Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 143 of 187
Found at i:43200241 original size:12 final size:12
Alignment explanation
Indices: 43200192--43200240 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
43200182 ATGTGAGGTA
*
43200192 AGTATTAATATT
1 AGTATTATTATT
43200204 AGTATT-TGTATT
1 AGTATTAT-TATT
43200216 AGTATTATTATT
1 AGTATTATTATT
*
43200228 ATTATTATTATT
1 AGTATTATTATT
43200240 A
1 A
43200241 TGAGTGGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 32 0.97
13 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (12 bp):
AGTATTATTATT
Found at i:43200875 original size:126 final size:125
Alignment explanation
Indices: 43200650--43200897 Score: 469
Period size: 126 Copynumber: 2.0 Consensus size: 125
43200640 TTGAATTTAA
* *
43200650 ATTGTATATACTAATTATGCATTACATGTTTATTATTTTTATAATTTGAATTATGGTAATACCAC
1 ATTGTATATACGAATTATGCATTACATGTTTATTATTGTTATAATTTGAATTATGGTAATACCAC
43200715 TGAGTATGAAATACTCAGCGTACGGTTGTTTCCGTGCGCAGGTCGATAGAAGTCAAAGGT
66 TGAGTATGAAATACTCAGCGTACGGTTGTTTCCGTGCGCAGGTCGATAGAAGTCAAAGGT
43200775 NATTGTATATACGAATTATGCATTACATGTTTATTATTGTTATAATTTGAATTATGGTAATACCA
1 -ATTGTATATACGAATTATGCATTACATGTTTATTATTGTTATAATTTGAATTATGGTAATACCA
43200840 CTGAGTATGAAATACTCAGCGTACGGTTGTTTCCGTGCGCAGGTCGATAGAAGTCAAA
65 CTGAGTATGAAATACTCAGCGTACGGTTGTTTCCGTGCGCAGGTCGATAGAAGTCAAA
43200898 TGTCCCGGTT
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 120 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (125 bp):
ATTGTATATACGAATTATGCATTACATGTTTATTATTGTTATAATTTGAATTATGGTAATACCAC
TGAGTATGAAATACTCAGCGTACGGTTGTTTCCGTGCGCAGGTCGATAGAAGTCAAAGGT
Found at i:43202743 original size:28 final size:26
Alignment explanation
Indices: 43202671--43202743 Score: 69
Period size: 29 Copynumber: 2.7 Consensus size: 26
43202661 TAGAAATTTT
*
43202671 TTTATCAAAAATTA-GAAATTATTAAA
1 TTTAT-AAAAATTATAAAATTATTAAA
*
43202697 TATT-TAAAAAATATTAAAATTGATATAAA
1 T-TTATAAAAATTA-TAAAATT-AT-TAAA
43202726 TTTATAAAAATTATAAAA
1 TTTATAAAAATTATAAAA
43202744 AAATTTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
25 7 0.18
26 2 0.05
27 7 0.18
28 9 0.24
29 13 0.34
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (26 bp):
TTTATAAAAATTATAAAATTATTAAA
Found at i:43202749 original size:21 final size:21
Alignment explanation
Indices: 43202723--43202765 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
43202713 AAATTGATAT
43202723 AAATTTATAAAAATTATAAAA
1 AAATTTATAAAAATTATAAAA
**
43202744 AAATTTATAAGTATTATAAAA
1 AAATTTATAAAAATTATAAAA
43202765 A
1 A
43202766 TATATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
AAATTTATAAAAATTATAAAA
Found at i:43202835 original size:21 final size:21
Alignment explanation
Indices: 43202801--43202905 Score: 64
Period size: 19 Copynumber: 5.3 Consensus size: 21
43202791 AATTTTTTTA
*
43202801 TAAAA-TTAATAAAACATAT-T
1 TAAAATTTTATAAAA-ATATAT
*
43202821 TAAAATTTTATAAAAATGTAT
1 TAAAATTTTATAAAAATATAT
*
43202842 TAAAATTCTATAAAAA-AT-T
1 TAAAATTTTATAAAAATATAT
* * *
43202861 AAAAATTATA-AAAAAAATA-
1 TAAAATTTTATAAAAATATAT
* * *
43202880 TAAGATATTAT-AAGA-ATAT
1 TAAAATTTTATAAAAATATAT
43202899 TAAAATT
1 TAAAATT
43202906 GATATGAACT
Statistics
Matches: 66, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
18 8 0.12
19 25 0.38
20 9 0.14
21 24 0.36
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (21 bp):
TAAAATTTTATAAAAATATAT
Found at i:43202872 original size:17 final size:18
Alignment explanation
Indices: 43202840--43202875 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
43202830 ATAAAAATGT
*
43202840 ATTAAAATTCTATAAAAA
1 ATTAAAAATCTATAAAAA
43202858 ATTAAAAAT-TATAAAAA
1 ATTAAAAATCTATAAAAA
43202875 A
1 A
43202876 AATATAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
ATTAAAAATCTATAAAAA
Found at i:43203454 original size:21 final size:21
Alignment explanation
Indices: 43203411--43203454 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
43203401 GTTTTCATAT
*
43203411 TTTTTTATAGTTTTTTTACAA
1 TTTTTTATAGTTTTTTAACAA
*
43203432 TTTTTTATTA-TTTTTTAAGAA
1 TTTTTTA-TAGTTTTTTAACAA
43203453 TT
1 TT
43203455 CTATCATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTTTATAGTTTTTTAACAA
Found at i:43203858 original size:20 final size:18
Alignment explanation
Indices: 43203826--43203876 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
43203816 GTTATTTATA
*
43203826 ATTTCTTATAATTCTTAAT
1 ATTTTTTATAATT-TTAAT
**
43203845 ATTTTTTAATAATTTTTGT
1 ATTTTTT-ATAATTTTAAT
43203864 ATTTTTTATAATT
1 ATTTTTTATAATT
43203877 ATTTAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 16 0.57
20 6 0.21
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTTTATAATTTTAAT
Found at i:43203881 original size:10 final size:9
Alignment explanation
Indices: 43203820--43203881 Score: 52
Period size: 10 Copynumber: 6.4 Consensus size: 9
43203810 AATCTAGTTA
43203820 TTTATAATT
1 TTTATAATT
43203829 TCTTATAATT
1 T-TTATAATT
* *
43203839 CTTAATATTT
1 -TTTATAATT
43203849 TTTAATAATT
1 TTT-ATAATT
* *
43203859 TTTGTATTT
1 TTTATAATT
43203868 TTTATAATT
1 TTTATAATT
43203877 ATTTA
1 -TTTA
43203882 AGAAACTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
9 14 0.34
10 26 0.63
11 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTATAATT
Found at i:43205420 original size:25 final size:25
Alignment explanation
Indices: 43205376--43205439 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
43205366 AATTTATGTA
*
43205376 TTTTTTTTAATTCGGCACTT-AAGTT
1 TTTTTTTTAATTCAGCACTTGAA-TT
* *
43205401 TTTTTTTTAATTTAGTACTTGAATT
1 TTTTTTTTAATTCAGCACTTGAATT
43205426 TAATTTTTTTAATT
1 T--TTTTTTTAATT
43205440 GAATTTAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 20 0.61
26 2 0.06
27 11 0.33
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.62
Consensus pattern (25 bp):
TTTTTTTTAATTCAGCACTTGAATT
Found at i:43212690 original size:14 final size:15
Alignment explanation
Indices: 43212665--43212693 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43212655 ATTGAATTAC
43212665 TTTTAGTTTTATTTA
1 TTTTAGTTTTATTTA
43212680 TTTTA-TTTTATTTA
1 TTTTAGTTTTATTTA
43212694 ACATAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTAGTTTTATTTA
Found at i:43216799 original size:31 final size:29
Alignment explanation
Indices: 43216735--43216803 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
43216725 ACGATAACGT
* *
43216735 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACATGTCAAACAA
* *
43216764 AAGTGACTAAAATGTAACCTGAGTCAAACAA
1 AAGTGACTAAAACGTAACAT--GTCAAACAA
43216795 AAGTGACTA
1 AAGTGACTA
43216804 TTTTGGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACATGTCAAACAA
Found at i:43216907 original size:29 final size:28
Alignment explanation
Indices: 43216875--43216936 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
43216865 AAAAAGCTGT
43216875 TTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* **
43216904 TTTTTTTATTATTTACCGAAATGGGCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
43216932 TTTTT
1 TTTTT
43216937 CGGGAAATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:43217289 original size:125 final size:125
Alignment explanation
Indices: 43217093--43217444 Score: 598
Period size: 125 Copynumber: 2.8 Consensus size: 125
43217083 TTATTTCGAG
*
43217093 TTGAAGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTAAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTAAGAAGAAATTGT
43217157 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTT
* * * *
43217218 TTGACGTTTCTGAGCAAATAGTATAAAATCACCTCTACCAGGATGCTATTTGAGAAGAAATTATG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTAAGAAGAAATTGTG
*
43217283 GAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTT
* *
43217343 TTGACATTTCTGAGCAAACAGTATAAAATCGCTTCTACCAGGATGCTATTTAAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTAAGAAGAAATTGTG
* *
43217408 AAATCGCGCCCTCGTGGATGCGATTTTACTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
43217445 CAAGTTTGGG
Statistics
Matches: 211, Mismatches: 15, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
125 210 1.00
126 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTAAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTT
Found at i:43220562 original size:10 final size:10
Alignment explanation
Indices: 43220547--43220571 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
43220537 CAAATCTAAC
43220547 ATTATGTAAA
1 ATTATGTAAA
43220557 ATTATGTAAA
1 ATTATGTAAA
43220567 ATTAT
1 ATTAT
43220572 TAAGTCCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:43220625 original size:10 final size:10
Alignment explanation
Indices: 43220610--43220636 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
43220600 TAAAATTATC
43220610 AAATTATGTA
1 AAATTATGTA
43220620 AAATTATGTA
1 AAATTATGTA
43220630 AAATTAT
1 AAATTAT
43220637 TAAGCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (10 bp):
AAATTATGTA
Found at i:43220681 original size:18 final size:18
Alignment explanation
Indices: 43220658--43220692 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43220648 AATTTTAATT
43220658 AAATTAGGTAAAATTATC
1 AAATTAGGTAAAATTATC
*
43220676 AAATTATGTAAAATTAT
1 AAATTAGGTAAAATTAT
43220693 TAAGTCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (18 bp):
AAATTAGGTAAAATTATC
Found at i:43220684 original size:56 final size:55
Alignment explanation
Indices: 43220620--43220746 Score: 161
Period size: 56 Copynumber: 2.3 Consensus size: 55
43220610 AAATTATGTA
43220620 AAATTATGTAAAATTATTAAG-CCAAAAAAAT-T-TTAATTAAATTAGGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCC-AAAAAATGTGTTAA-T-AATTA-GTAAAATTATC
* ** *
43220676 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAATTTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAAATGTGTTAATAATTAGTAAAATTATC
43220731 AAATTATGTAAAATTA
1 AAATTATGTAAAATTA
43220747 GGTTAGGGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
55 26 0.41
56 30 0.47
57 4 0.06
58 4 0.06
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (55 bp):
AAATTATGTAAAATTATTAAGTCCAAAAAATGTGTTAATAATTAGTAAAATTATC
Found at i:43220685 original size:66 final size:64
Alignment explanation
Indices: 43220547--43220692 Score: 206
Period size: 66 Copynumber: 2.2 Consensus size: 64
43220537 CAAATCTAAC
* * *
43220547 ATTATGTAAAATTATGTAAAATTATTAAGTCCCAAAATTTTGTTAATGGTTAGTAAAATTATCAA
1 ATTATGTAAAATTATGTAAAATTATTAAGTCCAAAAATTTTATTAA-GATTAGTAAAATTATCAA
43220612 ATTATGTAAAATTATGTAAAATTATTAAG-CCAAAAAAATTTTAATTAA-ATTAGGTAAAATTAT
1 ATTATGTAAAATTATGTAAAATTATTAAGTCC--AAAAATTTT-ATTAAGATTA-GTAAAATTAT
43220675 CAA
62 CAA
43220678 ATTATGTAAAATTAT
1 ATTATGTAAAATTAT
43220693 TAAGTCCAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
64 2 0.03
65 32 0.43
66 36 0.49
67 4 0.05
