Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 46 of 213
Found at i:12358891 original size:29 final size:29
Alignment explanation
Indices: 12358829--12358892 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
12358819 TATGATTTCT
*
12358829 ATTTTTATATATTTTTATAATTTATTAGA
1 ATTTTTATATATTTGTATAATTTATTAGA
* *
12358858 GTTTTTATATTATTTGTA-AGTTT-TTATGA
1 ATTTTTATA-TATTTGTATAATTTATTA-GA
12358887 ATTTTT
1 ATTTTT
12358893 TCAAGCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.10
29 19 0.66
30 7 0.24
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (29 bp):
ATTTTTATATATTTGTATAATTTATTAGA
Found at i:12359061 original size:10 final size:10
Alignment explanation
Indices: 12358957--12359063 Score: 71
Period size: 10 Copynumber: 10.9 Consensus size: 10
12358947 TTTTTATTTT
12358957 TATTTTTATA
1 TATTTTTATA
12358967 TATTTTTA-A
1 TATTTTTATA
* *
12358976 -GTTTTTATG
1 TATTTTTATA
* *
12358985 GATTCTTTAAA
1 TATT-TTTATA
*
12358996 TATTTTTTTA
1 TATTTTTATA
*
12359006 TCATTTTTCTA
1 T-ATTTTTATA
12359017 TATTTTT-TA
1 TATTTTTATA
** *
12359026 TAAGTTTATT
1 TATTTTTATA
12359036 TATTTATTA-A
1 TATTT-TTATA
12359046 TA-TTTTATA
1 TATTTTTATA
12359055 TATTTTTAT
1 TATTTTTAT
12359064 GATTATATGA
Statistics
Matches: 74, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
8 9 0.12
9 13 0.18
10 33 0.45
11 19 0.26
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (10 bp):
TATTTTTATA
Found at i:12364480 original size:17 final size:18
Alignment explanation
Indices: 12364449--12364482 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12364439 CTCTAATTTA
*
12364449 CATTATAATTTAGTAAAC
1 CATTATAATTAAGTAAAC
12364467 CATTA-AATTAAGTAAA
1 CATTATAATTAAGTAAA
12364483 TAGTTAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (18 bp):
CATTATAATTAAGTAAAC
Found at i:12365543 original size:24 final size:24
Alignment explanation
Indices: 12365511--12365579 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
12365501 GGGTAGGCTT
*
12365511 TGTGACTGCATCTGTATCTGAATC
1 TGTGTCTGCATCTGTATCTGAATC
*** *
12365535 TGTGTCTGCATCCACATTTGAATC
1 TGTGTCTGCATCTGTATCTGAATC
* * *
12365559 TGCGTCTACATTTGTATCTGA
1 TGTGTCTGCATCTGTATCTGA
12365580 TTCTAAATAT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (24 bp):
TGTGTCTGCATCTGTATCTGAATC
Found at i:12365560 original size:18 final size:18
Alignment explanation
Indices: 12365539--12365578 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12365529 TGAATCTGTG
12365539 TCTGCATCCACATTTGAA
1 TCTGCATCCACATTTGAA
* * *
12365557 TCTGCGTCTACATTTGTA
1 TCTGCATCCACATTTGAA
12365575 TCTG
1 TCTG
12365579 ATTCTAAATA
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:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (18 bp):
TCTGCATCCACATTTGAA
Found at i:12365633 original size:24 final size:24
Alignment explanation
Indices: 12365605--12365660 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
12365595 CGTATCTAAT
*
12365605 TATGAAAATACATTTGACTCTGTA
1 TATGAAAATACATTTGAATCTGTA
* **
12365629 TATGAGAATATGTTTGAATCTGTA
1 TATGAAAATACATTTGAATCTGTA
*
12365653 TCTGAAAA
1 TATGAAAA
12365661 CATATATGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (24 bp):
TATGAAAATACATTTGAATCTGTA
Found at i:12368140 original size:12 final size:12
Alignment explanation
Indices: 12368123--12368147 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12368113 CTCACGTCAG
12368123 TTTTCTTTCTTT
1 TTTTCTTTCTTT
12368135 TTTTCTTTCTTT
1 TTTTCTTTCTTT
12368147 T
1 T
12368148 CCTCTTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:12368753 original size:41 final size:41
Alignment explanation
Indices: 12368695--12368772 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
12368685 GTGTAGTAGG
* *
12368695 TCGTGTGGTTCACATGAGCTTGTGTTAGGCCATGTGGAAGC
1 TCGTGTGGGTCACATGAGCTTATGTTAGGCCATGTGGAAGC
*
12368736 TCGTGTGGGTCATATGAGCTTATGTTAGGCCATGTGG
1 TCGTGTGGGTCACATGAGCTTATGTTAGGCCATGTGG
12368773 GCCACACGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.17, C:0.15, G:0.35, T:0.33
Consensus pattern (41 bp):
TCGTGTGGGTCACATGAGCTTATGTTAGGCCATGTGGAAGC
Found at i:12368785 original size:29 final size:29
Alignment explanation
Indices: 12368753--12368808 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
12368743 GGTCATATGA
12368753 GCTTATGTTAGGCCATGTGGGCCACACGG
1 GCTTATGTTAGGCCATGTGGGCCACACGG
* ***
12368782 GCTTGTGTTAGGTTGTGTGGGCCACAC
1 GCTTATGTTAGGCCATGTGGGCCACAC
12368809 AGACTGGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.14, C:0.21, G:0.36, T:0.29
Consensus pattern (29 bp):
GCTTATGTTAGGCCATGTGGGCCACACGG
Found at i:12373040 original size:18 final size:17
Alignment explanation
Indices: 12373011--12373053 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
12373001 TTGTTAACTT
12373011 TGTTGATGTCACATACA
1 TGTTGATGTCACATACA
*
12373028 TGTTGATTGTCACATAGA
1 TGTTGA-TGTCACATACA
12373046 TGTT-ATGT
1 TGTTGATGT
12373054 AAGCAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 7 0.29
18 14 0.58
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.42
Consensus pattern (17 bp):
TGTTGATGTCACATACA
Found at i:12388155 original size:40 final size:40
Alignment explanation
Indices: 12388078--12388155 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
12388068 ACAAATTCAG
*
12388078 AATAAATAATCAAAATTTAAATTTAAAATATTTTTTTACA
1 AATAAATAATCAAAATTTAAATTTAAAATATTATTTTACA
* *
12388118 AATAAATAATTAATAA-TTAATATTTTAAATA-TATTTTA
1 AATAAATAATCAA-AATTTAA-ATTTAAAATATTATTTTA
12388156 AATTTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 22 0.67
41 11 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (40 bp):
AATAAATAATCAAAATTTAAATTTAAAATATTATTTTACA
Found at i:12393202 original size:44 final size:42
Alignment explanation
Indices: 12393139--12393255 Score: 130
Period size: 44 Copynumber: 2.7 Consensus size: 42
12393129 TATGTGTTGT
* *
12393139 CGTGTAAGACCACATCTGGGACGTTGGCATCGACT-TGTGATTTA
1 CGTGTAAGACCACGTCTGGGACG-TGGCATC-AATATGTGA-TTA
*
12393183 CGTGTAAGACC-CTGTCTGGGATAGTGGCATCAATATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGA-CGTGGCATCAATATGTGATTA
*
12393226 CATGTAAGACCACGTCTGGGACGATGGCAT
1 CGTGTAAGACCACGTCTGGGACG-TGGCAT
12393256 TGTACGAAAC
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
42 1 0.02
43 30 0.48
44 31 0.49
45 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACGTGGCATCAATATGTGATTA
Found at i:12393246 original size:43 final size:44
Alignment explanation
Indices: 12393141--12393255 Score: 121
Period size: 43 Copynumber: 2.6 Consensus size: 44
12393131 TGTGTTGTCG
* * * *
12393141 TGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGATTTACG
1 TGTAAGACCACGTCTGGGAAGTTGGCATCGAATTGTGATTTACA
12393185 TGTAAGACC-CTGTCTGGGATAG-TGGCATC-AATATGTGA-TTACA
1 TGTAAGACCAC-GTCTGGGA-AGTTGGCATCGAAT-TGTGATTTACA
* *
12393228 TGTAAGACCACGTCTGGGACGATGGCAT
1 TGTAAGACCACGTCTGGGAAGTTGGCAT
12393256 TGTACGAAAC
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
42 1 0.02
43 30 0.49
44 29 0.48
45 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGAAGTTGGCATCGAATTGTGATTTACA
Found at i:12394798 original size:23 final size:23
Alignment explanation
Indices: 12394763--12394953 Score: 195
Period size: 23 Copynumber: 8.2 Consensus size: 23
12394753 TGGTGCATAA
*
12394763 ATGCTGTCCAATTTTGTATATAT
1 ATGCTGTCAAATTTTGTATATAT
* * * *
12394786 TTGCTGTCAAATTTAGTGTATAA
1 ATGCTGTCAAATTTTGTATATAT
*
12394809 ATGCTGTCCAATTTTGTATATAT
1 ATGCTGTCAAATTTTGTATATAT
* * *
12394832 ATGCTGTCAAATCTTGGTGTATAA
1 ATGCTGTCAAAT-TTTGTATATAT
*
12394856 ATGCTGTCCAAA-TTGGTATATAT
1 ATGCTGT-CAAATTTTGTATATAT
** * * * *
12394879 ATGCTACCCAATTTGGTGTATAA
1 ATGCTGTCAAATTTTGTATATAT
*
12394902 ATGCTGTCCAATTTTGTATATAT
1 ATGCTGTCAAATTTTGTATATAT
12394925 ATGCTGTCAAATTTTGGTATATAT
1 ATGCTGTCAAATTTT-GTATATAT
12394949 ATGCT
1 ATGCT
12394954 CGCAACTCAA
Statistics
Matches: 137, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
22 3 0.02
23 102 0.74
24 28 0.20
25 4 0.03
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (23 bp):
ATGCTGTCAAATTTTGTATATAT
Found at i:12394809 original size:46 final size:46
Alignment explanation
Indices: 12394751--12394953 Score: 298
Period size: 46 Copynumber: 4.4 Consensus size: 46
12394741 GTTATCCAAT
* *
12394751 TTTGGTGCATAAATGCTGTCCAATTTTGTATATATTTGCTGTCAAA
1 TTTGGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
*
12394797 TTTAGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
1 TTTGGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
* * ** *
12394843 TCTTGGTGTATAAATGCTGTCCAAATTGGTATATATATGCTACCCAA
1 T-TTGGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
12394890 TTTGGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
1 TTTGGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
* *
12394936 TTTTGGTATATATATGCT
1 -TTTGGTGTATAAATGCT
12394954 CGCAACTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
46 84 0.60
47 55 0.40
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (46 bp):
TTTGGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
Found at i:12394911 original size:93 final size:93
Alignment explanation
Indices: 12394752--12394953 Score: 305
Period size: 93 Copynumber: 2.2 Consensus size: 93
12394742 TTATCCAATT
* * * * **
12394752 TTGGTGCATAAATGCTGTCCAATTTTGTATATATTTGCTGTCAAATTTAGTGTATAAATGCTGTC
1 TTGGTGTATAAATGCTGTCCAAATTGGTATATATATGCTACCAAATTTAGTGTATAAATGCTGTC
12394817 CAATTTTGTATATATATGCTGTCAAATC
66 CAATTTTGTATATATATGCTGTCAAATC
* *
12394845 TTGGTGTATAAATGCTGTCCAAATTGGTATATATATGCTACCCAATTTGGTGTATAAATGCTGTC
1 TTGGTGTATAAATGCTGTCCAAATTGGTATATATATGCTACCAAATTTAGTGTATAAATGCTGTC
*
12394910 CAATTTTGTATATATATGCTGTCAAATT
66 CAATTTTGTATATATATGCTGTCAAATC
* *
12394938 TTGGTATATATATGCT
1 TTGGTGTATAAATGCT
12394954 CGCAACTCAA
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 98 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (93 bp):
TTGGTGTATAAATGCTGTCCAAATTGGTATATATATGCTACCAAATTTAGTGTATAAATGCTGTC
CAATTTTGTATATATATGCTGTCAAATC
Found at i:12396071 original size:24 final size:25
Alignment explanation
Indices: 12396038--12396086 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
12396028 TGATAATTAT
*
12396038 TTTAGGATTTAATA-TTAAGATTTA
1 TTTAGAATTTAATATTTAAGATTTA
*
12396062 TTTAGAATTTAATATTTACGATTTA
1 TTTAGAATTTAATATTTAAGATTTA
12396087 AAATTCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (25 bp):
TTTAGAATTTAATATTTAAGATTTA
Found at i:12400467 original size:27 final size:27
Alignment explanation
Indices: 12400428--12400485 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
12400418 AAAGGTTTTT
12400428 AAATGACCGAAATACCCTCGAAG-GGTA
1 AAATGACCGAAATACCCT-GAAGAGGTA
* *
12400455 AAATGA-CGAAAATATCCTTAAGAGGTA
1 AAATGACCG-AAATACCCTGAAGAGGTA
12400482 AAAT
1 AAAT
12400486 TACCATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCTGAAGAGGTA
Found at i:12405923 original size:30 final size:30
Alignment explanation
Indices: 12405889--12405948 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
12405879 TCTTTCATTC
* * *
12405889 TTTGTATATTATTGTCTGGTGTGAACTTTA
1 TTTGTATACTATTGCCTGGTATGAACTTTA
*
12405919 TTTGTATACTATTGCCTGTTATGAACTTTA
1 TTTGTATACTATTGCCTGGTATGAACTTTA
12405949 GTCCAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.52
Consensus pattern (30 bp):
TTTGTATACTATTGCCTGGTATGAACTTTA
Found at i:12406295 original size:32 final size:33
Alignment explanation
Indices: 12406255--12406327 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
12406245 CAGTTTTTAT
12406255 AAAATATTTT-CAGAAAAT-T-TGCCAAACACTAG
1 AAAATATTTTACAG-AAATCTAT-CCAAACACTAG
* *
12406287 AAATTATTTTACAGAGATCTATCCAAACACTAG
1 AAAATATTTTACAGAAATCTATCCAAACACTAG
12406320 AAAATATT
1 AAAATATT
12406328 AACAGTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 12 0.34
33 22 0.63
34 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (33 bp):
AAAATATTTTACAGAAATCTATCCAAACACTAG
Found at i:12411250 original size:3 final size:3
Alignment explanation
Indices: 12411242--12411328 Score: 88
Period size: 3 Copynumber: 29.0 Consensus size: 3
12411232 CAAAATTTAG
* *
12411242 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
12411290 GTT ATT -TAT ATT ATT GTT -TT CATC ATC ATT ATT ATT ATT
1 ATT ATT AT-T ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
12411329 GTTTATGCAT
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
2 3 0.04
3 66 0.93
4 2 0.03
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:12412604 original size:30 final size:31
Alignment explanation
Indices: 12412559--12412627 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
12412549 CCAAATCGGG
* *
12412559 ATAACTCCACAATCTCATATTTTCTTCCTAAA
1 ATAACT-CACAATCTCACATTTTCCTCCTAAA
12412591 ATAACTC-CAATCTCACATTTTCCTCCTAAA
1 ATAACTCACAATCTCACATTTTCCTCCTAAA
*
12412621 ATCACTC
1 ATAACTC
12412628 GAGCACTCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 27 0.79
31 1 0.03
32 6 0.18
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.35
Consensus pattern (31 bp):
ATAACTCACAATCTCACATTTTCCTCCTAAA
Found at i:12435340 original size:2 final size:2
Alignment explanation
Indices: 12435329--12435360 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
12435319 TTTAGTTTTT
12435329 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
12435361 TTCCCGGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12437889 original size:42 final size:42
Alignment explanation
Indices: 12437842--12437927 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
12437832 AAGTAAATTT
12437842 AAATAAAATAATAATATTATTAATATGAATCAAACTACTTTC
1 AAATAAAATAATAATATTATTAATATGAATCAAACTACTTTC
12437884 AAATAAAATAATAATATTATTAATATGAATCAAACTACTTTC
1 AAATAAAATAATAATATTATTAATATGAATCAAACTACTTTC
12437926 AA
1 AA
12437928 TTATAAGCTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.35
Consensus pattern (42 bp):
AAATAAAATAATAATATTATTAATATGAATCAAACTACTTTC
Found at i:12439789 original size:15 final size:18
Alignment explanation
Indices: 12439748--12439789 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
12439738 TCTTTAATTT
12439748 TTTTGTA-AT-TTTATTA
1 TTTTGTATATATTTATTA
12439764 TTTTGTATATATTTATTA
1 TTTTGTATATATTTATTA
12439782 TTTT-TATA
1 TTTTGTATA
12439790 ATTCTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.29
17 6 0.25
18 11 0.46
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTTGTATATATTTATTA
Found at i:12440046 original size:32 final size:31
Alignment explanation
Indices: 12440010--12440069 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
12440000 AACCGTTAAA
* *
12440010 TTTTAACGGTCAAAAGTTCTAATTGGGTGTAT
1 TTTTAAAGGTCAAAAGTGC-AATTGGGTGTAT
* *
12440042 TTTTAAAGTTCAATAGTGCAATTGGGTG
1 TTTTAAAGGTCAAAAGTGCAATTGGGTG
12440070 CAAAAAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 9 0.38
32 15 0.62
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.40
Consensus pattern (31 bp):
TTTTAAAGGTCAAAAGTGCAATTGGGTGTAT
Found at i:12444546 original size:5 final size:5
Alignment explanation
Indices: 12444532--12444614 Score: 58
Period size: 5 Copynumber: 15.8 Consensus size: 5
12444522 GGCATATCTT
* * * * *
12444532 ATATC GTATC TTATC ATATC ATATTTC ATATA ATGTC ATATCAC ATTTC
1 ATATC ATATC ATATC ATATC ATA--TC ATATC ATATC ATAT--C ATATC
* * *
12444581 ATATC TTATC ATATC ATATC TTAAC ATATC ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATAT
12444615 TCTAACCCCA
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
5 50 0.85
7 9 0.15
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (5 bp):
ATATC
Found at i:12444570 original size:22 final size:22
Alignment explanation
Indices: 12444543--12444599 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
12444533 TATCGTATCT
12444543 TATCATATCATATTTCATATAA
1 TATCATATCATATTTCATATAA
* * **
12444565 TGTCATATCACATTTCATATCT
1 TATCATATCATATTTCATATAA
12444587 TATCATATCATAT
1 TATCATATCATAT
12444600 CTTAACATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.46
Consensus pattern (22 bp):
TATCATATCATATTTCATATAA
Found at i:12444599 original size:15 final size:15
Alignment explanation
Indices: 12444532--12444614 Score: 73
Period size: 15 Copynumber: 5.6 Consensus size: 15
12444522 GGCATATCTT
*
12444532 ATATCGTATCTTATC
1 ATATCATATCTTATC
12444547 ATATCATA--TT-TC
1 ATATCATATCTTATC
* * *
12444559 ATATAATGTCATATCAC
1 ATATCATATCTTAT--C
*
12444576 ATTTCATATCTTATC
1 ATATCATATCTTATC
*
12444591 ATATCATATCTTAAC
1 ATATCATATCTTATC
12444606 ATATCATAT
1 ATATCATAT
12444615 TCTAACCCCA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
12 8 0.15
13 2 0.04
14 1 0.02
15 31 0.58
17 11 0.21
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (15 bp):
ATATCATATCTTATC
Found at i:12448199 original size:27 final size:27
Alignment explanation
Indices: 12448147--12448199 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
12448137 TTATTTACAA
* *
12448147 TATTTTTATAATATTTTTATAGTTTCT
1 TATTTTTATAATATTTTCATACTTTCT
*
12448174 TATTTTT-TAATAATTTTCCTACTTTC
1 TATTTTTATAAT-ATTTTCATACTTTC
12448200 ATATCATACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (27 bp):
TATTTTTATAATATTTTCATACTTTCT
Found at i:12448349 original size:9 final size:9
Alignment explanation
Indices: 12448335--12448415 Score: 50
Period size: 9 Copynumber: 9.4 Consensus size: 9
12448325 AATCGATATG
12448335 TTTTATAAT
1 TTTTATAAT
12448344 TTTTAT-AT
1 TTTTATAAT
12448352 TAATTT-TAAT
1 T--TTTATAAT
12448362 TTTTA-AAT
1 TTTTATAAT
12448370 TTTTA-AAT
1 TTTTATAAT
12448378 TTTT-T-AT
1 TTTTATAAT
**
12448385 TTACA-ATAT
1 TTTTATA-AT
*
12448394 TTTTATAGT
1 TTTTATAAT
*
12448403 TTTTATAGT
1 TTTTATAAT
12448412 TTTT
1 TTTT
12448416 TTTTATTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
7 4 0.07
8 21 0.36
9 26 0.45
10 7 0.12
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTATAAT
Found at i:12448465 original size:244 final size:248
Alignment explanation
Indices: 12448027--12448473 Score: 581
Period size: 244 Copynumber: 1.8 Consensus size: 248
12448017 TACAACAACA
*
12448027 TAAATATGATATGAAGTTATATAAATTGCAATTATAAACTATGAGTTAATTGACATGTTTATAAT
1 TAAATATGATATGAAGTTATATAAATTGCAATTATAAACTATGAGTTAATCGACATGTTTATAAT
* * *
12448092 TTATAGCTTTTATTAGTTTTATATTAATTGTAATTTTTTAATTTTTTATTTACAATATTTTTATA
66 TTATA--TTATATTAATTTTATATT-ATTGTAATTTTTAAATTTTTTATTTACAATATTTTTATA
* * * *
12448157 ATATTTTTATAGTTTCTTATTTTTTAATAATTTTCCTACTTTCATATCATACGCCCCTTCTTTTA
128 ATATTTTTATAGTTTCTTATTTTTCAATAATTTTCCAACTCTCATATCATACGCCCCATCTTTTA
12448222 CCTAGTTAACATAGTTAATATCAGTAACTAATTGATTTTAGTTTCAATCAGTAACT
193 CCTAGTTAACATAGTTAATATCAGTAACTAATTGATTTTAGTTTCAATCAGTAACT
* * * * * *
12448278 TAAATATGATTTGTAGTTATATGAATTGCAATTATAAATTTTGAGTTAATCGATATGTTTTATAA
1 TAAATATGATATGAAGTTATATAAATTGCAATTATAAACTATGAGTTAATCGACATG-TTTATAA
12448343 -TT-T-TTATATTAATTTTA-ATT-TT-TAAATTTTTAAATTTTTTATTTACAATATTTTTAT-A
65 TTTATATTATATTAATTTTATATTATTGT-AATTTTTAAATTTTTTATTTACAATATTTTTATAA
* * * *
12448401 -GTTTTTATAGTTTTTTTTTATTTTTCAAT-ATTTTCCAAC-CTCATATCATGTCGCCTCATCTT
129 TATTTTTATAG---TTTCTTATTTTTCAATAATTTTCCAACTCTCATATCAT-ACGCCCCATCTT
12448463 TTACCTAGTTA
190 TTACCTAGTTA
12448474 GCACAAAGTT
Statistics
Matches: 172, Mismatches: 18, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
242 9 0.05
243 11 0.06
244 63 0.37
245 14 0.08
246 3 0.02
247 12 0.07
250 1 0.01
251 52 0.30
252 7 0.04
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.52
Consensus pattern (248 bp):
TAAATATGATATGAAGTTATATAAATTGCAATTATAAACTATGAGTTAATCGACATGTTTATAAT
TTATATTATATTAATTTTATATTATTGTAATTTTTAAATTTTTTATTTACAATATTTTTATAATA
TTTTTATAGTTTCTTATTTTTCAATAATTTTCCAACTCTCATATCATACGCCCCATCTTTTACCT
AGTTAACATAGTTAATATCAGTAACTAATTGATTTTAGTTTCAATCAGTAACT
Found at i:12453613 original size:17 final size:16
Alignment explanation
Indices: 12453591--12453662 Score: 81
Period size: 17 Copynumber: 4.1 Consensus size: 16
12453581 ATTTGAATCT
12453591 TTTTTTATTTATTTATG
1 TTTTTT-TTTATTTATG
12453608 TTTTTTTATTATTTATG
1 TTTTTTT-TTATTTATG
*
12453625 TTATTTTTTATTTGATG
1 TTTTTTTTTATTT-ATG
12453642 TTTTTTCTTATATTCTATG
1 TTTTTT-TT-TATT-TATG
12453661 TT
1 TT
12453663 GTATTAACAG
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.15
17 29 0.60
18 2 0.04
19 9 0.19
20 1 0.02
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.74
Consensus pattern (16 bp):
TTTTTTTTTATTTATG
Found at i:12453619 original size:21 final size:20
Alignment explanation
Indices: 12453590--12453633 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
12453580 GATTTGAATC
12453590 TTTTTTTATTTAT-TTATGTT
1 TTTTTTTATTTATGTTAT-TT
12453610 TTTTTATTATTTATGTTATTT
1 TTTTT-TTATTTATGTTATTT
12453631 TTT
1 TTT
12453634 ATTTGATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.80
Consensus pattern (20 bp):
TTTTTTTATTTATGTTATTT
Found at i:12462319 original size:125 final size:124
Alignment explanation
Indices: 12461921--12462487 Score: 744
Period size: 125 Copynumber: 4.5 Consensus size: 124
12461911 GATAAAATCA
* * * * * * *
12461921 AAGCAGGATGATTTATCAGAAGGATTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTAGAGT
1 AAGCA-GATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * *
12461986 ATGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAAATGCTTC
65 AGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * *
12462046 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGTTTTTACTACAGT
1 AAGCA-GATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * *
12462111 TGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTTTTAAAAAACGCTTC
65 AGGTCCT-GAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAG-TATAAAAAACGCTTC
* *
12462173 AAGCAAGATGCTTTATAAGAAGAATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGC-AGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
