Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 89 of 356
Found at i:27996133 original size:81 final size:81
Alignment explanation
Indices: 27996071--27996268 Score: 326
Period size: 81 Copynumber: 2.5 Consensus size: 81
27996061 CTCTCGATTT
*
27996071 GTAGAATTATTGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTACT
1 GTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTACT
27996136 AAAATACCCCTGTAGG
66 AAAATACCCCTGTAGG
* *
27996152 GTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAG-ATTACC
1 GTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTACT
*
27996216 AAAATACCCTTGTAGG
66 AAAATACCCCTGTAGG
* * *
27996232 GTAGAAATATCGAAATACTCCTATAGGGTAGAATTAC
1 GTAGAATTATCGAAATACCCCTGTAGGGTAGAATTAC
27996269 CGAGATACCC
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
80 54 0.49
81 56 0.51
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (81 bp):
GTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTACT
AAAATACCCCTGTAGG
Found at i:27996258 original size:27 final size:26
Alignment explanation
Indices: 27996071--27996278 Score: 256
Period size: 27 Copynumber: 7.7 Consensus size: 26
27996061 CTCTCGATTT
*
27996071 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTA-CGAAATACCCCTGTAGG
*
27996098 GTAGAATTACTAAAATACCCCTGTAGG
1 GTAGAATTAC-GAAATACCCCTGTAGG
*
27996125 GTAGAATTACTAAAATACCCCTGTAGG
1 GTAGAATTAC-GAAATACCCCTGTAGG
27996152 GTAGAATTATCGAAATACCCCTGTAGG
1 GTAGAATTA-CGAAATACCCCTGTAGG
27996179 GTAGAATTACTGAAATACCCCTGTAGG
1 GTAGAATTAC-GAAATACCCCTGTAGG
* *
27996206 GTAG-ATTACCAAAATACCCTTGTAGG
1 GTAGAATTA-CGAAATACCCCTGTAGG
* * *
27996232 GTAGAAATATCGAAATACTCCTATAGG
1 GTAGAATTA-CGAAATACCCCTGTAGG
*
27996259 GTAGAATTACCGAGATACCC
1 GTAGAATTA-CGAAATACCC
27996279 TTGGGTAAAA
Statistics
Matches: 161, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
26 23 0.14
27 137 0.85
28 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (26 bp):
GTAGAATTACGAAATACCCCTGTAGG
Found at i:27996532 original size:25 final size:25
Alignment explanation
Indices: 27996498--27996586 Score: 117
Period size: 25 Copynumber: 3.6 Consensus size: 25
27996488 AGGAAGTGCT
*
27996498 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAAGGCTTTGCCCCAGTTTACCG
*
27996523 AAAAAAGCTTTGCCCCAGTTTACCG
1 AAAAAGGCTTTGCCCCAGTTTACCG
* * *
27996548 AAAAGGGCTTTGCCCTAGTTTATC-
1 AAAAAGGCTTTGCCCCAGTTTACCG
27996572 AAAAAGGGCTTTGCC
1 AAAAA-GGCTTTGCC
27996587 TCGGTTATTA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
24 4 0.07
25 52 0.93
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAAGGCTTTGCCCCAGTTTACCG
Found at i:27996594 original size:24 final size:25
Alignment explanation
Indices: 27996498--27996599 Score: 82
Period size: 25 Copynumber: 4.1 Consensus size: 25
27996488 AGGAAGTGCT
* * *
27996498 AAAAGGGCTTTGCCCCAGTTTACCGA
1 AAAAGGGCTTTGCCCTAGGTTATC-A
* * * * *
27996524 AAAA-AGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCTAGGTTATCA
*
27996548 AAAAGGGCTTTGCCCTAGTTTATCA
1 AAAAGGGCTTTGCCCTAGGTTATCA
* *
27996573 AAAAGGGCTTTG-CCTCGGTTATTA
1 AAAAGGGCTTTGCCCTAGGTTATCA
27996597 AAA
1 AAA
27996600 GAGGTTAGGC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
24 16 0.24
25 46 0.70
26 4 0.06
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCTAGGTTATCA
Found at i:27999530 original size:27 final size:28
Alignment explanation
Indices: 27999446--27999543 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
27999436 CATGAGATTG
* * * *
27999446 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
27999475 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
27999503 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
27999530 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
27999544 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:27999554 original size:27 final size:27
Alignment explanation
Indices: 27999474--27999556 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
27999464 TAAATTGTAC
* *
27999474 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
27999502 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
27999529 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
27999556 A
1 A
27999557 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:27999557 original size:29 final size:27
Alignment explanation
Indices: 27999446--27999557 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
27999436 CATGAGATTG
** * *
27999446 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
27999475 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
27999503 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
27999530 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
27999558 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:28003220 original size:27 final size:27
Alignment explanation
Indices: 28002343--28003410 Score: 300
Period size: 27 Copynumber: 39.6 Consensus size: 27
28002333 TTAGTTTACT
* * * *
28002343 AAATTACTAAAATGCCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* * *
28002370 AAATTACCAAAGTACCCTTGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
**** * *
28002397 AAATTACCGTTTTACCCTTGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* *** *
28002424 GAATTACCATTTTACCCTCAATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* * *** *
28002451 GAATTAAC-GTTTCACCCTTGATTTATA
1 AAATTACCAAAAT-ACCCTCGATTTATA
**** *
28002478 AAATTACCGTTTTACCCTCAATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* *** * *
28002505 GAATTACCATTTTACCCTCAATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* **** ** *
28002532 GAATTACCGTTTTACCCTTAATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
** * * * *
28002559 AAATTACTGAAATACCATTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTATA
*
28002586 AAATTACCAAAATACCCTCGA-TCAGTA
1 AAATTACCAAAATACCCTCGATTTA-TA
* *
28002613 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTATA
* * * *
28002640 CAATTTCTAAAATACTCC-CTG-TTTGTA
1 AAATTACCAAAATAC-CCTC-GATTTATA
* * * *
28002667 AAATTATCGAAATACTCTCGATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* * *
28002694 AAA-TATCAAAATACCC-CTGATTTTTG
1 AAATTACCAAAATACCCTC-GATTTATA
* ***
28002720 AAATTAAC-GTTTCACCCTCGATTTATA
1 AAATTACCAAAAT-ACCCTCGATTTATA
* * *** * *
28002747 GAATTATC-GTTTCACCTTTGATTTATA
1 AAATTACCAAAAT-ACCCTCGATTTATA
* **** *
28002774 GAATTACCGTTTTACCCTTGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* *** * *
28002801 GAATTACCATTTTACCCTTGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* * ***
28002828 GAATTACTATTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* **** * * *
28002855 GAATTACCGTTTTACCCTTGATTCACA
1 AAATTACCAAAATACCCTCGATTTATA
** * * * *
28002882 AAATTACTGAAATACCATTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTATA
*
28002909 AAATTACCAAAATACCCTCGA-TCAGTA
1 AAATTACCAAAATACCCTCGATTTA-TA
* * *
28002936 AAATTACCAAAATATCCT-GGTTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* * * *
28002962 TAATTACTAAAATACTCCT-GGTTTGTA
1 AAATTACCAAAATAC-CCTCGATTTATA
* ** *
28002989 AAATTACCAAAATACCCTTGGCTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* *
28003016 AAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACCAAAATACCCTC-GATTTATA
* ***
28003043 AAATTAAC-GTTTCACCCTCGATTTATA
1 AAATTACCAAAAT-ACCCTCGATTTATA
* * *** *
28003070 GAATTATC-GTTTCACCCTCGATTTACA
1 AAATTACCAAAAT-ACCCTCGATTTATA
* ****
28003097 GAATTACCGTTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* *** * *
28003124 GAATTACCATTTTACCCTCAATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* ***** *
28003151 GAATTACTGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
****
28003178 AAATTACCGTTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* * * *
28003205 AAATTACTAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTATA
*
28003232 AAATTACCAAAATACCCTCGA-TCAGTA
1 AAATTACCAAAATACCCTCGATTTA-TA
* *
28003259 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTATA
* * *
28003286 AAATTACTAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTATA
* ** *
28003313 AAATTACCAAAATACCCTTGGCTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* * *
28003340 AAATTACCAAAATACCCTTGATTTGTG
1 AAATTACCAAAATACCCTCGATTTATA
* * * *
28003367 AAATTATCAAAATACTCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* *
28003394 GAATTACCGAAATACCC
1 AAATTACCAAAATACCC
28003411 CTATAGGGTA
Statistics
Matches: 845, Mismatches: 170, Indels: 52
0.79 0.16 0.05
Matches are distributed among these distances:
25 1 0.00
26 53 0.06
27 773 0.91
28 18 0.02
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTATA
Found at i:28003421 original size:27 final size:27
Alignment explanation
Indices: 28003391--28003533 Score: 184
Period size: 27 Copynumber: 5.4 Consensus size: 27
28003381 CTCTCAATTT
28003391 GTAGAATTACCGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCCTATAGG
* *
28003418 GTAGAATTACGGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTATAGG
* * *
28003445 GTAGAATTACCAAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTATAGG
* *
28003472 GTAGAAATATCGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCCTATAGG
*
28003499 GTAGAATTACCGAGATA-CCCT-T-GG
1 GTAGAATTACCGAAATACCCCTATAGG
*
28003523 GTAAAATTACC
1 GTAGAATTACC
28003534 ATTTGCCCCT
Statistics
Matches: 102, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
24 12 0.12
25 1 0.01
26 4 0.04
27 85 0.83
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTATAGG
Found at i:28003426 original size:81 final size:78
Alignment explanation
Indices: 28003260--28003518 Score: 195
Period size: 81 Copynumber: 3.2 Consensus size: 78
28003250 CGATCAGTAA
* * * *
28003260 AATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAA
1 AATTACCAAAATACCCCT-GTTTGTGAAATTAC-AAAATACCTC-AGTTTGTAGAATTACCGAAA
*
28003325 TA-CCCT-T-GGCTTGTAA
63 TACCCCTATAGG---GTAG
* *
28003341 AATTACCAAAATACCCTTGATTTGTGAAATTATCAAAATACTCTCAATTTGTAGAATTACCGAAA
1 AATTACCAAAATACCCCTG-TTTGTGAAATTA-CAAAATAC-CTCAGTTTGTAGAATTACCGAAA
28003406 TACCCCTATAGGGTAG
63 TACCCCTATAGGGTAG
** * * * ** * *
28003422 AATTACGGAAATACCCCTG-TAGGGTAGAATTACCAAAATACC-CTTGTAGGGTAGAAATATCGA
1 AATTACCAAAATACCCCTGTTTGTG-A-AATTA-CAAAATACCTC-AGT-TTGTAGAATTACCGA
28003485 AATACCCCTATAGGGTAG
61 AATACCCCTATAGGGTAG
* *
28003503 AATTACCGAGATACCC
1 AATTACCAAAATACCC
28003519 TTGGGTAAAA
Statistics
Matches: 147, Mismatches: 21, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
79 4 0.03
80 4 0.03
81 129 0.88
82 7 0.05
83 1 0.01
84 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (78 bp):
AATTACCAAAATACCCCTGTTTGTGAAATTACAAAATACCTCAGTTTGTAGAATTACCGAAATAC
CCCTATAGGGTAG
Found at i:28003771 original size:25 final size:25
Alignment explanation
Indices: 28003737--28003856 Score: 195
Period size: 25 Copynumber: 4.8 Consensus size: 25
28003727 AGGAAGTGCT
* *
28003737 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