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (64 bp):
ATTATGTAAAATTATGTAAAATTATTAAGTCCAAAAATTTTATTAAGATTAGTAAAATTATCAA
Found at i:43220778 original size:29 final size:29
Alignment explanation
Indices: 43220744--43220806 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
43220734 TTATGTAAAA
43220744 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
43220773 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
43220802 TTAGG
1 TTAGG
43220807 GTTTTAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (29 bp):
TTAGGTTAGGGTTAGGGTTTTTAATTAAG
Found at i:43220813 original size:17 final size:18
Alignment explanation
Indices: 43220783--43221129 Score: 116
Period size: 18 Copynumber: 19.7 Consensus size: 18
43220773 TTAGGTTAGG
43220783 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
43220801 GTTAGGG-TTTTAATTAAACTA
1 GTTAGGGTTTTTAATT--A--A
43220822 TGTTAGGGTTAGGATTTTTAATTAA
1 -GTTAGGG-T-----TTTTAATTAA
43220847 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
**
43220865 GTTA-GG---TT-A--GG
1 GTTAGGGTTTTTAATTAA
*
43220876 GTTAGGATTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
43220894 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
* **** *
43220912 ATTA-GG-TTAGGGTTAGG
1 GTTAGGGTTTTTAATTA-A
* *
43220929 GTTAGAGTTTTTAATTTA
1 GTTAGGGTTTTTAATTAA
**
43220947 GTTA-GG---TT-A--GG
1 GTTAGGGTTTTTAATTAA
43220958 GTTAGGGTTTTTAATTAAATTA
1 GTTAGGGTTTTTAATT--A--A
43220980 GGTTAGGGTTTTTAATTAA
1 -GTTAGGGTTTTTAATTAA
*
43220999 GTTAAGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
43221017 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
* **** *
43221035 ATTA-GG-TTAGGGTTAGG
1 GTTAGGGTTTTTAATTA-A
43221052 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
* **
43221070 ATTA-GG---TT-A--GG
1 GTTAGGGTTTTTAATTAA
43221081 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
43221099 GTTAGGGTTTTTAATCAA
1 GTTAGGGTTTTTAATTAA
* *
43221117 ATTTGGGTTTTTA
1 GTTAGGGTTTTTA
43221130 TTACATCAAA
Statistics
Matches: 237, Mismatches: 48, Indels: 88
0.64 0.13 0.24
Matches are distributed among these distances:
11 11 0.05
12 5 0.02
13 3 0.01
14 6 0.03
15 6 0.03
16 13 0.05
17 23 0.10
18 116 0.49
19 11 0.05
21 2 0.01
22 7 0.03
23 17 0.07
24 7 0.03
25 1 0.00
27 1 0.00
29 8 0.03
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:43220860 original size:93 final size:94
Alignment explanation
Indices: 43220754--43220928 Score: 316
Period size: 93 Copynumber: 1.9 Consensus size: 94
43220744 TTAGGTTAGG
*
43220754 GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGG-TTTTAATTAA
1 GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGATTTTTAATTAAGTTAGGGTTTTTAATTAA
*
43220818 ACTATGTTAGGGTTAGGATTTTTAATTAA
66 ACTAGGTTAGGGTTAGGATTTTTAATTAA
43220847 GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGATTTTTAATTAAGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGATTTTTAATTAAGTTAGGGTTTTTAATTAA
*
43220912 ATTAGGTTAGGGTTAGG
66 ACTAGGTTAGGGTTAGG
43220929 GTTAGAGTTT
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
93 53 0.68
94 25 0.32
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (94 bp):
GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGATTTTTAATTAAGTTAGGGTTTTTAATTAA
ACTAGGTTAGGGTTAGGATTTTTAATTAA
Found at i:43220877 original size:47 final size:47
Alignment explanation
Indices: 43220754--43221119 Score: 312
Period size: 47 Copynumber: 7.4 Consensus size: 47
43220744 TTAGGTTAGG
* *
43220754 GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGATTTTTAATTAA
* *
43220801 GTTAGGG-TTTTAATTAAACTATGTTAGGGTTAGGATTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGATTTTTAATTAA
*
43220847 GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGATTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGATTTTTAATTAA
43220894 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGAGTTTTTAATTTAGTTA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA--G---GA-TTTTTAA-TTA---A
** *
43220951 GGTTAGGGTTAGGGTTT--TT-AATTAAATTA-GGTTAGGGTTTTTAATTAA
1 -GTTAGGGTT----TTTAATTAAATTAGGTTAGGGTTAGGATTTTTAATTAA
* * **** * * * *
43220999 GTTAAGGTTTTTAATTAAGTTAGGGTTTTTAATTA-AATTAGGTTAGGGTTAGG
1 GTTAGGGTTTTTAATTAAATTA-GG-TTAGGGTTAGGATT--TTTA--ATTA-A
*
43221052 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGATTTTTAATTAA
*
43221099 GTTAGGGTTTTTAATCAAATT
1 GTTAGGGTTTTTAATTAAATT
43221120 TGGGTTTTTA
Statistics
Matches: 256, Mismatches: 35, Indels: 56
0.74 0.10 0.16
Matches are distributed among these distances:
43 3 0.01
45 2 0.01
46 46 0.18
47 103 0.40
48 8 0.03
49 4 0.02
50 6 0.02
51 8 0.03
52 16 0.06
53 28 0.11
54 3 0.01
56 1 0.00
57 1 0.00
58 14 0.05
59 8 0.03
60 2 0.01
62 3 0.01
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.46
Consensus pattern (47 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGATTTTTAATTAA
Found at i:43220889 original size:29 final size:29
Alignment explanation
Indices: 43220847--43221104 Score: 200
Period size: 29 Copynumber: 8.8 Consensus size: 29
43220837 TTTTAATTAA
43220847 GTTAGGGTTTTTAATTAAGTTAGGTTAGG
1 GTTAGGGTTTTTAATTAAGTTAGGTTAGG
*
43220876 GTTAGGATTTTTAATTAAGTTAGGGTT---
1 GTTAGGGTTTTTAATTAAGTTA-GGTTAGG
* * * *
43220903 TTTA----ATTAAATTAGGTTAGGGTTAGG
1 GTTAGGGTTTTTAATTAAGTTA-GGTTAGG
* *
43220929 GTTAGAGTTTTTAATTTAGTTAGGTTAGG
1 GTTAGGGTTTTTAATTAAGTTAGGTTAGG
43220958 GTTAGGGTTTTTAATTAA---A--TTA-G
1 GTTAGGGTTTTTAATTAAGTTAGGTTAGG
**
43220981 GTTAGGGTTTTTAATTAAGTTAAGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAGTT-AGG---TT-A--GG
43221017 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG
1 GTTAGGGTTTTTAATT--A--A-GTTA-GGTTAGG
*
43221052 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAGTTAGGTTAGG
43221081 GTTAGGGTTTTTAATTAAGTTAGG
1 GTTAGGGTTTTTAATTAAGTTAGG
43221105 GTTTTTAATC
Statistics
Matches: 185, Mismatches: 17, Indels: 54
0.72 0.07 0.21
Matches are distributed among these distances:
23 35 0.19
24 3 0.02
26 4 0.02
27 4 0.02
29 74 0.40
30 17 0.09
31 1 0.01
32 2 0.01
33 2 0.01
35 16 0.09
36 16 0.09
37 1 0.01
38 3 0.02
40 2 0.01
41 5 0.03
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (29 bp):
GTTAGGGTTTTTAATTAAGTTAGGTTAGG
Found at i:43221039 original size:123 final size:123
Alignment explanation
Indices: 43220883--43221104 Score: 408
Period size: 123 Copynumber: 1.8 Consensus size: 123
43220873 AGGGTTAGGA
* *
43220883 TTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGAGTTTTTAATTTAG
1 TTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGAGTTTTTAATTAAA
43220948 TTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGTTAAGG
66 TTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGTTAAGG
*
43221006 TTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAA
1 TTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGAGTTTTTAATTAAA
*
43221071 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGG
66 TTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
43221105 GTTTTTAATC
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 95 1.00
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (123 bp):
TTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGAGTTTTTAATTAAA
TTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGTTAAGG
Found at i:43221056 original size:35 final size:35
Alignment explanation
Indices: 43221017--43221089 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
43221007 TTTTAATTAA
43221017 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG
43221052 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG
43221087 GTT
1 GTT
43221090 TTTAATTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.44
Consensus pattern (35 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG
Found at i:43221094 original size:100 final size:92
Alignment explanation
Indices: 43220939--43221129 Score: 265
Period size: 100 Copynumber: 2.0 Consensus size: 92
43220929 GTTAGAGTTT
*
43220939 TTAATTTAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGTTAA
1 TTAAATTAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGTTAA
* *
43221004 GGTTTTTAATTAAGTTAGGGTTTTTAA
66 GGTTTTTAATCAAATTAGGGTTTTTAA
43221031 TTAAATTAGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAT
1 TTAAATTA-GTTA-GGTTAGGGTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAAT
* *
43221096 TAAGTTAGGGTTTTTAATCAAATTTGGGTTTTTA
58 TAAGTTAAGGTTTTTAATCAAATTAGGGTTTTTA
43221130 TTACATCAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
92 7 0.08
93 4 0.05
94 23 0.27
95 2 0.02
97 1 0.01
99 3 0.03
100 46 0.53
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.48
Consensus pattern (92 bp):
TTAAATTAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGTTAA
GGTTTTTAATCAAATTAGGGTTTTTAA
Found at i:43221096 original size:24 final size:27
Alignment explanation
Indices: 43221045--43221107 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 27
43221035 ATTAGGTTAG
43221045 GGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGG-TTTT-ATTAAATTA
43221074 GGTTAGGGTTAGGG-TTT-TT-AATTA
1 GGTTAGGGTTAGGGTTTTATTAAATTA
*
43221098 AGTTAGGGTT
1 GGTTAGGGTT
43221108 TTTAATCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 14 0.42
25 2 0.06
27 3 0.09
29 14 0.42
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (27 bp):
GGTTAGGGTTAGGGTTTTATTAAATTA
Found at i:43221177 original size:25 final size:26
Alignment explanation
Indices: 43221125--43221188 Score: 103
Period size: 25 Copynumber: 2.5 Consensus size: 26
43221115 AAATTTGGGT
43221125 TTTTATTACATCAAATATAACTTCTA
1 TTTTATTACATCAAATATAACTTCTA
* *
43221151 TTTTATTATATTAAATA-AACTTCTA
1 TTTTATTACATCAAATATAACTTCTA
43221176 TTTTATTACATCA
1 TTTTATTACATCA
43221189 GATAATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTTATTACATCAAATATAACTTCTA
Found at i:43221624 original size:18 final size:18
Alignment explanation
Indices: 43221597--43221631 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43221587 CAGAAAAGGA
* *
43221597 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
43221615 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
43221632 AAACACACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:43222293 original size:7 final size:7
Alignment explanation
Indices: 43222283--43222314 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
43222273 TTATATACAT
43222283 AATACTA
1 AATACTA
43222290 AATACTA
1 AATACTA
43222297 AATACTA
1 AATACTA
43222304 AATACTA
1 AATACTA
43222311 AATA
1 AATA
43222315 TCAATCGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:43222700 original size:51 final size:51
Alignment explanation
Indices: 43222624--43222725 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
43222614 GGCAACCTCC
* * *
