Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 169 of 199
Found at i:49396086 original size:18 final size:18
Alignment explanation
Indices: 49396043--49396087 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
49396033 ACCGATTTGC
49396043 ATGAAAAGAAAAAGAAAA
1 ATGAAAAGAAAAAGAAAA
** * *
49396061 GGGCAAAGAAAAATAAAA
1 ATGAAAAGAAAAAGAAAA
49396079 ATGAAAAGA
1 ATGAAAAGA
49396088 GCGTAAAACA
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.07
Consensus pattern (18 bp):
ATGAAAAGAAAAAGAAAA
Found at i:49399430 original size:26 final size:25
Alignment explanation
Indices: 49399401--49399466 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
49399391 ACGTTATAAG
49399401 AAATAAATAATAAAATAATAAAAATA
1 AAATAAATAAT-AAATAATAAAAATA
* **
49399427 AAATGTAATAATAAATTTTAAAAATA
1 AAAT-AAATAATAAATAATAAAAATA
*
49399453 ACAT-AATAA-AAATA
1 AAATAAATAATAAATA
49399467 TTTATTATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
23 4 0.12
24 5 0.15
26 19 0.56
27 6 0.18
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (25 bp):
AAATAAATAATAAATAATAAAAATA
Found at i:49399760 original size:21 final size:22
Alignment explanation
Indices: 49399734--49399781 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
49399724 ATGCCAAAAA
* *
49399734 TAAAAATATATATATTTT-TTT
1 TAAAAATATAAACATTTTATTT
*
49399755 TAAAAATCTAAACATTTTATTT
1 TAAAAATATAAACATTTTATTT
49399777 TAAAA
1 TAAAA
49399782 TTTTATTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAAAATATAAACATTTTATTT
Found at i:49401115 original size:95 final size:94
Alignment explanation
Indices: 49400972--49401145 Score: 224
Period size: 94 Copynumber: 1.8 Consensus size: 94
49400962 TCAATTAAAT
* * * * * ** *
49400972 TAATTAAAAAATTTTCAAAATTAGATTAGTTTTCGTGTTTATTATTTTTTAAGAAAAAATCAATT
1 TAATTAAAAAATTTTAAAAATTAGATTAGATTTAGAGTTAAAGA-TTTTTAAGAAAAAATCAAAT
49401037 AAATTAGGGTTTAGGGTTACTTGAGTAATA
65 AAATTAGGGTTTAGGGTTACTTGAGTAATA
* * *
49401067 TAATTAAAAAA-TTTAAAAATTAGATTAGAATTTAGAGTTAAAGGTTTTTAAGGAAAAATTAAAT
1 TAATTAAAAAATTTTAAAAATTAGATTAG-ATTTAGAGTTAAAGATTTTTAAGAAAAAATCAAAT
49401131 AAATTAGGGTTTAGG
65 AAATTAGGGTTTAGG
49401146 ATTTTTTATT
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
94 48 0.72
95 19 0.28
ACGTcount: A:0.43, C:0.02, G:0.15, T:0.40
Consensus pattern (94 bp):
TAATTAAAAAATTTTAAAAATTAGATTAGATTTAGAGTTAAAGATTTTTAAGAAAAAATCAAATA
AATTAGGGTTTAGGGTTACTTGAGTAATA
Found at i:49401571 original size:125 final size:126
Alignment explanation
Indices: 49401348--49401630 Score: 453
Period size: 125 Copynumber: 2.3 Consensus size: 126
49401338 TAATTTAAAG
* *
49401348 AAGC-TCCTACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAGAAAATAATGTCGAGTAGACGTT
1 AAGCTTCC-ACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAGAAAAAAATGTCGAGTAGACGTT
*
49401412 TCTGAGTAAACAGTATCAGAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTAAAAA
65 TCTGAGTAAACAGTATCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTAAAAA
* *
49401474 AAGCTTCCACGTGGACACGCTTTTGCTACAGTAGCTCCTGA-AAAAAAATTTCGAGTAGACGTTT
1 AAGCTTCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAGAAAAAAATGTCGAGTAGACGTTT
* * * *
49401538 CTGAGTAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTATTGAAAG
66 CTGAGTAAACAGTATCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTAAAAA
*
49401599 AAGCTCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCTTCCACGTGGACGCGCTTTTGCTACAGT
49401631 GGCGCATGGC
Statistics
Matches: 145, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
125 107 0.74
126 35 0.24
127 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (126 bp):
AAGCTTCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAGAAAAAAATGTCGAGTAGACGTTT
CTGAGTAAACAGTATCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTAAAAA
Found at i:49405224 original size:18 final size:18
Alignment explanation
Indices: 49405198--49405237 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
49405188 GACTAGAAAA
* *
49405198 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
49405216 AGGACACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
49405234 AGGA
1 AGGA
49405238 TACGCACCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.30, T:0.15
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:49407105 original size:22 final size:21
Alignment explanation
Indices: 49407079--49407131 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
49407069 AAATATGGAT
*
49407079 TTGAGAGAAATTTGAAAGGAGA
1 TTGAGAGAAA-TTGAAAGGAAA
*
49407101 TTGAGAGCAAATTGAGAGGAAA
1 TTGAGAG-AAATTGAAAGGAAA
49407123 TT-AGAGAAA
1 TTGAGAGAAA
49407132 GGATTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 4 0.14
22 18 0.64
23 3 0.11
ACGTcount: A:0.47, C:0.02, G:0.30, T:0.21
Consensus pattern (21 bp):
TTGAGAGAAATTGAAAGGAAA
Found at i:49407914 original size:53 final size:53
Alignment explanation
Indices: 49407851--49407957 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
49407841 GAAAAAGAGT
49407851 ACACATATCTATAATATGCATAACATACTGCCTCATTAAAAACTTTATCAGGA
1 ACACATATCTATAATATGCATAACATACTGCCTCATTAAAAACTTTATCAGGA
49407904 ACACATATCTATAATATGCATAACATACTGCCTCATTAAAAACTTTATCAGGA
1 ACACATATCTATAATATGCATAACATACTGCCTCATTAAAAACTTTATCAGGA
49407957 A
1 A
49407958 AACCCAATGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (53 bp):
ACACATATCTATAATATGCATAACATACTGCCTCATTAAAAACTTTATCAGGA
Found at i:49426936 original size:2 final size:2
Alignment explanation
Indices: 49426929--49426959 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49426919 AACTCTCCTT
49426929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49426960 TCATGACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49428613 original size:40 final size:40
Alignment explanation
Indices: 49428536--49428642 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 40
49428526 AGCGGCACTT
* * *
49428536 TTAGCGGCGTTTGGAGCAAAAACGCTGCTAAAGAGTGAGCA
1 TTAGCGGCGTTT-AAGCAAAAACGCCGCTAAAGAGTGAACA
* *
49428577 TTAGCGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAACA
1 TTAGCGGCGTTTAAGCAAAAACGCCGCTAAAGAGTGAACA
*
49428617 TTAGCAGCGTTTATA--AAAAACGCCGC
1 TTAGCGGCGTTTA-AGCAAAAACGCCGC
49428643 AAATAATACA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 10 0.17
40 35 0.60
41 13 0.22
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.20
Consensus pattern (40 bp):
TTAGCGGCGTTTAAGCAAAAACGCCGCTAAAGAGTGAACA
Found at i:49428777 original size:112 final size:111
Alignment explanation
Indices: 49428594--49428829 Score: 427
Period size: 112 Copynumber: 2.1 Consensus size: 111
49428584 CGTTTAAGGA
49428594 AAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
1 AAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
*
49428659 CAGTGCCGTTTTGTGGCTTTTGGGGGGGAATTAGTGGCGTTTTTTGT
66 CAGTGCCGTTTTGTGGCCTTT-GGGGGGAATTAGTGGCGTTTTTTGT
*
49428706 AAAGCGCCGCTAAAGAGTTAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
1 AAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
* *
49428771 CGGTGCCGTTTTGTGTCCTTTGGGGGGAATTAGTGGCGTTTTTTGT
66 CAGTGCCGTTTTGTGGCCTTTGGGGGGAATTAGTGGCGTTTTTTGT
49428817 AAAGCGCCGCTAA
1 AAAGCGCCGCTAA
49428830 TCTAGGTGTT
Statistics
Matches: 120, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
111 38 0.32
112 82 0.68
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (111 bp):
AAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCGCAAATAATACACCCAGA
CAGTGCCGTTTTGTGGCCTTTGGGGGGAATTAGTGGCGTTTTTTGT
Found at i:49430429 original size:22 final size:21
Alignment explanation
Indices: 49430378--49430430 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
49430368 TAGCTAGGGG
49430378 TTTAGGGGTTACAAGTTACGA
1 TTTAGGGGTTACAAGTTACGA
* *
49430399 TCTAGGGGTTA-AAGATTTAGGA
1 TTTAGGGGTTACAAG--TTACGA
49430421 TTTAGGGGTT
1 TTTAGGGGTT
49430431 TAGGGGTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.11
21 10 0.37
22 14 0.52
ACGTcount: A:0.26, C:0.06, G:0.32, T:0.36
Consensus pattern (21 bp):
TTTAGGGGTTACAAGTTACGA
Found at i:49431491 original size:84 final size:84
Alignment explanation
Indices: 49431350--49431786 Score: 705
Period size: 84 Copynumber: 5.1 Consensus size: 84
49431340 ATTTGTGCTT
* *
49431350 AAAACGCCAGAAATAATGCAATTATTCCAGACCATGCAAAACGGTGTCGTTTCTGTTCACAGCTG
1 AAAACGCCACAAATAATGC-A--ATTCCAGACCACG-AAAACGGTGTCGTTTCTGTTCACAGCTG
*
49431415 TAATATCTAGTGGCGTTTTTAGG
62 TAATATTTAGTGGCGTTTTTAGG
*
49431438 AAAACGCCACAAATAATACAATTCCAGACCACGAAAACGGTGTCGTTTCTGTTCACAGCTGTAAT
1 AAAACGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTGTTCACAGCTGTAAT
49431503 ATTTAGTGGCGTTTTTAGG
66 ATTTAGTGGCGTTTTTAGG
49431522 AAAACGCCACAAATAATGCAATTATTCCAGACCACGCAAAACGGTGTCGTTTCTGTTCACAGCTG
1 AAAACGCCACAAATAATGC-A--ATTCCAGACCACG-AAAACGGTGTCGTTTCTGTTCACAGCTG
49431587 TAATATTTAGTGGCGTTTTTAGG
62 TAATATTTAGTGGCGTTTTTAGG
* *
49431610 AAAACGCCACAAATAATGCAATTCCAGACCACAAAAACGGTGTCGTTTCTATTCACAGCTGTAAT
1 AAAACGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTGTTCACAGCTGTAAT
*
49431675 ATTTAGTGGCATTTTT-GG
66 ATTTAGTGGCGTTTTTAGG
*
49431693 AAAAACGCCACAAATAATACAATTCCAGACCACGAAAACGGTGTCGTTTCTGTTCACAGCTGTAA
1 -AAAACGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTGTTCACAGCTGTAA
49431758 TATTTAGTGGCGTTTTTTAGG
65 TATTTAGTGGCG-TTTTTAGG
49431779 AAAACGCC
1 AAAACGCC
49431787 GGAAATGTGG
Statistics
Matches: 330, Mismatches: 12, Indels: 17
0.92 0.03 0.05
Matches are distributed among these distances:
83 2 0.01
84 186 0.56
85 38 0.12
86 2 0.01
87 15 0.05
88 87 0.26
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (84 bp):
AAAACGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTGTTCACAGCTGTAAT
ATTTAGTGGCGTTTTTAGG
Found at i:49431636 original size:172 final size:172
Alignment explanation
Indices: 49431331--49431786 Score: 751
Period size: 172 Copynumber: 2.7 Consensus size: 172
49431321 TTTGACAAAT
* ** * *
49431331 TTTAGTGGCATTTGTGCTTAAAACGCCAGAAATAATGCAATTATTCCAGACCATGCAAAACGGTG
1 TTTAGTGGCATTTTTG-GAAAAACGCCACAAATAATGCAATTATTCCAGACCACGCAAAACGGTG
*
49431396 TCGTTTCTGTTCACAGCTGTAATATCTAGTGGCGTTTTTAGGAAAACGCCACAAATAATACAATT
65 TCGTTTCTGTTCACAGCTGTAATATTTAGTGGCGTTTTTAGGAAAACGCCACAAATAATACAATT
* *
49431461 CCAGACCACGAAAACGGTGTCGTTTCTGTTCACAGCTGTAATA
130 CCAGACCACAAAAACGGTGTCGTTTCTATTCACAGCTGTAATA
*
49431504 TTTAGTGGCGTTTTTAGG-AAAACGCCACAAATAATGCAATTATTCCAGACCACGCAAAACGGTG