28003762 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
28003787 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
28003812 AAAAGGGCTTTGCCCTAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
* *
28003837 AAAAAGGCTTTGCCTCAGTT
1 AAAAGGGCTTTGCCCCAGTT
28003857 ATTAAAAGAG
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 89 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:28003880 original size:50 final size:50
Alignment explanation
Indices: 28003737--28003881 Score: 159
Period size: 50 Copynumber: 2.9 Consensus size: 50
28003727 AGGAAGTGCT
* * * ** *
28003737 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAAGGCTTTGCCCCAGTTTATCAAAAAGGGCTAGGCCCTAGTTTATCA
* **
28003787 AAAAGGGCTTTGCCCCAGTTTATCAAAAAGGGCTTTGCCCTAGTTTATCA
1 AAAAAGGCTTTGCCCCAGTTTATCAAAAAGGGCTAGGCCCTAGTTTATCA
* *
28003837 AAAAAGGCTTTGCCTCAG-TTAT-TAAAAGAGGCTAGGCCTCTAGTT
1 AAAAAGGCTTTGCCCCAGTTTATCAAAAAG-GGCTAGGCC-CTAGTT
28003882 ATATGATAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
48 5 0.06
49 11 0.13
50 69 0.81
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (50 bp):
AAAAAGGCTTTGCCCCAGTTTATCAAAAAGGGCTAGGCCCTAGTTTATCA
Found at i:28004161 original size:28 final size:29
Alignment explanation
Indices: 28004075--28004156 Score: 96
Period size: 28 Copynumber: 2.8 Consensus size: 29
28004065 CGTTTACAGT
* *
28004075 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGT-ATATG-TTAAAGA
*
28004106 AAAGGCTT-GGCCCAGTA-ACCGTTAAAGA
1 AAAGGCTTCGGCCCAGTATA-TGTTAAAGA
28004134 AAAGGCTTCGGCCCAGTATATGT
1 AAAGGCTTCGGCCCAGTATATGT
28004157 CAAGACTGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
28 14 0.32
29 13 0.30
30 9 0.20
31 8 0.18
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (29 bp):
AAAGGCTTCGGCCCAGTATATGTTAAAGA
Found at i:28008740 original size:24 final size:23
Alignment explanation
Indices: 28008701--28008765 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
28008691 AAAAAATTTG
*
28008701 AATTAT-AGAG-ACAAAAAAATC
1 AATTATAAGAGAAAAAAAAAATC
* *
28008722 AATT-TACAGAGACAAAAAAAATTG
1 AATTATA-AGAGA-AAAAAAAAATC
28008746 AATTATAAGAGAAAAAAAAA
1 AATTATAAGAGAAAAAAAAA
28008766 CAAACAACAG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.03
21 4 0.11
22 4 0.11
23 8 0.22
24 17 0.47
25 2 0.06
ACGTcount: A:0.65, C:0.06, G:0.11, T:0.18
Consensus pattern (23 bp):
AATTATAAGAGAAAAAAAAAATC
Found at i:28008747 original size:45 final size:45
Alignment explanation
Indices: 28008691--28008830 Score: 142
Period size: 45 Copynumber: 3.1 Consensus size: 45
28008681 TACATGAACT
* * *
28008691 AAAAAATTTGAATTATAGAGACAAAAAAATCAATTTACAGAGACA
1 AAAAAAATTGAATTATAGAGACAAAAAAATCAAATTACAGGGACA
* **
28008736 AAAAAAATTGAATTATAAGAGA-AAAAAAAACAAACAACAGGGAC-
1 AAAAAAATTGAATTAT-AGAGACAAAAAAATCAAATTACAGGGACA
* * * *
28008780 AAACAAATTAGAATTATA-AGGACCAAAAATTCAAATTACAGGGATA
1 AAAAAAATT-GAATTATAGA-GACAAAAAAATCAAATTACAGGGACA
28008826 AAAAA
1 AAAAA
28008831 GACGAAATAC
Statistics
Matches: 76, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
43 1 0.01
44 11 0.14
45 55 0.72
46 9 0.12
ACGTcount: A:0.61, C:0.09, G:0.12, T:0.18
Consensus pattern (45 bp):
AAAAAAATTGAATTATAGAGACAAAAAAATCAAATTACAGGGACA
Found at i:28008760 original size:22 final size:22
Alignment explanation
Indices: 28008691--28008764 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 22
28008681 TACATGAACT
*
28008691 AAAAAATTTGAATTAT-AGAGA
1 AAAAAAATTGAATTATAAGAGA
*
28008712 CAAAAAAA-TCAATT-TACAGAGACA
1 -AAAAAAATTGAATTATA-AGAG--A
28008736 AAAAAAATTGAATTATAAGAGA
1 AAAAAAATTGAATTATAAGAGA
28008758 AAAAAAA
1 AAAAAAA
28008765 ACAAACAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
20 1 0.02
21 5 0.12
22 18 0.42
23 7 0.16
24 10 0.23
25 2 0.05
ACGTcount: A:0.64, C:0.05, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAAAAATTGAATTATAAGAGA
Found at i:28013002 original size:10 final size:10
Alignment explanation
Indices: 28012979--28013053 Score: 66
Period size: 10 Copynumber: 7.8 Consensus size: 10
28012969 ATGATAAAAA
* *
28012979 TAAAAATAAA
1 TAAAAATTAT
*
28012989 TAAAATTTAT
1 TAAAAATTAT
** *
28012999 TAAATTTTAA
1 TAAAAATTAT
28013009 TAAAAATTAT
1 TAAAAATTAT
28013019 T-AAAA-TAT
1 TAAAAATTAT
28013027 TAAAAATTAT
1 TAAAAATTAT
*
28013037 AAAAAATTA-
1 TAAAAATTAT
28013046 TAAAAATT
1 TAAAAATT
28013054 GTAAAATTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
8 4 0.08
9 15 0.28
10 34 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:28013042 original size:19 final size:18
Alignment explanation
Indices: 28013008--28013089 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 18
28012998 TTAAATTTTA
*
28013008 ATAAAAATTATTAAAA-T
1 ATAAAAATTATAAAAATT
28013025 ATTAAAAATTATAAAAAATT
1 A-TAAAAATTAT-AAAAATT
* *
28013045 ATAAAAATTGTAAAATTTT
1 ATAAAAATTATAAAA-ATT
*
28013064 ATAAAAATCATAAAAAATTT
1 ATAAAAATTAT-AAAAA-TT
28013084 ATAAAA
1 ATAAAA
28013090 TGCATCAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
17 1 0.02
18 14 0.26
19 24 0.45
20 14 0.26
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (18 bp):
ATAAAAATTATAAAAATT
Found at i:28013068 original size:10 final size:9
Alignment explanation
Indices: 28013008--28013089 Score: 76
Period size: 9 Copynumber: 8.7 Consensus size: 9
28012998 TTAAATTTTA
28013008 ATAAAAATT
1 ATAAAAATT
*
28013017 ATTAAAA-T
1 ATAAAAATT
28013025 ATTAAAAATT
1 A-TAAAAATT
28013035 ATAAAAAATT
1 AT-AAAAATT
28013045 ATAAAAATT
1 ATAAAAATT
* *
28013054 GTAAAATTTT
1 ATAAAA-ATT
*
28013064 ATAAAAATC
1 ATAAAAATT
28013073 ATAAAAAATTT
1 AT-AAAAA-TT
28013084 ATAAAA
1 ATAAAA
28013090 TGCATCAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
8 2 0.03
9 27 0.46
10 27 0.46
11 3 0.05
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:28013070 original size:11 final size:10
Alignment explanation
Indices: 28012990--28013089 Score: 75
Period size: 10 Copynumber: 10.3 Consensus size: 10
28012980 AAAAATAAAT
*
28012990 AAAATTTATT
1 AAAATTTATA
*
28013000 AAATTTTAATA
1 AAAATTT-ATA
*
28013011 AAAA-TTATT
1 AAAATTTATA
*
28013020 AAAATAT-TA
1 AAAATTTATA
28013029 AAAA-TTATA
1 AAAATTTATA
*
28013038 AAAAATTATA
1 AAAATTTATA
*
28013048 AAAA-TTGTA
1 AAAATTTATA
*
28013057 AAATTTTATA
1 AAAATTTATA
*
28013067 AAAA-TCATAA
1 AAAATTTAT-A
28013077 AAAATTTATA
1 AAAATTTATA
28013087 AAA
1 AAA
28013090 TGCATCAAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
8 1 0.01
9 27 0.39
10 34 0.49
11 8 0.11
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (10 bp):
AAAATTTATA
Found at i:28013071 original size:28 final size:28
Alignment explanation
Indices: 28012978--28013079 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 28
28012968 AATGATAAAA
* *
28012978 ATAAAAATAAATAAAATTTATT-AAATTTT
1 ATAAAAAT-TATAAAA-ATATTAAAATTTT
* *
28013007 AATAAAAATTATTAAAATATTAAAA-ATT
1 -ATAAAAATTATAAAAATATTAAAATTTT
28013035 ATAAAAAATTATAAAAAT-TGTAAAATTTT
1 AT-AAAAATTATAAAAATAT-TAAAATTTT
*
28013064 ATAAAAATCATAAAAA
1 ATAAAAATTATAAAAA
28013080 ATTTATAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
27 3 0.05
28 38 0.62
29 12 0.20
30 8 0.13
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (28 bp):
ATAAAAATTATAAAAATATTAAAATTTT
Found at i:28013667 original size:11 final size:11
Alignment explanation
Indices: 28013651--28013677 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28013641 TGTTTGCTCG
28013651 TTTTGAATTTA
1 TTTTGAATTTA
28013662 TTTTGAATTTA
1 TTTTGAATTTA
28013673 TTTTG
1 TTTTG
28013678 TTTTAGTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (11 bp):
TTTTGAATTTA
Found at i:28013817 original size:53 final size:53
Alignment explanation
Indices: 28013759--28013964 Score: 394
Period size: 53 Copynumber: 3.9 Consensus size: 53
28013749 TCTAAAGCTA
28013759 CTAGCTATTTAATTAAGTTAGTTAATATAGTTTAGTCTAAATAAATGAAGTTG
1 CTAGCTATTTAATTAAGTTAGTTAATATAGTTTAGTCTAAATAAATGAAGTTG
* *
28013812 CTAGCTATTTAATTAAGTTAGTTAATATAGTTTAGTCTAAATAAATGAAGCTA
1 CTAGCTATTTAATTAAGTTAGTTAATATAGTTTAGTCTAAATAAATGAAGTTG
28013865 CTAGCTATTTAATTAAGTTAGTTAATATAGTTTAGTCTAAATAAATGAAGTTG
1 CTAGCTATTTAATTAAGTTAGTTAATATAGTTTAGTCTAAATAAATGAAGTTG
28013918 CTAGCTATTTAATTAAGTTAGTTAATATAGTTTAGTCTAAATAAATG
1 CTAGCTATTTAATTAAGTTAGTTAATATAGTTTAGTCTAAATAAATG
28013965 TGTTTAAATT
Statistics
Matches: 149, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 149 1.00
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.41
Consensus pattern (53 bp):
CTAGCTATTTAATTAAGTTAGTTAATATAGTTTAGTCTAAATAAATGAAGTTG
Found at i:28014239 original size:63 final size:63
Alignment explanation
Indices: 28014140--28014266 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
28014130 TAAATATGTG
*
28014140 TTATAATTATGTCTTAGTTTAAACTTGATTTTAATGTGTTTGTTAATGCTTGTAGGTGACTAT
1 TTATAATTATGTCTTAATTTAAACTTGATTTTAATGTGTTTGTTAATGCTTGTAGGTGACTAT
*
28014203 TTATAATTATGTCTTAATTTAAGCTTGATTTTAATGTGTTTGTTAATGCTTGTAGGTGACTAT
1 TTATAATTATGTCTTAATTTAAACTTGATTTTAATGTGTTTGTTAATGCTTGTAGGTGACTAT
28014266 T
1 T
28014267 CAGCTGGAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.51
Consensus pattern (63 bp):
TTATAATTATGTCTTAATTTAAACTTGATTTTAATGTGTTTGTTAATGCTTGTAGGTGACTAT
Found at i:28014482 original size:42 final size:41
Alignment explanation
Indices: 28014404--28014489 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 41
28014394 TATCGACAAA
* * * *
28014404 ATTGTTGGTGTCTATTGGCTGCCAGATGGAATTTAAAGCTT
1 ATTGCTGGTGTCTATTGGCTACCAGAGGGAATTTAAAACTT
*
28014445 ATTGCTGGTGTTTATGTGGCTACCAAGAGGGAA-TTAAAACTT
1 ATTGCTGGTGTCTAT-TGGCTACC-AGAGGGAATTTAAAACTT
28014487 ATT
1 ATT
28014490 CTAAAAACTC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
41 13 0.34
42 18 0.47
43 7 0.18
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.37
Consensus pattern (41 bp):
ATTGCTGGTGTCTATTGGCTACCAGAGGGAATTTAAAACTT
Found at i:28016338 original size:18 final size:18
Alignment explanation
Indices: 28016304--28016355 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
28016294 GAGAGACGAA
28016304 AAAAAGAAA-TG--AAAG
1 AAAAAGAAATTGAAAAAG
*
28016319 AATAAGAAATTGAAAAAG
1 AAAAAGAAATTGAAAAAG
*
28016337 AAAAAGAGATTGAAAAAG
1 AAAAAGAAATTGAAAAAG
28016355 A
1 A
28016356 GAGAATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.26
16 2 0.06
18 21 0.68
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (18 bp):
AAAAAGAAATTGAAAAAG
Found at i:28022424 original size:20 final size:21
Alignment explanation
Indices: 28022399--28022442 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
28022389 GGTAAGACCG
28022399 ATTTCTA-TTTTTATCTCGGT
1 ATTTCTATTTTTTATCTCGGT
*
28022419 ATTTCTATTTTTTATCTTGGT
1 ATTTCTATTTTTTATCTCGGT
28022440 ATT
1 ATT
28022443 GGTTTATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.16, C:0.11, G:0.09, T:0.64
Consensus pattern (21 bp):
ATTTCTATTTTTTATCTCGGT
Found at i:28023518 original size:43 final size:43
Alignment explanation