43222624 GATGTTTGCTTTCCTCGGTTGCGTCGCCCCGTACATCTCCCGATATAATGT
1 GATGTTTGCTCTCCTCGGTCGCGTCGCCCCGCACATCTCCCGATATAATGT
43222675 GATGTTTGCTCTCCTCGGTCGCGTCGCCCCGCACATCTCCCGATATAATGT
1 GATGTTTGCTCTCCTCGGTCGCGTCGCCCCGCACATCTCCCGATATAATGT
43222726 TGCCAAGACG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.14, C:0.32, G:0.22, T:0.32
Consensus pattern (51 bp):
GATGTTTGCTCTCCTCGGTCGCGTCGCCCCGCACATCTCCCGATATAATGT
Found at i:43223465 original size:10 final size:10
Alignment explanation
Indices: 43223446--43223496 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
43223436 GCCATTGATG
*
43223446 AAAATATAAA
1 AAAATTTAAA
43223456 AAAATTTAAA
1 AAAATTTAAA
* * *
43223466 ATTATTTTTAA
1 A-AAATTTAAA
43223477 AAAATTTAAA
1 AAAATTTAAA
43223487 AAAATTTAAA
1 AAAATTTAAA
43223497 TTTATTTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
10 26 0.79
11 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:43223487 original size:31 final size:30
Alignment explanation
Indices: 43223446--43223509 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
43223436 GCCATTGATG
43223446 AAAATATAAAAAAATTTAAAATTATTTTTAA
1 AAAATATAAAAAAATTTAAAATTA-TTTTAA
* *
43223477 AAAATTTAAAAAAATTTAAATTTATTTTAA
1 AAAATATAAAAAAATTTAAAATTATTTTAA
43223507 AAA
1 AAA
43223510 TGAAATTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
AAAATATAAAAAAATTTAAAATTATTTTAA
Found at i:43223493 original size:21 final size:21
Alignment explanation
Indices: 43223454--43223493 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43223444 TGAAAATATA
**
43223454 AAAAAATTTAAAATTATTTTT
1 AAAAAATTTAAAAAAATTTTT
43223475 AAAAAATTTAAAAAAATTT
1 AAAAAATTTAAAAAAATTT
43223494 AAATTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAAATTTAAAAAAATTTTT
Found at i:43223566 original size:51 final size:51
Alignment explanation
Indices: 43223511--43223623 Score: 190
Period size: 51 Copynumber: 2.2 Consensus size: 51
43223501 TTTTAAAAAT
*
43223511 GAAATTAAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTAAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
* *
43223562 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTAAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
43223613 GAAATTGAGAG
1 GAAATTAAGAG
43223624 AATTTTGGAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.28
Consensus pattern (51 bp):
GAAATTAAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:43223620 original size:22 final size:22
Alignment explanation
Indices: 43223595--43223645 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
43223585 AAATATGGGT
43223595 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
43223617 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
43223639 TTGAGAG
1 TTGAGAG
43223646 GATTAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:43223927 original size:29 final size:28
Alignment explanation
Indices: 43223860--43223941 Score: 74
Period size: 29 Copynumber: 2.9 Consensus size: 28
43223850 TGATTTCCCG
* * * *
43223860 AAAAATGGCCCATTTCGATAAATAATCA
1 AAAAATGGCTCATTTCGGTAAATTATAA
*
43223888 AAAAATCGGCTCATTTCGGTAAATTTTGAA
1 AAAAAT-GGCTCATTTCGGTAAATTAT-AA
** *
43223918 AAAAATGGCTTTTTTAGGTAAATT
1 AAAAATGGCTCATTTCGGTAAATT
43223942 GCCCTAAAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
28 6 0.14
29 31 0.70
30 7 0.16
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (28 bp):
AAAAATGGCTCATTTCGGTAAATTATAA
Found at i:43226180 original size:13 final size:13
Alignment explanation
Indices: 43226162--43226186 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43226152 TACTAAATTT
43226162 TCATGGATTCAAG
1 TCATGGATTCAAG
43226175 TCATGGATTCAA
1 TCATGGATTCAA
43226187 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:43229662 original size:27 final size:27
Alignment explanation
Indices: 43229632--43229774 Score: 162
Period size: 27 Copynumber: 5.3 Consensus size: 27
43229622 CTCGATTTAC
*
43229632 AAAATTATTGAAATACCCTTGTAGGGT
1 AAAATTACTGAAATACCCTTGTAGGGT
* * *
43229659 AAAATTACTGAAACACCCCTATAGGGT
1 AAAATTACTGAAATACCCTTGTAGGGT
* *
43229686 AGAATTACCGAAATACCCTTGTAGGGT
1 AAAATTACTGAAATACCCTTGTAGGGT
* *
43229713 AGAAA-TACCGAAATACCCCTGTAGGGT
1 A-AAATTACTGAAATACCCTTGTAGGGT
* * * *
43229740 AGAATTACTGAGATACCCTTATGGGGT
1 AAAATTACTGAAATACCCTTGTAGGGT
43229767 AAAATTAC
1 AAAATTAC
43229775 CATTTTGCCC
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
26 2 0.02
27 92 0.96
28 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGTAGGGT
Found at i:43229699 original size:54 final size:54
Alignment explanation
Indices: 43229641--43229775 Score: 191
Period size: 54 Copynumber: 2.5 Consensus size: 54
43229631 CAAAATTATT
*
43229641 GAAATACCCTTGTAGGGTAAAATTACTGAAACACCCCTATAGGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAAAATTACCGAAACACCCCTATAGGGTAGAATTACC
* * *
43229695 GAAATACCCTTGTAGGGTAGAAA-TACCGAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCTTGTAGGGTA-AAATTACCGAAACACCCCTATAGGGTAGAATTACC
* * *
43229749 GAGATACCCTTATGGGGTAAAATTACC
1 GAAATACCCTTGTAGGGTAAAATTACC
43229776 ATTTTGCCCC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
53 3 0.04
54 66 0.92
55 3 0.04
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (54 bp):
GAAATACCCTTGTAGGGTAAAATTACCGAAACACCCCTATAGGGTAGAATTACC
Found at i:43230310 original size:20 final size:20
Alignment explanation
Indices: 43230270--43230310 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43230260 TGTGTGCTGT
* *
43230270 TATTGTGGGCTTTGTATCGA
1 TATTGTGGGCTTCGTACCGA
*
43230290 TATTGTGGGCTTCGTGCCGA
1 TATTGTGGGCTTCGTACCGA
43230310 T
1 T
43230311 TATAGACCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.15, G:0.32, T:0.41
Consensus pattern (20 bp):
TATTGTGGGCTTCGTACCGA
Found at i:43230530 original size:6 final size:6
Alignment explanation
Indices: 43230521--43230608 Score: 63
Period size: 6 Copynumber: 14.3 Consensus size: 6
43230511 TTTCATTCAC
* * *
43230521 ATTCTG ATTCTA ATTCTG TTATCTG ATTCTG ATTCTG ATTCTG -TCACATG
1 ATTCTG ATTCTG ATTCTG AT-TCTG ATTCTG ATTCTG ATTCTG AT-TC-TG
* * * *
43230571 GTTCTG ATTCTA ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
43230609 AATGTTTCTT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
5 2 0.03
6 52 0.81
7 9 0.14
8 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:43230549 original size:25 final size:25
Alignment explanation
Indices: 43230521--43230587 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
43230511 TTTCATTCAC
*
43230521 ATTCTGATTCTAATTCTGTTATC-TG
1 ATTCTGATTCTAATTCTGTCA-CATG
*
43230546 ATTCTGATTCTGATTCTGTCACATG
1 ATTCTGATTCTAATTCTGTCACATG
*
43230571 GTTCTGATTCTAATTCT
1 ATTCTGATTCTAATTCT
43230588 CATTTTGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 1 0.03
25 36 0.97
ACGTcount: A:0.19, C:0.18, G:0.13, T:0.49
Consensus pattern (25 bp):
ATTCTGATTCTAATTCTGTCACATG
Found at i:43233183 original size:34 final size:34
Alignment explanation
Indices: 43233114--43233188 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 34
43233104 TAGAGTTTAA
* **
43233114 CAGTCTGGGCCTAAGCCCATATCAGTCGCAATAT
1 CAGTGTGGGCCTAAGCCCATATCAGTAACAATAT
* *
43233148 CAGTGTGGGCCTTAGCCCAATAT-AGTAACAGTAT
1 CAGTGTGGGCCTAAGCCC-ATATCAGTAACAATAT
*
43233182 CAATGTG
1 CAGTGTG
43233189 CATACAAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 30 0.88
35 4 0.12
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (34 bp):
CAGTGTGGGCCTAAGCCCATATCAGTAACAATAT
Found at i:43243128 original size:229 final size:229
Alignment explanation
Indices: 43242704--43243164 Score: 755
Period size: 229 Copynumber: 2.0 Consensus size: 229
43242694 TTCAAAGGCT
* *
43242704 AATGTGGGAGATTCGAGTAGAGATCGTACTAAATCACATTCAAGTTTTAGAGCTCCAGCTACATC
1 AATGTGGGAGATTCAAGTAGAGATCGTACTAAATCACATTCAAGCTTTAGAGCTCCAGCTACATC
* * *
43242769 TGTTGCTAGTGTTGAAAATGTTCGATCTGATTGATCCAAGTGTAAACACTGTGGTAAAAGACATT
66 TGTTGCCAGTGTTGAAAATGTTCGATCTGATCGATCCAAGTGTAAACACTGTGGTAAAAGACATC
43242834 CAGGAAATTGTAGACTGTACGATCGGGCTTGTTTCAGATTTGGATCATTAGAGAATTTCATCCGT
131 CAGGAAATTGTAGACTGTACGATCGGGCTTGTTTCAGATTTGGATCATTAGAGAATTTCATCCGT
43242899 GATTGTCCCGAATCTATCAGCAAGAAATTGTGCAA
196 GATTGTCCCGAATCTATCAGCAAGAAATT-TGCAA
* * * *
43242934 AATGTGGGAGATTCAAGTAGAGATCGTGCTAGATCACATTCGAGCTTTAGAGCTCTAGCTACATC
1 AATGTGGGAGATTCAAGTAGAGATCGTACTAAATCACATTCAAGCTTTAGAGCTCCAGCTACATC
* * *
43242999 TGTTGCCAGTGTTGGAAATGTTCGATCTGATCGA-CCTAGTGTAAACACTGTGGTAAAAGATATC
66 TGTTGCCAGTGTTGAAAATGTTCGATCTGATCGATCCAAGTGTAAACACTGTGGTAAAAGACATC
*
43243063 CA-GACAATTGTAGATTGTACGATCGGGCTTGTTTCAGATTTGGATCATTAGAGAATTTCATCCG
131 CAGGA-AATTGTAGACTGTACGATCGGGCTTGTTTCAGATTTGGATCATTAGAGAATTTCATCCG
* *
43243127 TGATTGTCTCGAATCTATTAGCAAGAAATTTGCAA
195 TGATTGTCCCGAATCTATCAGCAAGAAATTTGCAA
43243162 AAT
1 AAT
43243165 CTGAGGAAGT
Statistics
Matches: 215, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
228 10 0.05
229 115 0.53
230 90 0.42
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (229 bp):
AATGTGGGAGATTCAAGTAGAGATCGTACTAAATCACATTCAAGCTTTAGAGCTCCAGCTACATC
TGTTGCCAGTGTTGAAAATGTTCGATCTGATCGATCCAAGTGTAAACACTGTGGTAAAAGACATC
CAGGAAATTGTAGACTGTACGATCGGGCTTGTTTCAGATTTGGATCATTAGAGAATTTCATCCGT
GATTGTCCCGAATCTATCAGCAAGAAATTTGCAA
Found at i:43247160 original size:42 final size:42
Alignment explanation
Indices: 43247056--43247215 Score: 173
Period size: 43 Copynumber: 3.7 Consensus size: 42
43247046 ATATGTGTTA
* * *
43247056 TCGTGTAAGACCACGTCTAGGACGTTGGCATTG-ACTTATGATT
1 TCGTGTAAGACCACATCTGGGACGTTGGCATCGTA-TT-TGATT
43247099 TACGTGTAAGACCACATCTGGGACGTTGGCATCGTATTTGATT
1 T-CGTGTAAGACCACATCTGGGACGTTGGCATCGTATTTGATT
*
43247142 TCGTGTAAGACC-CTATCTGGGATAG-TGGCATCGATATTTGATT
1 TCGTGTAAGACCAC-ATCTGGGA-CGTTGGCATCG-TATTTGATT
* * * *
43247185 ACATGTAAGACCACATTTGGGACATTGGCAT
1 TCGTGTAAGACCACATCTGGGACGTTGGCAT
43247216 TGTACGAGAT
Statistics
Matches: 101, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
41 1 0.01
42 27 0.27
43 40 0.40
44 32 0.32
45 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (42 bp):
TCGTGTAAGACCACATCTGGGACGTTGGCATCGTATTTGATT
Found at i:43254382 original size:43 final size:43
Alignment explanation
Indices: 43254317--43254474 Score: 187
Period size: 43 Copynumber: 3.7 Consensus size: 43
43254307 TATGTGTTAT
** *
43254317 CATGTAAGACCACGTCTTGGACGTTGGCATCTTATTTGATTTA
1 CATGTAAGACCATATCTGGGACGTTGGCATCTTATTTGATTTA
* *
43254360 CGTGTAAGACCATATTTGGGACGTTGGCATCTTATTTGATTT-
1 CATGTAAGACCATATCTGGGACGTTGGCATCTTATTTGATTTA
* * *
43254402 CATGTAAGACCCTATCTAGGACAG-TGGCATCGATATTTGA-TTA
1 CATGTAAGACCATATCTGGGAC-GTTGGCATC-TTATTTGATTTA
* *
43254445 CATGTAAGACCACATCTGGGACATTGGCAT
1 CATGTAAGACCATATCTGGGACGTTGGCAT
43254475 TGTACGAGAT
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
42 27 0.28
43 70 0.72
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (43 bp):
