *
5855449 TATATATACATATACTATAGGTTA
1 TATATATACATATACAATAGATTA
5855473 TATATATACATA
1 TATATATACATA
5855485 GTTTATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 6 0.19
23 7 0.23
24 18 0.58
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (24 bp):
TATATATACATATACAATAGATTA
Found at i:5855493 original size:15 final size:18
Alignment explanation
Indices: 5855453--5855500 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
5855443 AGATTGTATA
*
5855453 TATACATATACTATAGGT
1 TATATATATACTATAGGT
5855471 TATATATATAC-ATA-GT
1 TATATATATACTATAGGT
5855487 T-TATATATACTATA
1 TATATATATACTATA
5855501 CATAGTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 9 0.32
16 6 0.21
17 3 0.11
18 10 0.36
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (18 bp):
TATATATATACTATAGGT
Found at i:5855541 original size:35 final size:36
Alignment explanation
Indices: 5855502--5855571 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
5855492 TATACTATAC
*
5855502 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
**
5855537 ATAGTTTACATGTATACATATACTATAAGTTACAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACAT
5855572 TACATATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 7 0.23
37 23 0.77
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:5855618 original size:7 final size:7
Alignment explanation
Indices: 5855602--5855646 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
5855592 TATGTATAGT
*
5855602 GTTTATG
1 GTTTAGG
5855609 GTTTAGG
1 GTTTAGG
5855616 GTTTAGG
1 GTTTAGG
*
5855623 GTTTAGT
1 GTTTAGG
*
5855630 GCTTAGG
1 GTTTAGG
5855637 GTTTAGG
1 GTTTAGG
5855644 GTT
1 GTT
5855647 CTTATAAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.13, C:0.02, G:0.38, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:5855799 original size:2 final size:2
Alignment explanation
Indices: 5855776--5855890 Score: 53
Period size: 2 Copynumber: 57.5 Consensus size: 2
5855766 TATAAGTTAC
* * *
5855776 AT AT AT AGT -T AT AC AT AC AT AT AT AT ACT AT AT -T A- AT AT AA
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * *
5855817 AT -T AT A- AT AT AT AA ACT AT AT AT -T TT AT AT AGT TT AT AC AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT
* *
5855858 AT AT AGT TT AT AC AT AT ACT AT AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT A
5855891 AATAATATTT
Statistics
Matches: 84, Mismatches: 17, Indels: 24
0.67 0.14 0.19
Matches are distributed among these distances:
1 6 0.07
2 70 0.83
3 8 0.10
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Done.