Indices: 28023449--28023530 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
28023439 AAAATTGTTA
* * *
28023449 GTGTCTATTCGGCTGCTAAGAGGGAATTTAAAGCTTATTGCCG
1 GTGTCTATTCGGCTGCCAAGAAGGAATTTAAAACTTATTGCCG
*
28023492 GTGTCTATTTGGCTGCCAAGAAGGAATTTAAAACTTATT
1 GTGTCTATTCGGCTGCCAAGAAGGAATTTAAAACTTATT
28023531 CTAAAAACTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (43 bp):
GTGTCTATTCGGCTGCCAAGAAGGAATTTAAAACTTATTGCCG
Found at i:28026658 original size:20 final size:19
Alignment explanation
Indices: 28026636--28026672 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
28026626 TGATTTTTGA
28026636 AAAATGATTTACTTTTCTG
1 AAAATGATTTACTTTTCTG
28026655 AAAATGATTTACTTTTCT
1 AAAATGATTTACTTTTCT
28026673 AGTGTTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (19 bp):
AAAATGATTTACTTTTCTG
Found at i:28030318 original size:48 final size:48
Alignment explanation
Indices: 28030246--28030533 Score: 183
Period size: 48 Copynumber: 6.0 Consensus size: 48
28030236 AAGACATTTG
* *** *
28030246 GTTGATATGTGTGCTAGCAAAAGACCATGTTTGGGACATGGCATCGGT
1 GTTGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGT
** *
28030294 GTTGATATGTGTTCTAGTGTAAGACCATGTCTAGGACATGGCATCGG-
1 GTTGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGT
* ** * * * * *
28030341 CTACATTATGAGAGCCAGTATAAGACCATGTCTGGGACATGGCATCAGC
1 GTTGA-TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGT
* ** * * * * *
28030390 CTCAATATGCGAGCAAGTGTAAGACCATGTTTGGAACATGACATCGGCATT
1 GTTGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG---T
* * *
28030441 GTT-ATATGTG-TC-AGTGTAAGACCATGCCTGGGACATGGCATCGACACT
1 GTTGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCG---GT
* * * *
28030489 GATG-TATGAGAGCCAGTGTAAGACCATG-CTTGGGACATGACATCG
1 GTTGATATGTGAGCTAGTGTAAGACCATGTC-TGGGACATGGCATCG
28030534 ACATTTTACC
Statistics
Matches: 189, Mismatches: 39, Indels: 22
0.76 0.16 0.09
Matches are distributed among these distances:
47 2 0.01
48 146 0.77
49 6 0.03
50 34 0.18
51 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.26
Consensus pattern (48 bp):
GTTGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGT
Found at i:28030435 original size:96 final size:97
Alignment explanation
Indices: 28030309--28030533 Score: 244
Period size: 96 Copynumber: 2.3 Consensus size: 97
28030299 TATGTGTTCT
* * *
28030309 AGTGTAAGACCATGTCTAGGACATGGCATCGGC-TACATTATGA-GAGCCAGTATAAGACCATGT
1 AGTGTAAGACCATGT-TTGGACATGACATCGGCAT-CATTAT-ATGAGCCAGTATAAGACCATGC
*
28030372 CTGGGACATGGCATC-AGC-CTCA-ATATGCGAGCA
63 CTGGGACATGGCATCGA-CACTCATATATGAGAGCA
** * * *
28030405 AGTGTAAGACCATGTTTGGAACATGACATCGGCATTGTTATATGTGTCAGTGTAAGACCATGCCT
1 AGTGTAAGACCATGTTTGG-ACATGACATCGGCATCATTATATGAGCCAGTATAAGACCATGCCT
* * *
28030470 GGGACATGGCATCGACACTGATGTATGAGAGCC
65 GGGACATGGCATCGACACTCATATATGAGAGCA
*
28030503 AGTGTAAGACCATGCTTGGGACATGACATCG
1 AGTGTAAGACCATG-TTTGGACATGACATCG
28030534 ACATTTTACC
Statistics
Matches: 109, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
95 4 0.04
96 63 0.58
97 5 0.05
98 33 0.30
99 4 0.04
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (97 bp):
AGTGTAAGACCATGTTTGGACATGACATCGGCATCATTATATGAGCCAGTATAAGACCATGCCTG
GGACATGGCATCGACACTCATATATGAGAGCA
Found at i:28030533 original size:98 final size:96
Alignment explanation
Indices: 28030356--28030538 Score: 251
Period size: 98 Copynumber: 1.9 Consensus size: 96
28030346 TTATGAGAGC
* * *
28030356 CAGTATAAGACCATGTCTGGGACATGGCATCAGCCTCAATATGCGAGCAAGTGTAAGACCATGTT
1 CAGTATAAGACCATGCCTGGGACATGGCATCAGCCTCAATATGAGAGCAAGTGTAAGACCATGCT
*
28030421 TGGAACATGACATCGGCATTGTTATATGTGT
66 TGGAACATGACATCGACATTGTTATATGTGT
* * * *
28030452 CAGTGTAAGACCATGCCTGGGACATGGCATC-GACACTGATGTATGAGAGCCAGTGTAAGACCAT
1 CAGTATAAGACCATGCCTGGGACATGGCATCAG-C-CTCA-ATATGAGAGCAAGTGTAAGACCAT
*
28030516 GCTTGGGACATGACATCGACATT
63 GCTTGGAACATGACATCGACATT
28030539 TTACCCTTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
95 1 0.01
96 30 0.40
97 3 0.04
98 41 0.55
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (96 bp):
CAGTATAAGACCATGCCTGGGACATGGCATCAGCCTCAATATGAGAGCAAGTGTAAGACCATGCT
TGGAACATGACATCGACATTGTTATATGTGT
Found at i:28031157 original size:22 final size:22
Alignment explanation
Indices: 28031131--28031174 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28031121 ATTAATATGA
28031131 GTAAATTCTTAATTAGTCTATT
1 GTAAATTCTTAATTAGTCTATT
28031153 GTAAATTCTTAATTAGTCTATT
1 GTAAATTCTTAATTAGTCTATT
28031175 TTCAATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (22 bp):
GTAAATTCTTAATTAGTCTATT
Found at i:28031845 original size:11 final size:11
Alignment explanation
Indices: 28031829--28031859 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
28031819 ATGAATACCC
28031829 ATAAAATTCAT
1 ATAAAATTCAT
28031840 ATAAAATTCAT
1 ATAAAATTCAT
28031851 ATAAAATTC
1 ATAAAATTC
28031860 TTTGAATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAAAATTCAT
Found at i:28036039 original size:17 final size:19
Alignment explanation
Indices: 28036003--28036047 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
28035993 ACGCTCGTGT
*
28036003 ACACTACCCGTGTGGGCCC
1 ACACGACCCGTGTGGGCCC
28036022 ACAC-ACCCGTGT-GGCCC
1 ACACGACCCGTGTGGGCCC
28036039 ACACGACCC
1 ACACGACCC
28036048 AAATTTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.36
18 12 0.48
19 4 0.16
ACGTcount: A:0.20, C:0.47, G:0.22, T:0.11
Consensus pattern (19 bp):
ACACGACCCGTGTGGGCCC
Found at i:28044783 original size:50 final size:50
Alignment explanation
Indices: 28044708--28044936 Score: 246
Period size: 50 Copynumber: 4.6 Consensus size: 50
28044698 TTGTGAGTCA
* *
28044708 CATGTGTAGCACTAAGTGCAGGCTACTACGTGTACTAGATTGATAGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATTGATAGGTCT
* * * ** * * * *
28044758 CATGTGTAGTACAAAGTACAGGCTACTATGTGTACCCG-TTAACTTCGATCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATTGA--TAGGTCT
* * * *
28044809 CGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TCAGATGGTTAAGTCT
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACT-AGATTGATAGGTCT
* *
28044859 CGTGTGTAGTACTAAGTGCAGGCTACTACATGTACTAGATTGATAGGTCT
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATTGATAGGTCT
* *
28044909 CATGTGTAATACTAAGTGTAGGCTACTA
1 CATGTGTAGTACTAAGTGCAGGCTACTA
28044937 TGCGTACCAG
Statistics
Matches: 144, Mismatches: 30, Indels: 10
0.78 0.16 0.05
Matches are distributed among these distances:
49 3 0.02
50 104 0.72
51 36 0.25
52 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (50 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATTGATAGGTCT
Found at i:28044885 original size:101 final size:101
Alignment explanation
Indices: 28044705--28044886 Score: 267
Period size: 101 Copynumber: 1.8 Consensus size: 101
28044695 TCATTGTGAG
* *
28044705 TCACATGTGTAGCACTAAGTGCAGGCTACTACGTGTACTAGATTGATAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGCACTAAGTGCAGGCTACTACGTGTACTAGATGGATAAGTCGCATGTGTAGTAC
28044770 AAAGTACAGGCTACTATGTGTACCCGTTAACTTCGA
66 AAAGTACAGGCTACTATGTGTACCCGTTAACTTCGA
* * * * *
28044806 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TCAGATGGTTAAGTCTCGTGTGTAGTA
1 TCACATGTGTAGCACTAAGTGCAGGCTACTACGTGTACT-AGATGGATAAGTCGCATGTGTAGTA
* *
28044870 CTAAGTGCAGGCTACTA
65 CAAAGTACAGGCTACTA
28044887 CATGTACTAG
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 1 0.01
101 70 0.99
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (101 bp):
TCACATGTGTAGCACTAAGTGCAGGCTACTACGTGTACTAGATGGATAAGTCGCATGTGTAGTAC
AAAGTACAGGCTACTATGTGTACCCGTTAACTTCGA
Found at i:28045168 original size:16 final size:16
Alignment explanation
Indices: 28045147--28045178 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28045137 AGAATGGAGT
28045147 AAGTGAAATTATGTAA
1 AAGTGAAATTATGTAA
*
28045163 AAGTGAAATTTTGTAA
1 AAGTGAAATTATGTAA
28045179 TAAAACAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (16 bp):
AAGTGAAATTATGTAA
Found at i:28050237 original size:40 final size:40
Alignment explanation
Indices: 28050192--28050343 Score: 207
Period size: 40 Copynumber: 3.8 Consensus size: 40
28050182 ATAACCACAA
* * *
28050192 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
28050232 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
28050272 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
28050312 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
28050344 CATTCAAATG
Statistics
Matches: 102, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.01
40 97 0.95
41 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:28058101 original size:13 final size:13
Alignment explanation
Indices: 28058083--28058109 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28058073 GAAGTAATCG
28058083 CACACGGGCGTGT
1 CACACGGGCGTGT
28058096 CACACGGGCGTGT
1 CACACGGGCGTGT
28058109 C
1 C
28058110 CCTACCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:28060681 original size:41 final size:41
Alignment explanation
Indices: 28060624--28060706 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
28060614 ACTTGAGTAT
*
28060624 GGTCGTATGGGCCACATGGGCTAGGCCAAGTTGGGCATGTG
1 GGTCGTATGGGCCACATGGGCTAGCCCAAGTTGGGCATGTG
* *
28060665 GGTCGTGTGGGCCACATGGGTTAGCCCAAGTTGGGCATGTG
1 GGTCGTATGGGCCACATGGGCTAGCCCAAGTTGGGCATGTG
28060706 G
1 G
28060707 ATTATTAGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.16, C:0.19, G:0.42, T:0.23
Consensus pattern (41 bp):
GGTCGTATGGGCCACATGGGCTAGCCCAAGTTGGGCATGTG
Found at i:28064584 original size:17 final size:17
Alignment explanation
Indices: 28064564--28064599 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28064554 GCCATGAGGA
28064564 CCACACGGGCATGTCAG
1 CCACACGGGCATGTCAG
* *
28064581 CCACATGGGCATGTGAG
1 CCACACGGGCATGTCAG
28064598 CC
1 CC
28064600 CAAAATTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.33, G:0.31, T:0.14
Consensus pattern (17 bp):
CCACACGGGCATGTCAG
Found at i:28066851 original size:58 final size:58
Alignment explanation
Indices: 28066761--28066877 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
28066751 GATTAGACGT
28066761 TATTAGTCTTGAATAAGAATAATAACATAACTTAGGGATCTCTACGGAACAAGTTGAA
1 TATTAGTCTTGAATAAGAATAATAACATAACTTAGGGATCTCTACGGAACAAGTTGAA
28066819 TATTAGTCTTGAATAAGAATAATAACATAACTTAGGGATCTCTACGGAACAAGTTGAA
1 TATTAGTCTTGAATAAGAATAATAACATAACTTAGGGATCTCTACGGAACAAGTTGAA
28066877 T
1 T
28066878 GAATAAATCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (58 bp):
TATTAGTCTTGAATAAGAATAATAACATAACTTAGGGATCTCTACGGAACAAGTTGAA
Found at i:28067400 original size:36 final size:35
Alignment explanation
Indices: 28067340--28067418 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 35
28067330 TACTTTCTAT
*
28067340 TTGGTGTGTTTCGGTGGGACTAGCTCTTTTGAGCA
1 TTGGTGTGTTTCGGTGGGACTAGCTCTTATGAGCA
** * *
28067375 TCTGGTGTGTTTTTGTTGGATTAGCTCTTATGAGCA
1 T-TGGTGTGTTTCGGTGGGACTAGCTCTTATGAGCA
28067411 TTGGTGTG
1 TTGGTGTG
