Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 186 of 204
Found at i:54884553 original size:9 final size:9
Alignment explanation
Indices: 54884523--54884582 Score: 61
Period size: 9 Copynumber: 6.6 Consensus size: 9
54884513 TTTGTTTTGA
54884523 TTTTTGTTCT
1 TTTTTGTT-T
54884533 TTTTAT-TATT
1 TTTT-TGT-TT
54884543 TTTTTGTTT
1 TTTTTGTTT
* *
54884552 TTTAT-CTT
1 TTTTTGTTT
54884560 TTTTTGTTT
1 TTTTTGTTT
54884569 TTTTTGTTT
1 TTTTTGTTT
54884578 TTTTT
1 TTTTT
54884583 CCTCTACTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
8 6 0.14
9 23 0.55
10 11 0.26
11 2 0.05
ACGTcount: A:0.05, C:0.03, G:0.07, T:0.85
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:54886819 original size:4 final size:4
Alignment explanation
Indices: 54886792--54886867 Score: 50
Period size: 4 Copynumber: 19.2 Consensus size: 4
54886782 AATAAAATGA
* * * *
54886792 AAAT AAAT AGTAT ATAT AAA- AAAT AAAT AAA- AAAT AAAT -AAC GAAT
1 AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
54886838 AAAT GACT AAAT AAAT AGAT AAGAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT A
54886868 TAAATAATAT
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
3 8 0.14
4 41 0.73
5 7 0.12
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:54886841 original size:11 final size:11
Alignment explanation
Indices: 54886807--54886832 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54886797 AATAGTATAT
54886807 ATAAAAAATAA
1 ATAAAAAATAA
54886818 ATAAAAAATAA
1 ATAAAAAATAA
54886829 ATAA
1 ATAA
54886833 CGAATAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAAAATAA
Found at i:54886871 original size:23 final size:26
Alignment explanation
Indices: 54886818--54886874 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
54886808 TAAAAAATAA
54886818 ATAAA-AAATAAATAACGAATAAATG
1 ATAAATAAATAAATAACGAATAAATG
*
54886843 ACTAAATAAATAGATAA-G-ATAAAT-
1 A-TAAATAAATAAATAACGAATAAATG
54886867 ATAAATAA
1 ATAAATAA
54886875 TATTAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 7 0.24
24 1 0.03
25 7 0.24
26 5 0.17
27 9 0.31
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.23
Consensus pattern (26 bp):
ATAAATAAATAAATAACGAATAAATG
Found at i:54886944 original size:69 final size:67
Alignment explanation
Indices: 54886827--54887056 Score: 246
Period size: 69 Copynumber: 3.3 Consensus size: 67
54886817 AATAAAAAAT
* * * *
54886827 AAATAACGAATAAATGACTAAATAAATAGATAAGATAAATATAAATAATATTAAATTTAAGTATT
1 AAATAAAGAAT-AATAAATAAATAAATAGATAAAATAAATATAAATAATATTAAATTTAAGTATT
54886892 TAA
65 TAA
* * * * *
54886895 AAATTCAAAGAATGATAAATAAATAAATCGGTAAAATAAATATAAATAATATTATATTTAAATAT
1 AAA-T-AAAGAATAATAAATAAATAAATAGATAAAATAAATATAAATAATATTAAATTTAAGTAT
54886960 TTAA
64 TTAA
* * * * * * *
54886964 AAGGTAAAAGAATAATGAAA-AAGTAAATAAATAAAACATATATAAATAGTATTAAATTTAGGTA
1 AA-AT-AAAGAATAAT-AAATAAATAAATAGATAAAATAAATATAAATAATATTAAATTTAAGTA
54887028 TTTTAA
63 -TTTAA
54887034 AAATAAAGAATAATAAATAAATA
1 AAATAAAGAATAATAAATAAATA
54887057 TATAAATGCT
Statistics
Matches: 132, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
67 3 0.02
68 17 0.13
69 96 0.73
70 16 0.12
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (67 bp):
AAATAAAGAATAATAAATAAATAAATAGATAAAATAAATATAAATAATATTAAATTTAAGTATTT
AA
Found at i:54890556 original size:85 final size:84
Alignment explanation
Indices: 54890429--54890783 Score: 417
Period size: 85 Copynumber: 4.2 Consensus size: 84
54890419 ACGTCGTAAA
* * *
54890429 CTTTTGCGGCGCTTACAGAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAGA
1 CTTTAGCGGCGC-TA-AAAAAAAAACACCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAGA
54890494 AACGCCGCTAAAGATCATGTT
64 AACGCCGCTAAAGATCATGTT
* *
54890515 CTTTAGCGGCGCTAAAAAAATAAACACCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAAATAA
1 CTTTAGCGGCGCTAAAAAAA-AAACACCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAGAA
* *
54890580 ACGCCACTAAAGAGCATGTT
65 ACGCCGCTAAAGATCATGTT
* * * * *
54890600 CTTTAGCGGCGCTTAGAAATAAAA-GCCACTAAAGATCATGTTCTTTAGCGGCGCTAAAGAAATA
1 CTTTAGCGGCGC-TAAAAAAAAAACACCACTAAAGATCATGTTCTTTAGCGGCGCT-TAGAAAGA
54890664 AACGCCGCTAAAGATCATGTT
64 AACGCCGCTAAAGATCATGTT
* ** * * * * *
54890685 CTTTAGCGACGCTTAGGACAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTTGAAAGAA
1 CTTTAGCGGCGC-TAAAAAAAAAACACCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAG-A
* *
54890750 AACGCCTCTAAA-AGTAATGTT
64 AACGCCGCTAAAGA-TCATGTT
*
54890771 CTATAGCGGCGCT
1 CTTTAGCGGCGCT
54890784 TGTTTAAAAA
Statistics
Matches: 236, Mismatches: 27, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
84 34 0.14
85 128 0.54