1 TTTAGTGGCATTTTT-GGAAAAACGCCACAAATAATGCAATTATTCCAGACCACGCAAAACGGTG
*
49431568 TCGTTTCTGTTCACAGCTGTAATATTTAGTGGCGTTTTTAGGAAAACGCCACAAATAATGCAATT
65 TCGTTTCTGTTCACAGCTGTAATATTTAGTGGCGTTTTTAGGAAAACGCCACAAATAATACAATT
49431633 CCAGACCACAAAAACGGTGTCGTTTCTATTCACAGCTGTAATA
130 CCAGACCACAAAAACGGTGTCGTTTCTATTCACAGCTGTAATA
*
49431676 TTTAGTGGCATTTTTGGAAAAACGCCACAAATAATAC-A--ATTCCAGACCACG-AAAACGGTGT
1 TTTAGTGGCATTTTTGGAAAAACGCCACAAATAATGCAATTATTCCAGACCACGCAAAACGGTGT
49431737 CGTTTCTGTTCACAGCTGTAATATTTAGTGGCGTTTTTTAGGAAAACGCC
66 CGTTTCTGTTCACAGCTGTAATATTTAGTGGCG-TTTTTAGGAAAACGCC
49431787 GGAAATGTGG
Statistics
Matches: 269, Mismatches: 11, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
168 43 0.16
169 29 0.11
171 3 0.01
172 180 0.67
173 13 0.05
174 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (172 bp):
TTTAGTGGCATTTTTGGAAAAACGCCACAAATAATGCAATTATTCCAGACCACGCAAAACGGTGT
CGTTTCTGTTCACAGCTGTAATATTTAGTGGCGTTTTTAGGAAAACGCCACAAATAATACAATTC
CAGACCACAAAAACGGTGTCGTTTCTATTCACAGCTGTAATA
Found at i:49433951 original size:17 final size:17
Alignment explanation
Indices: 49433929--49434069 Score: 115
Period size: 17 Copynumber: 7.6 Consensus size: 17
49433919 GTTAAATTTA
49433929 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
49433946 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
*
49433963 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
49433986 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
*
49434003 TTACTAAAATAAATTAC
1 TTACTAAAATACATTAC
*
49434020 TTACTAAAATTTGATTAAATTTA-
1 TTACT-AAA----A-TACA-TTAC
49434043 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
49434060 TTACTAAAAT
1 TTACTAAAAT
49434070 TTGTTTAAAT
Statistics
Matches: 104, Mismatches: 4, Indels: 32
0.74 0.03 0.23
Matches are distributed among these distances:
16 6 0.06
17 63 0.61
18 4 0.04
22 4 0.04
23 21 0.20
24 6 0.06
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.40
Consensus pattern (17 bp):
TTACTAAAATACATTAC
Found at i:49434008 original size:57 final size:57
Alignment explanation
Indices: 49433920--49434069 Score: 282
Period size: 57 Copynumber: 2.6 Consensus size: 57
49433910 CGATTGAATG
* *
49433920 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTACTAAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGA
49433977 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGA
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGA
49434034 TTAAATTTATTACTAAAATACATTACTTACTAAAAT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAAT
49434070 TTGTTTAAAT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 91 1.00
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.41
Consensus pattern (57 bp):
TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGA
Found at i:49434047 original size:40 final size:40
Alignment explanation
Indices: 49434003--49434102 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
49433993 AATACATTAC
49434003 TTACTAAAATAAATTACTTACTAAAATTTGATTAAATTTA
1 TTACTAAAATAAATTACTTACTAAAATTTGATTAAATTTA
* *
49434043 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATAAATTACTTACTAAAATTTGATTAAATTTA
* **
49434083 TTACTTAAATATGTTACTTA
1 TTACTAAAATAAATTACTTA
49434103 AATACATTAC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (40 bp):
TTACTAAAATAAATTACTTACTAAAATTTGATTAAATTTA
Found at i:49434057 original size:97 final size:93
Alignment explanation
Indices: 49433946--49434124 Score: 286
Period size: 97 Copynumber: 1.9 Consensus size: 93
49433936 AATACATTAC
49433946 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAAT--A-T-CTTACTAAA
49434011 ATAAATTACTTACTAAAATTTGATTAAATTTA
62 ATAAATTACTTACTAAAATTTGATTAAATTTA
* * * *
49434043 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTTAAATATGTTACTTAAATAC
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATATCTTACTAAAATAA
49434108 ATTACTTACTAAAATTT
66 ATTACTTACTAAAATTT
49434125 AAGTATATAT
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
93 27 0.35
94 1 0.01
95 1 0.01
97 49 0.63
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.44
Consensus pattern (93 bp):
TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATATCTTACTAAAATAA
ATTACTTACTAAAATTTGATTAAATTTA
Found at i:49434092 original size:13 final size:13
Alignment explanation
Indices: 49434074--49434115 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
49434064 TAAAATTTGT
*
49434074 TTAAATTTATTAC
1 TTAAATATATTAC
*
49434087 TTAAATATGTTAC
1 TTAAATATATTAC
*
49434100 TTAAATACATTAC
1 TTAAATATATTAC
49434113 TTA
1 TTA
49434116 CTAAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (13 bp):
TTAAATATATTAC
Found at i:49434565 original size:9 final size:9
Alignment explanation
Indices: 49434548--49434578 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
49434538 TTTAATAACA
49434548 ATAACCTAC
1 ATAACCTAC
*
49434557 ATAAGCTAC
1 ATAACCTAC
49434566 ATAACCTAC
1 ATAACCTAC
49434575 ATAA
1 ATAA
49434579 TACATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.26, G:0.03, T:0.23
Consensus pattern (9 bp):
ATAACCTAC
Found at i:49434588 original size:18 final size:17
Alignment explanation
Indices: 49434548--49434598 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
49434538 TTTAATAACA
49434548 ATAACCTACATAAGCTAC
1 ATAACCTACATAA-CTAC
49434566 ATAACCTACATAA-TAC
1 ATAACCTACATAACTAC
*
49434582 ATTTAACTTACATAACT
1 A--TAACCTACATAACT
49434599 TGCATAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.14
18 24 0.83
19 1 0.03
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAACCTACATAACTAC
Found at i:49434662 original size:51 final size:51
Alignment explanation
Indices: 49434572--49434810 Score: 383
Period size: 51 Copynumber: 4.6 Consensus size: 51
49434562 CTACATAACC
* *
49434572 TACATAATACAT-TTAACTTACATAACTTGCATAATACATTTAACTTACAACT
1 TACATAATACATAATAACTTAC--AACTTACATAATACATTTAACTTACAACT
* *
49434624 TACATACTACATAATAACTTACAACTTACACAATACATTTAACTTACAACT
1 TACATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACT
49434675 TACATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACT
1 TACATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACT
49434726 TACATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACT
1 TACATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACT
*
49434777 TACATAATACAT-TTAACTTACATAACTTACATAA
1 TACATAATACATAATAACTTAC--AACTTACATAA
49434811 CTTACCATTG
Statistics
Matches: 177, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
50 8 0.05
51 139 0.79
52 22 0.12
53 8 0.05
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (51 bp):
TACATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACT
Found at i:49440368 original size:21 final size:21
Alignment explanation
Indices: 49440342--49440412 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
49440332 CTACAACTTA
*
49440342 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGAAGCGAGGG
* *
49440363 AAGCAGCGGCTGTAGCGAGGG
1 AAGCAGAGGCTGAAGCGAGGG
* *
49440384 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGAAGCGAGGG
49440405 AAGCAGAG
1 AAGCAGAG
49440413 CAGAACAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.32, C:0.17, G:0.46, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGAAGCGAGGG
Found at i:49448139 original size:16 final size:15
Alignment explanation
Indices: 49448118--49448165 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
49448108 GAAATAAAAC
49448118 CAATAACAATGAATAA
1 CAATAACAAT-AATAA
*
49448134 CAATAACGATAATAA
1 CAATAACAATAATAA
*
49448149 CATTAA-AATAATGAA
1 CAATAACAATAAT-AA
49448164 CA
1 CA
49448166 CAGTCATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 5 0.18
15 14 0.50
16 9 0.32
ACGTcount: A:0.60, C:0.12, G:0.06, T:0.21
Consensus pattern (15 bp):
CAATAACAATAATAA
Found at i:49449711 original size:50 final size:50
Alignment explanation
Indices: 49449648--49450531 Score: 840
Period size: 50 Copynumber: 17.7 Consensus size: 50
49449638 ACGTCAGGGG
*
49449648 GTAAGA-CCTGCTGTTGTAGCTTCAATATTTTTAATTGCAATGTCAGGAAA
1 GTAAGATCC-GCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGAAA
* ** * *
49449698 GTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTC-AGGAAA
* * * *
49449748 GTAAGATCCGCTGTTGTAGCTTTAATCTTCTTAACTGCAATGTCAGGGAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGAAA
* * *
49449798 GTAAGATCCGCTGTTGTAGCTTTAATCTTCTTAATTGCAATGTCAGGGAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGAAA
** * * ** *
49449848 GTAAGATCCGCTGTTGTAGCTTCAAT-TTGTTCCACTACACCG-CTTGGAAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTT-TTTAATTGCAATGTC-AGGAAA
* * * * * * *
49449898 -TAAGATTCGCCGTTGTGGCCTCAAT-GTTTTGATTGCAATGTCAGGGAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGAAA
* ** * ** * * * *
49449946 GTGAGATCCGCTGTTGTAGCTTCTTTCTGTTCCACTGCAAAG-CTAAGAGA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTC-AGGAAA
* *
49449996 GTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGAAA
* ** * *
49450046 GTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTC-AGGAAA
* *
49450096 GTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGAAA
* * ** *
49450146 GTAAGATCCGCTGTTGTAGCTTCAAT-TTGTTCCACTT-CACCG-CTTGGAAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTT-TT-TAATTGCAATGTC-AGGAAA
* * *
49450196 GTAAGATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGAAA
* ** * **
49450246 GTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAGCG-CTAGGAAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTC-AGGAAA
* *
49450296 GTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGAAA
* * ** * **** *
49450346 GTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCACCACCTGGAAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGAAA
* * *
49450396 GTAAGATCTGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGCCAGGAAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGAAA
* ** * *
49450446 GTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTC-AGGAAA
* *
49450496 GTAAGATCCACTGTTGTAGCTTCAATCTTCTTAATT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATT
49450532 ACAAACTATG
Statistics
Matches: 668, Mismatches: 145, Indels: 42
0.78 0.17 0.05
Matches are distributed among these distances:
48 11 0.02
49 55 0.08
50 590 0.88
51 12 0.02
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (50 bp):
GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGAAA
Found at i:49449763 original size:100 final size:100
Alignment explanation
Indices: 49449634--49450531 Score: 1233
Period size: 100 Copynumber: 9.0 Consensus size: 100
49449624 TTTATTCCAC
* * * * ** * *
49449634 TGCAACGTCAGGG-GGTAAGA-CCTGCTGTTGTAGCTTCAATATTTTTAATTGCAATG-TCAGGA
1 TGCAATGTCAGGGAAGTAAGATCC-GCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCT-AGGA
** *
49449696 AAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCAC
64 AAGTAAGATCCGCTGTTGTAGCTTCAATCT-TCTTAAT
* * * ** *
49449733 TGCAACG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTTAATCT-TCTTAACTGCAATG-TCAGG
1 TGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCT-AGG
* *
49449795 GAAGTAAGATCCGCTGTTGTAGCTTTAATCTTCTTAAT
63 AAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAAT
* * * *
49449833 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATTTGTTCCACTACACCGCTTGGAAA
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
* * * * * *
49449898 -TAAGATTCGCCGTTGTGGCCTCAATGTT-TTGAT
66 GTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAAT
* ** * * *
49449931 TGCAATGTCAGGGAAGTGAGATCCGCTGTTGTAGCTTCTTTCTGTTCCACTGCAAAGCTAAGAGA
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
49449996 GTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAAT
66 GTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAAT
49450031 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
49450096 GTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAAT
66 GTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAAT
* * * *
49450131 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATTTGTTCCACTTCACCGCTTGGAAA
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
*
49450196 GTAAGATCTGCTGTTGTAGCTTCAATCTTCTTAAT
66 GTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAAT
*
49450231 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAGCGCTAGGAAA
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
49450296 GTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAAT
66 GTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAAT
*
49450331 TGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCACCAC-CT-GGA
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCA--ACGCTAGGA
*
49450394 AAGTAAGATCTGCTGTTGTAGCTTCAATCTTCTTAAT
64 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAAT
* *
49450431 TGCAATGCCAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
*
49450496 GTAAGATCCACTGTTGTAGCTTCAATCTTCTTAAT
66 GTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAAT
49450531 T
1 T
49450532 ACAAACTATG
Statistics
Matches: 717, Mismatches: 68, Indels: 27
0.88 0.08 0.03
Matches are distributed among these distances:
98 62 0.09
99 59 0.08
100 588 0.82
101 7 0.01
102 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (100 bp):
TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
GTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAAT
Found at i:49463382 original size:16 final size:15
Alignment explanation
Indices: 49463361--49463408 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
49463351 GAAATAAAAC
49463361 CAATAACAATGAATAA
1 CAATAACAAT-AATAA
*
49463377 CAATAACGATAATAA
1 CAATAACAATAATAA
*
49463392 CATTAA-AATAATGAA
1 CAATAACAATAAT-AA
49463407 CA
1 CA
49463409 CAGTCATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 5 0.18
15 14 0.50
16 9 0.32
ACGTcount: A:0.60, C:0.12, G:0.06, T:0.21
Consensus pattern (15 bp):
CAATAACAATAATAA
Found at i:49477878 original size:41 final size:41
Alignment explanation
Indices: 49477833--49477977 Score: 227
Period size: 41 Copynumber: 3.5 Consensus size: 41
49477823 GACTTTAAGT
49477833 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATAAAC
*
49477874 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATAAAC
* * * * *
49477915 TTAGCAGGCTATGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATAAAC
*
49477956 CTAGCAGGCTAAGTGCGGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
49477978 ATACGTTAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATAAAC
Found at i:49478716 original size:13 final size:13
Alignment explanation
Indices: 49478698--49478723 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49478688 ATGCCTCGTA
49478698 ACCCTAATTCGGC
1 ACCCTAATTCGGC
49478711 ACCCTAATTCGGC
1 ACCCTAATTCGGC
49478724 GACGGATACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.23
Consensus pattern (13 bp):
ACCCTAATTCGGC
Found at i:49482303 original size:10 final size:9
Alignment explanation
Indices: 49482269--49482312 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
49482259 TACATTTTCA
49482269 AATTTTTAT
1 AATTTTTAT
*
49482278 ATTTTTTAT
1 AATTTTTAT
*
49482287 AACTTTTAGT
1 AATTTTTA-T
49482297 AATTTTTAAT
1 AATTTTT-AT
49482307 AATTTT
1 AATTTT
49482313 AATTTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 14 0.48
10 14 0.48
11 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
AATTTTTAT
Found at i:49482406 original size:2 final size:2
Alignment explanation
Indices: 49482399--49482424 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49482389 TCATTTTTAA
49482399 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
49482425 TAATTTTTAA
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:49482447 original size:18 final size:17
Alignment explanation
Indices: 49482424--49482459 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
49482414 TATATATATA
49482424 TTAATTTTTAAATAATTT
1 TTAATTTTTAAAT-ATTT
49482442 TTAATTTTTAAATATTT
1 TTAATTTTTAAATATTT
49482459 T
1 T
49482460 ACCAGTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTAATTTTTAAATATTT
Found at i:49486269 original size:97 final size:95
Alignment explanation
Indices: 49486144--49486322 Score: 259
Period size: 97 Copynumber: 1.9 Consensus size: 95
49486134 TAATGCTGAA
* * * *
49486144 TAACATTAAAAAATACAATACACAGTGAACAGTAAAAAATTCCATCGATTTTCATATTATAAATT
1 TAACATTAAAAAATACAATACACAGTGAACAATAAAAAATTCCACCCATTTTCATACTATAAATT
49486209 TGCAATTTTAATATATTACGTAACAAATAAGC
66 TGCAATTTT--TATATTACGTAACAAATAAGC
* * * *
49486241 TAACATTTAAAAATACACTACACTGTGAACAATAAAAAATTCCACCCATTTTCATACTATAGATT
1 TAACATTAAAAAATACAATACACAGTGAACAATAAAAAATTCCACCCATTTTCATACTATAAATT
*
49486306 TGCTATTTTTATATTAC
66 TGCAATTTTTATATTAC
49486323 ATAAACAATA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
95 8 0.11
97 65 0.89
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (95 bp):
TAACATTAAAAAATACAATACACAGTGAACAATAAAAAATTCCACCCATTTTCATACTATAAATT
TGCAATTTTTATATTACGTAACAAATAAGC
Found at i:49487528 original size:19 final size:19
Alignment explanation
Indices: 49487487--49487524 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
49487477 AAAAAGGTAT
* *
49487487 ATAAAGCAATTTTAAAGTA
1 ATAAAACAATTTTAAACTA
49487506 ATAAAACAATTTT-AACTA
1 ATAAAACAATTTTAAACTA
49487524 A
1 A
49487525 ATAATACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (19 bp):
ATAAAACAATTTTAAACTA
Found at i:49490857 original size:10 final size:10
Alignment explanation
Indices: 49490842--49490900 Score: 68
Period size: 10 Copynumber: 6.1 Consensus size: 10
49490832 CTTGTTTTTC
49490842 TTTTATAATT
1 TTTTATAATT
*
49490852 TTTTATAATG
1 TTTTATAATT
*
49490862 TTTTACAATT
1 TTTTATAATT
* *
49490872 TTTAAT-TTT
1 TTTTATAATT
49490881 TTTTAT-ATT
1 TTTTATAATT
49490890 TTTTATAATT
1 TTTTATAATT
49490900 T
1 T
49490901 AAGAAATTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
9 15 0.38
10 25 0.62
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:49490882 original size:28 final size:28
Alignment explanation
Indices: 49490842--49490900 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
49490832 CTTGTTTTTC
49490842 TTTTATAA-TTTTTTATAATGTTTTACAA
1 TTTTATAATTTTTTTAT-ATGTTTTACAA
* *
49490870 TTTT-TAATTTTTTTTATATTTTTTATAA
1 TTTTATAA-TTTTTTTATATGTTTTACAA
49490898 TTT
1 TTT
49490901 AAGAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.11
28 16 0.59
29 8 0.30
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (28 bp):
TTTTATAATTTTTTTATATGTTTTACAA
Found at i:49496328 original size:41 final size:41
Alignment explanation
Indices: 49496271--49496350 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
49496261 TGTAGGCCAT
49496271 TTTGCCCAGGCCCAATTACAACCCAAACCCAAACTAAAAAC
1 TTTGCCCAGGCCCAATTACAACCCAAACCCAAACTAAAAAC
49496312 TTTGCCCAGGCCCAATTACAACCCAAACCCAAACTAAAA
1 TTTGCCCAGGCCCAATTACAACCCAAACCCAAACTAAAA
49496351 TTAACCCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.41, C:0.36, G:0.07, T:0.15
Consensus pattern (41 bp):
TTTGCCCAGGCCCAATTACAACCCAAACCCAAACTAAAAAC
Found at i:49497077 original size:19 final size:19
Alignment explanation
Indices: 49497053--49497102 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
49497043 GCCGCCTACG
*
49497053 GCGGCGGCGGCGCCGGTGA
1 GCGGCGCCGGCGCCGGTGA
49497072 GCGGCGCCGGCGCCGGTGA
1 GCGGCGCCGGCGCCGGTGA
49497091 GCGGCGACCGGC
1 GCGGCG-CCGGC
49497103 ACGGCGGCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 24 0.83
20 5 0.17
ACGTcount: A:0.06, C:0.36, G:0.54, T:0.04
Consensus pattern (19 bp):
GCGGCGCCGGCGCCGGTGA
Found at i:49497882 original size:2 final size:2
Alignment explanation
Indices: 49497875--49497901 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49497865 TTTTATAACT
49497875 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
49497902 GTACTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49512497 original size:7 final size:7
Alignment explanation
Indices: 49512485--49512517 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
49512475 CTTTGCTTCC
49512485 TAAAAAA
1 TAAAAAA
49512492 TAAAAAAA
1 T-AAAAAA
49512500 TAAAAAA
1 TAAAAAA
49512507 TAAAAAA
1 TAAAAAA
49512514 TAAA
1 TAAA
49512518 TAAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:49513876 original size:41 final size:42
Alignment explanation
Indices: 49513719--49513997 Score: 170
Period size: 44 Copynumber: 6.5 Consensus size: 42
49513709 GATCAGTGAA
* * * *
49513719 GAATTGCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAAATC
1 GAATT-CAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGATC
** ** * * **
49513762 GAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGAT-
1 GAATTCA-GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGATC
* ** * * **
49513804 TAAAACGAGGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC
1 GAATTC-A-GG-TCTTATCTCCCTGAGGTTACAGTGGAGTAGATC
* *
49513849 GCA-TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACC
1 GAATTCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGATC
* * *
49513890 GAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT
1 ---GAA-TTCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGATC
** *
49513936 GAAGCCAGAGATCTTATCTCCCTGAGGTTACAGTGGAGTGGATC
1 GAATTCAG-G-TCTTATCTCCCTGAGGTTACAGTGGAGTAGATC
*
49513980 -ACATCCA-GTCTTATCTCC
1 GA-ATTCAGGTCTTATCTCC
49513998 TTGACATTGC
Statistics
Matches: 185, Mismatches: 39, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
41 38 0.21
42 12 0.06
43 37 0.20
44 63 0.34
45 1 0.01
46 34 0.18
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (42 bp):
GAATTCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGATC
Found at i:49513924 original size:46 final size:45
Alignment explanation
Indices: 49513814--49513974 Score: 163
Period size: 46 Copynumber: 3.7 Consensus size: 45
49513804 TAAAACGAGG
* * ** *
49513814 GATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC---GC-ATCA
1 GATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGCAATCA
*
49513855 GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAG-AATTTCA
1 GATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGCAA--TCA
* ** * *
49513901 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-GA
1 GATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGCAATCA
49513945 GATCTTATCTCCCTGAGGTTACAGTGGAGT
1 GATCTTATCTCCCTGAGGTTACAGTGGAGT
49513975 GGATCACATC
Statistics
Matches: 100, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
41 29 0.29
44 32 0.32
46 38 0.38
47 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (45 bp):
GATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGCAATCA
Found at i:49513963 original size:44 final size:44
Alignment explanation
Indices: 49513726--49513973 Score: 209
Period size: 44 Copynumber: 5.7 Consensus size: 44
49513716 GAAGAATTGC
* * *
49513726 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAAATCGAAGACA-
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGCCAG
** * * * ** * *
49513769 CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACGAG
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGCCAG
* * * ** * * *
49513813 GGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCA-TCAG
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGCCAG
* * * *
49513856 -G-TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAG-AATTTC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGCCA---G
*
49513900 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGCCAG
49513944 AGATCTTATCTCCCTGAGGTTACAGTGGAG
1 AGATCTTATCTCCCTGAGGTTACAGTGGAG
49513974 TGGATCACAT
Statistics
Matches: 159, Mismatches: 38, Indels: 15
0.75 0.18 0.07
Matches are distributed among these distances:
41 31 0.19
42 1 0.01
43 33 0.21
44 58 0.36
45 1 0.01
46 34 0.21
47 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGCCAG
Found at i:49513966 original size:131 final size:128
Alignment explanation
Indices: 49513729--49513997 Score: 317
Period size: 131 Copynumber: 2.1 Consensus size: 128
49513719 GAATTGCAGA
* *
49513729 TCTTATCTCCCTGAGGTTACAGCGGAGCAAATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGGTTACAGCGGAGCAAACCGAAGACACGATCCTATCTCCCTGAAGTTACAG
* * * * *
49513794 TGGAGCGGATTAAAACGAGGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCAT-CAGG
66 TGGAGCAGATTAAAACCAGAGATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCACATCCA-G
* * * * *
49513857 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTTCAGATCTTATCTCCCTGAGGTT
1 TCTTATCTCCCTGAGGTTACAGCGGAGCAAACCGAAGACA---C-GATCCTATCTCCCTGAAGTT
* * * ** *
49513921 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGGTTACAGTGGAGTGGATCACATCC
62 ACAGTGGAGCAGATTAAAACCAGAGATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCACATCC
49513986 AG
127 AG
49513988 TCTTATCTCC
1 TCTTATCTCC
49513998 TTGACATTGC
Statistics
Matches: 118, Mismatches: 18, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
127 1 0.01
128 34 0.29
130 1 0.01
131 80 0.68
132 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (128 bp):
TCTTATCTCCCTGAGGTTACAGCGGAGCAAACCGAAGACACGATCCTATCTCCCTGAAGTTACAG
TGGAGCAGATTAAAACCAGAGATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCACATCCAG
Found at i:49514011 original size:131 final size:131
Alignment explanation
Indices: 49513775--49514019 Score: 321
Period size: 131 Copynumber: 1.9 Consensus size: 131
49513765 GACACTATCC
* * * *
49513775 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACGAGGGATCTTATCTCTCTGAAGTTACAGCA
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCAGAGATCTTATCTCCCTGAAGTTACAGCA
* ** *
49513840 GAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATC
66 GAGTAGATCACATCAGGTCTTATCTCCCTGACATTACAGTGGAGCAGACCGAAGAATTTCAGATC
49513905 T
131 T
* * * * **
49513906 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGGTTACAGTG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCAGAGATCTTATCTCCCTGAAGTTACAGCA
* * *
49513971 GAGTGGATCACATCCA-GTCTTATCTCCTTGACATTGCAGTGGAGCAGAC
66 GAGTAGATCACAT-CAGGTCTTATCTCCCTGACATTACAGTGGAGCAGAC
49514020 TAAAACCACA
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
131 94 0.98
132 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (131 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCAGAGATCTTATCTCCCTGAAGTTACAGCA
GAGTAGATCACATCAGGTCTTATCTCCCTGACATTACAGTGGAGCAGACCGAAGAATTTCAGATC
T
Found at i:49516264 original size:108 final size:109
Alignment explanation
Indices: 49516075--49516379 Score: 465
Period size: 108 Copynumber: 2.8 Consensus size: 109
49516065 CTAATTGAGA
*
49516075 CAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
1 CAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
* **
49516140 TTAACCAAATGGCTTAATATCCTTT-TAAAATTTTAAAATAAGG
66 TTAACCAAATGGCTTAATATCCTTTAAAAAATTACAAAATAAGG
49516183 CAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
1 CAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
*
49516248 TCAACCAAATGGCTTAATATCCTTTCCAAAAAAATTACAAAATAAGG
66 TTAACCAAATGGCTTAATATCCTTT---AAAAAATTACAAAATAAGG
* * *
49516295 CAATGTTTTGCGTTTGGAAATTCGAG-GAACATGCCCTAAGGTGCTGGGTATTGA--TTTCTCGT
1 CAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
**
49516357 TTAACCAAATGGCCAAATATCCT
66 TTAACCAAATGGCTTAATATCCT
49516380 CTTGAATTTT
Statistics
Matches: 182, Mismatches: 11, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
108 88 0.48
109 28 0.15
111 25 0.14
112 41 0.23
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (109 bp):
CAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
TTAACCAAATGGCTTAATATCCTTTAAAAAATTACAAAATAAGG
Found at i:49526270 original size:6 final size:6
Alignment explanation
Indices: 49526259--49526292 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
49526249 GAAAAAGAAG
49526259 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGA
49526293 TACAGAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AGGAGA
Found at i:49526274 original size:24 final size:22
Alignment explanation
Indices: 49526230--49526292 Score: 54
Period size: 24 Copynumber: 2.7 Consensus size: 22
49526220 CGGTAGAGAC
* *
49526230 AGAAGAGAAGAAGGTCGAGGAAAA
1 AGAAGAGGAGAAGG-AGAGG-AAA
*
49526254 AGAAGAGGAGAAGGAGAAGGAGA
1 AGAAGAGGAGAAGGAG-AGGAAA
*
49526277 AGGAGAAGGAGAAGGA
1 AGAAG-AGGAGAAGGA
49526293 TACAGAGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 7 0.21
24 26 0.79
ACGTcount: A:0.52, C:0.02, G:0.44, T:0.02
Consensus pattern (22 bp):
AGAAGAGGAGAAGGAGAGGAAA
Found at i:49526319 original size:48 final size:48
Alignment explanation
Indices: 49526262--49526379 Score: 155
Period size: 48 Copynumber: 2.4 Consensus size: 48
49526252 AAAGAAGAGG
*
49526262 AGAAGGAGAAGGAGAAGGAGAAGGAGAAGGATACAGAGGTTAAGGAAAA
1 AGAA-GAGAAGGAGAAGGAGAAGGAGAAGGATAAAGAGGTTAAGGAAAA
* * * *
49526311 AGAAGAGAAGGAGAAGGAAAAGGATAAGGATAAAGAGGTTAAGGGAGA
1 AGAAGAGAAGGAGAAGGAGAAGGAGAAGGATAAAGAGGTTAAGGAAAA
* * *
49526359 CGAAGAGAAAGAGAAAGAGAA
1 AGAAGAGAAGGAGAAGGAGAA
49526380 AGAAAAGAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
48 56 0.93
49 4 0.07
ACGTcount: A:0.53, C:0.02, G:0.39, T:0.06
Consensus pattern (48 bp):
AGAAGAGAAGGAGAAGGAGAAGGAGAAGGATAAAGAGGTTAAGGAAAA
Found at i:49526372 original size:6 final size:6
Alignment explanation
Indices: 49526361--49526442 Score: 69
Period size: 6 Copynumber: 13.2 Consensus size: 6
49526351 AAGGGAGACG
* *
49526361 AAGAGA AAGAGA AAGAGA AAGA-A AAGAAA AAGA-A GAAGAAGA AAGACA
1 AAGAGA AAGAGA AAGAGA AAGAGA AAGAGA AAGAGA -AAG-AGA AAGAGA
* *
49526409 AAGATGGGA AAGAGA AAGAGA AAAAGA AAAAGA A
1 AAGA---GA AAGAGA AAGAGA AAGAGA AAGAGA A
49526443 GAAAAAGGAT
Statistics
Matches: 66, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
5 6 0.09
6 50 0.76
7 4 0.06
8 1 0.02
9 5 0.08
ACGTcount: A:0.70, C:0.01, G:0.28, T:0.01
Consensus pattern (6 bp):
AAGAGA
Found at i:49526567 original size:24 final size:24
Alignment explanation
Indices: 49526540--49526592 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
49526530 TTCCTCATCG
* *
49526540 TCGTCATCGTCATCTTCTTCTTCC
1 TCGTCATCATCATCATCTTCTTCC
* *
49526564 TCGTCATCATCTTCATCTTCTTCG
1 TCGTCATCATCATCATCTTCTTCC
49526588 TCGTC
1 TCGTC
49526593 TTCTGATTCA
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:0.09, C:0.36, G:0.09, T:0.45
Consensus pattern (24 bp):
TCGTCATCATCATCATCTTCTTCC
Found at i:49526567 original size:27 final size:27
Alignment explanation
Indices: 49526525--49526586 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
49526515 GGATAAAGGT
*
49526525 TCTTCTTCCTCATCGTCGTCATCGTCA
1 TCTTCTTCCTCATCGTCATCATCGTCA
* * *
49526552 TCTTCTTCTTCCTCGTCATCATCTTCA
1 TCTTCTTCCTCATCGTCATCATCGTCA
49526579 TCTTCTTC
1 TCTTCTTC
49526587 GTCGTCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.10, C:0.37, G:0.06, T:0.47
Consensus pattern (27 bp):
TCTTCTTCCTCATCGTCATCATCGTCA
Found at i:49526575 original size:21 final size:21
Alignment explanation
Indices: 49526549--49526589 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
49526539 GTCGTCATCG
*
49526549 TCATCTTCTTCTTCCTCGTCA
1 TCATCTTCATCTTCCTCGTCA
*
49526570 TCATCTTCATCTTCTTCGTC
1 TCATCTTCATCTTCCTCGTC