12462238 AGGTCCT-AAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAACAACGCTGC
65 AGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAA-AACGCTTC
* *
12462298 AAGCAGCATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAG
1 AAGCAG-ATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* *
12462362 TAGGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTC
64 TAGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * * * *
12462422 TAGCAGATGTTTTATGAGAAGAATTTGTGAAATCGTGCCCATGTGGACTCGCTTTTGCTACAGTA
1 AAGCAGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
12462487 G
66 G
12462488 CATGCTTAGG
Statistics
Matches: 390, Mismatches: 44, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
122 2 0.01
123 51 0.13
124 19 0.05
125 166 0.43
126 73 0.19
127 78 0.20
128 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (124 bp):
AAGCAGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
GGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
Found at i:12463707 original size:22 final size:22
Alignment explanation
Indices: 12463658--12464111 Score: 525
Period size: 22 Copynumber: 21.0 Consensus size: 22
12463648 TCAAATTATA
*
12463658 TTTAAGTTAAGGG-TTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
12463679 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * * *
12463701 TTAAATTTAAGTG-CTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
*
12463721 TTTAAGTTAAGGG-TTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
12463742 TTTAAGTTAAGGGTTTATGGAT
1 TTTAAGTTAAGGGTTTAGGGTT
*
12463764 TTTAATTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
*
12463785 TTTAATGTTAATGG-TTAGGGTT
1 TTTAA-GTTAAGGGTTTAGGGTT
12463807 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
12463829 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
12463851 TTTAAGTTACA-GGTTTAGGGTT
1 TTTAAGTTA-AGGGTTTAGGGTT
12463873 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
12463895 TTAAAGTTAAGGG-TTAGGATT
1 TTTAAGTTAAGGGTTTAGGGTT
*
12463916 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
12463938 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
12463960 TTTAATTTAAGAG-TTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
12463981 TTTAAGTTAAGGGTTTAGGATT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
12464003 TTAAAGTCAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* **
12464024 TTTAGGTTAAGGGGCTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
12464046 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * * **
12464068 TTTAGGTTTAGAGTTTAAGTTTT
1 TTTAAGTTAAGGGTTT-AGGGTT
*
12464091 TTTAATTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
12464112 AGGGGTAGGG
Statistics
Matches: 367, Mismatches: 54, Indels: 24
0.82 0.12 0.05
Matches are distributed among these distances:
20 15 0.04
21 108 0.29
22 230 0.63
23 14 0.04
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.45
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:12463722 original size:43 final size:43
Alignment explanation
Indices: 12463658--12464111 Score: 531
Period size: 43 Copynumber: 10.5 Consensus size: 43
12463648 TCAAATTATA
* *
12463658 TTTAAGTTAAGGGTTAAGGTTTTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * * *
12463701 TTAAATTTAAGTGCTAGGG-TTTTAAGTTAAGGG-TTAGTGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
12463742 TTTAAGTTAAGGGTTTATGGATTTTAATTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
*
12463785 TTTAATGTTAATGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAA-GTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
12463829 TTTAAGTTAAGGGGTTAGGGTTTTTAAGTTACA-GGTTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTA-AGGGTTTAGGGTT
* *
12463873 TTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGG-TTAGGATT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
12463916 TTTAGGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
12463960 TTTAATTTAAGAGTTAAGGTTTTTAAGTTAAGGGTTTAGGATT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * **
12464003 TTAAAGTCAAGGGTTAGGGTTTTTAGGTTAAGGGGCTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * **
12464046 TTTAAGTTAAGGGTTTAGGGTTTTTAGGTTTAGAGTTTAAGTTTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTT-AGGGTT
*
12464091 TTTAATTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
12464112 AGGGGTAGGG
Statistics
Matches: 350, Mismatches: 49, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
41 17 0.05
42 17 0.05
43 178 0.51
44 121 0.35
45 17 0.05
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.45
Consensus pattern (43 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
Found at i:12463811 original size:65 final size:64
Alignment explanation
Indices: 12463658--12464111 Score: 531
Period size: 65 Copynumber: 7.0 Consensus size: 64
12463648 TCAAATTATA
* * * * *
12463658 TTTAAGTTAAGGG-TTAAGGTTTTTAATTTAAGGGTTTAGGGTTTTAAATTTAAGTGCTAGGGT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTAGGGT
* * *
12463721 TTTAAGTTAAGGG-TTAGTGTTTTTAAGTTAAGGGTTTATGGATTTTAATTTAAGGGTTTAGGGT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTTAAGGG-TTAGGGT
* *
12463785 TTTAATGTTAATGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGGTTAGGG
1 TTTAA-GTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTTAA-GGGTTAGGG
12463849 TT
64 -T
* * *
12463851 TTTAAGTTACA-GGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGGTTAGGAT
1 TTTAAGTTA-AGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTAGG-G
12463915 T
64 T
* * * *
12463916 TTTAGGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTTAAGAGTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTT-AGGGT
* * * ** *
12463981 TTTAAGTTAAGGGTTTAGGATTTTAAAGTCAAGGG-TTAGGGTTTTTAGGTTAAGGGGCTAGGGT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTTAA-GGGTTAGGG-
12464045 T
64 T
* * * **
12464046 TTTAAGTTAAGGGTTTAGGGTTTTTAGGTTTAGAGTTTAAGTTTTTTTAATTTAAGGGTTAGGGT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTT-AGGGTTTTTAATTTAAGGGTTAGGGT
12464111 T
1 T
12464112 AGGGGTAGGG
Statistics
Matches: 337, Mismatches: 41, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
63 49 0.15
64 31 0.09
65 183 0.54
66 62 0.18
67 12 0.04
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.45
Consensus pattern (64 bp):
TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTAGGGT
Found at i:12464428 original size:21 final size:21
Alignment explanation
Indices: 12464404--12464450 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12464394 GCGGCGGTTG
*
12464404 TGGTTCTCCCAGT-GGGGATT
1 TGGTTCTCCCAGTAGGGCATT
*
12464424 CTGGTTCTTCCAGTAGGGCATT
1 -TGGTTCTCCCAGTAGGGCATT
12464446 TGGTT
1 TGGTT
12464451 GTCGGAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.11, C:0.19, G:0.32, T:0.38
Consensus pattern (21 bp):
TGGTTCTCCCAGTAGGGCATT
Found at i:12465362 original size:7 final size:7
Alignment explanation
Indices: 12465352--12465377 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12465342 TTATATACAT
12465352 AATACTA
1 AATACTA
12465359 AATACTA
1 AATACTA
12465366 AATACTA
1 AATACTA
12465373 AATAC
1 AATAC
12465378 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:12465583 original size:20 final size:20
Alignment explanation
Indices: 12465546--12465583 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12465536 TTTATTTTTA
*
12465546 AAAATCTACATAATAATTGC
1 AAAATCTACATAAAAATTGC
12465566 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
12465584 TACATCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGC
Found at i:12466618 original size:12 final size:11
Alignment explanation
Indices: 12466582--12466636 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
12466572 ATAAATATGG
12466582 ATTTGAGAGAA
1 ATTTGAGAGAA
*
12466593 ATTTTGA-AGGA
1 A-TTTGAGAGAA
12466604 ATTTGAGAGCAA
1 ATTTGAGAG-AA
12466616 A-TTGAGAGGAA
1 ATTTGAGA-GAA
*
12466627 ATTTAAGAGA
1 ATTTGAGAGA
12466637 GGATTAGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
10 5 0.14
11 18 0.50
12 13 0.36
ACGTcount: A:0.44, C:0.02, G:0.27, T:0.27
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:12466625 original size:22 final size:22
Alignment explanation
Indices: 12466582--12466636 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
12466572 ATAAATATGG
12466582 ATTTGAGAGAAATTTTGAAGG-A
1 ATTTGAGAGAAA-TTTGAAGGAA
12466604 ATTTGAGAGCAAA-TTGAGAGGAA
1 ATTTGAGAG-AAATTTGA-AGGAA
*
12466627 ATTTAAGAGA
1 ATTTGAGAGA
12466637 GGATTAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 4 0.14
22 13 0.45
23 12 0.41
ACGTcount: A:0.44, C:0.02, G:0.27, T:0.27
Consensus pattern (22 bp):
ATTTGAGAGAAATTTGAAGGAA
Found at i:12480125 original size:24 final size:23
Alignment explanation
Indices: 12480095--12480152 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
12480085 TATTAATTAA
*
12480095 TTAAAATTTAAAGTTTTTATATAT
1 TTAAAATTTAAA-TTCTTATATAT
*
12480119 TTAAAATTT-AATTCTTATATTT
1 TTAAAATTTAAATTCTTATATAT
*
12480141 TTTAAATTTAAA
1 TTAAAATTTAAA
12480153 AATTGGCCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.57
23 4 0.13
24 9 0.30
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TTAAAATTTAAATTCTTATATAT
Found at i:12494021 original size:40 final size:41
Alignment explanation
Indices: 12493961--12494041 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 41
12493951 GTAACAGTTT
* * *
12493961 GGGCCTTAGCTCATCTCAGTA-CAATATCAAACATGCAGTA
1 GGGCCTTAGCCCATCACAGTATCAATAGCAAACATGCAGTA
**
12494001 GGGCCTTAGCCCATCACAGTATCAATAGCAGTCATGCAGTA
1 GGGCCTTAGCCCATCACAGTATCAATAGCAAACATGCAGTA
12494042 TTCAGTATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 19 0.54
41 16 0.46
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (41 bp):
GGGCCTTAGCCCATCACAGTATCAATAGCAAACATGCAGTA
Found at i:12501554 original size:265 final size:261
Alignment explanation
Indices: 12501049--12501862 Score: 1147
Period size: 265 Copynumber: 3.1 Consensus size: 261
12501039 TGCGCGCAAC
12501049 AAACACAACCCTCTTTGAAGTGCATTTTTTTTATAAAAGTTTTATTATTTTTCAAGAAAAAAATA
1 AAACACAACCCTCTTTGAAGTGCATTTTTTTTATAAAAGTTTTATTATTTTTCAAG-AAAAAATA
* *
12501114 AAATCTTTAAACTATTTATTTTTTCAGTTTTACTGTTCCAAAAAATCTGGAATTGGAATATTTTT
65 AAAT-TTTAAACTATTTATTTTTCCAGTTTTACTGTTCCGAAAAATCTGGAATTGGAATA--TTT
* **
12501179 TTTGGCTATTGGGGCAGAAATAGTGGGGCAATTTTTTGTG-TTTTTTACTTCTTTGCCCCTACTT
127 TTTGGCTGTT-GGGCAGAAATAGTGGGGCAA-TTTCAGTGCTTTTTTACTTCTTTGCCCCTACTT
* *
12501243 ATTTATCATTTTGCCCTTCTATTACTAGTATAAATAGA-TAGTTGATTTCTTCATTCTTTTCACA
190 ATTTACCATTTTTCCCTTCTATTACTAGTATAAATAGAGT-GTTGATTTCTTCATTCTTTTCACA
12501307 CTGAACA-
254 CTGAACAG
* *
12501314 AAGACACAACTCTTTTTGAAGTGCA-TTTTTTTATAAAAGTTTTATTATTTTTCAAGAAAGAAAT
1 AA-ACACAACCCTCTTTGAAGTGCATTTTTTTTATAAAAGTTTTATTATTTTTCAAGAAA-AAAT
* * *
12501378 AAAATGTTTAAATTATTTATTTTTCCAGTTTTACTGTTTCGAAAAATCTGGAACTGGAATATTTT