86 74 0.31
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (84 bp):
CTTTAGCGGCGCTAAAAAAAAAACACCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAGAAA
CGCCGCTAAAGATCATGTT
Found at i:54890752 original size:43 final size:42
Alignment explanation
Indices: 54890429--54890784 Score: 446
Period size: 43 Copynumber: 8.3 Consensus size: 42
54890419 ACGTCGTAAA
*
54890429 CTTTTGCGGCGCTTACAGAAAAAAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCACTAAAGATCATGTT
* *
54890473 CTTTAGCGGCGCTTAGAAAGAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTT
* * * *
54890515 CTTTAGCGGCGCTAAAAAAATAAACACCACTAAAGACCATGTT
1 CTTTAGCGGCGCTTAGAAAA-AAACGCCACTAAAGATCATGTT
* *
54890558 CTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGAGCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTT
54890600 CTTTAGCGGCGCTTAGAAATAAAA-GCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAA-AAAACGCCACTAAAGATCATGTT
* * *
54890642 CTTTAGCGGCGCTAAAGAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCT-TAGAAAAAAACGCCACTAAAGATCATGTT
* * *
54890685 CTTTAGCGACGCTTAGGACAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-GAAAAAAACGCCACTAAAGATCATGTT
* * * *
54890728 CTTTAGCGGCACTTTGAAAGAAAACGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGAAA-AAAACGCCACTAAAGA-TCATGTT
*
54890771 CTATAGCGGCGCTT
1 CTTTAGCGGCGCTT
54890785 GTTTAAAAAC
Statistics
Matches: 274, Mismatches: 31, Indels: 15
0.86 0.10 0.05
Matches are distributed among these distances:
42 120 0.44
43 141 0.51
44 13 0.05
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTT
Found at i:54896866 original size:9 final size:9
Alignment explanation
Indices: 54896852--54897227 Score: 134
Period size: 9 Copynumber: 43.7 Consensus size: 9
54896842 AAGATATACA
54896852 TTATGTAAG
1 TTATGTAAG
54896861 TTATGTAAG
1 TTATGTAAG
54896870 TTATGTAAG
1 TTATGTAAG
*
54896879 TTGTGTAAG
1 TTATGTAAG
**
54896888 TTGCGTAAG
1 TTATGTAAG
* *
54896897 ATGTGT-A-
1 TTATGTAAG
* *
54896904 TTATGAAAC
1 TTATGTAAG
54896913 TTATGTAAG
1 TTATGTAAG
*
54896922 TTATGT--C
1 TTATGTAAG
54896929 TTATGTAAG
1 TTATGTAAG
*
54896938 TTATGTAAA
1 TTATGTAAG
*
54896947 ATATGT-A-
1 TTATGTAAG
*
54896954 TTATTTACA-
1 TTATGTA-AG
*
54896963 -CATGTAAG
1 TTATGTAAG
*
54896971 TTATGT--C
1 TTATGTAAG
54896978 TTATGTAAG
1 TTATGTAAG
**
54896987 TTGCGTAAG
1 TTATGTAAG
*
54896996 TTGTGT-A-
1 TTATGTAAG
*
54897003 TTATGAAAG
1 TTATGTAAG
*
54897012 TTATGT--C
1 TTATGTAAG
54897019 TTATGTAAG
1 TTATGTAAG
*
54897028 TTATGTAGG
1 TTATGTAAG
*
54897037 GTATGTATTA-
1 TTATGTA--AG
*
54897047 TTATGTAAC
1 TTATGTAAG
* *
54897056 TTATTTAAT
1 TTATGTAAG
*
54897065 TTATGTAGG
1 TTATGTAAG
*
54897074 GTATGTATTA-
1 TTATGTA--AG
*
54897084 TTATGTAAC
1 TTATGTAAG
* *
54897093 TTATTTAAT
1 TTATGTAAG
*
54897102 TTATGTAGG
1 TTATGTAAG
*
54897111 GTATGTAAG
1 TTATGTAAG
54897120 TTATGTAAG
1 TTATGTAAG
* *
54897129 CTCTGT-A-
1 TTATGTAAG
* *
54897136 TTATTTACG
1 TTATGTAAG
*
54897145 -CATGTAAG
1 TTATGTAAG
*
54897153 TTGTGT-A-
1 TTATGTAAG
54897160 TTATGTATTA-
1 TTATGTA--AG
* *
54897170 TTACGTAAC
1 TTATGTAAG
*
54897179 TTATTTAAG
1 TTATGTAAG
*
54897188 TTATGCAAG
1 TTATGTAAG
*
54897197 TTATAT-A-
1 TTATGTAAG
* *
54897204 TTAAGTAGG
1 TTATGTAAG
54897213 TTATGTAAG
1 TTATGTAAG
54897222 TTATGT
1 TTATGT
54897228 GTTATCTAAA
Statistics
Matches: 265, Mismatches: 73, Indels: 58
0.67 0.18 0.15
Matches are distributed among these distances:
7 42 0.16
8 20 0.08
9 184 0.69
10 19 0.07
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:54896920 original size:25 final size:25
Alignment explanation
Indices: 54896892--54896957 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
54896882 TGTAAGTTGC
*
54896892 GTAAGATGTGTATTATGAAACTTAT
1 GTAAGATATGTATTATGAAACTTAT
* * * *
54896917 GTAAGTTATGTCTTATGTAAGTTAT
1 GTAAGATATGTATTATGAAACTTAT
*
54896942 GTAAAATATGTATTAT
1 GTAAGATATGTATTAT
54896958 TTACACATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.35, C:0.03, G:0.18, T:0.44
Consensus pattern (25 bp):
GTAAGATATGTATTATGAAACTTAT
Found at i:54896931 original size:16 final size:16
Alignment explanation
Indices: 54896912--54897033 Score: 82
Period size: 16 Copynumber: 8.0 Consensus size: 16
54896902 TATTATGAAA
54896912 CTTATGTAAGTTATGT
1 CTTATGTAAGTTATGT
54896928 CTTATGTAAGTTATGT
1 CTTATGTAAGTTATGT
** *
54896944 AAAATATGT-A-TTATTT
1 --CTTATGTAAGTTATGT
**
54896960 ACACATGTAAGTTATGT
1 -CTTATGTAAGTTATGT
54896977 CTTATGTAAG-T-TG-
1 CTTATGTAAGTTATGT
*
54896990 C----GTAAGTTGTGT
1 CTTATGTAAGTTATGT
* *
54897002 ATTATGAAAGTTATGT
1 CTTATGTAAGTTATGT
54897018 CTTATGTAAGTTATGT
1 CTTATGTAAGTTATGT
54897034 AGGGTATGTA