CATGTAAGACCATATCTGGGACGTTGGCATCTTATTTGATTTA
Found at i:43254465 original size:85 final size:85
Alignment explanation
Indices: 43254316--43254474 Score: 207
Period size: 85 Copynumber: 1.9 Consensus size: 85
43254306 ATATGTGTTA
* * * * * *
43254316 TCATGTAAGACCACGTCTTGGACGTTGGCATCTTATTTGATTTACGTGTAAGACCATATTTGGGA
1 TCATGTAAGACCACATCTAGGACGTTGGCATCATATTTGATTTACATGTAAGACCACATCTGGGA
*
43254381 CGTTGGCATCTTATTTGATT
66 CATTGGCATCTTATTTGATT
43254401 TCATGTAAGACC-CTATCTAGGACAG-TGGCATCGATATTTGA-TTACATGTAAGACCACATCTG
1 TCATGTAAGACCAC-ATCTAGGAC-GTTGGCATC-ATATTTGATTTACATGTAAGACCACATCTG
43254463 GGACATTGGCAT
63 GGACATTGGCAT
43254475 TGTACGAGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
84 1 0.02
85 55 0.86
86 8 0.12
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (85 bp):
TCATGTAAGACCACATCTAGGACGTTGGCATCATATTTGATTTACATGTAAGACCACATCTGGGA
CATTGGCATCTTATTTGATT
Found at i:43260061 original size:50 final size:50
Alignment explanation
Indices: 43259944--43260283 Score: 256
Period size: 50 Copynumber: 6.7 Consensus size: 50
43259934 TGTGAGAACA
* *** ** *
43259944 CATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGACGGTTTTAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG--TTAGGTCG
* * * *
43259996 CGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTTAGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGTCG
** * * * *
43260046 CATGTACAGTACTAAGTGCAGGCTACTATGCGTATCC-GATAGCTTCGATCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTA-CCAGATAG-TTAGGTCG
** ** * * *
43260097 TGTGTGTAGTACTAAGTGCAGGCTACTATACGTACCCGATAGCTTCGAT--
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG-TTAGGTCG
* * * * * *
43260146 CATGAGTGTATTACTAAGTGCAGGCTACTATGTGTATCAAATGGTTAAGTCA
1 CAT--GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGTCG
* * * *
43260198 CGTGTGTAGTACTAAATGCAGGCTACTACGTGTACCAGATTGTTAGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGTCG
* *
43260248 CATGTGTAGTAC-ACAGTGCAGGCTAATATGCGTACC
1 CATGTGTAGTACTA-AGTGCAGGCTACTATGTGTACC
43260284 TAAGAGCTTC
Statistics
Matches: 229, Mismatches: 51, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
49 2 0.01
50 112 0.49
51 80 0.35
52 35 0.15
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (50 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGTCG
Found at i:43260123 original size:51 final size:51
Alignment explanation
Indices: 43260053--43260225 Score: 224
Period size: 51 Copynumber: 3.4 Consensus size: 51
43260043 TCGCATGTAC
43260053 AGTACTAAGTGCAGGCTACTATGCGTATCCGATAGCTTCGATCATGTGTGT
1 AGTACTAAGTGCAGGCTACTATGCGTATCCGATAGCTTCGATCATGTGTGT
* * *
43260104 AGTACTAAGTGCAGGCTACTATACGTACCCGATAGCTTCGATCATGAGTGT
1 AGTACTAAGTGCAGGCTACTATGCGTATCCGATAGCTTCGATCATGTGTGT
* * ** * * *
43260155 ATTACTAAGTGCAGGCTACTATGTGTATCAAAT-GGTT-AAGTCACGTGTGT
1 AGTACTAAGTGCAGGCTACTATGCGTATCCGATAGCTTCGA-TCATGTGTGT
*
43260205 AGTACTAAATGCAGGCTACTA
1 AGTACTAAGTGCAGGCTACTA
43260226 CGTGTACCAG
Statistics
Matches: 106, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
49 1 0.01
50 30 0.28
51 75 0.71
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (51 bp):
AGTACTAAGTGCAGGCTACTATGCGTATCCGATAGCTTCGATCATGTGTGT
Found at i:43267858 original size:22 final size:21
Alignment explanation
Indices: 43267833--43267873 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
43267823 TGTTGGAATG
43267833 CTCACACGGGCATGTTGCCCCT
1 CTCACACGGGCATG-TGCCCCT
* *
43267855 CTCACATGGGCGTGTGCCC
1 CTCACACGGGCATGTGCCC
43267874 TTGTGTCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.12, C:0.39, G:0.27, T:0.22
Consensus pattern (21 bp):
CTCACACGGGCATGTGCCCCT
Found at i:43270727 original size:40 final size:40
Alignment explanation
Indices: 43270644--43270829 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
43270634 TCGAATGATG
* * * *
43270644 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
43270684 TCCGGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCC-GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
43270724 TCCGGGTTAAGTCCCGAAGGTATTTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
43270764 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
43270805 -CCGGGCTATGTTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43270830 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
39 7 0.06
40 103 0.82
41 16 0.13
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:43270847 original size:80 final size:79
Alignment explanation
Indices: 43270644--43270852 Score: 201
Period size: 80 Copynumber: 2.6 Consensus size: 79
43270634 TCGAATGATG
** * * * *
43270644 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGGGCTAAGCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAAC-GAGTGACTATATCC-GGGTTAAGCCCAAAGGCATT
43270708 GGTGCGAGTTACTAAA
64 GGTGCGAGTTACTAAA
* * *** * * *
43270724 TCCGGGTTAAGTCCCGAAGGTATTTGTGTGAGTTACTAAATCCGGGTTAAGTCCCAAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTATATCCGGGTTAAG-CCCAAAGGCATTG
43270789 GTGCGAGTTACTATAA
65 GTGCGAGTTACTA-AA
* *
43270805 -CCGGGCTATGTTCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTATATCCGGGTTAA
43270853 ATTCCGAAGG
Statistics
Matches: 106, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
79 14 0.13
80 84 0.79
81 8 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTATATCCGGGTTAAGCCCAAAGGCATTGG
TGCGAGTTACTAAA
Found at i:43278767 original size:79 final size:81
Alignment explanation
Indices: 43278631--43278815 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
43278621 TTGAATGATG
*
43278631 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
43278695 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
43278710 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
43278772 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
43278790 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43278816 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:43278829 original size:40 final size:40
Alignment explanation
Indices: 43278632--43278815 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
43278622 TGAATGATGT
* * * *
43278632 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
43278672 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
43278712 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
43278750 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
43278791 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
43278816 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:43278837 original size:79 final size:79
Alignment explanation
Indices: 43278684--43278848 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
43278674 GGACTAAGAT
* **
43278684 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
43278749 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
43278763 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
43278826 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
43278842 CCGAAGG
1 CCGAAGG
43278849 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:43280546 original size:27 final size:27
Alignment explanation
Indices: 43280516--43280589 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
43280506 AGTCTGACGA
* *
43280516 GACATTAAATACAGGATAGTTTGA-TGG
1 GACATTAAACACAGGATAGTAT-ATTGG
43280543 GACATTAAACAC-GAGATAGTATATTGG
1 GACATTAAACACAG-GATAGTATATTGG
*
43280570 GATATTAAACACAGGATAGT
1 GACATTAAACACAGGATAGT
43280590 CGACCGGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.05
27 38 0.93
28 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (27 bp):
GACATTAAACACAGGATAGTATATTGG
Found at i:43295746 original size:18 final size:17
Alignment explanation
Indices: 43295723--43295757 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
43295713 GATGGGCCGA
*
43295723 AATGGGCTATGTGGGCCC
1 AATGGGCT-TGTAGGCCC
43295741 AATGGGCTTGTAGGCCC
1 AATGGGCTTGTAGGCCC
43295758 CACACGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.23, G:0.37, T:0.23
Consensus pattern (17 bp):
AATGGGCTTGTAGGCCC
Found at i:43296056 original size:27 final size:27
Alignment explanation
Indices: 43296003--43296056 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
43295993 ATGACCAAAA
* * *
43296003 TACCCTTATAGGGTAAAATGACTATTT
1 TACCCCTAGAGGGTAAAATGACGATTT
43296030 TACCCCTAGAGGGT-AAATGACAGATTT
1 TACCCCTAGAGGGTAAAATGAC-GATTT
43296057 GTGCTACGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (27 bp):
TACCCCTAGAGGGTAAAATGACGATTT
Found at i:43296232 original size:26 final size:26
Alignment explanation
Indices: 43296181--43296232 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
43296171 TTTGCCACAT
* **
43296181 ATACTGATACTGGTAGCTTTGTTGCG
1 ATACTGATACTGGCAGCTTTACTGCG
*
43296207 ATACTGTTACTGGCAGCTTTACTGCG
1 ATACTGATACTGGCAGCTTTACTGCG
43296233 CTATTGGTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTACTGCG
Found at i:43298509 original size:18 final size:18
Alignment explanation
Indices: 43298469--43298509 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
43298459 AGGCCATCTC
43298469 TGGGCTATGTGGGCCACA
1 TGGGCTATGTGGGCCACA
*
43298487 CGGGC-ATGTGGGCCCACA
1 TGGGCTATGTGGG-CCACA
43298505 TGGGC
1 TGGGC
43298510 CCGCAATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.15, C:0.27, G:0.41, T:0.17
Consensus pattern (18 bp):
TGGGCTATGTGGGCCACA
Found at i:43299082 original size:205 final size:205
Alignment explanation
Indices: 43298730--43299342 Score: 1109
Period size: 205 Copynumber: 3.0 Consensus size: 205
43298720 ATACCCGTAT
* *
43298730 TGTGACAGCCCAAAATTGACCCTAGTCGGGAAGTGGTTTCGGGACCGCTAAACCGAGTCACCGAA
1 TGTGACAGCCCAAAGTTGACCCTAGTCGGGAAGTAGTTTCGGGACCGCTAAACCGAGTCACCGAA
43298795 AGGTTTGAATGTGATGTTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAATTTCAAGCTTC
66 AGGTTTGAATGTGATGTTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAATTTCAAGCTTC
43298860 GATTTAGTCGATTGCATGTGAATTTAGTCAATAGGACTTATATGAGAAAATTTTAAAATGTGATA
131 GATTTAGTCGATTGCATGTGAATTTAGTCAATAGGACTTATATGAGAAAATTTTAAAATGTGATA
43298925 GGTCAATGCA
196 GGTCAATGCA
43298935 TGTGACAGCCCAAAGTTGACCCTAGTCGGGAAGTAGTTTCGGGACCGCTAAACCGAGTCACCGAA
1 TGTGACAGCCCAAAGTTGACCCTAGTCGGGAAGTAGTTTCGGGACCGCTAAACCGAGTCACCGAA
43299000 AGGTTTGAATGTGATGTTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAATTTCAAGCTTC
66 AGGTTTGAATGTGATGTTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAATTTCAAGCTTC
43299065 GATTTAGTCGATTGCATGTGAATTTAGTCAATAGGACTTATATGAGAAAATTTTAAAATGTGATA
131 GATTTAGTCGATTGCATGTGAATTTAGTCAATAGGACTTATATGAGAAAATTTTAAAATGTGATA
43299130 GGTCAATGCA
196 GGTCAATGCA
43299140 TGTGACAGCCCAAAGTTGACCCTAGTCGGGAAGTAGTTTCGGGACCGCTAAACCGAGTCACCGAA
1 TGTGACAGCCCAAAGTTGACCCTAGTCGGGAAGTAGTTTCGGGACCGCTAAACCGAGTCACCGAA
* ** *