28067419 ATTTGGAGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
35 8 0.21
36 30 0.79
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.44
Consensus pattern (35 bp):
TTGGTGTGTTTCGGTGGGACTAGCTCTTATGAGCA
Found at i:28077974 original size:15 final size:15
Alignment explanation
Indices: 28077933--28077995 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
28077923 GAAAACCAGA
*
28077933 ATAAAGAAATCCATG
1 ATAAAGAAATCCAAG
* * *
28077948 ACAGAGGAATCCAAG
1 ATAAAGAAATCCAAG
*
28077963 ATAAAGATATCCAAG
1 ATAAAGAAATCCAAG
* *
28077978 GTACAGAAATCCAAG
1 ATAAAGAAATCCAAG
28077993 ATA
1 ATA
28077996 CCATATCATA
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.51, C:0.16, G:0.17, T:0.16
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:28089217 original size:32 final size:32
Alignment explanation
Indices: 28089176--28089245 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
28089166 CCATAGGGTT
28089176 TTTATCTTAGAAAGGTTTTAACGAGGCACATTA
1 TTTA-CTTAGAAAGGTTTTAACGAGGCACATTA
*
28089209 TTTACTTAGTAAGGTTTTAACGAGGCACATTA
1 TTTACTTAGAAAGGTTTTAACGAGGCACATTA
28089241 TTTAC
1 TTTAC
28089246 CAATGGACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 32 0.89
33 4 0.11
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (32 bp):
TTTACTTAGAAAGGTTTTAACGAGGCACATTA
Found at i:28089546 original size:9 final size:8
Alignment explanation
Indices: 28089513--28089612 Score: 55
Period size: 9 Copynumber: 12.0 Consensus size: 8
28089503 ACTTTATAAA
28089513 AATTTT-T
1 AATTTTAT
*
28089520 AATTTTTT
1 AATTTTAT
28089528 AATTTCTAT
1 AATTT-TAT
28089537 ATATTTTAT
1 A-ATTTTAT
28089546 AATTTT-T
1 AATTTTAT
*
28089553 --TTCTTCT
1 AATT-TTAT
28089560 AATTTTTAAT
1 AA-TTTT-AT
28089570 AATTTTTAT
1 AA-TTTTAT
* *
28089579 ATTTTTTAA
1 A-ATTTTAT
*
28089588 AATTTAAT
1 AATTTTAT
28089596 AATTTTAT
1 AATTTTAT
28089604 AAATTTTAT
1 -AATTTTAT
28089613 TGATTTTTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 20
0.73 0.08 0.20
Matches are distributed among these distances:
5 2 0.03
6 2 0.03
7 8 0.11
8 22 0.30
9 26 0.35
10 14 0.19
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (8 bp):
AATTTTAT
Found at i:28089559 original size:25 final size:24
Alignment explanation
Indices: 28089514--28089601 Score: 74
Period size: 26 Copynumber: 3.5 Consensus size: 24
28089504 CTTTATAAAA
28089514 ATTTT-TAATTTTTTAATTTCTATAT
1 ATTTTATAATTTTTT-ATTTCTA-AT
28089539 ATTTTATAATTTTTT-TCTTCTAAT
1 ATTTTATAATTTTTTAT-TTCTAAT
* *
28089563 -TTTTAATAATTTTTATATTTTTTAAA
1 ATTTT-ATAATTTTT-TA-TTTCTAAT
*
28089589 ATTTAATAATTTT
1 ATTTTATAATTTT
28089602 ATAAATTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
23 4 0.08
24 12 0.23
25 11 0.21
26 22 0.42
27 4 0.08
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (24 bp):
ATTTTATAATTTTTTATTTCTAAT
Found at i:28090325 original size:34 final size:35
Alignment explanation
Indices: 28090287--28090412 Score: 143
Period size: 34 Copynumber: 3.7 Consensus size: 35
28090277 TTTTAAAAAA
* * *
28090287 TAAATCAAGGTTTAAAATCTTTTAA-AAAATTAAT
1 TAAATTAAGGTTTATAGTCTTTTAAGAAAATTAAT
*** *
28090321 TAAATT-AGGTTT-TAGGGGTTTAAGTAAATTAAT
1 TAAATTAAGGTTTATAGTCTTTTAAGAAAATTAAT
*
28090354 TAAATTAAGGTTTATGGT-TTTTAAGAAAATTAAT
1 TAAATTAAGGTTTATAGTCTTTTAAGAAAATTAAT
*
28090388 TAAATTAAGGTTTAGAGTCTTTTAA
1 TAAATTAAGGTTTATAGTCTTTTAA
28090413 AAATAATTTT
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
32 6 0.08
33 20 0.27
34 41 0.55
35 8 0.11
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.42
Consensus pattern (35 bp):
TAAATTAAGGTTTATAGTCTTTTAAGAAAATTAAT
Found at i:28090729 original size:125 final size:124
Alignment explanation
Indices: 28090505--28091479 Score: 995
Period size: 125 Copynumber: 7.9 Consensus size: 124
28090495 GTTTGTTTTT
* **
28090505 TTTTTCTACAGTAGTTTCTAAAAAAAATTAATTTTGAGAAGACGGTTCTGAAAAAATAGTGAAAA
1 TTTTTCTACAGTAGTTTCT-GAAAAAA-TAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAA
** * * * * * *
28090570 AAAATCTTCAAGCAAGATTCAGTGTAAGCAAAAGTACTGAAAAAAGCT-CCACGTGGTCGCTC
64 AAACGCTTCAAGTAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCACGTGGT-GCTC
* * * * * *
28090632 TTTTTCTACAGTAGTTTCTGAAAGAATAATTTTGAAAAGATGGTTTTGAAAAAATAATGTAAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * * * *
28090697 ACACTTCAAGTAGTATGCACTATTAGCAAAAGTACTAAAAAAGCTCCCACGT-G-G---
66 ACGCTTCAAGTAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACGTGGTGCTC
* * * *
28090751 ---------AGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTAAAAAAATAGTGTGAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
** * * *
28090807 ACATTTCAAGTAGGATGCATTGTCAACAAAATTACTGAAAAAAGCTCCCACGTGGAAGCTC
66 ACGCTTCAAGTAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCACGTGG-TGCTC
* * * ** * *
28090868 TTTTTCTACAATAGTTTTTGAGAAAATAATTTTGAGAAGACTATTATGAAAAAATAATGT-AAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * * * * *
28090932 ATGCTTAAAGTAGTATACACTGTCAGCAAAAGTACTAAAAAAGCTCCCACGTGGACGCTC
66 ACGCTTCAAGTAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACGTGG-TGCTC
* *
28090992 TTTTTCTATAGTAGTTGCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * * * *
28091057 ACGCTTCAAGCAGGATGCACTTTCAGAAAAACTACTAAAAAAGCTCCCACATGGATGCTC
66 ACGCTTCAAGTAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACGTGG-TGCTC
* *
28091117 TTTTTCTACAGTAG-TTCTTAAAAAA-AATTTTGAGAAGACGATTCT-AAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* ** * * * * *
28091179 ATGCTTCAAACAAGATGCACTGTCAACAAAATTATTAACAAAAGCTCCCACATAGATGCT-
66 ACGCTTCAAGTAGGATGCACTGTCAGCAAAATTACTAA-AAAAGCTCCCACGT-GGTGCTC
* * * *
28091239 TTTTTTTACAGTAGTTCCTGAAAAAATAATTTTGAG-AGACAGTTTTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * *
28091303 ACGCTTCAAGTAGGATGTATTGTCAGAAAAATTACTAAAACAAGCTCCCACGTGGATGCTC
66 ACGCTTCAAGTAGGATGCACTGTCAGCAAAATTACTAAAA-AAGCTCCCACGTGG-TGCTC
* * * * *
28091364 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTCCTAAAAAAATAGTTTC-AAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* *
28091428 ACTGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCAC
66 AC-GCTTCAAGTAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCAC
28091480 ATGAACACTC
Statistics
Matches: 706, Mismatches: 113, Indels: 59
0.80 0.13 0.07
Matches are distributed among these distances:
110 76 0.11
111 16 0.02
112 1 0.00
114 1 0.00
122 61 0.09
123 56 0.08
124 164 0.23
125 204 0.29
126 104 0.15
127 23 0.03
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (124 bp):
TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
ACGCTTCAAGTAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACGTGGTGCTC
Found at i:28090763 original size:110 final size:111
Alignment explanation
Indices: 28090641--28090862 Score: 295
Period size: 110 Copynumber: 2.0 Consensus size: 111
28090631 CTTTTTCTAC
* * * * *
28090641 AGTAGTTTCTGAAAGAATAATTTTGAA-AAGATGGTTTTGAAAAAATAATGTAAAAAACACTTCA
1 AGTAGTTCCTGAAAAAATAATTTT-AAGAAGACGGTTCTAAAAAAATAATGTAAAAAACACTTCA
* * *
28090705 AGTAGTATGCACTATTAGCAAAAGTACT-AAAAAAGCTCCCACGTGG
65 AGTAGGATGCACTATCAACAAAAGTACTGAAAAAAGCTCCCACGTGG
* * *
28090751 AGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTAAAAAAATAGTGTGAAAAACATTTCAA
1 AGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTAAAAAAATAATGTAAAAAACACTTCAA
* * *
28090816 GTAGGATGCATTGTCAACAAAATTACTGAAAAAAGCTCCCACGTGG
66 GTAGGATGCACTATCAACAAAAGTACTGAAAAAAGCTCCCACGTGG
28090862 A
1 A
28090863 AGCTCTTTTT
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
109 2 0.02
110 75 0.78
111 19 0.20
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.26
Consensus pattern (111 bp):
AGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTAAAAAAATAATGTAAAAAACACTTCAA
GTAGGATGCACTATCAACAAAAGTACTGAAAAAAGCTCCCACGTGG
Found at i:28090999 original size:124 final size:125
Alignment explanation
Indices: 28090751--28091509 Score: 904
Period size: 124 Copynumber: 6.1 Consensus size: 125
28090741 TCCCACGTGG
* * * * **
28090751 AGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTAAAAAAATAGTGTGAAAAACATTTCAA
1 AGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAAACGCTTCAA
* * * *
28090816 GTAGGATGCATTGTCAACAAAATTACTGAAAAAAGCTCCCACGTGGAAGCTCTTTTTCTAC
66 GTAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCACATGGATGCTCTTTTTCTAC
* ** * * * * * *
28090877 AATAGTTTTTGAGAAAATAATTTTGAGAAGACTATTATGAAAAAATAATGT-AAAAATGCTTAAA
1 AGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAAACGCTTCAA
* * * * * *
28090941 GTAGTATACACTGTCAGCAAAAGTACTAAAAAAGCTCCCACGTGGACGCTCTTTTTCTAT
66 GTAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACATGGATGCTCTTTTTCTAC
* *
28091001 AGTAGTTGCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCTTCAA
1 AGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAAACGCTTCAA
* * * *
28091066 GCAGGATGCACTTTCAGAAAAACTACTAAAAAAGCTCCCACATGGATGCTCTTTTTCTAC
66 GTAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACATGGATGCTCTTTTTCTAC
* *
28091126 AGTAGTT-CTTAAAAAA-AATTTTGAGAAGACGATTCT-AAAAAATAGTGTCAAAAATGCTTCAA
1 AGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAAACGCTTCAA
** * * * * *
28091188 ACAAGATGCACTGTCAACAAAATTATTAACAAAAGCTCCCACATAGATGCT-TTTTTTTAC
66 GTAGGATGCACTGTCAGCAAAATTACTAA-AAAAGCTCCCACATGGATGCTCTTTTTCTAC
*
28091248 AGTAGTTCCTGAAAAAATAATTTTGAG-AGAC-AGTTTTGAAAAAATAGTGTCAAAAACGCTTCA
1 AGTAGTTCCTGAAAAAATAATTTTGAGAAGACGA-TTCTGAAAAAATAGTGTCAAAAACGCTTCA
* * * * *
28091311 AGTAGGATGTATTGTCAGAAAAATTACTAAAACAAGCTCCCACGTGGATGCTCTTTTTCTAT
65 AGTAGGATGCACTGTCAGCAAAATTACTAAAA-AAGCTCCCACATGGATGCTCTTTTTCTAC
* * * *
28091373 AGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTCCTAAAAAAATAGTTTC-AAAACTGCTTCA
1 AGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAAAC-GCTTCA
* * * ** *
28091437 AGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGAACACTCTTTTTCTGC
65 AGTAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCACATGGATGCTCTTTTTCTAC
28091499 AGTAGTTCCTG
1 AGTAGTTCCTG
28091510 CTTGGCTTTA
Statistics
Matches: 538, Mismatches: 83, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
122 63 0.12
123 56 0.10
124 154 0.29
125 139 0.26
126 122 0.23
127 4 0.01
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (125 bp):
AGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAAACGCTTCAA
GTAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACATGGATGCTCTTTTTCTAC
Found at i:28091366 original size:372 final size:375
Alignment explanation
Indices: 28090751--28091506 Score: 1024
Period size: 372 Copynumber: 2.0 Consensus size: 375
28090741 TCCCACGTGG
* * *
28090751 AGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTAAAAAAATAGTGTGAAAAACATTTCAA
1 AGTAGTT-CTGAAAAAATAATTTTAAGAAGACGATTCTAAAAAAATAGTGTCAAAAACACTTCAA
** * * * *
28090816 GTAGGATGCATTGTCAACAAAATTACTGAAAAAAGCTCCCACGTGGAAGCTCTTTTTCTACAATA
65 ACAAGATGCACTGTCAACAAAATTACTGAAAAAAGCTCCCACATAGAAGCTCTTTTTCTACAATA