Statistics
Matches: 82, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
9 5 0.06
10 1 0.01
11 2 0.02
13 1 0.01
14 2 0.02
15 7 0.09
16 53 0.65
17 6 0.07
18 5 0.06
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.46
Consensus pattern (16 bp):
CTTATGTAAGTTATGT
Found at i:54897044 original size:41 final size:40
Alignment explanation
Indices: 54896968--54897117 Score: 114
Period size: 37 Copynumber: 3.9 Consensus size: 40
54896958 TTACACATGT
** * * *
54896968 AAGTTATGTCTTATGTAAGTTGCGTAAGTTGTGTATTATGA
1 AAGTTATGTCTTATGTAAGTTATGTAGGGTATGTATTAT-A
*
54897009 AAGTTATGTCTTATGTAAGTTATGTAGGGTATGTATTATT
1 AAGTTATGTCTTATGTAAGTTATGTAGGGTATGTATTATA
* * * * *
54897049 ATG-TA--ACTTATTTAATTTATGTAGGGTATGTATTATT
1 AAGTTATGTCTTATGTAAGTTATGTAGGGTATGTATTATA
* * * *
54897086 ATG-TA--ACTTATTTAATTTATGTAGGGTATGTA
1 AAGTTATGTCTTATGTAAGTTATGTAGGGTATGTA
54897118 AGTTATGTAA
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
37 61 0.62
39 2 0.02
40 2 0.02
41 34 0.34
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (40 bp):
AAGTTATGTCTTATGTAAGTTATGTAGGGTATGTATTATA
Found at i:54897069 original size:37 final size:37
Alignment explanation
Indices: 54897018--54897117 Score: 182
Period size: 37 Copynumber: 2.7 Consensus size: 37
54897008 AAAGTTATGT
* *
54897018 CTTATGTAAGTTATGTAGGGTATGTATTATTATGTAA
1 CTTATTTAATTTATGTAGGGTATGTATTATTATGTAA
54897055 CTTATTTAATTTATGTAGGGTATGTATTATTATGTAA
1 CTTATTTAATTTATGTAGGGTATGTATTATTATGTAA
54897092 CTTATTTAATTTATGTAGGGTATGTA
1 CTTATTTAATTTATGTAGGGTATGTA
54897118 AGTTATGTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.29, C:0.03, G:0.19, T:0.49
Consensus pattern (37 bp):
CTTATTTAATTTATGTAGGGTATGTATTATTATGTAA
Found at i:54897361 original size:12 final size:12
Alignment explanation
Indices: 54897344--54897368 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54897334 TATATGTAAG
54897344 TTATGTAAGTTA
1 TTATGTAAGTTA
54897356 TTATGTAAGTTA
1 TTATGTAAGTTA
54897368 T
1 T
54897369 GCAAGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:54897386 original size:22 final size:21
Alignment explanation
Indices: 54897340--54897391 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
54897330 TGAATATATG
* * *
54897340 TAAGTTATGTAAGTTATTATG
1 TAAGTTATGCAAGTTATAATA
54897361 TAAGTTATGCAAGATTATAATA
1 TAAGTTATGCAAG-TTATAATA
54897383 TAAGTTATG
1 TAAGTTATG
54897392 TATTATGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.42
Consensus pattern (21 bp):
TAAGTTATGCAAGTTATAATA
Found at i:54897405 original size:8 final size:7
Alignment explanation
Indices: 54897387--54897424 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
54897377 ATAATATAAG
54897387 TTATGTA
1 TTATGTA
54897394 TTATGTTA
1 TTATG-TA
54897402 TTATGTA
1 TTATGTA
54897409 TTATGTA
1 TTATGTA
54897416 --ATGTA
1 TTATGTA
54897421 TTAT
1 TTAT
54897425 CAGATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (7 bp):
TTATGTA
Found at i:54897450 original size:96 final size:95
Alignment explanation
Indices: 54897334--54897511 Score: 293
Period size: 96 Copynumber: 1.9 Consensus size: 95
54897324 CGTAAATGAA
* * * *
54897334 TATATGTAAGTTATGTAAGTTATTATGTAAGTTATGCAAGATTATAATATAAGTTATGTATTATG
1 TATATATAAGTTACGGAAGTTATTATGTAAGTTATACAAGATTAT-ATATAAGTTATGTATTATG
*
54897399 TTATTATGTATTATGTAATGTATTATCAGAT
65 TTATTATATATTATGTAATGTATTATCAGAT
*
54897430 TATATATAAGTTACGGAAGTTATTATGTAAGTTATACAAGCTTATATATAAGTTATGTATTATGT
1 TATATATAAGTTACGGAAGTTATTATGTAAGTTATACAAGATTATATATAAGTTATGTATTATGT
54897495 TATTATATATTATGTAA
66 TATTATATATTATGTAA
54897512 GTTATGCAAG
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
95 36 0.47
96 40 0.53
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.46
Consensus pattern (95 bp):
TATATATAAGTTACGGAAGTTATTATGTAAGTTATACAAGATTATATATAAGTTATGTATTATGT
TATTATATATTATGTAATGTATTATCAGAT
Found at i:54897481 original size:21 final size:20
Alignment explanation
Indices: 54897429--54897485 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
54897419 TATTATCAGA
***
54897429 TTATATATAAGTTACGGAAG
1 TTATATATAAGTTATACAAG
*
54897449 TTATTATGTAAGTTATACAAG
1 TTA-TATATAAGTTATACAAG
54897470 CTTATATATAAGTTAT
1 -TTATATATAAGTTAT
54897486 GTATTATGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (20 bp):
TTATATATAAGTTATACAAG
Found at i:54897526 original size:26 final size:26
Alignment explanation
Indices: 54897450--54897529 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 26
54897440 TTACGGAAGT
*
54897450 TATTATGTAAGTTATACAAGCTTATATA
1 TATTATGTAAGTTATGCAAGC-T-TATA
**
54897478 TAAGTTATGT-A-TTATGTTA--TTATA
1 T-A-TTATGTAAGTTATGCAAGCTTATA