43299205 ATGTTTGAATGTGATACTTATTGTCTAGAATATGTAATTATGAATGTGTGAAAATTTCAAGCTTC
66 AGGTTTGAATGTGATGTTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAATTTCAAGCTTC
* * * * * * *
43299270 AATTTGGTTGATTTCATGTAAATTTAGTCAATAGGACTTATGTGAGAAAATTCTAAAATGTGATA
131 GATTTAGTCGATTGCATGTGAATTTAGTCAATAGGACTTATATGAGAAAATTTTAAAATGTGATA
43299335 GGTCAATG
196 GGTCAATG
43299343 TGTGAGAACC
Statistics
Matches: 395, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
205 395 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (205 bp):
TGTGACAGCCCAAAGTTGACCCTAGTCGGGAAGTAGTTTCGGGACCGCTAAACCGAGTCACCGAA
AGGTTTGAATGTGATGTTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAATTTCAAGCTTC
GATTTAGTCGATTGCATGTGAATTTAGTCAATAGGACTTATATGAGAAAATTTTAAAATGTGATA
GGTCAATGCA
Found at i:43299859 original size:278 final size:278
Alignment explanation
Indices: 43299362--43299917 Score: 1112
Period size: 278 Copynumber: 2.0 Consensus size: 278
43299352 CTATTAGTGC
43299362 ATGTGGACAAAGGGGGGACTTGCATGTCAAATTCCCCCCTACTAGTAGTGGCCGGCCATGACAAG
1 ATGTGGACAAAGGGGGGACTTGCATGTCAAATTCCCCCCTACTAGTAGTGGCCGGCCATGACAAG
43299427 CATGGTAGACAAAGTTTGATGGCCAAGACATGTCATAGACATGTTTTGTTGGTGCATCATGGGTG
66 CATGGTAGACAAAGTTTGATGGCCAAGACATGTCATAGACATGTTTTGTTGGTGCATCATGGGTG
43299492 GAAAAAAATAAAATAATAGGCATGGAAATTAAATAATGAAAAGGAGTATGATGATTACACAAAAA
131 GAAAAAAATAAAATAATAGGCATGGAAATTAAATAATGAAAAGGAGTATGATGATTACACAAAAA
43299557 AAAAAGTGTGTAGTTGATTCTTTCCCCCCCCATTGCCGTGAGCTAAAGAAAAGAGAGGAGAAGAT
196 AAAAAGTGTGTAGTTGATTCTTTCCCCCCCCATTGCCGTGAGCTAAAGAAAAGAGAGGAGAAGAT
43299622 CTTTGTTCATCCTTTTCT
261 CTTTGTTCATCCTTTTCT
43299640 ATGTGGACAAAGGGGGGACTTGCATGTCAAATTCCCCCCTACTAGTAGTGGCCGGCCATGACAAG
1 ATGTGGACAAAGGGGGGACTTGCATGTCAAATTCCCCCCTACTAGTAGTGGCCGGCCATGACAAG
43299705 CATGGTAGACAAAGTTTGATGGCCAAGACATGTCATAGACATGTTTTGTTGGTGCATCATGGGTG
66 CATGGTAGACAAAGTTTGATGGCCAAGACATGTCATAGACATGTTTTGTTGGTGCATCATGGGTG
43299770 GAAAAAAATAAAATAATAGGCATGGAAATTAAATAATGAAAAGGAGTATGATGATTACACAAAAA
131 GAAAAAAATAAAATAATAGGCATGGAAATTAAATAATGAAAAGGAGTATGATGATTACACAAAAA
43299835 AAAAAGTGTGTAGTTGATTCTTTCCCCCCCCATTGCCGTGAGCTAAAGAAAAGAGAGGAGAAGAT
196 AAAAAGTGTGTAGTTGATTCTTTCCCCCCCCATTGCCGTGAGCTAAAGAAAAGAGAGGAGAAGAT
43299900 CTTTGTTCATCCTTTTCT
261 CTTTGTTCATCCTTTTCT
43299918 CACCTTCATT
Statistics
Matches: 278, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
278 278 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (278 bp):
ATGTGGACAAAGGGGGGACTTGCATGTCAAATTCCCCCCTACTAGTAGTGGCCGGCCATGACAAG
CATGGTAGACAAAGTTTGATGGCCAAGACATGTCATAGACATGTTTTGTTGGTGCATCATGGGTG
GAAAAAAATAAAATAATAGGCATGGAAATTAAATAATGAAAAGGAGTATGATGATTACACAAAAA
AAAAAGTGTGTAGTTGATTCTTTCCCCCCCCATTGCCGTGAGCTAAAGAAAAGAGAGGAGAAGAT
CTTTGTTCATCCTTTTCT
Found at i:43301086 original size:80 final size:80
Alignment explanation
Indices: 43301002--43301246 Score: 221
Period size: 80 Copynumber: 3.1 Consensus size: 80
43300992 GGACTAAGAT
* * *
43301002 CCGAAGGCATTTGTGCGGGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACT
43301066 AAATCCGGGTTAAATC
65 AAATCCGGGTTAAATC
* * * * * **
43301082 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTA
**
43301147 AATCCGGGTTATGTC
66 AATCCGGGTTAAATC
* * * * * * * ** *
43301162 CCGAAGGCA-TTGTGTGAGTTA-CTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGA-GC
1 CCGAAGGCATTTGTGCGAGATATC-AAATCCGGGTTAAGCCCCGAAGGCATTCGTGCGA-GATAC
*
43301224 TATATCC-GGTTAAATC
64 TAAATCCGGGTTAAATC
43301240 CCGAAGG
1 CCGAAGG
43301247 TACGTGATTT
Statistics
Matches: 136, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
78 14 0.10
79 45 0.33
80 74 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTA
AATCCGGGTTAAATC
Found at i:43301193 original size:39 final size:40
Alignment explanation
Indices: 43300949--43301211 Score: 255
Period size: 40 Copynumber: 6.6 Consensus size: 40
43300939 TTGAATGCTG
* * * * * *
43300949 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
43300989 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGGGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
* * * *
43301028 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
43301069 TCCGGGTTAAATCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
43301109 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
43301149 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
43301188 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
43301212 TGAACGAGGA
Statistics
Matches: 192, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
39 36 0.19
40 145 0.76
41 11 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:43301231 original size:79 final size:80
Alignment explanation
Indices: 43301064--43301246 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
43301054 GTGCGAGATA
* * *
43301064 CTAAATCCGGGTTAAATCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAATCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
43301129 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* ** * *
43301144 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAATCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
43301208 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
*
43301223 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAATCCCGAAGG
43301247 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 26 0.30
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAATCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:43302266 original size:85 final size:85
Alignment explanation
Indices: 43302139--43302305 Score: 298
Period size: 85 Copynumber: 2.0 Consensus size: 85
43302129 GTTCTTGTGG
*
43302139 AACAGGGCCGGAACAGTTTCTGGATTCCCTGTTCCGAATTTGGAAATTCACTATAAATTGACCAG
1 AACAGGGCCAGAACAGTTTCTGGATTCCCTGTTCCGAATTTGGAAATTCACTATAAATTGACCAG
43302204 AGATAATTAGGAGTCATTGT
66 AGATAATTAGGAGTCATTGT
**
43302224 AACAGGGCCAGAACAGTTTCTGGATTCCCTGTTCCGCCTTTGGAAATTCACTATAAATTGACCAG
1 AACAGGGCCAGAACAGTTTCTGGATTCCCTGTTCCGAATTTGGAAATTCACTATAAATTGACCAG
*
43302289 AGATAATTAGGGGTCAT
66 AGATAATTAGGAGTCAT
43302306 ACCATATATG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 78 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (85 bp):
AACAGGGCCAGAACAGTTTCTGGATTCCCTGTTCCGAATTTGGAAATTCACTATAAATTGACCAG
AGATAATTAGGAGTCATTGT
Found at i:43304332 original size:27 final size:27
Alignment explanation
Indices: 43304301--43304478 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43304291 TAAATTGTAC
43304301 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
43304328 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43304354 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
43304382 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
43304410 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43304437 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
43304464 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43304479 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:43304415 original size:82 final size:81
Alignment explanation
Indices: 43304302--43304457 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43304292 AAATTGTACA
* *
43304302 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
43304366 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
43304383 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
43304448 TGCGAGTTGA
65 TGCGAATTGA
43304458 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:43304469 original size:82 final size:81
Alignment explanation
Indices: 43304298--43304478 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
43304288 GATTAAATTG
* *
43304298 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
43304363 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
43304379 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
43304443 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
43304461 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
43304479 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:43310673 original size:43 final size:42
Alignment explanation
Indices: 43310602--43310731 Score: 129
Period size: 42 Copynumber: 3.1 Consensus size: 42
43310592 CAGAAAGCAT
* * *
43310602 ATACAATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAACC
1 ATACGATGCCAATGTCCCAGACAG-GGTCTTACATGAAATC-A-C
* * * *
43310646 AT-TGATGCCACTTTCCCAGACAGGGTCTTACATGAAATCAG
1 ATACGATGCCAATGTCCCAGACAGGGTCTTACATGAAATCAC
* * *
43310687 ATACGATGCCAATGTCCCAGACATGGTCTTACACGATATCAC
1 ATACGATGCCAATGTCCCAGACAGGGTCTTACATGAAATCAC
43310729 ATA
1 ATA
43310732 TCGAAAATCC
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
41 2 0.03
42 36 0.51
43 29 0.41
44 3 0.04
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAGACAGGGTCTTACATGAAATCAC
Found at i:43310708 original size:42 final size:41
Alignment explanation
Indices: 43310602--43310719 Score: 121
Period size: 43 Copynumber: 2.8 Consensus size: 41
43310592 CAGAAAGCAT
* * *
43310602 ATACAATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCA
1 ATACGATGCCAATGTCCCAGACAG-GGTCTTACATGAAATCA
* * * *
43310643 ACCATTGATGCCACTTTCCCAGACAGGGTCTTACATGAAATCA
1 A-TA-CGATGCCAATGTCCCAGACAGGGTCTTACATGAAATCA
*
43310686 GATACGATGCCAATGTCCCAGACATGGTCTTACA
1 -ATACGATGCCAATGTCCCAGACAGGGTCTTACA
43310720 CGATATCACA
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
41 1 0.02
42 27 0.44
43 31 0.51
44 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (41 bp):
ATACGATGCCAATGTCCCAGACAGGGTCTTACATGAAATCA
Found at i:43312668 original size:49 final size:48
Alignment explanation
Indices: 43312606--43312704 Score: 119
Period size: 48 Copynumber: 2.0 Consensus size: 48
43312596 CACACTCTTG
*
43312606 TCTTATCAAAATGGCT-AAGAAACATGAAATATATTCTTACCCACACTTA
1 TCTTATCAAAATGG-TGAAGAAACAT-AAATATATTCTCACCCACACTTA
* * * * *
43312655 TCTTATTAGAATGGTGGAGGAACATAAATATGTTCTCACCCACACTTA
1 TCTTATCAAAATGGTGAAGAAACATAAATATATTCTCACCCACACTTA
43312703 TC
1 TC
43312705 AGAATATTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
48 24 0.56
49 19 0.44
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (48 bp):
TCTTATCAAAATGGTGAAGAAACATAAATATATTCTCACCCACACTTA
Found at i:43314428 original size:57 final size:57
Alignment explanation
Indices: 43314351--43314487 Score: 145
Period size: 57 Copynumber: 2.4 Consensus size: 57
43314341 GTTATGGATT
* * * *
43314351 GGATTTAGCCCGGACGGGTAATCC-AGA-TCAAGCTC-TTTAGAGTATATGTCATAAAAA
1 GGATTTAGCCTGGACTGGTAATCCTA-ACT-AAGCTCAATT-GAGTATATATCATAAAAA
* ** * *
43314408 GGATTTAGCTTGGACTGGTAATCCTAACTAAGCTCAATTGAGTATATATTGTAGACA
1 GGATTTAGCCTGGACTGGTAATCCTAACTAAGCTCAATTGAGTATATATCATAAAAA
43314465 GGATTTAGCCTGGACTGGTAATC
1 GGATTTAGCCTGGACTGGTAATC
43314488 TTGTTGTCTA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
57 63 0.94