** * * *
28090881 GTTTTTGAGAAAATAATTTTGAGAAGACTATTATGAAAAAATAATGTAAAAATGCTTAAAGTAGT
130 GTTCCTGAAAAAATAATTTTGAGAAGACTATTATGAAAAAATAATGTAAAAACGCTTAAAGTAGG
* *
28090946 ATACACTGTCAGCAAAAGTACTAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAGTAGTTGCT
195 ATACACTGTCAGAAAAAGTACTAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAGTAGTTCCT
* *
28091011 GAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAAC-GCTTCAAGCAGGATGC
260 GAAAAAATAATTTTGAGAAGACGGTCCTAAAAAAATAGTGTC-AAAACTGCTTCAAGCAGGATGC
* * **
28091075 ACTTTCAGAAAAACTACT-AAAAAAGCTCCCACATGGATGCTCTTTTTCTAC
324 ACTATCAGAAAAACTACTGAAAAAAGCTCCCACATGAACACTCTTTTTCTAC
* * **
28091126 AGTAGTTCTTAAAAAA-AATTTTGAGAAGACGATTCT-AAAAAATAGTGTCAAAAATGCTTCAAA
1 AGTAGTTCTGAAAAAATAATTTTAAGAAGACGATTCTAAAAAAATAGTGTCAAAAACACTTCAAA
* * * *
28091189 CAAGATGCACTGTCAACAAAATTA-TTAACAAAAGCTCCCACATAGATGCT-TTTTTTTACAGTA
66 CAAGATGCACTGTCAACAAAATTACTGAA-AAAAGCTCCCACATAGAAGCTCTTTTTCTACAATA
* * *
28091252 GTTCCTGAAAAAATAATTTTGAG-AGAC-AGTTTTGAAAAAATAGTGTCAAAAACGCTTCAAGTA
130 GTTCCTGAAAAAATAATTTTGAGAAGACTA-TTATGAAAAAATAATGT-AAAAACGCTTAAAGTA
** * * *
28091315 GGATGTATTGTCAGAAAAATTACTAAAACAAGCTCCCACGTGGATGCTCTTTTTCTATAGTAGTT
193 GGATACACTGTCAGAAAAAGTACTAAAA-AAGCTCCCACGTGGACGCTCTTTTTCTATAGTAGTT
*
28091380 CCTGAAAAAATAATTTTGAGAAGACGGTCCTAAAAAAATAGTTTCAAAACTGCTTCAAGCAGGAT
257 CCTGAAAAAATAATTTTGAGAAGACGGTCCTAAAAAAATAGTGTCAAAACTGCTTCAAGCAGGAT
* * *
28091445 GCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGAACACTCTTTTTCTGC
322 GCACTATCAGAAAAACTACTGAAAAAAGCTCCCACATGAACACTCTTTTTCTAC
28091499 AGTAGTTC
1 AGTAGTTC
28091507 CTGCTTGGCT
Statistics
Matches: 333, Mismatches: 42, Indels: 14
0.86 0.11 0.04
Matches are distributed among these distances:
369 1 0.00
370 19 0.06
371 75 0.23
372 168 0.50
373 55 0.17
374 8 0.02
375 7 0.02
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (375 bp):
AGTAGTTCTGAAAAAATAATTTTAAGAAGACGATTCTAAAAAAATAGTGTCAAAAACACTTCAAA
CAAGATGCACTGTCAACAAAATTACTGAAAAAAGCTCCCACATAGAAGCTCTTTTTCTACAATAG
TTCCTGAAAAAATAATTTTGAGAAGACTATTATGAAAAAATAATGTAAAAACGCTTAAAGTAGGA
TACACTGTCAGAAAAAGTACTAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAGTAGTTCCTG
AAAAAATAATTTTGAGAAGACGGTCCTAAAAAAATAGTGTCAAAACTGCTTCAAGCAGGATGCAC
TATCAGAAAAACTACTGAAAAAAGCTCCCACATGAACACTCTTTTTCTAC
Found at i:28092911 original size:38 final size:38
Alignment explanation
Indices: 28092868--28092943 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
28092858 TTCATCCTTT
28092868 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
28092906 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
28092944 GGAGTTCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:28094224 original size:40 final size:40
Alignment explanation
Indices: 28094130--28094271 Score: 178
Period size: 40 Copynumber: 3.5 Consensus size: 40
28094120 TACTCGAATG
* *
28094130 ATATTCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
28094171 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
28094211 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
28094251 ATATCCGGGTTAAGACCCGAA
1 ATATCCGGGCTAAGTCCCGAA
28094272 AGCCTTGTGC
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 59 0.67
41 27 0.31
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:28098297 original size:18 final size:18
Alignment explanation
Indices: 28098260--28098298 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28098250 GGAAAATGAA
*
28098260 ACATATAAAGGTTATAAT
1 ACATATAAAGGTTAGAAT
* *
28098278 ACATATAACGGTTAGGAT
1 ACATATAAAGGTTAGAAT
28098296 ACA
1 ACA
28098299 CACCTAGCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (18 bp):
ACATATAAAGGTTAGAAT
Found at i:28099854 original size:25 final size:26
Alignment explanation
Indices: 28099826--28099878 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
28099816 AACTGTTATA
*
28099826 AAAAATTATA-AAAT-AAAAAATAATT
1 AAAAATTACATAAATGAAAAAAT-ATT
28099851 -AAAATTACATAAATGAAAAAATATT
1 AAAAATTACATAAATGAAAAAATATT
28099876 AAA
1 AAA
28099879 TAATATTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
24 8 0.33
25 7 0.29
26 9 0.38
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (26 bp):
AAAAATTACATAAATGAAAAAATATT
Found at i:28101330 original size:6 final size:6
Alignment explanation
Indices: 28101319--28101352 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
28101309 CATCCAATCT
*
28101319 CCATTG CCATTG CCAGTG CCATTG CCATTG CCAT
1 CCATTG CCATTG CCATTG CCATTG CCATTG CCAT
28101353 CAATATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.35, G:0.18, T:0.29
Consensus pattern (6 bp):
CCATTG
Found at i:28108062 original size:44 final size:44
Alignment explanation
Indices: 28108012--28108099 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
28108002 AAAAACTTTC
*
28108012 TATTTATACTAGTAATAGAAAGGTAAAATAGTAAATAGCAAGGG
1 TATTTATACTAGTAATAAAAAGGTAAAATAGTAAATAGCAAGGG
28108056 TATTTATACTAGTAATAAAAAGGTAAAATAGTAAATAGCAAGGG
1 TATTTATACTAGTAATAAAAAGGTAAAATAGTAAATAGCAAGGG
28108100 CAAAAGAGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (44 bp):
TATTTATACTAGTAATAAAAAGGTAAAATAGTAAATAGCAAGGG
Found at i:28115816 original size:18 final size:17
Alignment explanation
Indices: 28115787--28115822 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
28115777 ATCTCTCCCC
*
28115787 TTTTGAAATATTATAAA
1 TTTTGAAATATTAGAAA
28115804 TTTTGATAATATTAGAAA
1 TTTTGA-AATATTAGAAA
28115822 T
1 T
28115823 CAATTATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (17 bp):
TTTTGAAATATTAGAAA
Found at i:28116397 original size:21 final size:20
Alignment explanation
Indices: 28116372--28116411 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28116362 TCTAATTACG
*
28116372 ATCTATAATTTTTATTTATTA
1 ATCTATAATTATT-TTTATTA
*
28116393 ATCTATTATTATTTTTATT
1 ATCTATAATTATTTTTATT
28116412 CCAATTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
ATCTATAATTATTTTTATTA
Found at i:28120904 original size:19 final size:17
Alignment explanation
Indices: 28120867--28120933 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 17
28120857 AACAATATCT
*
28120867 TTATTTTAATTTTATAA
1 TTATTTTAATTTTAAAA
28120884 TTATTTTATATTTTTAAAA
1 TTATTTTA-A-TTTTAAAA
*
28120903 TTATGTTTTAATATTATAAA
1 TTA--TTTTAATTTTA-AAA
28120923 -TAGTTTTAATT
1 TTA-TTTTAATT
28120934 ATAATTCATT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
17 8 0.19
18 9 0.21
19 16 0.38
20 4 0.10
21 5 0.12
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TTATTTTAATTTTAAAA
Found at i:28121518 original size:21 final size:22
Alignment explanation
Indices: 28121492--28121532 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
28121482 AAAAATAAAT
28121492 TGCTATTTT-TTGTTATTTTAA
1 TGCTATTTTCTTGTTATTTTAA
*
28121513 TGCTATTTTCTTGTTGTTTT
1 TGCTATTTTCTTGTTATTTT
28121533 CTCCCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.68
Consensus pattern (22 bp):
TGCTATTTTCTTGTTATTTTAA
Found at i:28131188 original size:21 final size:20
Alignment explanation
Indices: 28131164--28131211 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
28131154 GTCACAGTTG
28131164 AAAATA-AAATAATTAAGTCTA
1 AAAATACAAATAA-TAA-TCTA
*
28131185 AAAATATCAAATAATAATCTT
1 AAAATA-CAAATAATAATCTA
28131206 AAAATA
1 AAAATA
28131212 TTTTTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 15 0.62
22 3 0.12
23 6 0.25
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAATACAAATAATAATCTA
Found at i:28131198 original size:23 final size:21
Alignment explanation
Indices: 28131170--28131212 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28131160 GTTGAAAATA
28131170 AAATAATTAAGTCTAAAAATATC
1 AAATAA-TAA-TCTAAAAATATC
*
28131193 AAATAATAATCTTAAAATAT
1 AAATAATAATCTAAAAATAT
28131213 TTTTAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 3 0.16
23 6 0.32
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
AAATAATAATCTAAAAATATC
Found at i:28131333 original size:12 final size:12
Alignment explanation
Indices: 28131316--28131345 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
28131306 GGATAGTGAG
28131316 ATATGAAGCTCA
1 ATATGAAGCTCA
28131328 ATATGAAGCTCA
1 ATATGAAGCTCA
28131340 ATATGA
1 ATATGA
28131346 GTTCAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (12 bp):
ATATGAAGCTCA
Found at i:28131969 original size:34 final size:34
Alignment explanation
Indices: 28131919--28132005 Score: 95
Period size: 34 Copynumber: 2.5 Consensus size: 34
28131909 TGATAACATT
* **
28131919 TAATAATGCTTTTAACAGAGTAATACGGCAGCAA-
1 TAAT-ATGCTTATAACAGAGTAATAAAGCAGCAAG
** *
28131953 TCAATATGCTTATAACAGTTTAATAAAGTAGCAAG
1 T-AATATGCTTATAACAGAGTAATAAAGCAGCAAG
28131988 TAATATGCTTATAACAGA
1 TAATATGCTTATAACAGA
28132006 TCACCTCAGT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
34 40 0.91
35 4 0.09
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (34 bp):
TAATATGCTTATAACAGAGTAATAAAGCAGCAAG
Found at i:28137021 original size:28 final size:28
Alignment explanation
Indices: 28136989--28137058 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
28136979 AATGAGATTG
28136989 GCACTAAGTGTGCGAGTTT-AAT-TGTATA
1 GCACTAAGTGTGCGAGTTTGAATAT-TA-A
*
28137017 GCACTAAGTGTGCGAGTTTGACTATTAA
1 GCACTAAGTGTGCGAGTTTGAATATTAA
28137045 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28137059 GACTTACTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 34 0.87
29 4 0.10
30 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATATTAA
Found at i:28144314 original size:24 final size:23
Alignment explanation
Indices: 28144260--28144314 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
28144250 GCGCGAATCA
* * *
28144260 TTATTTTATATTAAATTCTTTTT
1 TTATTTTAAATAAAATTATTTTT
*
28144283 TGTTTTTTAAATAAAATATATTTTT
1 T-TATTTTAAATAAAAT-TATTTTT
28144308 TTATTTT
1 TTATTTT
28144315 CGGGTTAGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 1 0.04
24 17 0.68
25 7 0.28
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
TTATTTTAAATAAAATTATTTTT
Found at i:28144391 original size:27 final size:27
Alignment explanation
Indices: 28144352--28144426 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
28144342 TACAGGTTGC
* * **
28144352 GCCTACCTGAGAGGCGCAGCTAATCGA
1 GCCTATCTCAGAGGCGCAAATAATCGA
* * *
28144379 GCCTATCTCAGAGGCGCAAATGATTGT
1 GCCTATCTCAGAGGCGCAAATAATCGA
28144406 GCCTATCTCAGAGGCGCAAAT
1 GCCTATCTCAGAGGCGCAAAT
28144427 GGTGGGGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (27 bp):
GCCTATCTCAGAGGCGCAAATAATCGA
Found at i:28147892 original size:33 final size:33
Alignment explanation
Indices: 28147850--28147926 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
28147840 ATGAACTTGA
28147850 GTCGGGAGGAGTGGAGTACGGCAATTGATACGG
1 GTCGGGAGGAGTGGAGTACGGCAATTGATACGG
* * *
28147883 GTCGGGAGGAGTGGAGTACTGCGATTGGTACGG
1 GTCGGGAGGAGTGGAGTACGGCAATTGATACGG
* *
28147916 GCCGGAAGGAG
1 GTCGGGAGGAG
28147927 CAGAGTACTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.22, C:0.13, G:0.48, T:0.17