49526590 GTCTTCTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.37, G:0.05, T:0.49
Consensus pattern (21 bp):
TCATCTTCATCTTCCTCGTCA
Found at i:49526621 original size:6 final size:6
Alignment explanation
Indices: 49526612--49526646 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
49526602 AGATTCAGAT
49526612 AAGAAA AAG-AA AAGAAA AGAGAAA AAGAAA AAGAA
1 AAGAAA AAGAAA AAGAAA A-AGAAA AAGAAA AAGAA
49526647 GCAAGAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:49526701 original size:24 final size:24
Alignment explanation
Indices: 49526674--49526729 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
49526664 ATAAAGAGCC
*
49526674 GAAAGAAGATGA-ACACAAAGAGAA
1 GAAAGAAGACGAGACA-AAAGAGAA
*
49526698 GAAAGATGACGAGACAAAAGAGAA
1 GAAAGAAGACGAGACAAAAGAGAA
49526722 -AAAGAAGA
1 GAAAGAAGA
49526730 AAAAGAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 7 0.25
24 18 0.64
25 3 0.11
ACGTcount: A:0.62, C:0.07, G:0.27, T:0.04
Consensus pattern (24 bp):
GAAAGAAGACGAGACAAAAGAGAA
Found at i:49527599 original size:35 final size:35
Alignment explanation
Indices: 49527553--49527629 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 35
49527543 TGCATTATAG
*
49527553 GTTCTGCGGGTTATGGATAACAGGATTACTTACAA
1 GTTCTGCGGGTTATGAATAACAGGATTACTTACAA
*
49527588 GTTCTGCGGGTTATGAATAACAGGATTACTTCCAA
1 GTTCTGCGGGTTATGAATAACAGGATTACTTACAA
49527623 GTTCTGC
1 GTTCTGC
49527630 AAGCACTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (35 bp):
GTTCTGCGGGTTATGAATAACAGGATTACTTACAA
Found at i:49531725 original size:13 final size:13
Alignment explanation
Indices: 49531707--49531731 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49531697 TATAATAAAT
49531707 TTTTTTATTTTTA
1 TTTTTTATTTTTA
49531720 TTTTTTATTTTT
1 TTTTTTATTTTT
49531732 TAACTTTAAA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:49531794 original size:51 final size:52
Alignment explanation
Indices: 49531736--49531847 Score: 174
Period size: 51 Copynumber: 2.2 Consensus size: 52
49531726 ATTTTTTAAC
*
49531736 TTTAAAATACTTTTAAAAATAC-TTTTTTAAATTTTTTAATTTTAAAATTTT
1 TTTAAAATACTTTTAAAAATACTTTTTTTAAATTTTTTAATTTTAAAATATT
* * *
49531787 TTTAAAAT-TTTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATT
1 TTTAAAATACTTTTAAAAATACTTTTTTTAAATTTTTTAATTTTAAAATATT
49531838 TTTAAAATAC
1 TTTAAAATAC
49531848 NNNNNNNNNN
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
50 11 0.20
51 43 0.80
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (52 bp):
TTTAAAATACTTTTAAAAATACTTTTTTTAAATTTTTTAATTTTAAAATATT
Found at i:49531812 original size:40 final size:40
Alignment explanation
Indices: 49531726--49531805 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
49531716 TTTATTTTTT
*
49531726 ATTTTTTAACTTTAAAATACTTTTAAAAATACTTTTTTAA
1 ATTTTTTAACTTTAAAATACTTTTAAAAATACTTTTTAAA
* * * *
49531766 ATTTTTTAATTTTAAAAT-TTTTTTAAAAT-TTTTTTAAA
1 ATTTTTTAACTTTAAAATACTTTTAAAAATACTTTTTAAA
49531804 AT
1 AT
49531806 ACTTTTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 9 0.26
39 9 0.26
40 17 0.49
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (40 bp):
ATTTTTTAACTTTAAAATACTTTTAAAAATACTTTTTAAA
Found at i:49531818 original size:23 final size:22
Alignment explanation
Indices: 49531775--49531825 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
49531765 AATTTTTTAA
49531775 TTTTAAAATTTTTTTAAAATTT
1 TTTTAAAATTTTTTTAAAATTT
*
49531797 TTTTAAAATACTTTTTT-TAATTT
1 TTTTAAAAT--TTTTTTAAAATTT
49531820 TTTTAA
1 TTTTAA
49531826 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 9 0.35
23 11 0.42
24 6 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTAAAATTTTTTTAAAATTT
Found at i:49532681 original size:19 final size:19
Alignment explanation
Indices: 49532627--49532704 Score: 77
Period size: 20 Copynumber: 4.0 Consensus size: 19
49532617 AACTTAAGAG
*
49532627 AAAGTATGAAAAATTATTA
1 AAAGTATTAAAAATTATTA
*
49532646 ATAGT-TATAAGAAATTATTA
1 AAAGTAT-TAA-AAATTATTA
* *
49532666 AAAGTATTAAAAATTAGTC
1 AAAGTATTAAAAATTATTA
*
49532685 AAAGTATTTAAAATTTATTA
1 AAAGTA-TTAAAAATTATTA
49532705 TAAAATCACA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
18 1 0.02
19 19 0.40
20 26 0.55
21 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (19 bp):
AAAGTATTAAAAATTATTA
Found at i:49534811 original size:20 final size:21
Alignment explanation
Indices: 49534786--49534833 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 21
49534776 TTTTGGAAAT
49534786 TTAAAAAATAAATA-TA-AAA
1 TTAAAAAATAAATATTATAAA
*
49534805 TTAAAAAATAAATATTATAAT
1 TTAAAAAATAAATATTATAAA
49534826 TTAAAAAA
1 TTAAAAAA
49534834 ATATTAGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 14 0.54
20 2 0.08
21 10 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAAAAAATAAATATTATAAA
Found at i:49541226 original size:8 final size:8
Alignment explanation
Indices: 49541213--49541266 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
49541203 AATTGAATTA
49541213 TTAATATT
1 TTAATATT
*
49541221 TTAATATA
1 TTAATATT
49541229 TTAA-ATCT
1 TTAATAT-T
49541237 TTAA-A-T
1 TTAATATT
*
49541243 ATAATATT
1 TTAATATT
49541251 TTAAATATT
1 TT-AATATT
49541260 TTAATAT
1 TTAATAT
49541267 AAAATTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 4 0.11
7 3 0.08
8 23 0.61
9 8 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (8 bp):
TTAATATT
Found at i:49541245 original size:17 final size:16
Alignment explanation
Indices: 49541211--49541266 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
49541201 AGAATTGAAT
49541211 TATTAATATTTTAATA
1 TATTAATATTTTAATA
49541227 TATTAA-ATCTTTAA-A
1 TATTAATAT-TTTAATA
49541242 TA-TAATATTTTAAATA
1 TATTAATATTTT-AATA
*
49541258 TTTTAATAT
1 TATTAATAT
49541267 AAAATTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
14 6 0.18
15 9 0.26
16 13 0.38
17 6 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTAATATTTTAATA
Found at i:49541248 original size:22 final size:21
Alignment explanation
Indices: 49541222--49541276 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
49541212 ATTAATATTT
*
49541222 TAATATATTAAATCTTTAAATA
1 TAATAT-TTAAATATTTAAATA
*
49541244 TAATATTTTAAATATTTTAATA
1 TAATA-TTTAAATATTTAAATA
*
49541266 TAAAATTTAAA
1 TAATATTTAAA
49541277 AAATATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 22 0.76
23 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATATTTAAATATTTAAATA
Found at i:49542509 original size:2 final size:2
Alignment explanation
Indices: 49542502--49542557 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
49542492 GTTTAGAAGC
49542502 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49542544 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
49542558 ACTCTATCAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49543495 original size:28 final size:28
Alignment explanation
Indices: 49543454--49543509 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
49543444 TAATTTACGA
* *
49543454 AATTCTTAGCATTTTATCGCATGTGATT
1 AATTCTTAGAATTTTATCACATGTGATT
49543482 AATTCTTAGAATTTTATCACATGTGATT
1 AATTCTTAGAATTTTATCACATGTGATT
49543510 CATATTGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (28 bp):
AATTCTTAGAATTTTATCACATGTGATT
Found at i:49543735 original size:43 final size:43
Alignment explanation
Indices: 49543681--49544021 Score: 551
Period size: 43 Copynumber: 8.0 Consensus size: 43
49543671 TTATGGAAAA
* * *
49543681 AAACGCTGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
49543724 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCAC-TTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
49543766 AAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
49543809 AAACGCCACTAAAGACCAAGACTTTTAGTGGCGC-TTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
49543851 AAACACCGCTAAAGACCAAGACCTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACC-TTTAGCGGCGCTTTTCCCAC
*
49543895 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
49543938 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
49543981 AAACACCGCTAAAGACCAAGACCTTTAGCGACGCTTTTCCC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
49544022 TTTAGAAAAA
Statistics
Matches: 276, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
42 66 0.24
43 180 0.65
44 30 0.11
ACGTcount: A:0.29, C:0.35, G:0.17, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:49546293 original size:2 final size:2
Alignment explanation
Indices: 49546286--49546310 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49546276 AGTAATTACT
49546286 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
49546311 CCATATAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49546939 original size:7 final size:7
Alignment explanation
Indices: 49546927--49547032 Score: 74
Period size: 7 Copynumber: 15.0 Consensus size: 7
49546917 TACCCTTGAC
49546927 ACCCTAA
1 ACCCTAA
49546934 ACCCTAA
1 ACCCTAA
49546941 ATCCCTAA
1 A-CCCTAA
*
49546949 CCCCTAA
1 ACCCTAA
*
49546956 TCCCTAA
1 ACCCTAA
49546963 ATCCCTAA
1 A-CCCTAA
*
49546971 CCCCTAA
1 ACCCTAA
*
49546978 CCCCT-A
1 ACCCTAA
49546984 ACCTCTAA
1 ACC-CTAA
*
49546992 ATCTCT-A
1 A-CCCTAA
49546999 ACCCTAA
1 ACCCTAA
*
49547006 CCCCTAA
1 ACCCTAA
* *
49547013 AACTTAA
1 ACCCTAA
*
49547020 TCCC-AA
1 ACCCTAA
49547026 ACCCTAA
1 ACCCTAA
49547033 TCCATACCCT
Statistics
Matches: 77, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
6 11 0.14
7 49 0.64
8 16 0.21
9 1 0.01
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (7 bp):
ACCCTAA
Found at i:49546955 original size:22 final size:22
Alignment explanation
Indices: 49546928--49546984 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
49546918 ACCCTTGACA
49546928 CCCTAAACCCTAAATCCCTAAC
1 CCCTAAACCCTAAATCCCTAAC
*
49546950 CCCTAATCCCTAAATCCCTAAC
1 CCCTAAACCCTAAATCCCTAAC
*
49546972 CCCTAACCCCTAA
1 CCCTAAACCCTAA
49546985 CCTCTAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.19
Consensus pattern (22 bp):
CCCTAAACCCTAAATCCCTAAC
Found at i:49546962 original size:29 final size:27
Alignment explanation
Indices: 49546929--49547032 Score: 111
Period size: 29 Copynumber: 3.7 Consensus size: 27
49546919 CCCTTGACAC
49546929 CCTAAA-CCCTAAATCCCTAACCCCTAATC
1 CCTAAATCCCT-AA-CCCTAACCCCTAA-C
49546958 CCTAAATCCCTAACCCCTAACCCCTAAC
1 CCTAAATCCCTAA-CCCTAACCCCTAAC
* *
49546986 CTCTAAATCTCTAACCCTAACCCCTAAA
1 C-CTAAATCCCTAACCCTAACCCCTAAC
* * *
49547014 ACTTAATCCCAAACCCTAA