58 4 0.06
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (57 bp):
GGATTTAGCCTGGACTGGTAATCCTAACTAAGCTCAATTGAGTATATATCATAAAAA
Found at i:43316256 original size:34 final size:34
Alignment explanation
Indices: 43316217--43316327 Score: 141
Period size: 34 Copynumber: 3.3 Consensus size: 34
43316207 ATAAATGTAT
* * *
43316217 ATATATATTCACCTTCGGTTATATCAAACCATAC
1 ATATATATTCACCTTCGATTATACCAAGCCATAC
* *
43316251 ATATATATTCACTTTCGATTATACCAAGCTATAC
1 ATATATATTCACCTTCGATTATACCAAGCCATAC
* * * *
43316285 ATTTATAATCATCTTCGATTATGCCAAGCCATAC
1 ATATATATTCACCTTCGATTATACCAAGCCATAC
43316319 ATATATATT
1 ATATATATT
43316328 TATGTACTTC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (34 bp):
ATATATATTCACCTTCGATTATACCAAGCCATAC
Found at i:43322775 original size:42 final size:41
Alignment explanation
Indices: 43322667--43322781 Score: 124
Period size: 44 Copynumber: 2.7 Consensus size: 41
43322657 TTCTGATATG
* * **
43322667 TGATTTCGTGCAAGACCAC-ATCTGGGACATTGGCATCGATT
1 TGATTTCGTGTAAGACC-CTGTCTGGGACATCAGCATCGATT
* *
43322708 TGAGATTTACGTGTAAGACCATGTCTAGGACATCAGCATCGTATT
1 T--GATTT-CGTGTAAGACCCTGTCTGGGACATCAGCATCG-ATT
43322753 TGATTTCGTGTAAGACCCTGTCTGGGACA
1 TGATTTCGTGTAAGACCCTGTCTGGGACA
43322782 GTGGTATAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
41 1 0.02
42 21 0.34
43 10 0.16
44 25 0.41
45 4 0.07
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (41 bp):
TGATTTCGTGTAAGACCCTGTCTGGGACATCAGCATCGATT
Found at i:43322797 original size:43 final size:42
Alignment explanation
Indices: 43322661--43322822 Score: 141
Period size: 43 Copynumber: 3.8 Consensus size: 42
43322651 ATAGGATTCT
* * *
43322661 GATATGTGATTTCGTGCAAGACCACATCTGGGACATTGGCATC
1 GATATTTGATTTCGTGTAAGACCACGTCTGGGACA-TGGCATC
* * * *
43322704 GAT-TTGAGATTTACGTGTAAGACCATGTCTAGGACATCAGCATC
1 GATATT-TGATTT-CGTGTAAGACCACGTCTGGGACAT-GGCATC
* *
43322748 G-TATTTGATTTCGTGTAAGACC-CTGTCTGGGACAGTGGTATA
1 GATATTTGATTTCGTGTAAGACCAC-GTCTGGGACA-TGGCATC
* * *
43322790 GATATTTGATTACATGTATGACCACGTCTGGGA
1 GATATTTGATTTCGTGTAAGACCACGTCTGGGA
43322823 TGTTGCCATT
Statistics
Matches: 95, Mismatches: 16, Indels: 16
0.75 0.13 0.13
Matches are distributed among these distances:
42 25 0.26
43 42 0.44
44 28 0.29
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (42 bp):
GATATTTGATTTCGTGTAAGACCACGTCTGGGACATGGCATC
Found at i:43331279 original size:43 final size:40
Alignment explanation
Indices: 43331190--43331300 Score: 114
Period size: 43 Copynumber: 2.6 Consensus size: 40
43331180 TAGTCTCAAG
*
43331190 CACAGCCTAGACACACGGGCGTGTCTGGTGGCCATGTGAGGCA
1 CACAGCCTAGACACACAGGCGTG--T-GTGGCCATGTGAGGCA
* * *
43331233 CACAGCCTTGGCACACAGGCGTGTGTGGCCATGTCGAAGGGTA
1 CACAGCCTAGACACACAGGCGTGTGTGGCCATGT-G-A-GGCA
* *
43331276 CACAGGCTAGACACACAGGCATGTG
1 CACAGCCTAGACACACAGGCGTGTG
43331301 GTTAGCCGTG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
40 10 0.18
41 2 0.04
42 1 0.02
43 44 0.77
ACGTcount: A:0.23, C:0.27, G:0.33, T:0.16
Consensus pattern (40 bp):
CACAGCCTAGACACACAGGCGTGTGTGGCCATGTGAGGCA
Found at i:43336974 original size:53 final size:54
Alignment explanation
Indices: 43336906--43337102 Score: 186
Period size: 55 Copynumber: 3.6 Consensus size: 54
43336896 TTTCCTTTTT
* * * * * *
43336906 GAACTTACCATTGCCATGTCTTTACATGGTCTTACGTGGTATTCTTGCTTTAT-
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATTCTTGCCTTATA
* *
43336959 GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCTT-TT-CCTTATA
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTA--TTCTTGCCTTATA
* * * *
43337013 GTAACTCATCAATGTCATGTCTTGACATGGTCTTACATGAT-TTCCTTGCCTTATA
1 G-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATT-CTTGCCTTATA
* * * *
43337068 GAACTTATCAATGTCATGCCTTGGCATGGTCTTAC
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTAC
43337103 GTGATATCCT
Statistics
Matches: 120, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
52 2 0.02
53 39 0.32
54 36 0.30
55 43 0.36
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (54 bp):
GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATTCTTGCCTTATA
Found at i:43337101 original size:54 final size:54
Alignment explanation
Indices: 43336930--43337113 Score: 194
Period size: 55 Copynumber: 3.4 Consensus size: 54
43336920 CATGTCTTTA
* * * * *
43336930 CATGGTCTTACGTGGTATT-CTTGCTTTAT-GAACTCACCAATGCCATGCCTTGG
1 CATGGTCTTACATGAT-TTCCTTGCCTTATAGAACTCATCAATGTCATGCCTTGG
*** * * *
43336983 CATGGTCTTACATG-GGACCTTTTCCTTATAGTAACTCATCAATGTCATGTCTTGA
1 CATGGTCTTACATGATTTCC-TTGCCTTATAG-AACTCATCAATGTCATGCCTTGG
*
43337038 CATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGTCATGCCTTGG
1 CATGGTCTTACATGATTTCCTTGCCTTATAGAACTCATCAATGTCATGCCTTGG
* *
43337092 CATGGTCTTACGTGATATCCTT
1 CATGGTCTTACATGATTTCCTT
43337114 ATCTTACCAA
Statistics
Matches: 107, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
52 1 0.01
53 20 0.19
54 41 0.38
55 43 0.40
56 2 0.02
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (54 bp):
CATGGTCTTACATGATTTCCTTGCCTTATAGAACTCATCAATGTCATGCCTTGG
Found at i:43337168 original size:47 final size:47
Alignment explanation
Indices: 43337092--43337213 Score: 181
Period size: 47 Copynumber: 2.6 Consensus size: 47
43337082 CATGCCTTGG
* * *
43337092 CATGGTCTTACGTGATATCCTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
* * *
43337139 CATGGTTTTACATGGTATCTTTGTCTTACCAAATGTCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
*
43337186 CATAGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
43337214 GTGCCAATGC
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
Found at i:43347154 original size:23 final size:22
Alignment explanation
Indices: 43347099--43347154 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
43347089 TTTATGTTTT
43347099 TATTTTTATTTTATTTTAAGAC
1 TATTTTTATTTTATTTTAAGAC
* *
43347121 TACTTTTTATTTTTTCTTTAAGCC
1 TA-TTTTTATTTTAT-TTTAAGAC
*
43347145 TATTTCTATT
1 TATTTTTATT
43347155 AGATTTTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.07
23 18 0.62
24 9 0.31
ACGTcount: A:0.21, C:0.11, G:0.04, T:0.64
Consensus pattern (22 bp):
TATTTTTATTTTATTTTAAGAC
Found at i:43355718 original size:58 final size:59
Alignment explanation
Indices: 43355611--43355725 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 59
43355601 AGGGAAATTA
43355611 TGACATGGCCGTGCTGATGACCCGTGTGGTTCACACAGCCTAAGCACAAGGGGACACTC
1 TGACATGGCCGTGCTGATGACCCGTGTGGTTCACACAGCCTAAGCACAAGGGGACACTC
* * *
43355670 TGACATGGCCGTGTTGATGGCCCGT-TGGTTCACACTGCCTAAGCACAAGGGGACAC
1 TGACATGGCCGTGCTGATGACCCGTGTGGTTCACACAGCCTAAGCACAAGGGGACAC
43355726 GACCCGTGTC
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 30 0.57
59 23 0.43
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.20
Consensus pattern (59 bp):
TGACATGGCCGTGCTGATGACCCGTGTGGTTCACACAGCCTAAGCACAAGGGGACACTC
Found at i:43358690 original size:27 final size:26
Alignment explanation
Indices: 43358653--43358970 Score: 336
Period size: 27 Copynumber: 11.8 Consensus size: 26
43358643 GCGAGGCTGC
* *
43358653 CAGATATTGTGACGA-AGTCACCAGAT
1 CAGATATTGTGGC-ATAGCCACCAGAT
* *
43358679 CAGATAATTGTGGCATCGCCACCAGAA
1 CAGAT-ATTGTGGCATAGCCACCAGAT
*
43358706 CAGATATGTGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCATAGCCACCAGAT
* *
43358733 CAGATAATCGTGGCATAGCCACCAGAA
1 CAGAT-ATTGTGGCATAGCCACCAGAT
* *
43358760 CAGATATATGTGGCAGAACCACCAGAT
1 CAGATAT-TGTGGCATAGCCACCAGAT
*
43358787 CAGATAATTGTGGCATAGCCACCAGAA
1 CAGAT-ATTGTGGCATAGCCACCAGAT
*
43358814 AAGATATATGTGGCATAGCCACCAGAAT
1 CAGATAT-TGTGGCATAGCCACCAG-AT
* *
43358842 -AGATATATGCGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCATAGCCACCAGAT
*
43358868 CAGATAATTGTGGCATAGCCACCAGAA
1 CAGAT-ATTGTGGCATAGCCACCAGAT
*
43358895 AAGATATATGTGGCATAGCCACCAGAAT
1 CAGATAT-TGTGGCATAGCCACCAG-AT
* *
43358923 -AGATATATGCGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCATAGCCACCAGAT
43358949 CAGATAATTGTGGCATAGCCAC
1 CAGAT-ATTGTGGCATAGCCAC
43358971 AAGGACGCTT
Statistics
Matches: 248, Mismatches: 30, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
26 18 0.07
27 220 0.89
28 10 0.04
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCATAGCCACCAGAT
Found at i:43358734 original size:54 final size:54
Alignment explanation
Indices: 43358671--43358970 Score: 410
Period size: 54 Copynumber: 5.6 Consensus size: 54
43358661 GTGACGAAGT
* *
43358671 CACCAGATCAGATAATTGTGGCATCGCCACCAGAACAGATATGTGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
* *
43358725 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
* *
43358779 CACCAGATCAGATAATTGTGGCATAGCCACCAGAAAAGATATATGTGGCATAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
* * * *
43358833 CACCAGAAT-AGAT-ATATGCGGCAGAGCCACCAGATCAGATA-ATTGTGGCATAGC
1 CACCAG-ATCAGATAAT-TGTGGCATAGCCACCAGAACAGATATA-TGTGGCAGAGC
** * *
43358887 CACCAGAAAAGAT-ATATGTGGCATAGCCACCAGAATAGATATATGCGGCAGAGC
1 CACCAGATCAGATAAT-TGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
43358941 CACCAGATCAGATAATTGTGGCATAGCCAC
1 CACCAGATCAGATAATTGTGGCATAGCCAC
43358971 AAGGACGCTT
Statistics
Matches: 219, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
53 4 0.02
54 210 0.96
55 5 0.02
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:43358765 original size:81 final size:81
Alignment explanation
Indices: 43358696--43358970 Score: 446
Period size: 81 Copynumber: 3.4 Consensus size: 81
43358686 TTGTGGCATC
* * **
43358696 GCCACCAGAACAGAT-ATGTGTGGCAGAGCCACCAGATCAGATA-ATCGTGGCATAGCCACCAGA
1 GCCACCAGATCAGATAAT-TGTGGCATAGCCACCAGAAAAGATATAT-GTGGCATAGCCACCAGA
*
43358759 ACAGATATATGTGGCAGA
64 ACAGATATATGCGGCAGA
* *
43358777 ACCACCAGATCAGATAATTGTGGCATAGCCACCAGAAAAGATATATGTGGCATAGCCACCAGAAT
1 GCCACCAGATCAGATAATTGTGGCATAGCCACCAGAAAAGATATATGTGGCATAGCCACCAGAAC
43358842 AGATATATGCGGCAGA
66 AGATATATGCGGCAGA
*
43358858 GCCACCAGATCAGATAATTGTGGCATAGCCACCAGAAAAGATATATGTGGCATAGCCACCAGAAT
1 GCCACCAGATCAGATAATTGTGGCATAGCCACCAGAAAAGATATATGTGGCATAGCCACCAGAAC
43358923 AGATATATGCGGCAGA
66 AGATATATGCGGCAGA
43358939 GCCACCAGATCAGATAATTGTGGCATAGCCAC
1 GCCACCAGATCAGATAATTGTGGCATAGCCAC
43358971 AAGGACGCTT
Statistics
Matches: 184, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
81 180 0.98
82 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.18
Consensus pattern (81 bp):
GCCACCAGATCAGATAATTGTGGCATAGCCACCAGAAAAGATATATGTGGCATAGCCACCAGAAC
AGATATATGCGGCAGA
Found at i:43360623 original size:26 final size:26
Alignment explanation
Indices: 43360592--43360699 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
43360582 TGAAATGCCC
*
43360592 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
43360618 ATCATGGAACATTTACTTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
43360644 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