64 AAAAT-TTTAAACTATTTATTTTTCCAGTTTTACTGTTCCGAAAAATCTGGAATTGGAATATTTT
12501443 TTGGCTGTTGGAGCAGAAATAGTGGGGCAATTTCAGTGCATTTTTTACTTCTTTGCCCCTACTTA
128 TTGGCTGTTGG-GCAGAAATAGTGGGGCAATTTCAGTGC-TTTTTTACTTCTTTGCCCCTACTTA
12501508 TTTACCATTTTTCCCTTCTATTACTAGTATAAGATAGAGTGTTGATTTCTTCATTCTTTTCACAC
191 TTTACCATTTTTCCCTTCTATTACTAGTATAA-ATAGAGTGTTGATTTCTTCATTCTTTTCACAC
12501573 TGAACAG
255 TGAACAG
*
12501580 AAACACAACCCTCTCTGAAGTGCATATTTTTTTTATAAAA-TTTTAATTATTTTTCAA-AAAAAA
1 AAACACAACCCTCTTTGAAGTGC--ATTTTTTTTATAAAAGTTTT-ATTATTTTTCAAGAAAAAA
* * *
12501643 TAAAAATTTTAAACTATTTATTTTTCTAGTTTTACTGTTCCGAAAAATCTGAAATTGGAATTTTT
63 T-AAAATTTTAAACTATTTATTTTTCCAGTTTTACTGTTCCGAAAAATCTGGAATTGGAATATTT
* * ** * *
12501708 TTTTGTTGTTGGGCAGAAATAGTAAGGCAATTTCAGTGCGTTTTTCACTTCTTTTCCCCTACTTA
127 TTTGGCTGTTGGGCAGAAATAGTGGGGCAATTTCAGTGC-TTTTTTACTTCTTTGCCCCTACTTA
* * *
12501773 TTTACCGTTTTGT-CCTTCTGTTACTAGTATAAATAGAGGGTTGATTTCTTCATTCTTTTCACAC
191 TTTACCATTTT-TCCCTTCTATTACTAGTATAAATAGAGTGTTGATTTCTTCATTCTTTTCACAC
*
12501837 TGAATAG
255 TGAACAG
* * *
12501844 AAATACAACCTTCTCTGAA
1 AAACACAACCCTCTTTGAA
12501863 AATATTTTTC
Statistics
Matches: 500, Mismatches: 35, Indels: 29
0.89 0.06 0.05
Matches are distributed among these distances:
262 8 0.02
263 30 0.06
264 112 0.22
265 222 0.44
266 90 0.18
267 13 0.03
268 25 0.05
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (261 bp):
AAACACAACCCTCTTTGAAGTGCATTTTTTTTATAAAAGTTTTATTATTTTTCAAGAAAAAATAA
AATTTTAAACTATTTATTTTTCCAGTTTTACTGTTCCGAAAAATCTGGAATTGGAATATTTTTTG
GCTGTTGGGCAGAAATAGTGGGGCAATTTCAGTGCTTTTTTACTTCTTTGCCCCTACTTATTTAC
CATTTTTCCCTTCTATTACTAGTATAAATAGAGTGTTGATTTCTTCATTCTTTTCACACTGAACA
G
Found at i:12503179 original size:17 final size:19
Alignment explanation
Indices: 12503157--12503200 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
12503147 AATTATTAAA
12503157 ATATTTA-AAAT-AAAATC
1 ATATTTATAAATAAAAATC
* *
12503174 ATATTTATATATAAAAATT
1 ATATTTATAAATAAAAATC
12503193 ATATTTAT
1 ATATTTAT
12503201 GTTATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 3 0.13
19 13 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATTTATAAATAAAAATC
Found at i:12505988 original size:20 final size:20
Alignment explanation
Indices: 12505963--12506006 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12505953 AAATAATATG
*
12505963 AAAAAA-AAGAAAAAACCTTT
1 AAAAAACAA-AAAAAACATTT
*
12505983 AAAAAACAAATAAAACATTT
1 AAAAAACAAAAAAAACATTT
12506003 AAAA
1 AAAA
12506007 TAAATAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAAACAAAAAAAACATTT
Found at i:12508176 original size:44 final size:45
Alignment explanation
Indices: 12508073--12508187 Score: 153
Period size: 44 Copynumber: 2.6 Consensus size: 45
12508063 TTAATTCGCT
* * * *
12508073 CCACTGCAACTTCAGAGAGATAGGA-TTAGTAGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTTAGTAGCCTCAATCTGCC
*
12508117 CCACTGCAACTTCAGGGAGATAAGACTT-GTATCCTCAATCTGCC
1 CCACTGCAACTTCAGGGAGATAAGACTTAGTAGCCTCAATCTGCC
* *
12508161 CCACTGCAACTTCAGGGGGATCAGACT
1 CCACTGCAACTTCAGGGAGATAAGACT
12508188 GGTGGCTTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
44 61 0.97
45 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (45 bp):
CCACTGCAACTTCAGGGAGATAAGACTTAGTAGCCTCAATCTGCC
Found at i:12508517 original size:45 final size:45
Alignment explanation
Indices: 12508457--12508925 Score: 518
Period size: 45 Copynumber: 10.4 Consensus size: 45
12508447 ACCAGCTTTT
* * * * *
12508457 GATCTGCTTCACTGCCAGTACAAGAAGACAAGATTTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
*
12508502 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCT-ATAATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT-ATCTTC
* * * *** * *
12508547 GACCTACTCCACTGCTGCT-CAGGGAGACAAGATCTGCTATCTTT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * *
12508591 GATATACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * *
12508636 GACCTACTTCGCTGCCAATACAAGAAGACAAGATCTGCTATCTTT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* *
12508681 GACCTACTTCGCTGCCAATACAAGAAGACAAGATCTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
** * *
12508726 -AGTCTACTTCGCTATCAATACAGGAAGACAAGACCTGTTATCTTC
1 GA-TCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * * * *
12508771 GATCTACTTCGCTACCAATATAGGAAGATAAGATCTGTTATCTTT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * * *
12508816 GA-CTTACTTTGCTGCTAATACAGGAAGATAAGATCTACTATCTTC
1 GATC-TACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* *
12508861 -AGTCTACTTCGCTGTCAATACAGGAAGACAAGA-CTTACTATCTTC
1 GA-TCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATCTTC
12508906 GATCTACTTCGCTGCCAATA
1 GATCTACTTCGCTGCCAATA
12508926 TAGAAAGATA
Statistics
Matches: 362, Mismatches: 52, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
44 37 0.10
45 322 0.89
46 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (45 bp):
GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
Found at i:12508928 original size:135 final size:135
Alignment explanation
Indices: 12508475--12508925 Score: 584
Period size: 135 Copynumber: 3.3 Consensus size: 135
12508465 TCACTGCCAG
* * *
12508475 TACAAGAAGACAAGATTTGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTAT
1 TACAGGAAGACAAGACTTGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGT
* * * * ** * * *
12508540 AATCTTCGACCTACTCCACTGCTGCT-CAGGGAGACAAGATCTGCTATCTT-TGATATACTTCGC
66 TATCTTTGACCTACTTCGCTGCTAATACAGGAAGACAAGATCTGCTATCTTCAG-TCTACTTCGC
*
12508603 TGCCAA
130 TGTCAA
* * * *
12508609 TATAGGAAGACAAGA-TCTGCTATCTTTGACCTACTTCGCTGCCAATACAAGAAGACAAGATCTG
1 TACAGGAAGACAAGACT-TGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTG
* * *
12508673 CTATCTTTGACCTACTTCGCTGCCAATACAAGAAGACAAGATCTGCTATCTTCAGTCTACTTCGC
65 TTATCTTTGACCTACTTCGCTGCTAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGC
*
12508738 TATCAA
130 TGTCAA
* * * * *
12508744 TACAGGAAGACAAGACCTGTTATCTTCGATCTACTTCGCTACCAATATAGGAAGATAAGATCTGT
1 TACAGGAAGACAAGACTTGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGT
* * * *
12508809 TATCTTTGACTTACTTTGCTGCTAATACAGGAAGATAAGATCTACTATCTTCAGTCTACTTCGCT
66 TATCTTTGACCTACTTCGCTGCTAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
12508874 GTCAA
131 GTCAA
*
12508879 TACAGGAAGACAAGACTTACTATCTTCGATCTACTTCGCTGCCAATA
1 TACAGGAAGACAAGACTTGCTATCTTCGATCTACTTCGCTGCCAATA
12508926 TAGAAAGATA
Statistics
Matches: 272, Mismatches: 41, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
133 1 0.00
134 75 0.28
135 195 0.72
136 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (135 bp):
TACAGGAAGACAAGACTTGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGT
TATCTTTGACCTACTTCGCTGCTAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
GTCAA
Found at i:12512683 original size:18 final size:17
Alignment explanation
Indices: 12512651--12512684 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12512641 TCTTTTATTT
12512651 TATTTTTTGTATATATG
1 TATTTTTTGTATATATG
*
12512668 TATTTGTTTTTATATAT
1 TATTT-TTTGTATATAT
12512685 ATGATTCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (17 bp):
TATTTTTTGTATATATG
Found at i:12528485 original size:14 final size:14
Alignment explanation
Indices: 12528468--12528512 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
12528458 AAATATGTAT
*
12528468 ATACATATATTTAA
1 ATACATATATATAA
*
12528482 ATACGTATATATAA
1 ATACATATATATAA
12528496 GTATACATATATATAA
1 --ATACATATATATAA
12528512 A
1 A
12528513 AAATGAATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (14 bp):
ATACATATATATAA
Found at i:12530518 original size:129 final size:130
Alignment explanation
Indices: 12530232--12530521 Score: 343
Period size: 130 Copynumber: 2.2 Consensus size: 130
12530222 TTATCTCTAG
* ** *
12530232 TCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGATGCAGTCTGCTCTACTGCAACTTCAGAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCGGATGCAGTCTACTCTACTGCAACTTCAGAGA
** * * * * * * **
12530297 GATAAGATCTGTGATTTTTAATCCACTCCACTGCAACCTCAAGGAGATAGGATTGGTTTCTTCTG
66 GATAAGATCCATCATTTTTAATCCACTCCACTACAACCTCAAGGAGATAGAATTGATTGCCTCAA
* *
12530362 TCTGCTCCACTGCAACTTCAGGGAGATAGGACCGGATGC-GATCTACTCTACTGCACCTTCAGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCGGATGCAG-TCTACTCTACTGCAACTTCAGAG
* * *
12530426 AGATAAGATCCATCA-TTTTAATCCGCTCCACTACAACTTCAGGGAGATAGAATT-ATTGGCCTC
65 AGATAAGATCCATCATTTTTAATCCACTCCACTACAACCTCAAGGAGATAGAATTGATT-GCCTC
12530489 AA
129 AA
* * *
12530491 TCTGCTCCGCTGCATCTCCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
12530522 TTCATCGTCG
Statistics
Matches: 135, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
128 2 0.01
129 65 0.48
130 68 0.50
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (130 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACCGGATGCAGTCTACTCTACTGCAACTTCAGAGA
GATAAGATCCATCATTTTTAATCCACTCCACTACAACCTCAAGGAGATAGAATTGATTGCCTCAA
Found at i:12530637 original size:99 final size:99
Alignment explanation
Indices: 12530526--12530706 Score: 267
Period size: 99 Copynumber: 1.8 Consensus size: 99
12530516 ATAAGATTCA
12530526 TCGTCGTAGCTTCAATCTGCTCCACTACACCGCCAAGA-AAGTAAGATT-AGCCATTGTGGATTC
1 TCGTCGTAGCTTCAATCTGCTCCACTACACCG-CAAGAGAAGTAAGATTCA-CCATTGTGGATTC
*
12530589 AATCTTTTCAATTGCAATGTCGGGAAACAAGATCCG
64 AATCTATTCAATTGCAATGTCGGGAAACAAGATCCG
* * * *
12530625 TCGTCGTGGCTTCAATCTGTTCCACTACACCGCTAGAGAAGTAAGATTCACCATTGTGGCTTCAA
1 TCGTCGTAGCTTCAATCTGCTCCACTACACCGCAAGAGAAGTAAGATTCACCATTGTGGATTCAA
* *
12530690 TCTATTCCATTGTAATG
66 TCTATTCAATTGCAATG
12530707 CCAAAGAGAT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
98 4 0.05
99 68 0.93
100 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (99 bp):
TCGTCGTAGCTTCAATCTGCTCCACTACACCGCAAGAGAAGTAAGATTCACCATTGTGGATTCAA
TCTATTCAATTGCAATGTCGGGAAACAAGATCCG
Found at i:12536058 original size:37 final size:37
Alignment explanation
Indices: 12536008--12536082 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
12535998 CACTATCTTG
12536008 CACGGAGGTGAAAACCTCACTAAGGACTAGTTTCTCA
1 CACGGAGGTGAAAACCTCACTAAGGACTAGTTTCTCA
12536045 CACGGAGGTGAAAACCTCACTAAGGACTAGTTTCTCA
1 CACGGAGGTGAAAACCTCACTAAGGACTAGTTTCTCA
12536082 C
1 C
12536083 TCTCACTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (37 bp):
CACGGAGGTGAAAACCTCACTAAGGACTAGTTTCTCA
Found at i:12537535 original size:9 final size:9
Alignment explanation
Indices: 12537521--12537545 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12537511 TATAGAAATA
12537521 ATAATAATG
1 ATAATAATG
12537530 ATAATAATG
1 ATAATAATG
12537539 ATAATAA
1 ATAATAA
12537546 CATTAAAATA
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (9 bp):
ATAATAATG
Found at i:12547253 original size:8 final size:8
Alignment explanation
Indices: 12547240--12547265 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
12547230 CACGTTTGCA