1 CCTAAATCCCTAACCCTAA
49547033 TCCATACCCT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
27 15 0.23
28 15 0.23
29 32 0.48
30 4 0.06
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (27 bp):
CCTAAATCCCTAACCCTAACCCCTAAC
Found at i:49547996 original size:41 final size:41
Alignment explanation
Indices: 49547951--49548124 Score: 140
Period size: 41 Copynumber: 4.2 Consensus size: 41
49547941 AATATTTTTT
*
49547951 GCGGCGCTTCCACAAAAACGCCGCTAAAACCCCTAACATTA
1 GCGGCGCTTCCATAAAAACGCCGCTAAAACCCCTAACATTA
* ** *
49547992 GCGGCGCTTCTCAAAAAAACGCCGCTAAAAATCTTAAC-TTCA
1 GCGGCGCTTC-CATAAAAACGCCGCTAAAACCCCTAACATT-A
* *** *
49548034 GCAGCGCTTATTTAAAAACGCCGCTAAATA-CCTTAACATTA
1 GCGGCGCTTCCATAAAAACGCCGCTAAA-ACCCCTAACATTA
* * * *
49548075 GCAGCAG-TT-GATTAAAAACGCCACTAAAACCCCCAACCATTA
1 GCGGC-GCTTCCA-TAAAAACGCCGCTAAAACCCCTAA-CATTA
49548117 GCGGCGCT
1 GCGGCGCT
49548125 AATTCAAAAA
Statistics
Matches: 108, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
40 1 0.01
41 61 0.56
42 46 0.43
ACGTcount: A:0.35, C:0.30, G:0.15, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTCCATAAAAACGCCGCTAAAACCCCTAACATTA
Found at i:49549421 original size:2 final size:2
Alignment explanation
Indices: 49549414--49549446 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49549404 TAATGGGGTT
49549414 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49549447 TATGTGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49550342 original size:2 final size:2
Alignment explanation
Indices: 49550335--49550368 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
49550325 CTTTTGGTTA
49550335 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
49550369 GTTTACGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49566771 original size:19 final size:16
Alignment explanation
Indices: 49566746--49566796 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 16
49566736 AATATGATGA
49566746 TAGTTAGTCTGTTAGT
1 TAGTTAGTCTGTTAGT
*
49566762 TAGCAGTTAGGCTGTTAG-
1 T---AGTTAGTCTGTTAGT
49566780 TAGTTAGTCTGTTAGT
1 TAGTTAGTCTGTTAGT
49566796 T
1 T
49566797 GCTATAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 13 0.45
16 2 0.07
18 1 0.03
19 13 0.45
ACGTcount: A:0.20, C:0.08, G:0.27, T:0.45
Consensus pattern (16 bp):
TAGTTAGTCTGTTAGT
Found at i:49567396 original size:3 final size:3
Alignment explanation
Indices: 49567384--49567421 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
49567374 CCTTACACCC
49567384 TCT T-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
49567422 ATATTAACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:49567698 original size:2 final size:2
Alignment explanation
Indices: 49567691--49567740 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
49567681 CTCAGTGACC
49567691 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
49567733 CT CT CT CT
1 CT CT CT CT
49567741 AATGATTCAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:49568446 original size:27 final size:28
Alignment explanation
Indices: 49568416--49568471 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
49568406 AATATTGTGA
*
49568416 TTATAAATTA--TATATTTATGTAAATTT
1 TTATAAATTAGTTATA-TTATCTAAATTT
*
49568443 TTATATATTAGTTATATTATCTAAATTT
1 TTATAAATTAGTTATATTATCTAAATTT
49568471 T
1 T
49568472 GATATATTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.36
28 12 0.48
29 4 0.16
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (28 bp):
TTATAAATTAGTTATATTATCTAAATTT
Found at i:49571596 original size:58 final size:58
Alignment explanation
Indices: 49571493--49571642 Score: 142
Period size: 58 Copynumber: 2.6 Consensus size: 58
49571483 GATAGAAGAA
* * * ** *
49571493 AGAACATGCAACAAATGC-GTAGCAATTCTTTTTTCTTCAATAACTTAGGCAGATTCCT
1 AGAACATGCAACAAA-ACTGTAGCAATTCTTTTTCCTTCAAGAACTTAAACAGACTCCT
* * *
49571551 AGACCATGCAACAAAACTGTAGCAATTCTTTTTCCCTT-GAGAACTTAAATAGACTCCT
1 AGAACATGCAACAAAACTGTAGCAATTCTTTTT-CCTTCAAGAACTTAAACAGACTCCT
** * *
49571609 AGAATGTGCAACATAACTGTAGCACTTCCTTTTT
1 AGAACATGCAACAAAACTGTAGCAATT-CTTTTT
49571643 TTCCCTCTAG
Statistics
Matches: 75, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
57 1 0.01
58 65 0.87
59 9 0.12
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (58 bp):
AGAACATGCAACAAAACTGTAGCAATTCTTTTTCCTTCAAGAACTTAAACAGACTCCT
Found at i:49577184 original size:17 final size:18
Alignment explanation
Indices: 49577150--49577187 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
49577140 GATAATTATA
49577150 TAAAAATTTTCAATAAAAT
1 TAAAAATTTT-AATAAAAT
49577169 TAAAAATTTT-ATAAAAT
1 TAAAAATTTTAATAAAAT
49577186 TA
1 TA
49577188 TTAAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
19 10 0.53
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAAATTTTAATAAAAT
Found at i:49579401 original size:50 final size:50
Alignment explanation
Indices: 49579342--49579457 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
49579332 CTAACATTGA
* * *
49579342 CAATAGTTGCACCTTTGACATTCTATTATGTAAATCT-GGGTTGTAAGAAT
1 CAATGGTTGCACCTTTGACATTCTACTATGT-AATCTCGGGTTGCAAGAAT
* * * **
49579392 CAATGGTTGCACCTTTGGCATTCTACTGTGTAATTTCGGGTTGCAATCAT
1 CAATGGTTGCACCTTTGACATTCTACTATGTAATCTCGGGTTGCAAGAAT
*
49579442 CCATGGTTGCACCTTT
1 CAATGGTTGCACCTTT
49579458 TATATACAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 4 0.07
50 52 0.93
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (50 bp):
CAATGGTTGCACCTTTGACATTCTACTATGTAATCTCGGGTTGCAAGAAT
Found at i:49581019 original size:17 final size:18
Alignment explanation
Indices: 49580997--49581041 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
49580987 ATTGGCTTAT
49580997 ACTTTTGGCTTG-ACACC
1 ACTTTTGGCTTGCACACC
*
49581014 ACTTTTGGCTTGCACGCC
1 ACTTTTGGCTTGCACACC
49581032 AC-TTTGGCTT
1 ACTTTTGGCTT
49581042 ACTTTTTGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.13, C:0.29, G:0.20, T:0.38
Consensus pattern (18 bp):
ACTTTTGGCTTGCACACC
Found at i:49581051 original size:29 final size:29
Alignment explanation
Indices: 49581016--49581122 Score: 94
Period size: 29 Copynumber: 3.7 Consensus size: 29
49581006 TTGACACCAC
49581016 TTTTGGCTTGCACGCCACTTTGGCTTACT
1 TTTTGGCTTGCACGCCACTTTGGCTTACT
** *
49581045 TTTTGGCTTGTTCGCCACTTTAGCTTACT
1 TTTTGGCTTGCACGCCACTTTGGCTTACT
* * **
49581074 CTTTAGAC-TGTC-CGCCACTTTGAATTGCAC-
1 -TTTTGGCTTG-CACGCCACTTTGGCTT--ACT
49581104 TTTTGGCTTGCACGCCACT
1 TTTTGGCTTGCACGCCACT
49581123 ATTGCATGGT
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
29 45 0.74
30 14 0.23
31 2 0.03
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.40
Consensus pattern (29 bp):
TTTTGGCTTGCACGCCACTTTGGCTTACT
Found at i:49581707 original size:13 final size:13
Alignment explanation
Indices: 49581689--49581713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49581679 TCATTATTGA
49581689 CTTTAGAAAAAGC
1 CTTTAGAAAAAGC
49581702 CTTTAGAAAAAG
1 CTTTAGAAAAAG
49581714 TTAAGATTAA
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:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
CTTTAGAAAAAGC
Found at i:49582369 original size:19 final size:20
Alignment explanation
Indices: 49582333--49582370 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
49582323 GTTTTAGGGA
49582333 TTAAATATAAGAAAAAAAAG
1 TTAAATATAAGAAAAAAAAG
*
49582353 TTAAATGTAAGAAAAAAA
1 TTAAATATAAGAAAAAAA
49582371 CATTAAAACA
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:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (20 bp):
TTAAATATAAGAAAAAAAAG
Found at i:49582376 original size:20 final size:19
Alignment explanation
Indices: 49582332--49582377 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
49582322 TGTTTTAGGG
49582332 ATTAAATATAAGAAAAAAA
1 ATTAAATATAAGAAAAAAA
*
49582351 AGTTAAATGTAAGAAAAAAA
1 A-TTAAATATAAGAAAAAAA
49582371 CATTAAA
1 -ATTAAA
49582378 ACATTAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (19 bp):
ATTAAATATAAGAAAAAAA
Found at i:49582387 original size:28 final size:30
Alignment explanation
Indices: 49582353--49582425 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 30
49582343 GAAAAAAAAG
49582353 TTAAATGTA-AGAAAAAAAC-ATTAAAACA
1 TTAAATGTAGAGAAAAAAACTATTAAAACA
* * *
49582381 TTAAATGCATAG--AAAAACTATTAAGACA
1 TTAAATGTAGAGAAAAAAACTATTAAAACA
49582409 TTAAATGTAGAGAAAAA
1 TTAAATGTAGAGAAAAA
49582426 TTTGTTGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
27 6 0.16
28 26 0.70
29 2 0.05
30 3 0.08
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.23
Consensus pattern (30 bp):
TTAAATGTAGAGAAAAAAACTATTAAAACA
Found at i:49588753 original size:36 final size:36
Alignment explanation
Indices: 49588647--49588755 Score: 164
Period size: 36 Copynumber: 3.0 Consensus size: 36
49588637 GGTAGTTTTA
* *
49588647 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAAT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
49588683 GTTATACTTATCTGATCAAGTGAAAAAATGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
49588719 GCTATACTTATCTGATCAAGTGACAAAGTAATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
49588755 G
1 G
49588756 GTAGCTTAGC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:49601946 original size:15 final size:15
Alignment explanation
Indices: 49601926--49601959 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
49601916 TAATCTAGTT
49601926 TGATTCAGATAACCA
1 TGATTCAGATAACCA
*
49601941 TGATTCAGATAATCA
1 TGATTCAGATAACCA
49601956 TGAT
1 TGAT
49601960 ATATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (15 bp):
TGATTCAGATAACCA
Found at i:49604004 original size:19 final size:19
Alignment explanation
Indices: 49603980--49604026 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
49603970 TTTCCTAAAA
*
49603980 ATTTTAATATGCTTCT-AGC
1 ATTTTAATATCCTT-TAAGC
*
49603999 ATTTTAA-ATCCTTTAAGG
1 ATTTTAATATCCTTTAAGC
49604017 ATTTTAATAT
1 ATTTTAATAT
49604027 AAACTTTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.04
18 14 0.58
19 9 0.38
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (19 bp):
ATTTTAATATCCTTTAAGC
Found at i:49605453 original size:16 final size:16
Alignment explanation
Indices: 49605428--49605458 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49605418 ATTTAATACC
49605428 ATTATCATTATTATTA
1 ATTATCATTATTATTA
*
49605444 ATTATTATTATTATT
1 ATTATCATTATTATT
49605459 TACTCATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATCATTATTATTA
Found at i:49605858 original size:2 final size:2
Alignment explanation
Indices: 49605851--49605875 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49605841 TGTATACATT
49605851 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
49605876 TTGTCTTCTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49609897 original size:3 final size:3
Alignment explanation
Indices: 49609889--49609919 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
49609879 TATTTCAAAA
49609889 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
49609920 AAATGAGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:49611276 original size:45 final size:45
Alignment explanation
Indices: 49611211--49611519 Score: 381
Period size: 45 Copynumber: 6.9 Consensus size: 45
49611201 TGAAAGCAGT
* *
49611211 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTATATCAAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAGC
* * *
49611256 AGATCTTGTCTTCCTATATTGGCAGCAAAGTAAATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAGC
* * *
49611301 AGATCTTGTCTTCCTGTATTGGCAACGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAGC
* * * * *
49611346 ATG-TCTTATCTTCCTGTATCGGCAGCGAAGTAGA-CTGAAGATAAC
1 A-GATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC-AAAGATAGC
* * *
49611391 AGATCTTGTCTTCCTATATTGGCAGCAAAGTTGATTAAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAGC
* *
49611436 AGGTCTTGTCTTCCTATATTGGCAGCAAAGTAGA-CTAAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC-AAAGATAGC
* * *
49611481 AGATCTTGTCTTCCTATACTGGCAGTGAAGCAGATCAAA
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAA
49611520 AGCACCAGCC
Statistics
Matches: 230, Mismatches: 28, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
44 2 0.01
45 226 0.98
46 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (45 bp):
AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAGC
Found at i:49611857 original size:45 final size:45
Alignment explanation
Indices: 49611772--49612166 Score: 257
Period size: 45 Copynumber: 8.7 Consensus size: 45
49611762 AGTTGAGGCT
* * * * *
49611772 ACAAGTCTTATCTCACTGAGGTTGCAGTAGAGTGGGCTGAAGATA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATA
*
49611817 ACAAGTCTTATCTCCCTGAAGTTACAGTGGAGTAGACTGAAGATA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATA
** * * * *
49611862 ACAAACCTTATCTCCCTAAAGTTGCAGTGGGGCA-AGTTGAAGAT-
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-CTGAAGATA
* * * * * * * **
49611906 ATAAGTCCTATCTCCCTGAATTTGTAGTGGAGCAGA-TTAAAACG
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATA
* * * * * **
49611950 ACGAA-TCATATAC-CTCTAAAGTTGCAATAGGTCAGATTAAATCT-ATCATA
1 AC-AAGTCTTAT-CTCCCTGAAGTTGCAGT-GG--AG--TAGA-CTGAAGATA
* * *
49612000 ACAAGTCTTATCTCCCTGAAGGTGCAGTGGAGTAGACTGTAGCTA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATA
* * * * *
49612045 ACAAGTCTTATCTACTTGAAGTTGCAGTGGAGCAAACTGATGATA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATA
** * * *
49612090 ACAAACCTTATCTCCCTGAAGTTGCAGTGGGGCA-AGTTGAAGAT-
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-CTGAAGATA
* *
49612134 ACAAGTCTTATCTCCCTAAATTTGCAGTGGAGT
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGT
49612167 GGATTAAAAC
Statistics
Matches: 266, Mismatches: 68, Indels: 33
0.72 0.19 0.09
Matches are distributed among these distances:
43 4 0.02
44 73 0.27
45 157 0.59
47 4 0.02
49 7 0.03
50 20 0.08
51 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (45 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATA
Found at i:49612174 original size:228 final size:228
Alignment explanation
Indices: 49611772--49612272 Score: 709
Period size: 228 Copynumber: 2.2 Consensus size: 228
49611762 AGTTGAGGCT
* * * * * *
49611772 ACAAGTCTTATCTCACTG-AGGTTGCAGTAGAGTGGGCTGAAGATAACAAGTCTTATCTCCCTGA
1 ACAAGTCTTATCTCCCTGAAGG-TGCAGTGGAGTAGACTGTAGATAACAAGTCTTATCTACCTGA
* *
49611836 AGTTACAGTGGAGTAGACTGAAGATAACAAACCTTATCTCCCTAAAGTTGCAGTGGGGCAAGTTG
65 AGTTACAGTGGAGCAAACTGAAGATAACAAACCTTATCTCCCTAAAGTTGCAGTGGGGCAAGTTG
* * * *
49611901 AAGATATAAGTCCTATCTCCCTGAATTTGTAGTGGAGCAGATTAAAACGACGAATCATATACCTC
130 AAGATACAAGTCCTATCTCCCTAAATTTGCAGTGGAGCAGATTAAAACAACGAATCATATACCTC
*
49611966 TAAAGTTGCA-ATAGGTCAGATTAAATCTATCATA
195 TAAAGTTGCAGA-AAGTCAGATTAAATCTATCATA
* *
49612000 ACAAGTCTTATCTCCCTGAAGGTGCAGTGGAGTAGACTGTAGCTAACAAGTCTTATCTACTTGAA
1 ACAAGTCTTATCTCCCTGAAGGTGCAGTGGAGTAGACTGTAGATAACAAGTCTTATCTACCTGAA
* * *
49612065 GTTGCAGTGGAGCAAACTGATGATAACAAACCTTATCTCCCTGAAGTTGCAGTGGGGCAAGTTGA
66 GTTACAGTGGAGCAAACTGAAGATAACAAACCTTATCTCCCTAAAGTTGCAGTGGGGCAAGTTGA
* ** * *
49612130 AGATACAAGTCTTATCTCCCTAAATTTGCAGTGGAGTGGATTAAAACAATGAATCCTATACCTCT
131 AGATACAAGTCCTATCTCCCTAAATTTGCAGTGGAGCAGATTAAAACAACGAATCATATACCTCT
*
49612195 GAAGTTGCAGAAAGTCAGATTAAATCTATCATA
196 AAAGTTGCAGAAAGTCAGATTAAATCTATCATA
* * * * *
49612228 ACAAGTTTTATCTCCCTAAAGTTGTAGTGGAGCAGACTGTAGATA
1 ACAAGTCTTATCTCCCTGAAGGTGCAGTGGAGTAGACTGTAGATA
49612273 GTGGATCTTA
Statistics
Matches: 241, Mismatches: 30, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
228 237 0.98
229 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (228 bp):
ACAAGTCTTATCTCCCTGAAGGTGCAGTGGAGTAGACTGTAGATAACAAGTCTTATCTACCTGAA
GTTACAGTGGAGCAAACTGAAGATAACAAACCTTATCTCCCTAAAGTTGCAGTGGGGCAAGTTGA
AGATACAAGTCCTATCTCCCTAAATTTGCAGTGGAGCAGATTAAAACAACGAATCATATACCTCT
AAAGTTGCAGAAAGTCAGATTAAATCTATCATA
Found at i:49613839 original size:3 final size:3
Alignment explanation
Indices: 49613831--49613866 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
49613821 AATAAATTTA
49613831 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
49613867 TACTCCTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:49619073 original size:3 final size:3
Alignment explanation
Indices: 49619065--49619102 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
49619055 TATTAGTTTG
49619065 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
49619103 AAGAAAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:49623571 original size:25 final size:25
Alignment explanation
Indices: 49623543--49623592 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
49623533 GAGCGTCCCA
* *
49623543 TTATTTAGCTCTTATGAGCATCTCG
1 TTATATAGCTCTCATGAGCATCTCG
* *
49623568 TTATATGGCTCTCATGAGCTTCTCG
1 TTATATAGCTCTCATGAGCATCTCG
49623593 ATAATTGGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (25 bp):
TTATATAGCTCTCATGAGCATCTCG
Found at i:49623605 original size:25 final size:25
Alignment explanation
Indices: 49623573--49623785 Score: 156
Period size: 25 Copynumber: 8.6 Consensus size: 25
49623563 TCTCGTTATA
*
49623573 TGGCTCTCATGAGCTTCTCGATAAT
1 TGGCTCTCATGAGCTTCCCGATAAT
* * * *
49623598 TGGGTCTCTTGAGCTTCCCGTTTA-
1 TGGCTCTCATGAGCTTCCCGATAAT
**
49623622 TGGCTCGT-ATGAGCTTCTTGATAAT
1 TGGCTC-TCATGAGCTTCCCGATAAT
49623647 TGGCTCTCCA-GAGCTTCCCGATAAT
1 TGGCTCT-CATGAGCTTCCCGATAAT
**
49623672 TGGCTCTCATGAGCTTCATGATTAA-
1 TGGCTCTCATGAGCTTCCCGA-TAAT
*
49623697 TGGCTCTC-CGAAGCTTCCCGATAA-
1 TGGCTCTCATG-AGCTTCCCGATAAT
* * * *
49623721 TGGCTCACATGAGCTTTCTGATTA-
1 TGGCTCTCATGAGCTTCCCGATAAT
* * *
49623745 TAGCTCTTATGAGCTTCCCGTTACA-
1 TGGCTCTCATGAGCTTCCCGATA-AT
49623770 TGGCTCAT-ATGAGCTT
1 TGGCTC-TCATGAGCTT
49623786 TCTATTCCCT
Statistics
Matches: 147, Mismatches: 31, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
24 56 0.38
25 86 0.59
26 5 0.03
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.35
Consensus pattern (25 bp):
TGGCTCTCATGAGCTTCCCGATAAT
Found at i:49623725 original size:74 final size:73
Alignment explanation
Indices: 49623572--49623785 Score: 191
Period size: 74 Copynumber: 2.9 Consensus size: 73
49623562 ATCTCGTTAT
* * * * * *
49623572 ATGGCTCTCATGAGCTTCTCGATAATTGGGTCTCTTGAGCTTCCCGTTTATGGCTCGTATGAGCT
1 ATGGCTCTCATGAGCTTCCCGATAATTGGCTCTCATGAGCTTCACGTTAATGGCTCGTACGAGCT
**
49623637 TCTTGATA
66 TCCCGATA
* *
49623645 ATTGGCTCTCCA-GAGCTTCCCGATAATTGGCTCTCATGAGCTTCATGATTAATGGCTC-TCCGA
1 A-TGGCTCT-CATGAGCTTCCCGATAATTGGCTCTCATGAGCTTCACG-TTAATGGCTCGTACG-
49623708 AGCTTCCCGATA
62 AGCTTCCCGATA
* * * * * * * * *
49623720 ATGGCTCACATGAGCTTTCTGATTA-TAGCTCTTATGAGCTTCCCGTTACATGGCTCATATGAGC
1 ATGGCTCTCATGAGCTTCCCGATAATTGGCTCTCATGAGCTTCACGTTA-ATGGCTCGTACGAGC
49623784 TT
65 TT
49623786 TCTATTCCCT
Statistics
Matches: 114, Mismatches: 20, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
72 3 0.03
73 31 0.27
74 58 0.51
75 22 0.19
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (73 bp):
ATGGCTCTCATGAGCTTCCCGATAATTGGCTCTCATGAGCTTCACGTTAATGGCTCGTACGAGCT
TCCCGATA
Found at i:49623788 original size:49 final size:47
Alignment explanation
Indices: 49623550--49623785 Score: 185
Period size: 49 Copynumber: 4.8 Consensus size: 47
49623540 CCATTATTTA
* *
49623550 GCTCTTATGAGCATCTCGTTATATGGCTCTCATGAGCTTCTCGATAATTG
1 GCTCTTATGAGCTTCCCGTTA-ATGGCTCT-ATGAGCTTCT-GATAATTG
* *
49623600 GGTCTCT-TGAGCTTCCCGTTTATGGCTCGTATGAGCTTCTTGATAATTG
1 GCTCT-TATGAGCTTCCCGTTAATGGCTC-TATGAGCTTC-TGATAATTG
* *
49623649 GCTCTCCA-GAGCTTCCCGATAATTGGCTCTCATGAGCTTCATGATTAA-TG
1 GCTCT-TATGAGCTTCCCGTTAA-TGGCTCT-ATGAGCTTC-TGA-TAATTG
** * * * *
49623699 GCTC-TCCGAAGCTTCCCGATAATGGCTCACATGAGCTTTCTGATTA-TA
1 GCTCTTATG-AGCTTCCCGTTAATGGCTC-TATGAGC-TTCTGATAATTG
49623747 GCTCTTATGAGCTTCCCGTTACATGGCTCATATGAGCTT
1 GCTCTTATGAGCTTCCCGTTA-ATGGCTC-TATGAGCTT
49623786 TCTATTCCCT
Statistics
Matches: 155, Mismatches: 18, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
48 20 0.13
49 74 0.48
50 57 0.37
51 4 0.03
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (47 bp):
GCTCTTATGAGCTTCCCGTTAATGGCTCTATGAGCTTCTGATAATTG
Found at i:49635528 original size:20 final size:20
Alignment explanation
Indices: 49635470--49635530 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
49635460 AATATTAACC
49635470 CATAAT-ATAATATTGTTATA
1 CATAATAATAA-ATTGTTATA
* ***
49635490 -ATTAATAACAAAAAATTATA
1 CA-TAATAATAAATTGTTATA
49635510 CATAATAATAAATTGTTATA
1 CATAATAATAAATTGTTATA
49635530 C
1 C
49635531 GCAATTTATT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
19 1 0.03
20 25 0.83
21 4 0.13
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (20 bp):
CATAATAATAAATTGTTATA
Found at i:49643641 original size:12 final size:12
Alignment explanation
Indices: 49643624--49643650 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