43360670 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
43360696 ATCA
1 ATCA
43360700 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:43362209 original size:45 final size:45
Alignment explanation
Indices: 43362154--43362244 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
43362144 CTGTAACAGT
*
43362154 CCAGAGGGTAATTGATGCTCAGATTTCACTTGTTGGCATGTCAGA
1 CCAGAAGGTAATTGATGCTCAGATTTCACTTGTTGGCATGTCAGA
*
43362199 CCAGAAGGTAATTGATGCTCAGCTTTCACTTGTTGGCATGTCAGA
1 CCAGAAGGTAATTGATGCTCAGATTTCACTTGTTGGCATGTCAGA
43362244 C
1 C
43362245 ACTTCCCTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (45 bp):
CCAGAAGGTAATTGATGCTCAGATTTCACTTGTTGGCATGTCAGA
Found at i:43366057 original size:27 final size:27
Alignment explanation
Indices: 43366027--43366166 Score: 171
Period size: 27 Copynumber: 5.2 Consensus size: 27
43366017 TGACGAAGTT
*
43366027 ACCAGATATAGATATTGTGGCAGAGCC
1 ACCAGATACAGATATTGTGGCAGAGCC
43366054 ACCAGA-ACAGATATATGTGGCAGAGCC
1 ACCAGATACAGATAT-TGTGGCAGAGCC
* *
43366081 ACCAGAT-CAGATAATCGTGGCATAGCC
1 ACCAGATACAGAT-ATTGTGGCAGAGCC
*
43366108 ACCAGA-ACAGATATATGTGGCAAAGCC
1 ACCAGATACAGATAT-TGTGGCAGAGCC
*
43366135 ACCAGAT-CAGATAATTGTGGCATAGCC
1 ACCAGATACAGAT-ATTGTGGCAGAGCC
43366162 ACCAG
1 ACCAG
43366167 GACGCTTCCT
Statistics
Matches: 100, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
26 9 0.09
27 87 0.87
28 4 0.04
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.18
Consensus pattern (27 bp):
ACCAGATACAGATATTGTGGCAGAGCC
Found at i:43366101 original size:54 final size:54
Alignment explanation
Indices: 43366043--43366166 Score: 221
Period size: 54 Copynumber: 2.3 Consensus size: 54
43366033 TATAGATATT
* *
43366043 GTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATC
1 GTGGCATAGCCACCAGAACAGATATATGTGGCAAAGCCACCAGATCAGATAATC
*
43366097 GTGGCATAGCCACCAGAACAGATATATGTGGCAAAGCCACCAGATCAGATAATT
1 GTGGCATAGCCACCAGAACAGATATATGTGGCAAAGCCACCAGATCAGATAATC
43366151 GTGGCATAGCCACCAG
1 GTGGCATAGCCACCAG
43366167 GACGCTTCCT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (54 bp):
GTGGCATAGCCACCAGAACAGATATATGTGGCAAAGCCACCAGATCAGATAATC
Found at i:43366603 original size:16 final size:15
Alignment explanation
Indices: 43366582--43366611 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
43366572 AAAATACCGA
43366582 CTTTTCGGCATTTTGG
1 CTTTTCGGC-TTTTGG
43366598 CTTTTCGGCTTTTG
1 CTTTTCGGCTTTTG
43366612 CCAATCTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.03, C:0.20, G:0.23, T:0.53
Consensus pattern (15 bp):
CTTTTCGGCTTTTGG
Found at i:43367774 original size:26 final size:26
Alignment explanation
Indices: 43367743--43367850 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
43367733 TGAAATGCCC
*
43367743 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
43367769 ATCATGGAACATTTACTTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
43367795 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
43367821 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
43367847 ATCA
1 ATCA
43367851 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:43368829 original size:13 final size:13
Alignment explanation
Indices: 43368811--43368837 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43368801 ACAACTTCTA
43368811 CAATATGTAGCAT
1 CAATATGTAGCAT
43368824 CAATATGTAGCAT
1 CAATATGTAGCAT
43368837 C
1 C
43368838 GTTCACAATA
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:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (13 bp):
CAATATGTAGCAT
Found at i:43371525 original size:20 final size:23
Alignment explanation
Indices: 43371495--43371535 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
43371485 TCCACATTAT
43371495 TATTAAAACAA-CAT-TACGACG
1 TATTAAAACAATCATATACGACG
43371516 TATT-AAACAATCATATACGA
1 TATTAAAACAATCATATACGA
43371536 GCTTACGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (23 bp):
TATTAAAACAATCATATACGACG
Found at i:43371766 original size:13 final size:13
Alignment explanation
Indices: 43371748--43371796 Score: 89
Period size: 13 Copynumber: 3.8 Consensus size: 13
43371738 CCTAAACAAG
43371748 CAATTCAATACTT
1 CAATTCAATACTT
*
43371761 CAATTCAATAGTT
1 CAATTCAATACTT
43371774 CAATTCAATACTT
1 CAATTCAATACTT
43371787 CAATTCAATA
1 CAATTCAATA
43371797 TTTTCAGCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.37
Consensus pattern (13 bp):
CAATTCAATACTT
Found at i:43375791 original size:48 final size:48
Alignment explanation
Indices: 43375668--43375952 Score: 231
Period size: 48 Copynumber: 5.9 Consensus size: 48
43375658 AAGGTAAGAT
*
43375668 GCCGATGCCATG-TCCTAGACATGTTCTTACACTAGCTCTCATATATC-AG
1 GCCGATGCCATGTTCC-AGACATGGTCTTACACTAGCTCTC--ATATCGAG
* *
43375717 TGCCGATGCCATGTTCCTA-ACATGGTCTTACACTAGCTCGCATGTCGAG
1 -GCCGATGCCATGTTCC-AGACATGGTCTTACACTAGCTCTCATATCGAG
* * * * * ** *
43375766 GCTGATACCATGTGCCAGACATGGTCGTACACTAGCTTTCATATAAAT
1 GCCGATGCCATGTTCCAGACATGGTCTTACACTAGCTCTCATATCGAG
* * *
43375814 ACCGATGCTATGTTCCAAACATGG-CATTACACTAGCT-T-ATATGTCGAG
1 GCCGATGCCATGTTCCAGACATGGTC-TTACACTAGCTCTCATA--TCGAG
* * ** *
43375862 GCCAATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAAT
1 GCCGATGCCATGTTCCAGACATGGTCTTACACTAGCTCTCATATCGAG
* * * * * *
43375910 GCCGTTGCCATTTTCCAAATATGGTCTTACACTGGCTCACATA
1 GCCGATGCCATGTTCCAGACATGGTCTTACACTAGCTCTCATA
43375953 ACCCTAGTAT
Statistics
Matches: 187, Mismatches: 39, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
46 3 0.02
47 3 0.02
48 137 0.73
49 4 0.02
50 35 0.19
51 5 0.03
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (48 bp):
GCCGATGCCATGTTCCAGACATGGTCTTACACTAGCTCTCATATCGAG
Found at i:43375848 original size:96 final size:95
Alignment explanation
Indices: 43375675--43375951 Score: 340
Period size: 96 Copynumber: 2.9 Consensus size: 95
43375665 GATGCCGATG
* * *
43375675 CCATGTCCTAGACATGTTCTTACACTAGCTCTCATATATCAGTGCCGATGCCATGTTCCTAACAT
1 CCATGTCC-AGACATGGTCTTACACTAGCTCTCATATA--AATGCCGATGCCATGTTCCAAACAT
* **
43375740 GGTCTTACACTAGCTCGCATGTCGAGGCTGATA
63 GGTCTTACACTAGCTCACATGTCGAGGCCAATA
* * * *
43375773 CCATGTGCCAGACATGGTCGTACACTAGCTTTCATATAAATACCGATGCTATGTTCCAAACATGG
1 CCATGT-CCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAACATGG
* * *
43375838 -CATTACACTAGCTTATATGTCGAGGCCAATG
65 TC-TTACACTAGCTCACATGTCGAGGCCAATA
* * *
43375869 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGTTGCCATTTTCCAAATATGG
1 CCATGT-CCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAACATGG
*
43375934 TCTTACACTGGCTCACAT
65 TCTTACACTAGCTCACAT
43375952 AACCCTAGTA
Statistics
Matches: 152, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
95 1 0.01
96 116 0.76
97 1 0.01
98 32 0.21
99 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (95 bp):
CCATGTCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAACATGGT
CTTACACTAGCTCACATGTCGAGGCCAATA
Found at i:43389477 original size:41 final size:41
Alignment explanation
Indices: 43389399--43389519 Score: 136
Period size: 41 Copynumber: 2.9 Consensus size: 41
43389389 ATACTCGATA
* * *
43389399 TCTCACACACTAAGTGCCAATACATAGCCGAAACTATTATAAT
1 TCTCGCACACTAAGTGCC-ATACATAGCCGAAGCTATT-TAAG
* * **
43389442 TCT-GCACACTAAGTGCCTTACATAGTCGAAGCTATTTTGG
1 TCTCGCACACTAAGTGCCATACATAGCCGAAGCTATTTAAG
* *
43389482 TCTCGCACACTAAGTGCCATATATAGCCAAAGCTATTT
1 TCTCGCACACTAAGTGCCATACATAGCCGAAGCTATTT
43389520 TGAATCACAC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
40 4 0.06
41 46 0.70
42 13 0.20
43 3 0.05
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (41 bp):
TCTCGCACACTAAGTGCCATACATAGCCGAAGCTATTTAAG
Found at i:43389520 original size:41 final size:40
Alignment explanation
Indices: 43389404--43389626 Score: 231
Period size: 40 Copynumber: 5.5 Consensus size: 40
43389394 CGATATCTCA
* * *
43389404 CACACTAAGTGCCAATACATAGCCGAAACTATTAT-AATTCTG
1 CACACTAAGTGCC-ATATATAGCCGAAGCTATTTTGAA-TC-G
* * * **
43389446 CACACTAAGTGCCTTACATAGTCGAAGCTATTTTGGTCTCG
1 CACACTAAGTGCCATATATAGCCGAAGCTATTTT-GAATCG
* *
43389487 CACACTAAGTGCCATATATAGCCAAAGCTATTTTGAATCA
1 CACACTAAGTGCCATATATAGCCGAAGCTATTTTGAATCG
*
43389527 CACACTAAGT-CTCATATATCA-CCGAGGCT-TTCTTGAATCG
1 CACACTAAGTGC-CATATAT-AGCCGAAGCTATT-TTGAATCG
*
43389567 CACACTAAGTGCCGTATATAGCCGAAGCT-TTCTTGAATCG
1 CACACTAAGTGCCATATATAGCCGAAGCTATT-TTGAATCG
43389607 CACACTAAGTGCCATATATA
1 CACACTAAGTGCCATATATA
43389627 TATCCGACTT
Statistics
Matches: 155, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
39 4 0.03
40 86 0.55
41 50 0.32
42 15 0.10
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (40 bp):
CACACTAAGTGCCATATATAGCCGAAGCTATTTTGAATCG
Found at i:43392713 original size:12 final size:12
Alignment explanation
Indices: 43392696--43392721 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43392686 CCACCCACGC
43392696 CCGTGTGCTAGG
1 CCGTGTGCTAGG
43392708 CCGTGTGCTAGG
1 CCGTGTGCTAGG
43392720 CC
1 CC
43392722 ATGCCAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.31, G:0.38, T:0.23
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:43395404 original size:10 final size:10
Alignment explanation
Indices: 43395389--43395449 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
43395379 ATATTGTTAT
43395389 ACATGATATG
1 ACATGATATG
43395399 ACATGATATG
1 ACATGATATG
43395409 CACATGATATG
1 -ACATGATATG
** *
43395420 TTATGAGATG
1 ACATGATATG
43395430 TACATGATATG
1 -ACATGATATG
43395441 -CTATGATAT
1 AC-ATGATAT
43395450 ACTCATTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 1 0.02
10 24 0.57
11 17 0.40
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (10 bp):
ACATGATATG
Found at i:43395414 original size:21 final size:20
Alignment explanation
Indices: 43395389--43395463 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
43395379 ATATTGTTAT
43395389 ACATGATATGACATGATATGC
1 ACATGATATG-CATGATATGC
* * *
43395410 ACATGATATGTTATGAGATGT
1 ACATGATATG-CATGATATGC
*
43395431 ACATGATATGCTATGATATAC
1 ACATGATATGC-ATGATATGC
* *
43395452 TCATTATATGCA
1 ACATGATATGCA
43395464 CGGGTTGGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
20 1 0.02
21 42 0.98
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (20 bp):
ACATGATATGCATGATATGC
Found at i:43398941 original size:12 final size:12
Alignment explanation
Indices: 43398924--43398950 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43398914 ATTCCGAAGT
43398924 ATATATATATAC
1 ATATATATATAC
43398936 ATATATATATAC
1 ATATATATATAC
43398948 ATA
1 ATA
43398951 AGTATGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:43399411 original size:42 final size:42
Alignment explanation
Indices: 43399352--43399458 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
43399342 TGTTGATCTC
*
43399352 GGCACTAAGTGTGCGGGTATAAACATTTATGATCCTGAGATT