12547240 GAATTCTT
1 GAATTCTT
12547248 GAATTCTT
1 GAATTCTT
12547256 GAATTCTT
1 GAATTCTT
12547264 GA
1 GA
12547266 GACCAAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (8 bp):
GAATTCTT
Found at i:12550219 original size:14 final size:14
Alignment explanation
Indices: 12550202--12550239 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
12550192 ATTTATATAT
12550202 AAATATAAATTTTA
1 AAATATAAATTTTA
12550216 AAATTATAAATTTTA
1 AAA-TATAAATTTTA
*
12550231 AAAAATAAA
1 AAATATAAA
12550240 AAAATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATATAAATTTTA
Found at i:12554538 original size:6 final size:6
Alignment explanation
Indices: 12554521--12554550 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
12554511 CAAGGTTCGG
12554521 GATTTAA GATTTA GATTTA GATTTA GATTT
1 GATTT-A GATTTA GATTTA GATTTA GATTT
12554551 GAGGTTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
GATTTA
Found at i:12555708 original size:28 final size:28
Alignment explanation
Indices: 12555664--12555724 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
12555654 AGTAGAAAAG
12555664 AAAAAGAAACAATAGAAAA-AAAAGGTGAA
1 AAAAAGAAACAATAGAAAATAAAA--TGAA
*
12555693 AAAAAGAAAGAA-AGAAAATAAAATGAA
1 AAAAAGAAACAATAGAAAATAAAATGAA
12555720 AAAAA
1 AAAAA
12555725 TATGGGTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 9 0.30
28 6 0.20
29 15 0.50
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.07
Consensus pattern (28 bp):
AAAAAGAAACAATAGAAAATAAAATGAA
Found at i:12556290 original size:19 final size:21
Alignment explanation
Indices: 12556254--12556292 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12556244 AGATAATAAT
12556254 ATTTATTATTTTTGTAAAATA
1 ATTTATTATTTTTGTAAAATA
12556275 ATTT-TTATTTTT-TAAAAT
1 ATTTATTATTTTTGTAAAAT
12556293 GACATTGACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
ATTTATTATTTTTGTAAAATA
Found at i:12558283 original size:21 final size:21
Alignment explanation
Indices: 12558257--12558298 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12558247 ACGAGATAGG
*
12558257 TGACGTGACCCGTTAACTAGC
1 TGACGTGACCAGTTAACTAGC
*
12558278 TGACGTGGCCAGTTAACTAGC
1 TGACGTGACCAGTTAACTAGC
12558299 CACAGTGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (21 bp):
TGACGTGACCAGTTAACTAGC
Found at i:12562644 original size:20 final size:20
Alignment explanation
Indices: 12562619--12562658 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12562609 CGGAAAATAA
*
12562619 TTTTTGGAGAATAATTTACT
1 TTTTTGGAAAATAATTTACT
*
12562639 TTTTTGGAAAATGATTTACT
1 TTTTTGGAAAATAATTTACT
12562659 GAAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (20 bp):
TTTTTGGAAAATAATTTACT
Found at i:12564072 original size:32 final size:32
Alignment explanation
Indices: 12564021--12564081 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
12564011 TGTCAATCAT
*
12564021 TTCAATATCCAACAGGCTTAAAACATAATTAA
1 TTCAATATCCAACAAGCTTAAAACATAATTAA
*
12564053 TTCAATATCTAACAAGCTTAAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
12564082 CAATATCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.30
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATTAA
Found at i:12564089 original size:27 final size:30
Alignment explanation
Indices: 12564021--12564094 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 30
12564011 TGTCAATCAT
* *
12564021 TTCAATATCCAACAGGCTTAAAACATAATTAA
1 TTCAATATCTAACAAGCTTAAAAC--AATTAA
12564053 TTCAATATCTAACAAGCTTAAAAC-A-TAA
1 TTCAATATCTAACAAGCTTAAAACAATTAA
12564081 -TCAATATCTAACAA
1 TTCAATATCTAACAA
12564095 ATTCAAGACA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 14 0.35
28 3 0.08
29 1 0.03
32 22 0.55
ACGTcount: A:0.49, C:0.19, G:0.04, T:0.28
Consensus pattern (30 bp):
TTCAATATCTAACAAGCTTAAAACAATTAA
Found at i:12564105 original size:27 final size:27
Alignment explanation
Indices: 12564054--12564107 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
12564044 CATAATTAAT
*
12564054 TCAATATCTAACAAGCTTAAAACATAA
1 TCAATATCTAACAAGATTAAAACATAA
*
12564081 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
12564108 AAATTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.52, C:0.19, G:0.04, T:0.26
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:12569142 original size:30 final size:30
Alignment explanation
Indices: 12569108--12569346 Score: 211
Period size: 30 Copynumber: 8.0 Consensus size: 30
12569098 ATTTTACATG
* *
12569108 TTATTTTATTGTCAGCTTGTGTGAGCAATC
1 TTATTATAATGTCAGCTTGTGTGAGCAATC
*
12569138 TTATTATAATGTCAGCTTGTGTGAACAATAC
1 TTATTATAATGTCAGCTTGTGTGAGCAAT-C
* * *
12569169 -TATTATAATGTCAACTTGTGTGAGTAAAGC
1 TTATTATAATGTCAGCTTGTGTGAG-CAATC
* * *
12569199 -TATTATAATATTAGCTTGTATGAGCAAT-
1 TTATTATAATGTCAGCTTGTGTGAGCAATC
* *
12569227 TCTATCATAATGTCAGCTTGTGTGAGTAAT-
1 T-TATTATAATGTCAGCTTGTGTGAGCAATC
* * *
12569257 TCCATCATAATGTCAGCTTGTGTAAGC-AT-
1 T-TATTATAATGTCAGCTTGTGTGAGCAATC
* * *
12569286 TTCCATCATAATGTCAGCTTGTGTGAGAAACC
1 TT--ATTATAATGTCAGCTTGTGTGAGCAATC
* *
12569318 TTATTATAATGTCAACTTGTCTGAGCAAT
1 TTATTATAATGTCAGCTTGTGTGAGCAAT
12569347 GTATTCACTT
Statistics
Matches: 171, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
29 5 0.03
30 160 0.94
31 4 0.02
32 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (30 bp):
TTATTATAATGTCAGCTTGTGTGAGCAATC
Found at i:12569191 original size:60 final size:60
Alignment explanation
Indices: 12569117--12569346 Score: 250
Period size: 60 Copynumber: 3.8 Consensus size: 60
12569107 GTTATTTTAT
* * *
12569117 TGTCAGCTTGTGTGAGCAATCTTATTATAATGTCAGCTTGTGTGAACAATACTATTATAA
1 TGTCAGCTTGTGTGAGAAATCTTATTATAATGTCAGCTTGTGTGAACAATTCTATCATAA
* * * * * *
12569177 TGTCAACTTGTGTGAGTAAAGC-TATTATAATATTAGCTTGTATGAGCAATTCTATCATAA
1 TGTCAGCTTGTGTGAG-AAATCTTATTATAATGTCAGCTTGTGTGAACAATTCTATCATAA
* * * * *
12569237 TGTCAGCTTGTGTGAGTAAT-TCCATCATAATGTCAGCTTGTGT-AAGCATTTCCATCATAA
1 TGTCAGCTTGTGTGAGAAATCT-TATTATAATGTCAGCTTGTGTGAA-CAATTCTATCATAA
* * * *
12569297 TGTCAGCTTGTGTGAGAAACCTTATTATAATGTCAACTTGTCTGAGCAAT
1 TGTCAGCTTGTGTGAGAAATCTTATTATAATGTCAGCTTGTGTGAACAAT
12569347 GTATTCACTT
Statistics
Matches: 136, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
59 3 0.02
60 128 0.94
61 5 0.04
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (60 bp):
TGTCAGCTTGTGTGAGAAATCTTATTATAATGTCAGCTTGTGTGAACAATTCTATCATAA
Found at i:12569297 original size:90 final size:90
Alignment explanation
Indices: 12569119--12569346 Score: 233
Period size: 90 Copynumber: 2.5 Consensus size: 90
12569109 TATTTTATTG
* * *
12569119 TCAGCTTGTGTGAGCAATCTTATTATAATGTCAGCTTGTGTGAACAATACTATTATAATGTCAAC
1 TCAGCTTGTGTGAGCAATCTTATCATAATGTCAGCTTGTGTGAACAATACCATCATAATGTCAAC
* * * *
12569184 TTGTGTGAGTAAAGCTATTATAATA
66 TTGTGTAAGCAAAGCCATCATAATA
* * ** * *
12569209 TTAGCTTGTATGAGCAAT-TCTATCATAATGTCAGCTTGTGTGAGTAATTCCATCATAATGTCAG
1 TCAGCTTGTGTGAGCAATCT-TATCATAATGTCAGCTTGTGTGAACAATACCATCATAATGTCAA
*** *
12569273 CTTGTGTAAGCATTTCCATCATAATG
65 CTTGTGTAAGCAAAGCCATCATAATA
* * * * * *
12569299 TCAGCTTGTGTGAGAAACCTTATTATAATGTCAACTTGTCTGAGCAAT
1 TCAGCTTGTGTGAGCAATCTTATCATAATGTCAGCTTGTGTGAACAAT
12569347 GTATTCACTT
Statistics
Matches: 111, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
89 1 0.01
90 109 0.98
91 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (90 bp):
TCAGCTTGTGTGAGCAATCTTATCATAATGTCAGCTTGTGTGAACAATACCATCATAATGTCAAC
TTGTGTAAGCAAAGCCATCATAATA
Found at i:12570170 original size:19 final size:20
Alignment explanation
Indices: 12570136--12570176 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
12570126 TTTAAAGCTT
12570136 AATTAACTAATGTTTAATTA
1 AATTAACTAATGTTTAATTA
*
12570156 AATTAATTAAT-TTTAATTA
1 AATTAACTAATGTTTAATTA
12570175 AA
1 AA
12570177 GTGAAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
AATTAACTAATGTTTAATTA
Found at i:12570767 original size:71 final size:70
Alignment explanation
Indices: 12570687--12570834 Score: 244
Period size: 71 Copynumber: 2.1 Consensus size: 70
12570677 GGAAGGGATA
* * *
12570687 AATTGAATTGAATTATTATATAAATCTTAAATTGGACCAAATCAGAAATAATCAGGGAAAATAAA
1 AATTGAATTGAATTATTATATAAATCATAAATTGGACCAAATAAAAAATAATCAGGGAAAATAAA
12570752 AAATT
66 AAATT
*
12570757 GAATTGAATTGAATTATTATATAGATCATAAATTGGACCAAATAAAAAATAATCAGGGAAAATAA
1 -AATTGAATTGAATTATTATATAAATCATAAATTGGACCAAATAAAAAATAATCAGGGAAAATAA
12570822 AAAATT
65 AAAATT
12570828 -ATTGAAT
1 AATTGAAT
12570835 AGCCCCTGAA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 7 0.10
71 66 0.90
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (70 bp):
AATTGAATTGAATTATTATATAAATCATAAATTGGACCAAATAAAAAATAATCAGGGAAAATAAA
AAATT
Found at i:12573158 original size:22 final size:21
Alignment explanation
Indices: 12573130--12573205 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 21
12573120 AGGGGAGCCA
12573130 TGTCTCGAGATAATTATGTATT
1 TGTCTCGAGA-AATTATGTATT
** *
12573152 TGTCTCGAGAAAACAGTGTATG
1 TGTCTCGAGAAATTA-TGTATT
* *
12573174 TGTCTCAAGAAAATTGTGTATT
1 TGTCTCGAG-AAATTATGTATT
* *
12573196 TTTCTTGAGA
1 TGTCTCGAGA
12573206 CATATACCTT
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
21 4 0.10
22 34 0.83
23 3 0.07
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (21 bp):
TGTCTCGAGAAATTATGTATT
Found at i:12575126 original size:15 final size:15
Alignment explanation
Indices: 12575106--12575136 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12575096 TAACTTGTGA
12575106 AACTATTAAAAGTTT
1 AACTATTAAAAGTTT
12575121 AACTATTAAAAGTTT
1 AACTATTAAAAGTTT
12575136 A
1 A
12575137 GGGACATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTATTAAAAGTTT
Found at i:12586103 original size:15 final size:15
Alignment explanation
Indices: 12586083--12586114 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12586073 TCCCTTAAAG
*
12586083 TTAACTCGATTTCAA
1 TTAACTCAATTTCAA
12586098 TTAACTCAATTTCAA
1 TTAACTCAATTTCAA
12586113 TT
1 TT
12586115 CAAAAAGCGC
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:0.34, C:0.19, G:0.03, T:0.44
Consensus pattern (15 bp):
TTAACTCAATTTCAA
Found at i:12586546 original size:16 final size:17
Alignment explanation
Indices: 12586520--12586556 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
12586510 TTATTTCCCA
12586520 ATTTAATTTAATTTTTG
1 ATTTAATTTAATTTTTG
*
12586537 ATTT-ATTTAATTTTTT
1 ATTTAATTTAATTTTTG
12586553 ATTT
1 ATTT
12586557 CTGCTATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
ATTTAATTTAATTTTTG
Found at i:12589859 original size:126 final size:126
Alignment explanation
Indices: 12589722--12590099 Score: 533
Period size: 126 Copynumber: 3.0 Consensus size: 126
12589712 AGTAGTTTTA
* * * *
12589722 GAAAAATTAATTTTGAGAAGATGATTTTGAAAAGATAATGTCAAAAACGCTTCAAGCAGAATGCA
1 GAAAAAATAATTTTGAGAAGATGATTTTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCA
* * *
12589787 CTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGTTATTTTTCTATAATAGTTCCT