49643614 TGTCTGAAAC
49643624 TGCCTTTTATGA
1 TGCCTTTTATGA
49643636 TGCCTTTTATGA
1 TGCCTTTTATGA
49643648 TGC
1 TGC
49643651 ACTCGTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.48
Consensus pattern (12 bp):
TGCCTTTTATGA
Found at i:49651701 original size:32 final size:32
Alignment explanation
Indices: 49651665--49651730 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
49651655 CATTTTGGTA
49651665 TTGAACTTGGGTTCCAAGGTTCAAATTACTAC
1 TTGAACTTGGGTTCCAAGGTTCAAATTACTAC
49651697 TTGAACTTGGGTTCCAAGGTTCAAATTACTAC
1 TTGAACTTGGGTTCCAAGGTTCAAATTACTAC
49651729 TT
1 TT
49651731 AAAGGGTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (32 bp):
TTGAACTTGGGTTCCAAGGTTCAAATTACTAC
Found at i:49651738 original size:29 final size:31
Alignment explanation
Indices: 49651673--49651738 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 31
49651663 TATTGAACTT
*
49651673 GGGTTCCAAGGTTCAAATTACTACTTGAACTT
1 GGGTTCCAAGGTTCAAATTACTACTTGAAC-A
49651705 GGGTTCCAAGGTTCAAATTACTACTT-AA-A
1 GGGTTCCAAGGTTCAAATTACTACTTGAACA
49651734 GGGTT
1 GGGTT
49651739 GCTTTTTGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 5 0.15
31 2 0.06
32 26 0.79
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (31 bp):
GGGTTCCAAGGTTCAAATTACTACTTGAACA
Found at i:49652386 original size:13 final size:12
Alignment explanation
Indices: 49652368--49652418 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
49652358 TCTATTCAAT
49652368 TCAATTAAATAAA
1 TCAATTAAA-AAA
*
49652381 TCAATTTAAAAAT
1 TCAA-TTAAAAAA
*
49652394 TC-ATGAAAAAAA
1 TCAAT-TAAAAAA
49652406 TCAATTAAAAAA
1 TCAATTAAAAAA
49652418 T
1 T
49652419 TCATGAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
11 1 0.03
12 15 0.48
13 10 0.32
14 5 0.16
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (12 bp):
TCAATTAAAAAA
Found at i:49652403 original size:12 final size:12
Alignment explanation
Indices: 49652388--49652428 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
49652378 AAATCAATTT
49652388 AAAAATTCATGA
1 AAAAATTCATGA
* *
49652400 AAAAAATCAATTA
1 AAAAATTC-ATGA
49652413 AAAAATTCATGA
1 AAAAATTCATGA
49652425 AAAA
1 AAAA
49652429 TAAAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (12 bp):
AAAAATTCATGA
Found at i:49652408 original size:25 final size:25
Alignment explanation
Indices: 49652378--49652428 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
49652368 TCAATTAAAT
*
49652378 AAATCAATTTAAAAATTCATGAAAA
1 AAATCAATTAAAAAATTCATGAAAA
49652403 AAATCAATTAAAAAATTCATGAAAA
1 AAATCAATTAAAAAATTCATGAAAA
49652428 A
1 A
49652429 TAAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.63, C:0.08, G:0.04, T:0.25
Consensus pattern (25 bp):
AAATCAATTAAAAAATTCATGAAAA
Found at i:49652428 original size:13 final size:13
Alignment explanation
Indices: 49652388--49652428 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
49652378 AAATCAATTT
49652388 AAAAATTCATGAA
1 AAAAATTCATGAA
*
49652401 AAAAA-TCAAT-TA
1 AAAAATTC-ATGAA
49652413 AAAAATTCATGAA
1 AAAAATTCATGAA
49652426 AAA
1 AAA
49652429 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (13 bp):
AAAAATTCATGAA
Found at i:49653324 original size:14 final size:14
Alignment explanation
Indices: 49653305--49653332 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49653295 TAACAACTTT
49653305 CTAACTGCTTAATA
1 CTAACTGCTTAATA
49653319 CTAACTGCTTAATA
1 CTAACTGCTTAATA
49653333 TTCATCCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
CTAACTGCTTAATA
Found at i:49658381 original size:14 final size:14
Alignment explanation
Indices: 49658362--49658390 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
49658352 TAACAACTTT
49658362 CTAACTGCTTAATA
1 CTAACTGCTTAATA
49658376 CTAACTGCTTAATA
1 CTAACTGCTTAATA
49658390 C
1 C
49658391 AGCTTTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (14 bp):
CTAACTGCTTAATA
Found at i:49662826 original size:30 final size:29
Alignment explanation
Indices: 49662783--49662849 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
49662773 ATAAATGTTT
* *
49662783 TAAATATATATAAATAAATTT-AAAAATATA
1 TAAAAATACATAAAT-AATTTCAAAAA-ATA
*
49662813 TAAAAATACATAAATATTTTCAAAAAATA
1 TAAAAATACATAAATAATTTCAAAAAATA
*
49662842 TAATAATA
1 TAAAAATA
49662850 AATTTAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (29 bp):
TAAAAATACATAAATAATTTCAAAAAATA
Found at i:49662843 original size:49 final size:51
Alignment explanation
Indices: 49662757--49662857 Score: 145
Period size: 49 Copynumber: 2.0 Consensus size: 51
49662747 AAAATCAAAG
* *
49662757 AAATATATAAAAACACATAAATGTTTTAAATATATAT-A-AATAAATTTAA
1 AAATATATAAAAACACATAAATATTTTAAATAAATATAATAATAAATTTAA
*
49662806 AAATATATAAAAATACATAAATATTTTCAAA-AAATATAATAATAAATTTAA
1 AAATATATAAAAACACATAAATATTTT-AAATAAATATAATAATAAATTTAA
49662857 A
1 A
49662858 TTTCATATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
49 30 0.65
50 4 0.09
51 12 0.26
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (51 bp):
AAATATATAAAAACACATAAATATTTTAAATAAATATAATAATAAATTTAA
Found at i:49662976 original size:95 final size:94
Alignment explanation
Indices: 49662871--49663085 Score: 269
Period size: 94 Copynumber: 2.3 Consensus size: 94
49662861 CATATAACAA
* *
49662871 TAATTGTTTTTTTTTTGAAAAAGTTTGAAGACCTTTTTTG-TGCATTTT-AGTAGTTCAAGTACC
1 TAATTG-TTTTTTTTTGAAAAAGTTTGAAGACC-TTTTTGATGCATTTTGA-AAGTACAAGTACC
* * *
49662934 C-ATTGAGTGCAAAAAATTAAAAG-GCAAGGGCT
63 CAATTGAATACAAAAAA--AAAAGAGCAAGAGCT
** *
49662966 TAATTGTTTTTTTTTGAAAAAAATTGAAGGCCTTTTTGATGCATTTTGAAAGTACAAGTACCCAA
1 TAATTGTTTTTTTTTGAAAAAGTTTGAAGACCTTTTTGATGCATTTTGAAAGTACAAGTACCCAA
49663031 TTGAATACAAAAAAAAAAGAGCAAGAGCT
66 TTGAATACAAAAAAAAAAGAGCAAGAGCT
*
49663060 TAATTG-ATTTTTTTGAAAAAGTTTGA
1 TAATTGTTTTTTTTTGAAAAAGTTTGA
49663086 GGGCTTTTTA
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
93 28 0.27
94 57 0.54
95 20 0.19
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (94 bp):
TAATTGTTTTTTTTTGAAAAAGTTTGAAGACCTTTTTGATGCATTTTGAAAGTACAAGTACCCAA
TTGAATACAAAAAAAAAAGAGCAAGAGCT
Found at i:49674692 original size:231 final size:231
Alignment explanation
Indices: 49674288--49674756 Score: 868
Period size: 231 Copynumber: 2.0 Consensus size: 231
49674278 AAATACTATG
49674288 GAATTGAATGGATTATAAATGGTTGAATGTTATATGATATAGGTTAGATTTGTATAAATTGAACT
1 GAATTGAATGGATTATAAATGGTTGAATGTTATATGATATAGGTTAGATTTGTATAAATTGAACT
*
49674353 GGTATGATTTAGGTACCATTTTGAGGTACATTAGTTTAGTTGAATGGAAATTAGTGGATGTTATG
66 GGTATGATTTAGGTACCATTTTGAGGTACATTAGTGTAGTTGAATGGAAATTAGTGGATGTTATG
49674418 ATTGATTATGAAATTGATATGTATATATTGATATTACATGGTTAAAATGTATATGAATTGCTATT
131 ATTGATTATGAAATTGATATGTATATATTGATATTACATGGTTAAAATGTATATGAATTGCTATT
*
49674483 TGAAATATGAAAAA-GTGTATACAGCTACAAAGGTT
196 TGAAATATGAAAAACATGTATACAGCTACAAAGGTT
* * *
49674518 GAAATTGAATGGATTATAAATGGTTGCATGTTATATGATATGGGTTAGATTTGTATAAATTGAAT
1 G-AATTGAATGGATTATAAATGGTTGAATGTTATATGATATAGGTTAGATTTGTATAAATTGAAC
49674583 TGGTATGATTTAGGTACCATTTTGAGGTACATTAGTGTAGTTGAATGGAAATTAGTGGATGTTAT
65 TGGTATGATTTAGGTACCATTTTGAGGTACATTAGTGTAGTTGAATGGAAATTAGTGGATGTTAT
*
49674648 GATTGATTATGAAATTGATATGTATATGTTGATATTACATGGTTAAAATGTATATGAATTGCTAT
130 GATTGATTATGAAATTGATATGTATATATTGATATTACATGGTTAAAATGTATATGAATTGCTAT
49674713 TTGAAATATGAAAAACATGTATACAGCTACAAAGGTT
195 TTGAAATATGAAAAACATGTATACAGCTACAAAGGTT
49674750 GAATTGA
1 GAATTGA
49674757 TACGAATTCG
Statistics
Matches: 231, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
230 1 0.00
231 209 0.90
232 21 0.09
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (231 bp):
GAATTGAATGGATTATAAATGGTTGAATGTTATATGATATAGGTTAGATTTGTATAAATTGAACT
GGTATGATTTAGGTACCATTTTGAGGTACATTAGTGTAGTTGAATGGAAATTAGTGGATGTTATG
ATTGATTATGAAATTGATATGTATATATTGATATTACATGGTTAAAATGTATATGAATTGCTATT
TGAAATATGAAAAACATGTATACAGCTACAAAGGTT
Found at i:49675659 original size:2 final size:2
Alignment explanation
Indices: 49675640--49675696 Score: 89
Period size: 2 Copynumber: 28.5 Consensus size: 2
49675630 GTTCTTGTGA
*
49675640 AT AT GT AT AT AT GA- 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
49675682 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
49675697 ATTGGAAGTG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 1 0.02
2 49 0.96
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:49689103 original size:126 final size:126
Alignment explanation
Indices: 49688944--49689188 Score: 429
Period size: 126 Copynumber: 1.9 Consensus size: 126
49688934 CTGTAGTAAA
* * *
49688944 AGAGCTTCTTTCAGTACTTTTGCTGACATTGCATCCT-GCTTGAAGCGTTTTTGACACTATTTGC
1 AGAGCTTCTTTCAGTACTTTTGCTAACACTGCATCCTAG-TTAAAGCGTTTTTGACACTATTTGC
*
49689008 TCAGAAACATCTTCTCAAAATTATTTTTTCAGAAACTACTGTAGCAAAAGAGCGTTTACGTG
65 TCAGAAACATCTTCTCAAAATTATTTTTTCAAAAACTACTGTAGCAAAAGAGCGTTTACGTG
49689070 AGAGCTTCTTTCAGTACTTTTGCTAACACTGCATCCTAGTTAAAGCGTTTTTGACACTATTTGCT
1 AGAGCTTCTTTCAGTACTTTTGCTAACACTGCATCCTAGTTAAAGCGTTTTTGACACTATTTGCT
*
49689135 CAGAAACGTCTTCTCAAAATTATTTTTTCAAAAACTACTGTAGCAAAAGAGCGT
66 CAGAAACATCTTCTCAAAATTATTTTTTCAAAAACTACTGTAGCAAAAGAGCGT
49689189 CCACATGGGA
Statistics
Matches: 113, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
126 112 0.99
127 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (126 bp):
AGAGCTTCTTTCAGTACTTTTGCTAACACTGCATCCTAGTTAAAGCGTTTTTGACACTATTTGCT
CAGAAACATCTTCTCAAAATTATTTTTTCAAAAACTACTGTAGCAAAAGAGCGTTTACGTG
Found at i:49689399 original size:98 final size:95
Alignment explanation
Indices: 49689239--49689420 Score: 294
Period size: 98 Copynumber: 1.9 Consensus size: 95
49689229 AGTAACCCTA
* * *
49689239 AACCCCAAACCCTAATTTATTTGATTTTTCTTTAAAAACCCAAAACACTAAATCCTAATCTAATT
1 AACCCCAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCAAAACACTAAACCCCAATCTAA--
49689304 TTTTTTAAAATTTATAATTAATTTACTCAAGT
64 TTTTTTAAAATTTATAATTAATTTACTCAAGT
49689336 AACCCCAAACCCTAATTTATTTGATTTTTTCCTTAAAAA-CCATAAACACTAAACCCCAATCTAA
1 AACCCCAAACCCTAATTTATTTGA-TTTTTCCTTAAAAACCCA-AAACACTAAACCCCAATCTAA
49689400 TTTTTTAAAATTTATAATTAA
64 TTTTTTAAAATTTATAATTAA
49689421 CCTAAACCCT
Statistics
Matches: 80, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
96 21 0.26
97 27 0.34
98 32 0.40
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (95 bp):
AACCCCAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCAAAACACTAAACCCCAATCTAATT
TTTTAAAATTTATAATTAATTTACTCAAGT
Done.