Consensus pattern (33 bp):
GTCGGGAGGAGTGGAGTACGGCAATTGATACGG
Found at i:28147933 original size:33 final size:33
Alignment explanation
Indices: 28147863--28147936 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
28147853 GGGAGGAGTG
* * * **
28147863 GAGTACGGCAATTGATACGGGTCGGGAGGAGTG
1 GAGTACTGCAATTGATACGGGCCGGAAGGAGCA
* *
28147896 GAGTACTGCGATTGGTACGGGCCGGAAGGAGCA
1 GAGTACTGCAATTGATACGGGCCGGAAGGAGCA
28147929 GAGTACTG
1 GAGTACTG
28147937 AGGTGGATAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.15, G:0.43, T:0.18
Consensus pattern (33 bp):
GAGTACTGCAATTGATACGGGCCGGAAGGAGCA
Found at i:28152575 original size:22 final size:21
Alignment explanation
Indices: 28152545--28152591 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
28152535 TACAAATTAA
28152545 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
28152567 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
28152588 ATCT
1 ATCT
28152592 AGGATTGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:28152599 original size:19 final size:19
Alignment explanation
Indices: 28152562--28152659 Score: 155
Period size: 19 Copynumber: 5.2 Consensus size: 19
28152552 AGATTACAAG
28152562 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
*
28152583 ATCATATCTAGGATTGCAT
1 ATCATATCTAAGATTGCAT
28152602 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
28152619 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
28152638 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
28152657 ATC
1 ATC
28152660 CTTAAAGATT
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
17 17 0.23
19 47 0.64
20 1 0.01
21 8 0.11
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:28152626 original size:36 final size:37
Alignment explanation
Indices: 28152562--28152659 Score: 144
Period size: 36 Copynumber: 2.6 Consensus size: 37
28152552 AGATTACAAG
*
28152562 ATCATATCTTCAAGATTGCATATCATATCTAGGATTGCAT
1 ATCATATC-T-AAGATTG-ATATCATATCTAAGATTGCAT
28152602 ATCATATCTAAGATTG-TATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
28152638 ATCATATCTAAGATTGCATATC
1 ATCATATCTAAGATTG-ATATC
28152660 CTTAAAGATT
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
36 35 0.64
38 11 0.20
39 1 0.02
40 8 0.15
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (37 bp):
ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
Found at i:28153395 original size:132 final size:132
Alignment explanation
Indices: 28153237--28154079 Score: 1389
Period size: 132 Copynumber: 6.4 Consensus size: 132
28153227 ATGGAGATGC
* * * *
28153237 CAGATCTGTTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTATCTTCAATTT
1 CAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTT
* * * * * * * *
28153302 GTTCCCTATAAACATAGGGATGTCATGTTGAAATCTTCGATCTGCTTTGCTATAAGCATAGGAAT
66 GTTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAAGAGT
28153367 GT
131 GT
*
28153369 CAGATCTGCTATCTTCGATTTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTT
1 CAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTT
* * * *
28153434 GTTCCCTATAAACACAGGGATGCCATGCTAAAATCTTCGATCTGCTTCGCTGTAATCACAGGAAT
66 GTTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAAGAGT
28153499 GT
131 GT
* *
28153501 CAGATCTGCTATCTTTGATTTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTT
1 CAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTT
*
28153566 GTTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAATCACAAGAGT
66 GTTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAAGAGT
28153631 GT
131 GT
* * *
28153633 TAGATCTGATATCTTCGATCTGTTCCCTATAAACAAAGGGATGCCAAATCTGCTATCTTCAACTT
1 CAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTT
28153698 GTTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAAGAGT
66 GTTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAAGAGT
28153763 GT
131 GT
*
28153765 CAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATATGCTATCTTCAACTT
1 CAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTT
* *
28153830 GTTCCCTATAAACACAGAGATGCCATGCTGAAATCTTCGATCTACTTCGCTGTAAGCACAAGAGT
66 GTTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAAGAGT
28153895 GT
131 GT
* *
28153897 CAGATCTGCTATCTTCGATCTATTCCCTATAAACATAGGGATGCCAAATCTGCTATCTTCAACTT
1 CAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTT
* *
28153962 GTTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTACTTCGCTGTAAGCACAGGAGT
66 GTTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAAGAGT
28154027 GT
131 GT
* * *
28154029 CAGATCTGCTATCTTCGATCTGTTCTCTATAAACAAAGAGATGCCAAATCT
1 CAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCT
28154080 TGTTTCTGTA
Statistics
Matches: 675, Mismatches: 36, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 675 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (132 bp):
CAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTT
GTTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAAGAGT
GT
Found at i:28154059 original size:88 final size:89
Alignment explanation
Indices: 28153229--28154074 Score: 534
Period size: 88 Copynumber: 9.6 Consensus size: 89
28153219 CCGTCGAAAT
* * * * *
28153229 GGAGATGCCAGATCTGTTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGCTAT
1 GGAGATGTCAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCC--ATGCTGATAT
* ** *
28153293 CTTCAAT-TTGTTCCCTATAAACATA
64 CTTCGATCTACTTCCCTATAAACACA
** ** * * * * *
28153318 GG-GATGTCATG-T-TGAAATCTTCGATCTGCTTTGCTATAAGCATAGGAATGTCA-GATCTGCT
1 GGAGATGTCA-GATCTGCTATCTTCGATCTG-TTCCCTATAAACACAGGGATGCCATG--CTGAT
**
28153379 ATCTTCGAT-TTGTTCCCTATAAACACA
62 ATCTTCGATCTACTTCCCTATAAACACA
* * * * *
28153406 GG-GATGCCAAATCTGCTATCTTC-AACTTGTTCCCTATAAACACAGGGATGCCATGCTAAAATC
1 GGAGATGTCAGATCTGCTATCTTCGATC-TGTTCCCTATAAACACAGGGATGCCATGCTGATATC
* * * *
28153469 TTCGATCTGCTTCGCTGTAATCACA
65 TTCGATCTACTTCCCTATAAACACA
* * *
28153494 GGA-ATGTCAGATCTGCTATCTTTGATTTGTTCCCTATAAACACAGGGATGCCAAAT-CTGCTAT
1 GGAGATGTCAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCC--ATGCTGATAT
* **
28153557 CTTC-AACTTGTTCCCTATAAACACA
64 CTTCGATCTACTTCCCTATAAACACA
* ** * * * *
28153582 GG-GATG-C-CATGCTGAAATCTTCGATCTGCTTCGCTGTAATCACAAGAGTGTTAG--AT-CTG
1 GGAGATGTCAGAT-CTGCTATCTTCGATCTG-TTCCCTATAAACAC-AG-G-GAT-GCCATGCTG
* *
28153641 ATATCTTCGATCT-GTTCCCTATAAACAAA
60 ATATCTTCGATCTACTTCCCTATAAACACA
* * * *
28153670 GG-GATGCCAAATCTGCTATCTTC-AACTTGTTCCCTATAAACACAGGGATGCCATGCTGAAATC
1 GGAGATGTCAGATCTGCTATCTTCGATC-TGTTCCCTATAAACACAGGGATGCCATGCTGATATC
* * * *
28153733 TTCGATCTGCTTCGCTGTAAGCACA
65 TTCGATCTACTTCCCTATAAACACA
* * *
28153758 AGAG-TGTCAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAAT-ATGCTAT
1 GGAGATGTCAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCC--ATGCTGATAT
* **
28153821 CTTC-AACTTGTTCCCTATAAACACA
64 CTTCGATCTACTTCCCTATAAACACA
* ** * * * * * * *
28153846 -GAGATG-C-CATGCTGAAATCTTCGATCTACTTCGCTGTAAGCACA-AGAGTGTCA-GATCTGC
1 GGAGATGTCAGAT-CTGCTATCTTCGATCT-GTTCCCTATAAACACAGGGA-TGCCATG--CTGA
*
28153906 TATCTTCGATCTA-TTCCCTATAAACATA
61 TATCTTCGATCTACTTCCCTATAAACACA
* * * *
28153934 GG-GATGCCAAATCTGCTATCTTC-AACTTGTTCCCTATAAACACAGGGATGCCATGCTGAAATC
1 GGAGATGTCAGATCTGCTATCTTCGATC-TGTTCCCTATAAACACAGGGATGCCATGCTGATATC
* * *
28153997 TTCGATCTACTTCGCTGTAAGCACA
65 TTCGATCTACTTCCCTATAAACACA
* * *
28154022 GGAG-TGTCAGATCTGCTATCTTCGATCTGTTCTCTATAAACAAAGAGATGCCA
1 GGAGATGTCAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCA
28154075 AATCTTGTTT
Statistics
Matches: 589, Mismatches: 118, Indels: 101
0.73 0.15 0.12
Matches are distributed among these distances:
84 1 0.00
85 2 0.00
86 9 0.02
87 90 0.15
88 403 0.68
89 72 0.12
90 9 0.02
91 2 0.00
92 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (89 bp):
GGAGATGTCAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCATGCTGATATCT
TCGATCTACTTCCCTATAAACACA
Found at i:28157560 original size:16 final size:14
Alignment explanation
Indices: 28157519--28157571 Score: 65
Period size: 14 Copynumber: 3.7 Consensus size: 14
28157509 TTTATAATTT
28157519 TGAATGCAAATG-A
1 TGAATGCAAATGCA
28157532 TGCAATG-AAATGCTA
1 TG-AATGCAAATGC-A
28157547 TGAGATGCAAATGCA
1 TGA-ATGCAAATGCA
28157562 TGAATGCAAA
1 TGAATGCAAA
28157572 AGGTATCGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 7 0.20
14 12 0.34
15 10 0.29
16 6 0.17
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (14 bp):
TGAATGCAAATGCA
Found at i:28157608 original size:13 final size:14
Alignment explanation
Indices: 28157590--28157618 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28157580 ATCTCGATTC
28157590 AATC-TTATTTAGA
1 AATCTTTATTTAGA
28157603 AATCTTTATTTAGA
1 AATCTTTATTTAGA
28157617 AA
1 AA
28157619 AAGAATATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
AATCTTTATTTAGA
Found at i:28160596 original size:19 final size:19
Alignment explanation
Indices: 28160547--28160615 Score: 84
Period size: 19 Copynumber: 3.5 Consensus size: 19
28160537 AAATTAAATC
* *
28160547 TCTAAAATTACAAGATCATA
1 TCTAAGATTAC-ATATCATA
*
28160567 TCTTCAAGATTGCATATCATA
1 TC-T-AAGATTACATATCATA
28160588 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
28160607 TCTAAGATT
1 TCTAAGATT
28160616 TAAGATTGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
19 24 0.56
20 3 0.07
21 10 0.23
22 6 0.14
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:28161077 original size:21 final size:20
Alignment explanation
Indices: 28161030--28161078 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
28161020 CTTTTTTTTT
* *
28161030 CTTTTT-TTCTTTTTTCTTT
1 CTTTTTATTCTTTCTTCTTC
*
28161049 CTTCTTATTCTCTTCTTCTTC
1 CTTTTTATTCT-TTCTTCTTC
28161070 CTTTTTATT
1 CTTTTTATT
28161079 TCTCCTTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 5 0.21
20 4 0.17
21 15 0.62
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.73
Consensus pattern (20 bp):
CTTTTTATTCTTTCTTCTTC
Found at i:28161081 original size:31 final size:30
Alignment explanation
Indices: 28161029--28161098 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
28161019 CCTTTTTTTT
* * * *
28161029 TCTTTTTTTCTTTTTTCTTTCTTCTTAT-TC
1 TCTTTTCTTCCTTTTTATTTCTCCTT-TGTC
28161059 TCTTCTTCTTCCTTTTTATTTCTCCTTTGTC
1 TCTT-TTCTTCCTTTTTATTTCTCCTTTGTC
28161090 TCTTTTCTT
1 TCTTTTCTT
28161099 TCCCTCTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.03, C:0.24, G:0.01, T:0.71
Consensus pattern (30 bp):
TCTTTTCTTCCTTTTTATTTCTCCTTTGTC
Found at i:28161292 original size:32 final size:32
Alignment explanation
Indices: 28161230--28161316 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 32
28161220 AGGGGGCATG
* *
28161230 CATGCAGGCTGCAGGGAGGATTGATCGGGCAA
1 CATGCAGGCTGCAGGGAGAACTGATCGGGCAA
* * *
28161262 CATGCAGGTTGCAGGGAGAACT-ATTTGGGCAG
1 CATGCAGGCTGCAGGGAGAACTGA-TCGGGCAA
* * *
28161294 CAGGTAGGCTGCAGGGAGGACTG
1 CATGCAGGCTGCAGGGAGAACTG