66 CTGTTAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAATAGTTCCT
* *
12589848 GAAAAAATAATTCTGAGAAGATGATTTTGAAAAAATAGTGTCAAAAACGCTTCAAACAGGATGCA
1 GAAAAAATAATTTTGAGAAGATGATTTTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCA
* * * ** *
12589913 CTGTTAACAAAATTACTAAAAAAAGCTCCCACGTGGACGCTCTTTTACTACGATAGTTCTT
66 CTGTTAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAATAGTTCCT
* * *
12589974 G-AAAAATAATTTTGGGAAGATGGTTTTGAAAAAATAGTGTAAAAAACGCTTCAAGCAGGATGCA
1 GAAAAAATAATTTTGAGAAGATGATTTTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCA
* * * * * *
12590038 CTATTAGCAAAATTACTGAAAAGAGCTCCTACGTGAACACTCTTTTTCTATAGTAGTTCCT
66 CTGTTAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAATAGTTCCT
12590099 G
1 G
12590100 CTTGGCCTTA
Statistics
Matches: 220, Mismatches: 32, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
125 108 0.49
126 112 0.51
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (126 bp):
GAAAAAATAATTTTGAGAAGATGATTTTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCA
CTGTTAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAATAGTTCCT
Found at i:12593649 original size:18 final size:18
Alignment explanation
Indices: 12593623--12593665 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
12593613 GACTGGAAAA
* *
12593623 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
12593641 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
12593659 AGGATAC
1 AGGATAC
12593666 GCAGCTGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:12595433 original size:32 final size:32
Alignment explanation
Indices: 12595386--12595452 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
12595376 GGAAATAATT
12595386 AATTAAAGAGA-TTTTTGAGAAATTTT-GAGAGA
1 AATTAAAGAGATTTTTTGAG-AATTTTGGA-AGA
* *
12595418 AATTTAAGAGCTTTTTTGAGAATTTTGGAAGA
1 AATTAAAGAGATTTTTTGAGAATTTTGGAAGA
12595450 AAT
1 AAT
12595453 GTTTGTGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.40, C:0.01, G:0.21, T:0.37
Consensus pattern (32 bp):
AATTAAAGAGATTTTTTGAGAATTTTGGAAGA
Found at i:12598218 original size:16 final size:16
Alignment explanation
Indices: 12598199--12598230 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12598189 TTTTGATTTG
12598199 GAGCAATTATACAACT
1 GAGCAATTATACAACT
12598215 GAGCAATTATACAACT
1 GAGCAATTATACAACT
12598231 TTTGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (16 bp):
GAGCAATTATACAACT
Found at i:12601977 original size:21 final size:21
Alignment explanation
Indices: 12601951--12602007 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
12601941 ATGTAAAAGG
*
12601951 AAAAATGAAAATAAAATAGAA
1 AAAAATGAAAATAAAATACAA
* *
12601972 AAAAATGAAAA-AAGATTCAA
1 AAAAATGAAAATAAAATACAA
*
12601992 AACAA-GAAAATAAAAT
1 AAAAATGAAAATAAAAT
12602008 CCTCTCAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.17
20 14 0.47
21 11 0.37
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAATAAAATACAA
Found at i:12602988 original size:132 final size:132
Alignment explanation
Indices: 12602829--12603086 Score: 372
Period size: 132 Copynumber: 2.0 Consensus size: 132
12602819 GGTTTGATTC
* * * * * *
12602829 AATCTGGTTCCCTATTTCCTTGGGAAGATAAGATTCATTGTCTTTGATCTGCTCCACTACCGCTT
1 AATCTGCTTCCCTACTACCTTAGGAAGATAAGATTCATCGTCTTCGATCTGCTCCACTACCGCTT
* * * * *
12602894 AGGGAGACAGGATCTGCAATCTTCAGCCTACTCCGCTTCTGCTCAGGGAGATAAGGCTAGTGGCT
66 AGGGAGACAGGATATGCAATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAAGGCTAGTGGCT
12602959 TA
131 TA
* *
12602961 AATCTGCTTCCCTACTACCTTAGGAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTT
1 AATCTGCTTCCCTACTACCTTAGGAAGATAAGATTCATCGTCTTCGATCTGCTCCACTACCGCTT
* * *
12603026 AGGGAGGCAGGATATGCAATTTTCAACCTACTCTACTGCTGCTCAAGGAGATAAGGCTAGT
66 AGGGAGACAGGATATGCAATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAAGGCTAGT
12603087 TTTTTTTTAC
Statistics
Matches: 110, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
132 110 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (132 bp):
AATCTGCTTCCCTACTACCTTAGGAAGATAAGATTCATCGTCTTCGATCTGCTCCACTACCGCTT
AGGGAGACAGGATATGCAATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAAGGCTAGTGGCT
TA
Found at i:12603236 original size:44 final size:44
Alignment explanation
Indices: 12603187--12603898 Score: 312
Period size: 44 Copynumber: 16.6 Consensus size: 44
12603177 GATCTACTTT
* * *
12603187 ACTGTAACTTCAGAGAGATAAGATCCTTTATTTAAATCCGCTCC
1 ACTGTAACTTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCC
* * *
12603231 ACTGTAA-TCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGCTCC
1 ACTGTAACT-TCAGGGAGATAAGATCCT-TTA-TTTCAATCTGCTCC
* * ** * * *
12603275 GCTGTAATCTT-AGGGAGATAAGAT-C-TGACAT-GATCTACTCT
1 ACTGTAA-CTTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCC
* * *
12603316 ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
1 ACTGTAACTTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCC
* * *
12603360 ACTGTAA-TCTCAGGGAGATAGGATTCC--TAGCTTCAATTTGCTCC
1 ACTGTAACT-TCAGGGAGATAAGA-TCCTTTA-TTTCAATCTGCTCC
* * * * * * *
12603404 GCTGTAA-TCTGAGGGAGATAAGA--CTTGA-TGCGATCTACTCT
1 ACTGTAACT-TCAGGGAGATAAGATCCTTTATTTCAATCTGCTCC
* * * *
12603445 GCTGTAACTTCAGAGAGATAAGATCCTCTACTTT-AGTCTGCTCC
1 ACTGTAACTTCAGGGAGATAAGATCCTTTA-TTTCAATCTGCTCC
* * * * *
12603489 ACTGTAA-TCTCAGGGAGATAAGA-CC-TGA-TGCGATCTACTCT
1 ACTGTAACT-TCAGGGAGATAAGATCCTTTATTTCAATCTGCTCC
* * * *
12603530 ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCT
1 ACTGTAACTTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCC
* * * * *
12603574 ACTGTAACTTCAGGGAGATAGGA-CAGTGT-CTTCGATCTGCTCC
1 ACTGTAACTTCAGGGAGATAAGATC-CTTTATTTCAATCTGCTCC
** * * **
12603617 GTTGTAA-TCTCAGGGAAATAAGAT-ATTTGGCTTCAATCTGCTCC
1 ACTGTAACT-TCAGGGAGATAAGATCCTTT-ATTTCAATCTGCTCC
**
12603661 ACTGTAACTTCAGGGAGATAAGAT--TTCTGGCTTCAATCTGCTCC
1 ACTGTAACTTCAGGGAGATAAGATCCTT-T-ATTTCAATCTGCTCC
* ** ** *
12603705 ACTGTAACATCAGGGAGATAAGAT-CTGAAATTCTTCGGTCTACTCC
1 ACTGTAACTTCAGGGAGATAAGATCCT-TTA-T-TTCAATCTGCTCC
** * * *
12603751 ACTGTAACTTCAGGGAGATAAGA-CC--TGGTGCGATCT-CTCT
1 ACTGTAACTTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCC
* * *
12603791 ACTGTAACTTTAGAGAGATAAGATCC----TTT-AATCCGCTCC
1 ACTGTAACTTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCC
* * * * * *
12603830 ACTGTAA-TCTCAGGGAGATAGGATTAC-TAAATTCACTCTGCTCT
1 ACTGTAACT-TCAGGGAGATAAGA-TCCTTTATTTCAATCTGCTCC
*
12603874 GCTGTAA-TCTCAGGGAGATAAGATC
1 ACTGTAACT-TCAGGGAGATAAGATC
12603899 TGAGATTCTT
Statistics
Matches: 507, Mismatches: 115, Indels: 93
0.71 0.16 0.13
Matches are distributed among these distances:
38 4 0.01
39 22 0.04
40 30 0.06
41 87 0.17
42 12 0.02
43 51 0.10
44 260 0.51
45 7 0.01
46 34 0.07
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (44 bp):
ACTGTAACTTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCC
Found at i:12603395 original size:129 final size:129
Alignment explanation
Indices: 12603165--12603508 Score: 555
Period size: 129 Copynumber: 2.7 Consensus size: 129
12603155 ACAGGAAGAC
* *
12603165 AAGATCTGACACGATCTACTTTACTGTAACTTCAGAGAGATAAGATCCTTTATTTAAATCCGCTC
1 AAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTC
*
12603230 CACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTTAGGGAGAT
66 CACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTGAGGGAGAT
*
12603294 AAGATCTGACATGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTC
1 AAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTC
* *
12603359 CACTGTAATCTCAGGGAGATAGGATTCCTAGCTTCAATTTGCTCCGCTGTAATCTGAGGGAGAT
66 CACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTGAGGGAGAT
** * * * * *
12603423 AAGA-CTTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTCTACTTTAGTCTGCT
1 AAGATC-TGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCT
12603487 CCACTGTAATCTCAGGGAGATA
65 CCACTGTAATCTCAGGGAGATA
12603509 AGACCTGATG
Statistics
Matches: 200, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
128 1 0.00
129 199 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (129 bp):
AAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTC
CACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTGAGGGAGAT
Found at i:12603450 original size:85 final size:85
Alignment explanation
Indices: 12603360--12603849 Score: 351
Period size: 85 Copynumber: 5.8 Consensus size: 85
12603350 AATCCGCTCC
* * * * * *
12603360 ACTGTAA-TCTCAGGGAGATAGGATTC-CTAGCTTCAATTTGCTCCGCTGTAATCTGAGGGAGAT
1 ACTGTAACT-TCAGAGAGATAAGATCCTCTA-CTTCAATCTGCTCCACTGTAATCTCAGGGAGAT
*
12603423 AAGACTTGATGCGATCTACTCT
64 AAGACCTGATGCGATCTACTCT
* * *
12603445 GCTGTAACTTCAGAGAGATAAGATCCTCTACTTTAGTCTGCTCCACTGTAATCTCAGGGAGATAA
1 ACTGTAACTTCAGAGAGATAAGATCCTCTACTTCAATCTGCTCCACTGTAATCTCAGGGAGATAA
12603510 GACCTGATGCGATCTACTCT
66 GACCTGATGCGATCTACTCT
* * * * *
12603530 ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCTACTGTAA-CTTCAGGGAGATA
1 ACTGTAACTTCAGAGAGATAAGATCCTCTACTTCAATCTGCTCCACTGTAATC-TCAGGGAGATA
* * * * * *
12603594 GGACAGTGTCTTCGATCTGCTCC
65 AGAC-CTG-ATGCGATCTACTCT
** * * * * *
12603617 GTTGTAA-TCTCAGGGAAATAAGAT-ATTTGGCTTCAATCTGCTCCACTGTAA-CTTCAGGGAGA
1 ACTGTAACT-TCAGAGAGATAAGATCCTCT-ACTTCAATCTGCTCCACTGTAATC-TCAGGGAGA
* * * * * *
12603679 TAAGATTTCTGGCTTCAATCTGCTCC
63 TAAGA--CCT-GATGCGATCTACTCT
* * * * ** *
12603705 ACTGTAACATCAGGGAGATAAGAT-CTGAAATTCTTCGGTCTACTCCACTGTAA-CTTCAGGGAG
1 ACTGTAACTTCAGAGAGATAAGATCCT---CTACTTCAATCTGCTCCACTGTAATC-TCAGGGAG
*
12603768 ATAAGACCTGGTGCGATCT-CTCT
62 ATAAGACCTGATGCGATCTACTCT
* *
12603791 ACTGTAACTTTAGAGAGATAAGAT-C-CT--TT-AATCCGCTCCACTGTAATCTCAGGGAGATA
1 ACTGTAACTTCAGAGAGATAAGATCCTCTACTTCAATCTGCTCCACTGTAATCTCAGGGAGATA
12603850 GGATTACTAA
Statistics
Matches: 331, Mismatches: 59, Indels: 36
0.78 0.14 0.08
Matches are distributed among these distances:
79 24 0.07
80 3 0.01
82 1 0.00
84 1 0.00
85 128 0.39
86 35 0.11
87 67 0.20
88 36 0.11
89 1 0.00
90 34 0.10
91 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (85 bp):
ACTGTAACTTCAGAGAGATAAGATCCTCTACTTCAATCTGCTCCACTGTAATCTCAGGGAGATAA
GACCTGATGCGATCTACTCT
Found at i:12603463 original size:41 final size:41
Alignment explanation
Indices: 12603418--12603552 Score: 132
Period size: 41 Copynumber: 3.2 Consensus size: 41
12603408 TAATCTGAGG
*
12603418 GAGATAAGACTTGATGCGATCTACTCTGCTGTAACTTCAGA
1 GAGATAAGACTTGATGCGATCTACTCTACTGTAACTTCAGA
** * * *
12603459 GAGATAAGATCCTCT-ACT-TTAGTCTGCTCCACTGTAA-TCTCAGG
1 GAGATAAGA--CT-TGA-TGCGA-TCTACTCTACTGTAACT-TCAGA
*
12603503 GAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGA
1 GAGATAAGACTTGATGCGATCTACTCTACTGTAACTTCAGA
12603544 GAGATAAGA
1 GAGATAAGA
12603553 TCCTTTATTT
Statistics
Matches: 73, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
41 37 0.51
42 4 0.05
43 5 0.07
44 27 0.37
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