54897502 TATTATGTAAGTTATGCAAGCTTATA
1 TATTATGTAAGTTATGCAAGCTTATA
54897528 TA
1 TA
54897530 CCAATTATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
22 6 0.15
23 2 0.05
24 11 0.27
25 1 0.02
26 7 0.17
28 6 0.15
29 2 0.05
30 6 0.15
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.46
Consensus pattern (26 bp):
TATTATGTAAGTTATGCAAGCTTATA
Found at i:54897528 original size:52 final size:52
Alignment explanation
Indices: 54897450--54897558 Score: 166
Period size: 52 Copynumber: 2.1 Consensus size: 52
54897440 TTACGGAAGT
*
54897450 TATTATGTAAGTTATACAAGCTTATATA-TAAGTTATGTATTATGTTATTATA
1 TATTATGTAAGTTATACAAGCTTATATACCAA-TTATGTATTATGTTATTATA
* * *
54897502 TATTATGTAAGTTATGCAAGCTTATATACCAATTATGTATTGTGTTATTATG
1 TATTATGTAAGTTATACAAGCTTATATACCAATTATGTATTATGTTATTATA
54897554 TATTA
1 TATTA
54897559 AGTTATATAC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 50 0.96
53 2 0.04
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTATGTAAGTTATACAAGCTTATATACCAATTATGTATTATGTTATTATA
Found at i:54898860 original size:52 final size:52
Alignment explanation
Indices: 54898798--54898896 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
54898788 GGTTATGTAA
*
54898798 ATTATTACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTTACCGT
1 ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTTACCGT
*
54898850 ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAGTTTGAATTT
1 ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTT
54898897 TCTTATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.44
Consensus pattern (52 bp):
ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTTACCGT
Found at i:54898881 original size:27 final size:27
Alignment explanation
Indices: 54898803--54898881 Score: 65
Period size: 25 Copynumber: 3.0 Consensus size: 27
54898793 TGTAAATTAT
54898803 TACCTAAAAATGTTCTTACTTTCTTAA
1 TACCTAAAAATGTTCTTACTTTCTTAA
* ** * ** *
54898830 -CCCT-AATTTGAAT-TTACCGTATTAA
1 TACCTAAAAATG-TTCTTACTTTCTTAA
54898855 TACCTAAAAATGTTCTTACTTTCTTAA
1 TACCTAAAAATGTTCTTACTTTCTTAA
54898882 CCCTAGTTTG
Statistics
Matches: 34, Mismatches: 14, Indels: 8
0.61 0.25 0.14
Matches are distributed among these distances:
25 13 0.38
26 8 0.24
27 13 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (27 bp):
TACCTAAAAATGTTCTTACTTTCTTAA
Found at i:54901319 original size:86 final size:86
Alignment explanation
Indices: 54901217--54901389 Score: 283
Period size: 86 Copynumber: 2.0 Consensus size: 86
54901207 TTAAATCCCT
** * ** *
54901217 GAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAAACCTTGAAAGCTAAGAAAACGGTGTCGTT
1 GAGCATTAGCAACGCTTTACTAAAAACGCCGCTAAAACCCCGAAAGCAAAGAAAACGGTGTCGTT
54901282 GGGTTTAATTTTTTTTGCGGC
66 GGGTTTAATTTTTTTTGCGGC
*
54901303 GAGCATTAGCAACGCTTTACTAAAAACGCCGCTAAACCCCCGAAAGCAAAGAAAACGGTGTCGTT
1 GAGCATTAGCAACGCTTTACTAAAAACGCCGCTAAAACCCCGAAAGCAAAGAAAACGGTGTCGTT
54901368 GGGTTTAATTTTTTTTGCGGC
66 GGGTTTAATTTTTTTTGCGGC
54901389 G
1 G
54901390 CTTCCATAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (86 bp):
GAGCATTAGCAACGCTTTACTAAAAACGCCGCTAAAACCCCGAAAGCAAAGAAAACGGTGTCGTT
GGGTTTAATTTTTTTTGCGGC
Found at i:54901512 original size:112 final size:112
Alignment explanation
Indices: 54901305--54901522 Score: 271
Period size: 112 Copynumber: 1.9 Consensus size: 112
54901295 TTTGCGGCGA
* *
54901305 GCATTAGCAACGCTTTACTAAAAACGCCGCTAAACCCCCGAAAGCAAAGAAAACGGTGTCGTTGG
1 GCATTAGCAACGCATTACTAAAAACGCCGCTAAACCCCCGAAAGCAAAGAAAACGGCGTCGTTGG
* * *
54901370 GTTTAATTTTTTTTGCGGCGCTTCCATAAAAACGCCGCTAAAGCCCT
66 GCTTAATGTTTTTTGCGGCGCTTCCATAAAAACACCGCTAAAGCCCT
** * * **
54901417 GCATTAGCGGCGCATTATTAAAAACGCCGCTAAACCCCCCCGGAAGCTTAGAAAACGGCGTCGTT
1 GCATTAGCAACGCATTACTAAAAACGCCGCTAAA--CCCCCGAAAGCAAAGAAAACGGCGTCGTT
* *
54901482 GGGCTT-A-GTTTTTTGCGGCGCTT-TAGTAAAAGCACCGCTAA
64 GGGCTTAATGTTTTTTGCGGCGCTTCCA-TAAAAACACCGCTAA
54901523 TTCTTATTTC
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
111 1 0.01
112 58 0.64
113 1 0.01
114 30 0.33
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (112 bp):
GCATTAGCAACGCATTACTAAAAACGCCGCTAAACCCCCGAAAGCAAAGAAAACGGCGTCGTTGG
GCTTAATGTTTTTTGCGGCGCTTCCATAAAAACACCGCTAAAGCCCT
Found at i:54904054 original size:4 final size:4
Alignment explanation
Indices: 54904047--54904089 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
54904037 AATAAATAAA
* *
54904047 ATAC ATAC ATAC ATAC TTAC ATAC TTAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
54904090 ACGTAGGAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (4 bp):
ATAC
Found at i:54904823 original size:28 final size:28
Alignment explanation