28161317 TTCGAGCAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 1 0.02
32 43 0.98
ACGTcount: A:0.24, C:0.17, G:0.41, T:0.17
Consensus pattern (32 bp):
CATGCAGGCTGCAGGGAGAACTGATCGGGCAA
Found at i:28161390 original size:21 final size:22
Alignment explanation
Indices: 28161364--28161411 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
28161354 TGCCAGGCGC
28161364 GACCCATTTTTA-CCGTATTTT
1 GACCCATTTTTACCCGTATTTT
28161385 GACCCATTTTTACCCGTATTTT
1 GACCCATTTTTACCCGTATTTT
28161407 GACCC
1 GACCC
28161412 GTATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.19, C:0.29, G:0.10, T:0.42
Consensus pattern (22 bp):
GACCCATTTTTACCCGTATTTT
Found at i:28161411 original size:12 final size:12
Alignment explanation
Indices: 28161376--28161415 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
28161366 CCCATTTTTA
28161376 CCGTATTTTGAC
1 CCGTATTTTGAC
*
28161388 CC--ATTTTTAC
1 CCGTATTTTGAC
28161398 CCGTATTTTGAC
1 CCGTATTTTGAC
28161410 CCGTAT
1 CCGTAT
28161416 ATATATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.17, C:0.28, G:0.12, T:0.42
Consensus pattern (12 bp):
CCGTATTTTGAC
Found at i:28162832 original size:12 final size:11
Alignment explanation
Indices: 28162814--28162857 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
28162804 TTGCTCGGCC
28162814 CAAAAAATAAA
1 CAAAAAATAAA
*
28162825 CAAAAAAAAAA
1 CAAAAAATAAA
28162836 CAAAAAATAAA
1 CAAAAAATAAA
28162847 CCAAAAAATAA
1 -CAAAAAATAA
28162858 TAAAAGTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.82, C:0.11, G:0.00, T:0.07
Consensus pattern (11 bp):
CAAAAAATAAA
Found at i:28164270 original size:16 final size:16
Alignment explanation
Indices: 28164224--28164278 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
28164214 AACTTTTATA
*
28164224 TATATAAAATTATTTT
1 TATATATAATTATTTT
* *
28164240 TAT-TACACATGATTTT
1 TATATATA-ATTATTTT
28164256 TATATATAATTATTTT
1 TATATATAATTATTTT
*
28164272 CATATAT
1 TATATAT
28164279 TATTGATCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 3 0.09
16 26 0.81
17 3 0.09
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (16 bp):
TATATATAATTATTTT
Found at i:28164649 original size:69 final size:64
Alignment explanation
Indices: 28164601--28164813 Score: 176
Period size: 56 Copynumber: 3.3 Consensus size: 64
28164591 TATTTATTTC
* *
28164601 TTATATTTGCATGAAATATTAATATATGTATTATGTAATTTATGTTG-T-TTTTTAG------G
1 TTATATTTGCATGAAATATTAATATATATATTATGTAATTTATGTTGTTATTTTTAGTTTTTTA
* * * *
28164657 TTATATTTGCATGAAATATTATTGTATATATTATGTAATTTATATTTCTATATTTATTA-TTTTC
1 TTATATTTGCATGAAATATTAATATATATATTATGTAATTTAT-GTTGT-TATTT-TTAGTTTT-
28164721 TATGA
62 T-T-A
* * * *
28164726 TTATATTTGCATGAAATGTCAATACATATATTATGTAATTTATGTCGTTATTTGTT-GTTTTCTA
1 TTATATTTGCATGAAATATTAATATATATATTATGTAATTTATGTTGTTATTT-TTAGTTTT-T-
28164790 TA
63 TA
*
28164792 TTATATTTGCATGAAATGTTAA
1 TTATATTTGCATGAAATATTAA
28164814 AGTATGTATC
Statistics
Matches: 126, Mismatches: 16, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
56 40 0.32
57 2 0.02
59 1 0.01
60 3 0.02
61 3 0.02
66 22 0.17
67 15 0.12
68 2 0.02
69 38 0.30
ACGTcount: A:0.31, C:0.05, G:0.11, T:0.53
Consensus pattern (64 bp):
TTATATTTGCATGAAATATTAATATATATATTATGTAATTTATGTTGTTATTTTTAGTTTTTTA
Found at i:28164828 original size:66 final size:68
Alignment explanation
Indices: 28164643--28164828 Score: 200
Period size: 66 Copynumber: 2.8 Consensus size: 68
28164633 ATGTAATTTA
* ** * ** *
28164643 TGTTGTTTTTTAGGTTATATTTGCATGAAATATTATTGTATATATTATGTAATTTATATTTCTAT
1 TGTTGTTTTCTATATTATATTTGCATGAAATGTTAAAGTATATATTATGTAATTTATATGTCTAT
28164708 ATT
66 ATT
* * * *
28164711 TATTATTTTCTATGATTATATTTGCATGAAATGTCAATA-CATATATTATGTAA-TT-TATGTCG
1 TGTTGTTTTCTAT-ATTATATTTGCATGAAATGTTAA-AGTATATATTATGTAATTTATATGTC-
28164773 T-TATT
63 TATATT
* *
28164778 TGTTGTTTTCTATATTATATTTGCATGAAATGTTAAAGTATGTATCATGTA
1 TGTTGTTTTCTATATTATATTTGCATGAAATGTTAAAGTATATATTATGTA
28164829 GTTTGTTTTT
Statistics
Matches: 97, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
65 1 0.01
66 32 0.33
67 20 0.21
68 12 0.12
69 32 0.33
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (68 bp):
TGTTGTTTTCTATATTATATTTGCATGAAATGTTAAAGTATATATTATGTAATTTATATGTCTAT
ATT
Found at i:28168072 original size:14 final size:16
Alignment explanation
Indices: 28168053--28168084 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
28168043 TCGATATCTT
28168053 TTTGCAT-TCAT-GCA
1 TTTGCATCTCATCGCA
28168067 TTTGCATCTCATCGCA
1 TTTGCATCTCATCGCA
28168083 TT
1 TT
28168085 ATATGCATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.44
Consensus pattern (16 bp):
TTTGCATCTCATCGCA
Found at i:28195057 original size:46 final size:46
Alignment explanation
Indices: 28195007--28195179 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
28194997 TGGTTGAGCA
28195007 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
28195053 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
28195098 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
28195146 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
28195180 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 60 0.57
47 28 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28195163 original size:93 final size:93
Alignment explanation
Indices: 28195004--28195174 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
28194994 GGATGGTTGA
* *
28195004 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
28195069 TGAGTCTGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
28195097 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28195162 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
28195175 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:28200581 original size:46 final size:46
Alignment explanation
Indices: 28200531--28200703 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
28200521 TGGTTGAGCA
28200531 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
28200577 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
28200622 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
28200670 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
28200704 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28200687 original size:93 final size:93
Alignment explanation
Indices: 28200528--28200698 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
28200518 GGATGGTTGA
* *
28200528 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28200593 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
28200621 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28200686 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
28200699 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:28203334 original size:21 final size:21
Alignment explanation
Indices: 28203298--28203340 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28203288 CACCATGCCG
*
28203298 TGTGACCCAATAGCCATACCA
1 TGTGACCCAATAGCCAAACCA
* *
28203319 TGTGACCCATTTGCCAAACCA
1 TGTGACCCAATAGCCAAACCA
28203340 T
1 T
28203341 CAAAAGGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.33, G:0.14, T:0.23
Consensus pattern (21 bp):
TGTGACCCAATAGCCAAACCA
Found at i:28206270 original size:16 final size:16
Alignment explanation
Indices: 28206237--28206270 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28206227 GTAGAATGTT
* *
28206237 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
28206253 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
28206269 AA
1 AA
28206271 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:28209096 original size:21 final size:21
Alignment explanation
Indices: 28209070--28209110 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28209060 AGACGAGCAA
* *
28209070 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
28209091 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
28209111 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:28211049 original size:16 final size:16
Alignment explanation
Indices: 28211016--28211049 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28211006 GGAGATTGTT
* *
28211016 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
28211032 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
28211048 AA
1 AA
28211050 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:28217966 original size:16 final size:17
Alignment explanation
Indices: 28217938--28217976 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
28217928 AGGAGAAAAG
* *
28217938 AAAGAAAATGAAGGAGA
1 AAAGAAAATGAAGAACA
28217955 AAAGAAAA-GAAGAACA
1 AAAGAAAATGAAGAACA
28217971 AAAGAA
1 AAAGAA
28217977 GAAAAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.03
Consensus pattern (17 bp):
AAAGAAAATGAAGAACA
Found at i:28222671 original size:30 final size:30
Alignment explanation
Indices: 28222637--28222697 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
28222627 CCTTAACTCA
28222637 AAACTTTTGCAAAATTACAATTTTACCCCT
1 AAACTTTTGCAAAATTACAATTTTACCCCT
* * * *
28222667 AAACTTTTGCATATTTACAGTTTTTCCCCT
1 AAACTTTTGCAAAATTACAATTTTACCCCT
28222697 A
1 A
28222698 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTACCCCT
Found at i:28227223 original size:29 final size:29
Alignment explanation
Indices: 28227180--28227252 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
28227170 GTATTTTAAG
* **
28227180 AAAATGATAAATAAAGACAAAAAGAAATGC
1 AAAATGAAAAATAAA-ACAAAAAGAAAAAC
*
28227210 AAAAT-AAAAATAAAATAAAAAGAAAAAC
1 AAAATGAAAAATAAAACAAAAAGAAAAAC
*
28227238 AAATTGAAAAATAAA
1 AAAATGAAAAATAAA
28227253 TGAACTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.41
29 17 0.46
30 5 0.14
ACGTcount: A:0.74, C:0.04, G:0.08, T:0.14
Consensus pattern (29 bp):
AAAATGAAAAATAAAACAAAAAGAAAAAC
Found at i:28236436 original size:40 final size:40
Alignment explanation
Indices: 28236382--28236499 Score: 209
Period size: 40 Copynumber: 3.0 Consensus size: 40
28236372 CGGATGTAAC
* *
28236382 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
28236422 AACCCGCATGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
28236462 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATA
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATA
28236500 TTTTTTTTTC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:28237208 original size:18 final size:18
Alignment explanation
Indices: 28237185--28237220 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28237175 ACCAAATAGA
28237185 TCATATGTGTATAACACT
1 TCATATGTGTATAACACT
28237203 TCATATGTGTATAACACT
1 TCATATGTGTATAACACT
28237221 ACTCATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (18 bp):
TCATATGTGTATAACACT
Found at i:28241470 original size:63 final size:63
Alignment explanation
Indices: 28241383--28241505 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 63
28241373 CACTTACCCG
* *
28241383 TGTGGTCCTAATGTACAAAAAGTGTGTTACATGGCCTAGACACAGGCCCGTGTCATTGGCCTA