GAGATAAGACTTGATGCGATCTACTCTACTGTAACTTCAGA
Found at i:12603579 original size:129 final size:128
Alignment explanation
Indices: 12603178--12603820 Score: 474
Period size: 129 Copynumber: 5.0 Consensus size: 128
12603168 ATCTGACACG
* * *
12603178 ATCTACTTTACTGTAACTTCAGAGAGATAAGATCCTTTA-TTTAAATCCGCTCCACTGTAATCTC
1 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTACTTT-AGTCTGCTCCACTGTAATCTC
* * * *
12603242 AGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTT-AGGGAGATAAGATC-TGA--
65 AGGGAGATAAGA--CCTAGCTTCAATCTGCTCCACTGTAA-CTTCAGGGAGATAAGATCTTTATT
12603303 CA
127 CA
* * *
12603305 TGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
1 --ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTACTTTAGTCTGCTCCACTGTAATCT
* * * * *
12603370 CAGGGAGATAGGATTCCTAGCTTCAATTTGCTCCGCTGTAA-TCTGAGGGAGATAAGA-CTTGAT
64 CAGGGAGATAAGA--CCTAGCTTCAATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCTTTAT
* *
12603433 GCG
126 TCA
* *
12603436 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTCTACTTTAGTCTGCTCCACTGTAATCTCA
1 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTACTTTAGTCTGCTCCACTGTAATCTCA
* * * * * * *
12603501 GGGAGATAAGACCT-GATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
66 GGGAGATAAGACCTAGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGAT-CTTTA-TTCA
** * * * * * **
12603565 ATCCGCTCTACTGTAACTTCAGGGAGATAGGA-CAGTGT-C-TTCGATCTGCTCCGTTGTAATCT
1 ATCTACTCTACTGTAACTTCAGAGAGATAAGATC-CTTTACTTTAG-TCTGCTCCACTGTAATCT
* ** *
12603627 CAGGGAAATAAGATATTTGGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGAT-TTCTGG
64 CAGGGAGATAAG--ACCTAGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTT-T--
*
12603691 CTTCA
124 ATTCA
* * * * ** *
12603696 ATCTGCTCCACTGTAACATCAGGGAGATAAGAT-CTGAAATT-CTTCGGTCTACTCCACTGTAA-
1 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT----TTACTTTAGTCTGCTCCACTGTAAT
* * * * * *
12603758 CTTCAGGGAGATAAGACCT-GGTGCGATCT-CTCTACTGTAACTTTAGAGAGATAAGATCCTTTA
62 C-TCAGGGAGATAAGACCTAGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGAT-CTTTA
12603821 ATCCGCTCCA
Statistics
Matches: 422, Mismatches: 65, Indels: 54
0.78 0.12 0.10
Matches are distributed among these distances:
126 27 0.06
127 8 0.02
128 35 0.08
129 214 0.51
130 32 0.08
131 73 0.17
132 4 0.01
133 1 0.00
134 26 0.06
135 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (128 bp):
ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTACTTTAGTCTGCTCCACTGTAATCTCA
GGGAGATAAGACCTAGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTATTCA
Found at i:12605314 original size:13 final size:14
Alignment explanation
Indices: 12605288--12605321 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
12605278 TTAGCCTCTC
*
12605288 CATTTTTCATTTTT
1 CATTTTTCAGTTTT
12605302 CATTTTTC-GTTTT
1 CATTTTTCAGTTTT
12605315 CATTTTT
1 CATTTTT
12605322 TTGACTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.12, C:0.15, G:0.03, T:0.71
Consensus pattern (14 bp):
CATTTTTCAGTTTT
Found at i:12605322 original size:8 final size:7
Alignment explanation
Indices: 12605288--12605321 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
12605278 TTAGCCTCTC
12605288 CATTTTT
1 CATTTTT
12605295 CATTTTT
1 CATTTTT
12605302 CATTTTT
1 CATTTTT
*
12605309 C-GTTTT
1 CATTTTT
12605315 CATTTTT
1 CATTTTT
12605322 TTGACTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.12, C:0.15, G:0.03, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:12606179 original size:14 final size:15
Alignment explanation
Indices: 12606156--12606189 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
12606146 TTGACCTCTC
*
12606156 CTTTTTCTTC-TTTT
1 CTTTTCCTTCTTTTT
12606170 CTTTTCCTTCTTTTT
1 CTTTTCCTTCTTTTT
12606185 CTTTT
1 CTTTT
12606190 ATTTTTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTCCTTCTTTTT
Found at i:12606221 original size:20 final size:20
Alignment explanation
Indices: 12606157--12606221 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
12606147 TGACCTCTCC
* *
12606157 TTTTTCTTCTTTTCTTTTCCT
1 TTTTTCTT-TTTTTTTTTGCT
* *
12606178 TCTTTT-TCTTTTATTTTTGAT
1 T-TTTTCT-TTTTTTTTTTGCT
12606199 TTTTTCTTTTTTTTTTTGCT
1 TTTTTCTTTTTTTTTTTGCT
12606219 TTT
1 TTT
12606222 GCTTTTGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
20 18 0.51
21 12 0.34
22 5 0.14
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTTTTTTTTTGCT
Found at i:12606234 original size:6 final size:6
Alignment explanation
Indices: 12606212--12606244 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
12606202 TTCTTTTTTT
*
12606212 TTTTGC TTTTGC TTTTGC TTTTGA TTTTG- TTTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
12606245 TTTTAATTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.03, C:0.09, G:0.15, T:0.73
Consensus pattern (6 bp):
TTTTGC
Found at i:12612147 original size:20 final size:20
Alignment explanation
Indices: 12612106--12612161 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
12612096 ATGTAAAAGG
*
12612106 AAAAATGAAATAAAATAGAA
1 AAAAATGAAATAAAATACAA
*
12612126 AAAAATGAAA-AAAGATTCAA
1 AAAAATGAAATAAA-ATACAA
*
12612146 AACAA-GAAAATAAAAT
1 AAAAATG-AAATAAAAT
12612162 CCTCTCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 4 0.13
20 23 0.77
21 3 0.10
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.14
Consensus pattern (20 bp):
AAAAATGAAATAAAATACAA
Found at i:12612812 original size:22 final size:22
Alignment explanation
Indices: 12612780--12612836 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
12612770 AGGATATCCA
* *
12612780 ATATAGTTGCAGAATAGATCGG
1 ATATAGATGCAAAATAGATCGG
**
12612802 ATATAGATGCAAAATAGATCAA
1 ATATAGATGCAAAATAGATCGG
*
12612824 ATACAGATGCAAA
1 ATATAGATGCAAA
12612837 TTCCTAACTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (22 bp):
ATATAGATGCAAAATAGATCGG
Found at i:12613119 original size:15 final size:16
Alignment explanation
Indices: 12613083--12613112 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12613073 CAACCCAATG
12613083 CAGATA-CAGATTTAA
1 CAGATATCAGATTTAA
12613098 CAGATATCAGATTTA
1 CAGATATCAGATTTA
12613113 CATATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (16 bp):
CAGATATCAGATTTAA
Found at i:12622362 original size:20 final size:22
Alignment explanation
Indices: 12622303--12622363 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
12622293 AAATTAATTC
*
12622303 AATCGTAATCAACGTATAAACT
1 AATCGTAATCAACATATAAACT
12622325 AATCGTAATCAACATATAAACT
1 AATCGTAATCAACATATAAACT
12622347 AA-C-TAATC-ACATTATAA
1 AATCGTAATCAACA-TATAA
12622364 TATGCAAGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 3 0.08
20 10 0.27
21 1 0.03
22 23 0.62
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.28
Consensus pattern (22 bp):
AATCGTAATCAACATATAAACT
Found at i:12644900 original size:12 final size:12
Alignment explanation
Indices: 12644883--12644924 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
12644873 TATTAATTAA
12644883 TCATTTCATATT
1 TCATTTCATATT
12644895 TCATTTCAT-TT
1 TCATTTCATATT
*
12644906 CTCATCTCATA-T
1 -TCATTTCATATT
12644918 TCATTTC
1 TCATTTC
12644925 TCCTCTTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (12 bp):
TCATTTCATATT
Found at i:12649549 original size:20 final size:20
Alignment explanation
Indices: 12649513--12649550 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12649503 TATATATAGA
*
12649513 TATGTAAACAAATTATAAAC
1 TATGTAAACAAAATATAAAC
12649533 TATGTATAA-AAAATATAA
1 TATGTA-AACAAAATATAA
12649551 GGGTGCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
TATGTAAACAAAATATAAAC
Found at i:12649631 original size:10 final size:10
Alignment explanation
Indices: 12649616--12649649 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
12649606 AAAATGTATG
12649616 TATGTATATA
1 TATGTATATA
12649626 TATGTATGTATA
1 TATGTA--TATA
12649638 TATGTATATA
1 TATGTATATA
12649648 TA
1 TA
12649650 AATTACAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 12 0.55
12 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (10 bp):
TATGTATATA
Found at i:12649631 original size:14 final size:14
Alignment explanation
Indices: 12649612--12649640 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12649602 TATAAAAATG
12649612 TATGTATGTATATA
1 TATGTATGTATATA
12649626 TATGTATGTATATA
1 TATGTATGTATATA
12649640 T
1 T
12649641 GTATATATAA
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:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TATGTATGTATATA
Found at i:12649772 original size:3 final size:3
Alignment explanation
Indices: 12649748--12649802 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
12649738 TAAATGAGTA
* * *
12649748 AAT AAC AAT AAT GAT GAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12649795 AAT AAT AA
1 AAT AAT AA
12649803 GATTAAAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12670551 original size:15 final size:15
Alignment explanation
Indices: 12670528--12670563 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
12670518 ATATATCTCC
*
12670528 AAACTATTAAACTAT
1 AAACAATTAAACTAT
12670543 AAACAATTAAACTAT
1 AAACAATTAAACTAT
12670558 AAACAA
1 AAACAA
12670564 GGCCTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (15 bp):
AAACAATTAAACTAT
Found at i:12678440 original size:12 final size:12
Alignment explanation
Indices: 12678423--12678447 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12678413 GAATGTTAAT
12678423 AATAATAATAAC
1 AATAATAATAAC
12678435 AATAATAATAAC
1 AATAATAATAAC
12678447 A
1 A
12678448 CAAAAGATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:12678618 original size:20 final size:20
Alignment explanation
Indices: 12678584--12678625 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
12678574 AACTATTTAA
** *
12678584 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
12678604 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
12678624 AT
1 AT
12678626 GTGTTTATTT
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:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:12691697 original size:54 final size:54
Alignment explanation
Indices: 12691450--12691705 Score: 200
Period size: 54 Copynumber: 4.7 Consensus size: 54
12691440 ATTACCATGC
* * * * *
12691450 ATGTAGGAAGTCCGTTAGGACAAT-TGCAATATGGAAGTCCGTCAGAATAATCTTA
1 ATGT-GGAAGTCCGTCAGGACAATCT-TAATGTGGAAGTCCGTCAGGACAATCTTA
* * * *
12691505 ATGTGGGAAGTCTGTCAGGACTATCTTAA-GTGGGAAGTCCCTCAGGACAATCGTA
1 ATGT-GGAAGTCCGTCAGGACAATCTTAATGT-GGAAGTCCGTCAGGACAATCTTA
** * * * ** * *
12691560 ATGTGGAAGTCCACCAGAACAATCATAATGTGAAAGTTTGCCAAGACAAT-TATA
1 ATGTGGAAGTCCGTCAGGACAATCTTAATGTGGAAGTCCGTCAGGACAATCT-TA
* *
12691614 ATGTGGAAGTCTG-CTAGGTA-AAT-TGTAATGTGGAAGTCCGTTAGGACAATCTTA
1 ATGTGGAAGTCCGTC-AGG-ACAATCT-TAATGTGGAAGTCCGTCAGGACAATCTTA
* *
12691668 ATGTGGCAGTCCGTCAGGACAATCTTAATGTAGAAGTC
1 ATGTGGAAGTCCGTCAGGACAATCTTAATGTGGAAGTC
12691706 TGCTAGGACG