Indices: 54904769--54904823 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
54904759 TGTTTCCTAA
*
54904769 AAAATAAAATATAAAAATGAAACAAACG
1 AAAATAAAATATAAAAATGAAAAAAACG
54904797 AAAATAAAA-A-AAAAATAGAAGAAAAAC
1 AAAATAAAATATAAAAAT-GAA-AAAAAC
54904824 TACCTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.25
27 4 0.17
28 14 0.58
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.11
Consensus pattern (28 bp):
AAAATAAAATATAAAAATGAAAAAAACG
Found at i:54905177 original size:15 final size:16
Alignment explanation
Indices: 54905149--54905178 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54905139 GGTTTGTAAA
54905149 TGGACTATTTATTTTT
1 TGGACTATTTATTTTT
54905165 TGGACTA-TTATTTT
1 TGGACTATTTATTTT
54905179 ATTTTTGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (16 bp):
TGGACTATTTATTTTT
Found at i:54905610 original size:21 final size:22
Alignment explanation
Indices: 54905572--54905615 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
54905562 CATTCTAGAA
*
54905572 TTATAAAAACATAAATTTTTTT
1 TTATAAAAACATAAATTTGTTT
* *
54905594 TTATAAAAA-TTAGATTTGTTT
1 TTATAAAAACATAAATTTGTTT
54905615 T
1 T
54905616 AAAACTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
TTATAAAAACATAAATTTGTTT
Found at i:54905660 original size:9 final size:9
Alignment explanation
Indices: 54905615--54905678 Score: 56
Period size: 10 Copynumber: 6.6 Consensus size: 9
54905605 AGATTTGTTT
54905615 TAAAACTTTA
1 TAAAA-TTTA
*
54905625 TAAAATGTAA
1 TAAAAT-TTA
*
54905635 TAGAAATTAA
1 TA-AAATTTA
*
54905645 TTAAAATTCA
1 -TAAAATTTA
54905655 TAAAATTTTA
1 TAAAA-TTTA
54905665 TAAAATTTA
1 TAAAATTTA
54905674 TAAAA
1 TAAAA
54905679 ATAATTTATT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
9 15 0.32
10 26 0.55
11 6 0.13
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (9 bp):
TAAAATTTA
Found at i:54905668 original size:19 final size:18
Alignment explanation
Indices: 54905615--54905678 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
54905605 AGATTTGTTT
54905615 TAAAACTTTATAAAATGTAA
1 TAAAA-TTTATAAAAT-TAA
* *
54905635 TAGAAATTAATTAAAATTCA
1 TA-AAATTTA-TAAAATTAA
*
54905655 TAAAATTTTATAAAATTTA
1 TAAAA-TTTATAAAATTAA
54905674 TAAAA
1 TAAAA
54905679 ATAATTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 16 0.43
20 12 0.32
21 9 0.24
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAAATTTATAAAATTAA
Found at i:54905856 original size:17 final size:18
Alignment explanation
Indices: 54905819--54905862 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
54905809 CTATTCATTA
54905819 TTATAATTTTAATAATCTT
1 TTATAATTTT-ATAATCTT
*
54905838 TTATAATTTT-TAATGTT
1 TTATAATTTTATAATCTT
54905855 TTATAATT
1 TTATAATT
54905863 GTAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 14 0.58
19 10 0.42
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TTATAATTTTATAATCTT
Found at i:54907014 original size:26 final size:26
Alignment explanation
Indices: 54906985--54907039 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
54906975 CTTCAAAGAT
54906985 ATCCACTTGACCATAAAATCTATTCC
1 ATCCACTTGACCATAAAATCTATTCC
54907011 ATCCACTTGACCATAAAATCTATTCC
1 ATCCACTTGACCATAAAATCTATTCC
54907037 ATC
1 ATC
54907040 TCAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.31
Consensus pattern (26 bp):
ATCCACTTGACCATAAAATCTATTCC
Found at i:54920168 original size:23 final size:23
Alignment explanation
Indices: 54920157--54920212 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
54920147 ATATTAAATT
54920157 TACATAAAAAATATATAAAATAA
1 TACATAAAAAATATATAAAATAA
*
54920180 TACATAACAAAT-T-TGAAGAATAA
1 TACATAAAAAATATAT-AA-AATAA
*
54920203 TACATCAAAA
1 TACATAAAAA
54920213 CTTAAAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 1 0.04
22 3 0.11
23 24 0.86
ACGTcount: A:0.62, C:0.09, G:0.04, T:0.25
Consensus pattern (23 bp):
TACATAAAAAATATATAAAATAA
Found at i:54920266 original size:23 final size:22
Alignment explanation
Indices: 54920238--54920295 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
54920228 AAAAGAAACC
*
54920238 TTTAAAAATAATAATACAATAGA
1 TTTAAAAATAATAA-ACAATAAA
*
54920261 TTTAAACAAT-ATCAACAATAAA
1 TTTAAA-AATAATAAACAATAAA
*
54920283 TTT-ATAATAATAA
1 TTTAAAAATAATAA
54920296 GTTTAATTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 3 0.10
21 4 0.14
22 10 0.34
23 9 0.31
24 3 0.10
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
TTTAAAAATAATAAACAATAAA
Found at i:54925265 original size:30 final size:30
Alignment explanation
Indices: 54925214--54925272 Score: 77
Period size: 32 Copynumber: 2.0 Consensus size: 30
54925204 TAATAAAAAA