1 TGTGGTCCTAATGTACAAAAAGTGTGTTACACGGCCTAGACACACGCCCGTGTCATTGGCCTA
** * * *
28241446 TGTGGTTCC-AATGTACAAGCAGTGTGTTACACGGCCTGGACACACGTCCGTGTCCTTGGC
1 TGTGG-TCCTAATGTACAAAAAGTGTGTTACACGGCCTAGACACACGCCCGTGTCATTGGC
28241506 TGGTGTGAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
63 49 0.94
64 3 0.06
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (63 bp):
TGTGGTCCTAATGTACAAAAAGTGTGTTACACGGCCTAGACACACGCCCGTGTCATTGGCCTA
Found at i:28242106 original size:17 final size:16
Alignment explanation
Indices: 28242080--28242159 Score: 74
Period size: 17 Copynumber: 4.9 Consensus size: 16
28242070 CAGAAGTAAG
28242080 AAAAAGGAAAGAAAAT
1 AAAAAGGAAAGAAAAT
28242096 AAAAGAGGAAAGAAAAT
1 AAAA-AGGAAAGAAAAT
* * *
28242113 AAGAA-CAAA-AGAAT
1 AAAAAGGAAAGAAAAT
* *
28242127 AAAAAGGAAGGAAAAA
1 AAAAAGGAAAGAAAAT
28242143 AAAAAGAGAAAAGAAAA
1 AAAAAG-G-AAAGAAAA
28242160 ACGGTTAAGA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
14 8 0.16
15 5 0.10
16 14 0.28
17 16 0.32
18 7 0.14
ACGTcount: A:0.75, C:0.01, G:0.20, T:0.04
Consensus pattern (16 bp):
AAAAAGGAAAGAAAAT
Found at i:28242125 original size:33 final size:31
Alignment explanation
Indices: 28242087--28242160 Score: 78
Period size: 33 Copynumber: 2.3 Consensus size: 31
28242077 AAGAAAAAGG
*
28242087 AAAGAAAATAAAAG-AGGAAAGAAAATAAGAACA
1 AAAGAAAA-AAAAGAAGGAAA-AAAAAAAG-ACA
* *
28242120 AAAGAATAAAAAGGAAGGAAAAAAAAAAGAGA
1 AAAGAA-AAAAAAGAAGGAAAAAAAAAAGACA
28242152 AAAGAAAAA
1 AAAGAAAAA
28242161 CGGTTAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 3 0.08
32 8 0.22
33 17 0.47
34 8 0.22
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (31 bp):
AAAGAAAAAAAAGAAGGAAAAAAAAAAGACA
Found at i:28245911 original size:24 final size:24
Alignment explanation
Indices: 28245858--28245942 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 24
28245848 TGTAACTAAA
*
28245858 TATCAGGCTTTGTGTCAATGTTTATC
1 TATCAGGC-TTGTGCCAATG-TTATC
*
28245884 TATCAGGCTTGTGCCGATGTTATC
1 TATCAGGCTTGTGCCAATGTTATC
* * **
28245908 TATCAAGCCTTGTGCCAATATCGTC
1 TATC-AGGCTTGTGCCAATGTTATC
28245933 TATCAGGCTT
1 TATCAGGCTT
28245943 TGAGCCGGTG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
24 14 0.28
25 28 0.56
26 8 0.16
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (24 bp):
TATCAGGCTTGTGCCAATGTTATC
Found at i:28246153 original size:111 final size:111
Alignment explanation
Indices: 28245947--28246153 Score: 238
Period size: 111 Copynumber: 1.9 Consensus size: 111
28245937 AGGCTTTGAG
* ** * *
28245947 CCGGTGATACAAACTGTAGTGATGGCTTGACATCCTGCATGTGTTGCGGATTCTCTACAACTTGT
1 CCGGTGATACAAACCGTAGCAATAGCTTGACATCCTACATGTGTTGCGGATTCTCTACAACTTGT
** * **
28246012 GTGAGCAGCACTGGGAGTCGGTGATTATTTTACTAGGTATTATGTA
66 GTGAGCAGCACTGGGAGTCAATAAAAATTTTACTAGGTATTATGTA
* * * *
28246058 CCGGTGATACAGACCGTAGCAATAGCTTGAGATCCTACATGTGTTGCGGATTCTCTATAGCTTGT
1 CCGGTGATACAAACCGTAGCAATAGCTTGACATCCTACATGTGTTGCGGATTCTCTACAACTTGT
* *
28246123 GTGAGTAGTA-TCGTGG-GTCAATAAAAATTTT
66 GTGAGCAGCACT-G-GGAGTCAATAAAAATTTT
28246154 GAAGTTAACT
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
110 1 0.01
111 75 0.96
112 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (111 bp):
CCGGTGATACAAACCGTAGCAATAGCTTGACATCCTACATGTGTTGCGGATTCTCTACAACTTGT
GTGAGCAGCACTGGGAGTCAATAAAAATTTTACTAGGTATTATGTA
Found at i:28255135 original size:39 final size:39
Alignment explanation
Indices: 28255072--28255195 Score: 160
Period size: 39 Copynumber: 3.2 Consensus size: 39
28255062 GGACTTTAGC
* *
28255072 CCGGACAT-ATTTCCAGCACGTAGCCTGCGGATCTTAAGT
1 CCGGATATAATTT-CAGCACATAGCCTGCGGATCTTAAGT
* * *
28255111 CCGGTTATAATTTCAGCACATAGCCTGCAGACCTTAAGT
1 CCGGATATAATTTCAGCACATAGCCTGCGGATCTTAAGT
* * *
28255150 CCGGATATAATTCCAGCACATAGCTTGCGGATCCTAAGT
1 CCGGATATAATTTCAGCACATAGCCTGCGGATCTTAAGT
28255189 CCGGATA
1 CCGGATA
28255196 AACATCACTG
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 69 0.95
40 4 0.05
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
CCGGATATAATTTCAGCACATAGCCTGCGGATCTTAAGT
Found at i:28266810 original size:17 final size:18
Alignment explanation
Indices: 28266784--28266817 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28266774 TTTTTGTTTA
28266784 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
28266801 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
28266818 ATATTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:28269761 original size:22 final size:22
Alignment explanation
Indices: 28269730--28269773 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28269720 AAATATGAAC
**
28269730 ATAATGAATTTTACTTAATTTT
1 ATAATGAATTTTAAGTAATTTT
*
28269752 ATAATTAATTTTAAGTAATTTT
1 ATAATGAATTTTAAGTAATTTT
28269774 GGTTATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
ATAATGAATTTTAAGTAATTTT
Found at i:28272379 original size:68 final size:64
Alignment explanation
Indices: 28272293--28272514 Score: 198
Period size: 67 Copynumber: 3.4 Consensus size: 64
28272283 TAATACGGGA
* * *
28272293 TGTATACCATGTGTACAAGAGAGCTTCGAGACATTATGAGGTAGCTAGGTCTCATGGGTGATACT
1 TGTACACCATGTGTACAAGAGAGCTACGAG--A-TA-GAAGTAGCTAGGTCTCATGGGTGATACT
28272358 ATG
62 ATG
* * * * * *
28272361 TGTACACCATGTAG-ACAAGAAAGCTACGAGATAGATGTAGCTAGGT-TGCATGTGTGGTTCCAG
1 TGTACACCATGT-GTACAAGAGAGCTACGAGATAGAAGTAGCTAGGTCT-CATGGGTGATACTA-
28272424 GTG
63 -TG
* * ** * *
28272427 AAGGACACCATGTAAACAAGAGAGCTACGAGATA-AAGTGGCTAGGTCACATGGGTGATACTATG
1 -TGTACACCATGTGTACAAGAGAGCTACGAGATAGAAGTAGCTAGGTCTCATGGGTGATACTATG
*
28272491 TGTACACCATCTGTACAAGAGAGC
1 TGTACACCATGTGTACAAGAGAGC
28272515 CAAAATTATG
Statistics
Matches: 123, Mismatches: 24, Indels: 19
0.74 0.14 0.11
Matches are distributed among these distances:
63 20 0.16
64 24 0.20
65 2 0.02
66 23 0.19
67 28 0.23
68 25 0.20
69 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (64 bp):
TGTACACCATGTGTACAAGAGAGCTACGAGATAGAAGTAGCTAGGTCTCATGGGTGATACTATG
Found at i:28272514 original size:63 final size:63
Alignment explanation
Indices: 28272265--28272514 Score: 189
Period size: 68 Copynumber: 3.8 Consensus size: 63
28272255 CAGATGGTAT
* * ** * *
28272265 GTAGCTAGGTCACATGTGTAATAC-GGGATGTATACCATGTGTACAAGAGAGCTTCGAGACATTA
1 GTAGCTAGGTCACATGGGTGATACTATG-TGTACACCATGTG-ACAAGAGAGCTACGAG--A-TA
*
28272329 TGAG
61 -GAA
* * *
28272333 GTAGCTAGGTCTCATGGGTGATACTATGTGTACACCATGTAGACAAGAAAGCTACGAGATAGAT
1 GTAGCTAGGTCACATGGGTGATACTATGTGTACACCATGT-GACAAGAGAGCTACGAGATAGAA
** * * * * * * *
28272397 GTAGCTAGGTTGCATGTGTGGTTCCAGGTGAAGGACACCATGTAAACAAGAGAGCTACGAGATA-
1 GTAGCTAGGTCACATGGGTGATACTA--TG-TGTACACCATGT-GACAAGAGAGCTACGAGATAG
28272461 AA
62 AA
* *
28272463 GTGGCTAGGTCACATGGGTGATACTATGTGTACACCATCTGTACAAGAGAGC
1 GTAGCTAGGTCACATGGGTGATACTATGTGTACACCATGTG-ACAAGAGAGC
28272515 CAAAATTATG
Statistics
Matches: 145, Mismatches: 31, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
63 19 0.13
64 24 0.17
65 2 0.01
66 23 0.16
67 29 0.20
68 46 0.32
69 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.24
Consensus pattern (63 bp):
GTAGCTAGGTCACATGGGTGATACTATGTGTACACCATGTGACAAGAGAGCTACGAGATAGAA
Found at i:28275387 original size:46 final size:46
Alignment explanation
Indices: 28275331--28275480 Score: 130
Period size: 46 Copynumber: 3.2 Consensus size: 46
28275321 CCCAGACACG
*
28275331 GTCTTACACTGGCTTATATC-TCAAGTCGAAGCCATGTC-CAAGACAT
1 GTCTTACACTGGCTTACATCTTCAAGTCGAAG-CATGTCTC-AGACAT
* * * *
28275377 GTCTTACACTGGCTTACGTCTTGAGGTCGATGCATGTCTCAGACAT
1 GTCTTACACTGGCTTACATCTTCAAGTCGAAGCATGTCTCAGACAT
* * *
28275423 GTCTTACACTAGC--AC-TCGTCTCAATGCCGATGCCATGTCTCAGACAT
1 GTCTTACACTGGCTTACATC-T-TCAA-GTCGAAG-CATGTCTCAGACAT
28275470 GGTCTTACACT
1 -GTCTTACACT
28275481 AGCTCTCACA
Statistics
Matches: 88, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
43 2 0.02
44 3 0.03
45 2 0.02
46 48 0.55
47 23 0.26
48 10 0.11
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.30
Consensus pattern (46 bp):
GTCTTACACTGGCTTACATCTTCAAGTCGAAGCATGTCTCAGACAT
Found at i:28280279 original size:40 final size:40
Alignment explanation
Indices: 28280185--28280329 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
28280175 TACTCGAACG
*
28280185 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
28280226 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
28280266 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
28280306 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
28280330 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:28285949 original size:25 final size:25
Alignment explanation
Indices: 28285921--28285998 Score: 86
Period size: 25 Copynumber: 3.1 Consensus size: 25
28285911 CTTCTCGATT
* *
28285921 ATGGCTCGGATGAGCTTCCCGTTAC
1 ATGGCTCGAATGAGCTTCCCATTAC
* *
28285946 ATGGCTC-ACATGAGCTTCCAATTAT
1 ATGGCTCGA-ATGAGCTTCCCATTAC
*
28285971 ATGGCTCGAAAGAGCTTCCCATTTAC
1 ATGGCTCGAATGAGCTTCCCA-TTAC
28285997 AT
1 AT
28285999 ATTTGCATGA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
25 37 0.86
26 6 0.14
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (25 bp):
ATGGCTCGAATGAGCTTCCCATTAC
Found at i:28287259 original size:22 final size:20
Alignment explanation
Indices: 28287208--28287259 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 20
28287198 GGTTGATCTT
**
28287208 AATTTTAAAAAATTTAAAGA
1 AATTTTAAAAAACATAAAGA
*
28287228 AATATATAAAAATACATAAAGAA
1 AAT-TTTAAAAA-ACATAAAG-A
28287251 AATTTTAAA
1 AATTTTAAA
28287260 TTTTAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
21 7 0.28
22 11 0.44
23 4 0.16
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (20 bp):
AATTTTAAAAAACATAAAGA
Found at i:28287277 original size:19 final size:19
Alignment explanation
Indices: 28287255--28287298 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28287245 AAAGAAAATT
*
28287255 TTAAAT-TTTAAATTTTATA
1 TTAAATATTTAAA-TTCATA
28287274 TT-AATATTTAAATTCATA
1 TTAAATATTTAAATTCATA
28287292 TTAAATA
1 TTAAATA
28287299 AATATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAAATATTTAAATTCATA
Found at i:28295721 original size:20 final size:21
Alignment explanation
Indices: 28295693--28295740 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
28295683 AAAGATTAAT
* *
28295693 AAATAAATTTAACTTAAAATA
1 AAATAAATTCAAATTAAAATA
28295714 AAAT-AATTCAAATTAAAA-A
1 AAATAAATTCAAATTAAAATA
*
28295733 AATTAAAT
1 AAATAAAT
28295741 ATTGAGTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 15 0.65
21 4 0.17
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAAATTCAAATTAAAATA
Found at i:28300777 original size:12 final size:12
Alignment explanation
Indices: 28300760--28300784 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28300750 TAATTAGAAT
28300760 CCTTAAACTATC
1 CCTTAAACTATC
28300772 CCTTAAACTATC
1 CCTTAAACTATC
28300784 C
1 C
28300785 TAAAAAAGGA
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:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (12 bp):
CCTTAAACTATC
Done.