1 GGCACTAAGTGTGCGGGTATAAACATTTATGATCATGAGATT
43399394 GGCACTAAGTGTGCGGGTATAAACATTTATGATCATGAGATT
1 GGCACTAAGTGTGCGGGTATAAACATTTATGATCATGAGATT
*
43399436 GGCACTAAGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
43399459 TTGTACAGCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAACATTTATGATCATGAGATT
Found at i:43399521 original size:27 final size:28
Alignment explanation
Indices: 43399437--43399534 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
43399427 CATGAGATTG
* * * *
43399437 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
43399466 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
43399494 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
43399521 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
43399535 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:43399545 original size:27 final size:27
Alignment explanation
Indices: 43399465--43399547 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
43399455 TAAATTGTAC
* *
43399465 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
43399493 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
43399520 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
43399547 A
1 A
43399548 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:43399548 original size:29 final size:27
Alignment explanation
Indices: 43399437--43399548 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
43399427 CATGAGATTG
** * *
43399437 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
43399466 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
43399494 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
43399521 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
43399549 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:43400201 original size:41 final size:41
Alignment explanation
Indices: 43400144--43400225 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
43400134 ATTATGTTGT
*
43400144 GTTTGAACTTTGGTATGTAAACTTTCAGCCATGCGAAAATG
1 GTTTGAACTTTGGTATGTAAACTTTCAGCCATGCAAAAATG
43400185 GTTTGAACTTTGGTATGTAAACTTTCAGCCATGCAAAAATG
1 GTTTGAACTTTGGTATGTAAACTTTCAGCCATGCAAAAATG
43400226 ACATAAATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (41 bp):
GTTTGAACTTTGGTATGTAAACTTTCAGCCATGCAAAAATG
Found at i:43401255 original size:278 final size:278
Alignment explanation
Indices: 43400758--43401313 Score: 1085
Period size: 278 Copynumber: 2.0 Consensus size: 278
43400748 CTGTTCCGAC
*
43400758 TTTAGAGATTCGCCATAAATTAATCAGAGACAATTAGAAGTCATGCCTTATATGTATAGATTCCC
1 TTTAGAGATTCACCATAAATTAATCAGAGACAATTAGAAGTCATGCCTTATATGTATAGATTCCC
*
43400823 TTTTTAGTCTAGTTTCATTAGAAACAAATGGCATAAGTATTGAAGCTCTGTAAAGGGAGATATCT
66 TTTTGAGTCTAGTTTCATTAGAAACAAATGGCATAAGTATTGAAGCTCTGTAAAGGGAGATATCT
43400888 AAGTCGTAATGCACAAAGGTCAGAGTAGTCGAACCCAGGAACAGGGACGACTTTAACTAATAAAC
131 AAGTCGTAATGCACAAAGGTCAGAGTAGTCGAACCCAGGAACAGGGACGACTTTAACTAATAAAC
43400953 TGTACCAATTGGCCCAACCAAAAATTCTACAAAAATTCTACCATATAGATATATGAGTCTAGTTC
196 TGTACCAATTGGCCCAACCAAAAATTCTACAAAAATTCTACCATATAGATATATGAGTCTAGTTC
43401018 CGGGAAAAATTTACGGAA
261 CGGGAAAAATTTACGGAA
43401036 TTTAGAGATTCACCATAAATTAATCAGAGACAATTAGAAGTCATGCCTTATATGTATAGATTCCC
1 TTTAGAGATTCACCATAAATTAATCAGAGACAATTAGAAGTCATGCCTTATATGTATAGATTCCC
43401101 TTTTGAGTCTAGTTTCATTAGAAACAAATGGCATAAGTATTGAAGCTCTGTAAAGGGAGATATCT
66 TTTTGAGTCTAGTTTCATTAGAAACAAATGGCATAAGTATTGAAGCTCTGTAAAGGGAGATATCT
43401166 AAGTCGTAATGCACAAAGGTCAGAGTAGTCGAACCCAGGAACAGGGACGACTTTAACTAATAAAC
131 AAGTCGTAATGCACAAAGGTCAGAGTAGTCGAACCCAGGAACAGGGACGACTTTAACTAATAAAC
43401231 TGTACCAATTGGCCCAACCAAAAATTCTACAAAAATTCTACCATATAGATATATGAGTCTAGTTC
196 TGTACCAATTGGCCCAACCAAAAATTCTACAAAAATTCTACCATATAGATATATGAGTCTAGTTC
*
43401296 CGGGGAAAATTTACGGAA
261 CGGGAAAAATTTACGGAA
43401314 CTGGATTTCG
Statistics
Matches: 275, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
278 275 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (278 bp):
TTTAGAGATTCACCATAAATTAATCAGAGACAATTAGAAGTCATGCCTTATATGTATAGATTCCC
TTTTGAGTCTAGTTTCATTAGAAACAAATGGCATAAGTATTGAAGCTCTGTAAAGGGAGATATCT
AAGTCGTAATGCACAAAGGTCAGAGTAGTCGAACCCAGGAACAGGGACGACTTTAACTAATAAAC
TGTACCAATTGGCCCAACCAAAAATTCTACAAAAATTCTACCATATAGATATATGAGTCTAGTTC
CGGGAAAAATTTACGGAA
Found at i:43411049 original size:46 final size:45
Alignment explanation
Indices: 43410993--43411168 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 45
43410983 TGTTTGGGCA
43410993 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
43411039 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* * *
43411086 TCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTATTGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
43411132 CCCGAGCTCGTTCAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
43411169 GCGAGTTACA
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 65 0.61
47 31 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:43411149 original size:93 final size:93
Alignment explanation
Indices: 43410989--43411160 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
43410979 AGGATGTTTG
* * *
43410989 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTCAG
43411054 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
43411082 GGCATCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTATTGATGCGAACGCCCGAGCTCGTTCAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTCAG
43411147 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
43411161 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTCAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:43414133 original size:15 final size:15
Alignment explanation
Indices: 43414113--43414181 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
43414103 GTATCTTGGG
43414113 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
43414128 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
43414143 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
43414158 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
43414173 TTTCTTTAT
1 TTTCTTTAT
43414182 TTCGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:43414182 original size:30 final size:30
Alignment explanation
Indices: 43414104--43414182 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
43414094 CATAGTATCG
* * *
43414104 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATCTCTC
* *
43414134 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATCTCTC
43414164 TATCTTGGATTTCTTTATT
1 TATCTTGGATTTCTTTATT
43414183 TCGTTTTCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 1 0.02
30 40 0.95
31 1 0.02
ACGTcount: A:0.11, C:0.16, G:0.15, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATCTCTC
Found at i:43422200 original size:10 final size:10
Alignment explanation
Indices: 43422185--43422245 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
43422175 ATATTGTTAT
43422185 ACATGATATG
1 ACATGATATG
43422195 ACATGATATG
1 ACATGATATG
43422205 CACATGATATG
1 -ACATGATATG
** *
43422216 TTATGAGATG
1 ACATGATATG
43422226 CACATGATATG
1 -ACATGATATG
43422237 -CTATGATAT
1 AC-ATGATAT
43422246 ACTCATTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 1 0.02
10 24 0.57
11 17 0.40
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (10 bp):
ACATGATATG
Found at i:43422209 original size:21 final size:20
Alignment explanation
Indices: 43422185--43422261 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 20
43422175 ATATTGTTAT
43422185 ACATGATATGACATGATATGC
1 ACATGATATG-CATGATATGC
* *
43422206 ACATGATATGTTATGAGATGC
1 ACATGATATG-CATGATATGC
*
43422227 ACATGATATGCTATGATATAC
1 ACATGATATGC-ATGATATGC
* *
43422248 TCATTATATGCATG
1 ACATGATATGCATG
43422262 GGTTGGGTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 3 0.06
21 44 0.94
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (20 bp):
ACATGATATGCATGATATGC
Found at i:43423767 original size:40 final size:40
Alignment explanation
Indices: 43423683--43423769 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
43423673 TATAGTTTTG
* *
43423683 CACACTAAGTGCCATATATAGCCAAAGCTATTCCGAATCG
1 CACACTAAGTGCCATATATAGCCAAAGCTATTCCAAATCA
* *
43423723 CACACTAAGTGTCATATATAGCCAAAGCT-TTCTTAAATCA
1 CACACTAAGTGCCATATATAGCCAAAGCTATTC-CAAATCA
43423763 CACACTA
1 CACACTA
43423770 TGTAACAGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 3 0.07
40 39 0.93
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.25
Consensus pattern (40 bp):
CACACTAAGTGCCATATATAGCCAAAGCTATTCCAAATCA
Found at i:43424987 original size:42 final size:42
Alignment explanation
Indices: 43424928--43425039 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 42
43424918 CGAGATTATG
*
43424928 TGTAAG-GCCATATCTGGGATATGGCATCGATATGAGACTTCA
1 TGTAAGAG-CATATCTGGGATATGGCATCGATACGAGACTTCA
* * *
43424970 TGTAAGAGCATAACTGGGCTATTGGCATCGATACGAGATTTCA
1 TGTAAGAGCATATCTGGGATA-TGGCATCGATACGAGACTTCA
* * *
43425013 TTTAAGACCATATCTAGGATATGGCAT
1 TGTAAGAGCATATCTGGGATATGGCAT
43425040 TGGTATGGTA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 23 0.39
43 36 0.61
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.29
Consensus pattern (42 bp):
TGTAAGAGCATATCTGGGATATGGCATCGATACGAGACTTCA
Found at i:43426672 original size:48 final size:48
Alignment explanation
Indices: 43426599--43426734 Score: 191
Period size: 48 Copynumber: 2.8 Consensus size: 48
43426589 AATGAGAGCT
* *
43426599 AGTGTAAGACCATGTCTGAGACATGGCATTGGCATTTACATGTGTGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATTGGCATTGACATGTGTGCC
* ** * *
43426647 ATTGTAAGACCATGTCTGGGACATGGCACCGGCATTGATATGTGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATTGGCATTGACATGTGTGCC
* *
43426695 AGTGTAAGACCATGTTTGGGACATGGCATTGGCACTGACA
1 AGTGTAAGACCATGTCTGGGACATGGCATTGGCATTGACA
43426735 AGAGATTTCA
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATTGGCATTGACATGTGTGCC
Found at i:43426769 original size:96 final size:96
Alignment explanation
Indices: 43426596--43426770 Score: 208
Period size: 96 Copynumber: 1.8 Consensus size: 96
43426586 ATTAATGAGA
* * * * * * *
43426596 GCTAGTGTAAGACCATGTCTGAGACATGGCATTGGCATTTACATGTGTGCCATTGTAAGACCATG
1 GCTAGTGTAAGACCATGTCTGAGACATGGCATTGGCACTGACAAGAGTGCCATTATAAAACCATA
**
43426661 TCTGGGACATGGCACCGGCATTGATATGTGT
66 TCCAGGACATGGCACCGGCATTGATATGTGT
* * **
43426692 GCTAGTGTAAGACCATGTTTGGGACATGGCATTGGCACTGACAAGAGATTTCA-TATAAAACCAT
1 GCTAGTGTAAGACCATGTCTGAGACATGGCATTGGCACTGACAAGAG-TGCCATTATAAAACCAT
*
43426756 ATCCAGGATATGGCA
65 ATCCAGGACATGGCA
43426771 TTGATATTTG
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
96 61 0.95
97 3 0.05
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (96 bp):
GCTAGTGTAAGACCATGTCTGAGACATGGCATTGGCACTGACAAGAGTGCCATTATAAAACCATA
TCCAGGACATGGCACCGGCATTGATATGTGT
Done.