*
54925214 TTTAAAATATATATATGAAATTTATATAATTT
1 TTTAAAATATATAAATGAAA-TTATA-AATTT
54925246 TTTAAAATATA-AAAT-AAATTATAAATT
1 TTTAAAATATATAAATGAAATTATAAATT
54925273 ATAAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 3 0.12
31 3 0.12
32 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (30 bp):
TTTAAAATATATAAATGAAATTATAAATTT
Found at i:54930666 original size:26 final size:26
Alignment explanation
Indices: 54930629--54930680 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
54930619 GAATCAGCAA
*
54930629 ACACACACATATCTGCACATATAGAC
1 ACACACACATATCTGCACAGATAGAC
*
54930655 ACACACATATATCTGCACAGATAGAC
1 ACACACACATATCTGCACAGATAGAC
54930681 TACTAGGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (26 bp):
ACACACACATATCTGCACAGATAGAC
Found at i:54937581 original size:31 final size:31
Alignment explanation
Indices: 54937538--54937611 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
54937528 AACATGGCGT
54937538 TATGCTTTGTTGAGTTTAATGGTGTGGAAGAG
1 TATG-TTTGTTGAGTTTAATGGTGTGGAAGAG
*
54937570 TATGTTTGTTGAGTTTAATGGTGTGGAAGTG
1 TATGTTTGTTGAGTTTAATGGTGTGGAAGAG
*
54937601 TATGTTCGTTG
1 TATGTTTGTTG
54937612 TCTCCTGTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 36 0.90
32 4 0.10
ACGTcount: A:0.19, C:0.03, G:0.34, T:0.45
Consensus pattern (31 bp):
TATGTTTGTTGAGTTTAATGGTGTGGAAGAG
Found at i:54939640 original size:14 final size:14
Alignment explanation
Indices: 54939621--54939659 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
54939611 AAGTTACTGT
* *
54939621 TTTAGGGTTTGATG
1 TTTAGGGTTTAAGG
54939635 TTTAGGGTTTAAGG
1 TTTAGGGTTTAAGG
*
54939649 TTTAGAGTTTA
1 TTTAGGGTTTA
54939660 TGATTTAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTAAGG
Found at i:54940041 original size:29 final size:29
Alignment explanation
Indices: 54939999--54940059 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
54939989 AAAATTCTAA
54939999 CAATGAAAAATAATGTCATATTAATGTAT
1 CAATGAAAAATAATGTCATATTAATGTAT
*
54940028 CAATTAAAAATAATGTCATATTAATGTAT
1 CAATGAAAAATAATGTCATATTAATGTAT
54940057 CAA
1 CAA
54940060 ATTTATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.34
Consensus pattern (29 bp):
CAATGAAAAATAATGTCATATTAATGTAT
Found at i:54945831 original size:42 final size:42
Alignment explanation
Indices: 54945767--54945908 Score: 121
Period size: 43 Copynumber: 3.3 Consensus size: 42
54945757 AATCTACCAA
* *
54945767 TTTTAGTGGCGTTT-TTAGTAAAATG-CCGCTAAAGAACA-GTAC
1 TTTTAGCGGCGTTTGCTA-TAAAA-GACCGCTAAAGAACATG-AC
*
54945809 TTTTAGCGGCGTTTGCTATAAAAGCACCGCTAAAGAATATGAC
1 TTTTAGCGGCGTTTGCTATAAAAG-ACCGCTAAAGAACATGAC
* * **
54945852 ATTTAGCGGCGTTTGCTACAAAA-ACTTCGCTAAAGGTCATGAC
1 TTTTAGCGGCGTTTGCTATAAAAGAC--CGCTAAAGAACATGAC
* *
54945895 CTTTAGCAGCGTTT
1 TTTTAGCGGCGTTT
54945909 ATGTGAAAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
41 3 0.04
42 18 0.21
43 62 0.74
44 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (42 bp):
TTTTAGCGGCGTTTGCTATAAAAGACCGCTAAAGAACATGAC
Found at i:54945857 original size:43 final size:43
Alignment explanation
Indices: 54945792--54945874 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
54945782 TAGTAAAATG
* *
54945792 CCGCTAAAGAACAGTACTTTTAGCGGCGTTTGCTATAAAAGCA
1 CCGCTAAAGAACAGTACATTTAGCGGCGTTTGCTACAAAAGCA
*
54945835 CCGCTAAAGAATA-TGACATTTAGCGGCGTTTGCTACAAAA
1 CCGCTAAAGAACAGT-ACATTTAGCGGCGTTTGCTACAAAA
54945875 ACTTCGCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (43 bp):
CCGCTAAAGAACAGTACATTTAGCGGCGTTTGCTACAAAAGCA
Found at i:54946045 original size:21 final size:21
Alignment explanation
Indices: 54946002--54946046 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
54945992 TTTAGCGGCA
* * *
54946002 CTAAAAAGCGCCGCTATAGGC
1 CTAAAAAACGCCGCTAAAAGC
*
54946023 CTAAAAAATGCCGCTAAAAGC
1 CTAAAAAACGCCGCTAAAAGC
54946044 CTA
1 CTA
54946047 TTTTGCTGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.16
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:54946652 original size:17 final size:18
Alignment explanation
Indices: 54946620--54946663 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
54946610 CTATTCATTA
54946620 TTATAATTTTAATAATATT
1 TTATAATTTT-ATAATATT
*
54946639 TTATAATTTT-TAATGTT
1 TTATAATTTTATAATATT
54946656 TTATAATT
1 TTATAATT
54946664 GTAAAATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 14 0.58
19 10 0.42
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TTATAATTTTATAATATT
Found at i:54947687 original size:18 final size:20
Alignment explanation
Indices: 54947664--54947703 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
54947654 TTAAGCTTTA
*