Statistics
Matches: 154, Mismatches: 36, Indels: 23
0.72 0.17 0.11
Matches are distributed among these distances:
53 2 0.01
54 100 0.65
55 51 0.33
56 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (54 bp):
ATGTGGAAGTCCGTCAGGACAATCTTAATGTGGAAGTCCGTCAGGACAATCTTA
Found at i:12691713 original size:27 final size:27
Alignment explanation
Indices: 12691498--12691714 Score: 160
Period size: 27 Copynumber: 8.0 Consensus size: 27
12691488 CCGTCAGAAT
12691498 AATCTTAATGTGGGAAGTCTG-TCAGGAC
1 AATCTTAATGT-GGAAGTCTGCT-AGGAC
* *
12691526 TATCTTAA-GTGGGAAGTC-CCTCAGGAC
1 AATCTTAATGT-GGAAGTCTGCT-AGGAC
* ** * *
12691553 AATCGTAATGTGGAAGTCCACCAGAAC
1 AATCTTAATGTGGAAGTCTGCTAGGAC
* * * * *
12691580 AATCATAATGTGAAAGTTTGCCAAGAC
1 AATCTTAATGTGGAAGTCTGCTAGGAC
12691607 AAT-TATAATGTGGAAGTCTGCTAGGTA-
1 AATCT-TAATGTGGAAGTCTGCTAGG-AC
* *
12691634 AAT-TGTAATGTGGAAGTCCGTTAGGAC
1 AATCT-TAATGTGGAAGTCTGCTAGGAC
* *
12691661 AATCTTAATGTGGCAGTCCG-TCAGGAC
1 AATCTTAATGTGGAAGTCTGCT-AGGAC
*
12691688 AATCTTAATGTAGAAGTCTGCTAGGAC
1 AATCTTAATGTGGAAGTCTGCTAGGAC
12691715 GATTGTATTT
Statistics
Matches: 154, Mismatches: 26, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
26 2 0.01
27 139 0.90
28 13 0.08
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (27 bp):
AATCTTAATGTGGAAGTCTGCTAGGAC
Found at i:12691720 original size:81 final size:81
Alignment explanation
Indices: 12691450--12691721 Score: 264
Period size: 81 Copynumber: 3.3 Consensus size: 81
12691440 ATTACCATGC
* * * * *
12691450 ATGTAGGAAGTCCGTTAGGACAATTGCAATATGGAAGTCCGTCAGAATAATCTTAATGTGGGAAG
1 ATGTA-GAAGTCTGCTAGGACAATTGTAATGTGGAAGTCCGTCAGAACAATCTTAATGT-GGAAG
*
12691515 TCTGTCAGGACTATCTTA
64 TCTGTCAGGACAATCTTA
* * * ** * *
12691533 A-GTGGGAAGTC-CCTCAGGACAATCGTAATGTGGAAGTCCACCAGAACAATCATAATGTGAAAG
1 ATGT-AGAAGTCTGCT-AGGACAATTGTAATGTGGAAGTCCGTCAGAACAATCTTAATGTGGAAG
* * *
12691596 TTTGCCAAGACAAT-TATA
64 TCTGTCAGGACAATCT-TA
* * * *
12691614 ATGTGGAAGTCTGCTAGGTA-AATTGTAATGTGGAAGTCCGTTAGGACAATCTTAATGTGGCAGT
1 ATGTAGAAGTCTGCTAGG-ACAATTGTAATGTGGAAGTCCGTCAGAACAATCTTAATGTGGAAGT
*
12691678 CCGTCAGGACAATCTTA
65 CTGTCAGGACAATCTTA
*
12691695 ATGTAGAAGTCTGCTAGGACGATTGTA
1 ATGTAGAAGTCTGCTAGGACAATTGTA
12691722 TTTGTGAAGT
Statistics
Matches: 151, Mismatches: 30, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
80 2 0.01
81 98 0.65
82 50 0.33
83 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (81 bp):
ATGTAGAAGTCTGCTAGGACAATTGTAATGTGGAAGTCCGTCAGAACAATCTTAATGTGGAAGTC
TGTCAGGACAATCTTA
Found at i:12692814 original size:9 final size:9
Alignment explanation
Indices: 12692800--12692875 Score: 91
Period size: 9 Copynumber: 8.4 Consensus size: 9
12692790 GTAGTGATTC
*
12692800 AATTCGATT
1 AATTCGGTT
12692809 AATTCGAG-T
1 AATTCG-GTT
*
12692818 AATTTGGTT
1 AATTCGGTT
*
12692827 AATTTGGTT
1 AATTCGGTT
*
12692836 AATTCGGGT
1 AATTCGGTT
12692845 AATTCGGTT
1 AATTCGGTT
12692854 AATTCGGTT
1 AATTCGGTT
*
12692863 AATTCAGTT
1 AATTCGGTT
12692872 AATT
1 AATT
12692876 TTTAACCAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
8 1 0.02
9 58 0.98
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:12692838 original size:27 final size:27
Alignment explanation
Indices: 12692800--12692876 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
12692790 GTAGTGATTC
*
12692800 AATTCGATTAATTCGAGTAATTTGGTT
1 AATTCGGTTAATTCGAGTAATTTGGTT
* * *
12692827 AATTTGGTTAATTCGGGTAATTCGGTT
1 AATTCGGTTAATTCGAGTAATTTGGTT
12692854 AATTCGGTTAATTC-AGTTAATTT
1 AATTCGGTTAATTCGAG-TAATTT
12692877 TTAACCAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.45
Consensus pattern (27 bp):
AATTCGGTTAATTCGAGTAATTTGGTT
Found at i:12693687 original size:44 final size:46
Alignment explanation
Indices: 12693597--12693688 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
12693587 TTTGGATCGC
*
12693597 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
12693643 TGTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
12693687 TG
1 TG
12693689 GAATAGAGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 20 0.44
45 3 0.07
46 22 0.49
ACGTcount: A:0.26, C:0.04, G:0.30, T:0.39
Consensus pattern (46 bp):
TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
Found at i:12693689 original size:39 final size:44
Alignment explanation
Indices: 12693597--12693705 Score: 147
Period size: 46 Copynumber: 2.5 Consensus size: 44
12693587 TTTGGATCGC
*
12693597 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--A
12693643 TGTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTA
*
12693683 TG-AATGGAATAGAGGTGTAATAG
1 TGTAATGGAATAGAGGCGTAATAG
12693706 CATAAGGAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
39 18 0.30
40 3 0.05
43 1 0.02
44 13 0.22
45 3 0.05
46 22 0.37
ACGTcount: A:0.28, C:0.04, G:0.31, T:0.37
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTA
Found at i:12693965 original size:122 final size:109
Alignment explanation
Indices: 12693848--12694092 Score: 285
Period size: 122 Copynumber: 2.1 Consensus size: 109
12693838 ATAATTGTTG
12693848 TAAAATATAATTTAATAAAAATATATAATTTAATAAAATGATTAATAAATATTCTTAAATATGAA
1 TAAAATATAATTTAATAAAAATATATAATTTAAT-AAA--ATT-AT---TATTCTT--ATATGAA
*
12693913 TTTACTAATAAAATCATAATATATAACACTATAAAATATAATTTAAAATAATTATAA
57 TTTAC---TAAAATCATAATATATAACAATAT-AAATATAATTTAAAATAATTATAA
* * *
12693970 TTAAATATAATTTAATAATAATATATAATTTAATAAAATTCTTATTCTTATATGAATTTACTAAA
1 TAAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTATTCTTATATGAATTTACTAAA
* * *
12694035 ATCATAATATATAATAATATAAATATAATTT-AACTAATTATTAT
66 ATCATAATATATAACAATATAAATATAATTTAAAATAATTA-TAA
*
12694079 TAAATTATAATTTA
1 TAAAATATAATTTA
12694093 TAATCTACTT
Statistics
Matches: 113, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
108 8 0.07
109 25 0.22
110 22 0.19
113 12 0.11
115 7 0.06
118 1 0.01
119 3 0.03
121 3 0.03
122 32 0.28
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (109 bp):
TAAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTATTCTTATATGAATTTACTAAA
ATCATAATATATAACAATATAAATATAATTTAAAATAATTATAA
Found at i:12693970 original size:16 final size:17
Alignment explanation
Indices: 12693949--12694003 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
12693939 CACTATAAAA
12693949 TATAATTTAAA-ATAAT
1 TATAATTTAAATATAAT
12693965 TATAA-TTAAATATAAT
1 TATAATTTAAATATAAT
*
12693981 T-TAATAATAATATATAAT
1 TATAAT-TTAA-ATATAAT
12693999 T-TAAT
1 TATAAT
12694004 AAAATTCTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 8 0.24
16 11 0.32
17 3 0.09
18 12 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATAATTTAAATATAAT
Found at i:12693976 original size:26 final size:28
Alignment explanation
Indices: 12693946--12694009 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
12693936 TAACACTATA
12693946 AAATATAATTTAA-AATAAT-TATAATT
1 AAATATAATTTAATAATAATATATAATT
12693972 AAATATAATTTAATAATAATATATAATT
1 AAATATAATTTAATAATAATATATAATT
* *
12694000 TAATAAAATT
1 AAATATAATT
12694010 CTTATTCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 13 0.38
27 6 0.18
28 15 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
AAATATAATTTAATAATAATATATAATT
Found at i:12696661 original size:22 final size:22
Alignment explanation
Indices: 12696636--12696677 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12696626 TTTGCTGCAC
*
12696636 TAAATAAGAACACATTCAAATT
1 TAAATAAGAACACATCCAAATT
12696658 TAAATAAGAACACATCCAAA
1 TAAATAAGAACACATCCAAA
12696678 CGCAAGCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.17, G:0.05, T:0.21
Consensus pattern (22 bp):
TAAATAAGAACACATCCAAATT
Found at i:12696913 original size:24 final size:25
Alignment explanation
Indices: 12696885--12696945 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
12696875 ATTCAAACCA
12696885 GAATTGCAACTATAAAA-ACCTCTT
1 GAATTGCAACTATAAAATACCTCTT
12696909 GAATTGCAACTATAAAATACCTCTT
1 GAATTGCAACTATAAAATACCTCTT
*
12696934 AAATTGCAACTA
1 GAATTGCAACTA
12696946 AAGCTTTAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 17 0.49
25 18 0.51
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.30
Consensus pattern (25 bp):
GAATTGCAACTATAAAATACCTCTT
Found at i:12698559 original size:12 final size:12
Alignment explanation
Indices: 12698542--12698582 Score: 82
Period size: 12 Copynumber: 3.4 Consensus size: 12
12698532 AAACAGAGTG
12698542 TTATTATTTATT
1 TTATTATTTATT
12698554 TTATTATTTATT
1 TTATTATTTATT
12698566 TTATTATTTATT
1 TTATTATTTATT
12698578 TTATT
1 TTATT
12698583 TTTTCTTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTATTTATT
Found at i:12705959 original size:20 final size:20
Alignment explanation
Indices: 12705922--12705959 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12705912 TCCCCCCGAA
**
12705922 TCTTTTTCTTTTCATTTTTT
1 TCTTTTTCTCCTCATTTTTT
12705942 TCTTTTTCTCCTC-TTTTT
1 TCTTTTTCTCCTCATTTTT
12705960 GTTGTCGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (20 bp):
TCTTTTTCTCCTCATTTTTT
Found at i:12706604 original size:44 final size:44
Alignment explanation
Indices: 12706556--12706661 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 44
12706546 TGTTCTACTG
* * *
12706556 CAACTTCAGAGAGATAAGATCTAT-TACTTTAATCTGCTCCACTA
1 CAACTTCAGAGAGATAAGAT-TATCGAATTCAATCTGCTCCACTA
* * * *
12706600 CAACTTCAGGGGGATAGGATTATCGAATTCAATCTGCTCCACTG
1 CAACTTCAGAGAGATAAGATTATCGAATTCAATCTGCTCCACTA
*
12706644 CAACCTCA-AGGAGATAAG
1 CAACTTCAGA-GAGATAAG
12706662 TTTTGCTTCT
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
43 3 0.06
44 46 0.94
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (44 bp):
CAACTTCAGAGAGATAAGATTATCGAATTCAATCTGCTCCACTA
Found at i:12706947 original size:87 final size:86
Alignment explanation
Indices: 12706845--12707110 Score: 397
Period size: 87 Copynumber: 3.1 Consensus size: 86
12706835 ACCTGTAATC
* ** * **
12706845 TTCGATCTGCCTTACTGTCGACGCAGGAGGGTAAGATCTGCTATCTTTAACCAGCTCCACTGGAA
1 TTCGATCTGCTTTACTGTTAACGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTACAA
12706910 CCGATGGAGGCAATGCTTTGTT
66 CCGATGGAGGCAA-GCTTTGTT
*
12706932 TTCGATCTGCTTTACTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAA
1 TTCGATCTGCTTTACTGTTAACGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTACAA
*
12706997 CCGATGGAGGCAAGGTTTTGTT
66 CCGATGGAGGCAA-GCTTTGTT
* * * * *
12707019 TTCGATCTGCTTCACTGTTAATGTAGGAAGGTAAGATTTGCTATCTTTAATCAGCTCCACTACAA
1 TTCGATCTGCTTTACTGTTAACGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTACAA
12707084 CCGATGGAGGCAAGCTTTGTT
66 CCGATGGAGGCAAGCTTTGTT
12707105 TTCGAT
1 TTCGAT
12707111 TTTGACTGAT
Statistics
Matches: 163, Mismatches: 16, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
86 13 0.08
87 150 0.92
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (86 bp):
TTCGATCTGCTTTACTGTTAACGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTACAA
CCGATGGAGGCAAGCTTTGTT
Done.