54947664 TTTAAT-AT-TTTAATAAAT
1 TTTAATAATGTTTAAAAAAT
54947682 TTTAATAATGTTTAAAAAAT
1 TTTAATAATGTTTAAAAAAT
54947702 TT
1 TT
54947704 AAAACATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTAATAATGTTTAAAAAAT
Found at i:54948875 original size:16 final size:16
Alignment explanation
Indices: 54948854--54948923 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
54948844 TTTGGTTCGC
* *
54948854 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
54948870 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
54948886 TGTAATGGAATAGAGA
1 TGTAATGGAATAGAGG
54948902 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
54948918 TGTAAT
1 TGTAAT
54948924 AGCAAATCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.33, C:0.00, G:0.34, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:54949007 original size:39 final size:42
Alignment explanation
Indices: 54948904--54949011 Score: 123
Period size: 39 Copynumber: 2.6 Consensus size: 42
54948894 AATAGAGATG
54948904 TAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATA
1 TAATGGAATAGAGGTGTAATAGC-AATC-ACTG-TTGGTTGAATA
* * * *
54948949 TAATGGAATAGAGGCGTAATAGCAATC-CTG-TGTTTG-GTT
1 TAATGGAATAGAGGTGTAATAGCAATCACTGTTGGTTGAATA
*
54948988 TAATGTAATAGAGGTGTAATAGCA
1 TAATGGAATAGAGGTGTAATAGCA
54949012 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
39 23 0.40
40 5 0.09
42 3 0.05
44 4 0.07
45 22 0.39
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.31
Consensus pattern (42 bp):
TAATGGAATAGAGGTGTAATAGCAATCACTGTTGGTTGAATA
Found at i:54949177 original size:18 final size:17
Alignment explanation
Indices: 54949156--54949190 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54949146 TTATTATTAA
*
54949156 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
54949174 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
54949191 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:54949320 original size:16 final size:16
Alignment explanation
Indices: 54949283--54949324 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
54949273 TTAATCATAT
*
54949283 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
54949299 TT-AAATATATTATAA
1 TTAAAATATATTATAA
54949314 TTAAAATATAT
1 TTAAAATATAT
54949325 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:54949331 original size:14 final size:15
Alignment explanation
Indices: 54949292--54949333 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54949282 TTTAAACATA
*
54949292 ATTATTATTAAATAT
1 ATTATAATTAAATAT
54949307 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
54949321 A-TATAATTTAATA
1 ATTATAATTAAATA
54949334 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:54949344 original size:147 final size:147
Alignment explanation
Indices: 54949077--54949349 Score: 503
Period size: 147 Copynumber: 1.9 Consensus size: 147
54949067 ATGATTATTG
*
54949077 TTATTGTTATTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTTAAC
1 TTATTGTTATTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAAC
*
54949142 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
66 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
54949207 AAATTTGTTTTGGTAAA
131 AAATTTGTTTTGGTAAA
*
54949224 TTATT-TTATTTAAATTTTAATAAGATTATTAATATCAATAGTAAATAATTTAATCATATTTAAA
1 TTATTGTTA-TTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAA
54949288 CATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
65 CATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
54949350 ATATTCTTAT
Statistics
Matches: 122, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
146 3 0.02
147 119 0.98
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:54949442 original size:16 final size:16
Alignment explanation
Indices: 54949402--54949444 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
54949392 GTAAAATATA
*
54949402 AATTAACATA-ATTAT
1 AATTAAAATATATTAT
*
54949417 TATT-AAATATATTAT
1 AATTAAAATATATTAT
54949432 AATTAAAATATAT
1 AATTAAAATATAT
54949445 GATTTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 4 0.17
15 11 0.48
16 8 0.35
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTAAAATATATTAT
Found at i:54951060 original size:11 final size:11
Alignment explanation
Indices: 54951046--54951072 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
54951036 AAAAATCAAT
54951046 ACAAAAGTTTC
1 ACAAAAGTTTC
54951057 ACAAAAGTTTC
1 ACAAAAGTTTC
54951068 ACAAA
1 ACAAA
54951073 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:54951436 original size:14 final size:14
Alignment explanation
Indices: 54951417--54951447 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
54951407 AAAATATTAA
54951417 CAACAAATAGTTCC
1 CAACAAATAGTTCC
54951431 CAACAAATAGTTCC
1 CAACAAATAGTTCC
54951445 CAA
1 CAA
54951448 TTGCCAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.19
Consensus pattern (14 bp):
CAACAAATAGTTCC
Found at i:54953313 original size:163 final size:168
Alignment explanation
Indices: 54953006--54953313 Score: 482
Period size: 163 Copynumber: 1.8 Consensus size: 168
54952996 AATAATCTTA
54953006 CAATTTCAACAGAAACTACTGAAGAGTAAAAAATATTCATAATAATGCACAAATCTTAACAATTT
1 CAATTTCAACAGAAACTACTGAAGAGT--AAAATATTCATAATAATG-ACAAA--TTAACAATTT
*
54953071 GATAAAAGAGTGTCGAACAAAGAATTGCCAGATTTATTTGGGTCCGAAATAAAAATCACCCGATC
61 GATAAAAGAGTGTCGAACAAAGAATTGCCAGATTAATTTGGGTCCGAAATAAAAATCACCCGATC
54953136 TTGGATTAGAGGTGAATAAGCAACAATGAATAAAATCCAATAG
126 TTGGATTAGAGGTGAATAAGCAACAATGAATAAAATCCAATAG
* *
54953179 CAATTTCAACAGAAACTACTGAAGAGT-AAATATTCATACTAATG-C-AA-T-ACAATTTTATAA
1 CAATTTCAACAGAAACTACTGAAGAGTAAAATATTCATAATAATGACAAATTAACAATTTGATAA
* * *
54953239 AAGATTGTCGAACAAAGAATTGGCAGATTAATTTGGGTCCGAAATAAAACTCACCCGATCTTGGA
66 AAGAGTGTCGAACAAAGAATTGCCAGATTAATTTGGGTCCGAAATAAAAATCACCCGATCTTGGA
54953304 TTAGAGGTGA
131 TTAGAGGTGA
54953314 TGACCCGAAA
Statistics
Matches: 129, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
163 82 0.64
164 1 0.01
167 2 0.02
168 1 0.01
170 16 0.12
173 27 0.21
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (168 bp):
CAATTTCAACAGAAACTACTGAAGAGTAAAATATTCATAATAATGACAAATTAACAATTTGATAA
AAGAGTGTCGAACAAAGAATTGCCAGATTAATTTGGGTCCGAAATAAAAATCACCCGATCTTGGA
TTAGAGGTGAATAAGCAACAATGAATAAAATCCAATAG
Found at i:54959943 original size:14 final size:14
Alignment explanation
Indices: 54959924--54959950 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54959914 GACGTCATTT
54959924 CAGTGAGTGTGGTG
1 CAGTGAGTGTGGTG
54959938 CAGTGAGTGTGGT
1 CAGTGAGTGTGGT
54959951 CAAACTTCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.48, T:0.30
Consensus pattern (14 bp):
CAGTGAGTGTGGTG
Found at i:54965763 original size:22 final size:22
Alignment explanation
Indices: 54965738--54965819 Score: 128
Period size: 22 Copynumber: 3.7 Consensus size: 22
54965728 TGATTCAAAA
*
54965738 GTACTAAGCTCTCATGTTTCAC
1 GTACTAAGCTCTCATGTTTAAC
54965760 GTACTAAGCTCTCATGTTTAAC
1 GTACTAAGCTCTCATGTTTAAC
54965782 GTACTAAGCTCTCATGTTTAAC
1 GTACTAAGCTCTCATGTTTAAC
* * *
54965804 GAACTAAACCCTCATG
1 GTACTAAGCTCTCATG
54965820 GCTAACCAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (22 bp):
GTACTAAGCTCTCATGTTTAAC
Found at i:54972161 original size:69 final size:69
Alignment explanation
Indices: 54972069--54972277 Score: 226
Period size: 70 Copynumber: 3.0 Consensus size: 69
54972059 AATAAATGAC
* * * *
54972069 TAAATAAATAGATAAGACAAATATAAGTAATATTAAATTTAAGTA-TTTAAAAATTAAAAGAATG
1 TAAATAAATCGATAAAACAAATATAAATAATATTAAATTTAAGTATTTTAAAAA-TAAAAGAATA
54972133 ATAAA
65 ATAAA
* * ** *
54972138 TAAATAAATCGGTAAAACAAATATAAATAATATTAAATTTAAATATTTTAAAAGGCAAAAGAATT
1 TAAATAAATCGATAAAACAAATATAAATAATATTAAATTTAAGTATTTTAAAA-ATAAAAGAATA
*
54972203 ATGAA
65 ATAAA
* * * * * *
54972208 CAAACAAA-CAAATAAAACAGATATAAATAGTATTAAATTTAGGTATTTTAAAAAT-AAAGAATA
1 TAAATAAATC-GATAAAACAAATATAAATAATATTAAATTTAAGTATTTTAAAAATAAAAGAATA
54972271 ATAAA
65 ATAAA
54972276 TA
1 TA
54972278 TATATATATA
Statistics
Matches: 115, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
68 12 0.10
69 41 0.36
70 62 0.54
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (69 bp):
TAAATAAATCGATAAAACAAATATAAATAATATTAAATTTAAGTATTTTAAAAATAAAAGAATAA
TAAA
Found at i:54975857 original size:4 final size:4
Alignment explanation
Indices: 54975842--54975873 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
54975832 AATAAGAGTG
*
54975842 TAAA TGAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
54975874 GAAAATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:54976021 original size:2 final size:2
Alignment explanation
Indices: 54976014--54976062 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
54976004 ATCCACATGA
54976014 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54976056 AT AT AT A
1 AT AT AT A
54976063 CTTTGAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54976164 original size:6 final size:6
Alignment explanation
Indices: 54976153--54976205 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
54976143 TCGTGAGAAA
* * * *
54976153 AAATAT AAATAT AAATAT ACATATAT AAATAT ATATCT ATATAT ATATAT
1 AAATAT AAATAT AAATAT A-A-ATAT AAATAT AAATAT AAATAT AAATAT
54976203 AAA
1 AAA
54976206 ATGAGTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 34 0.83
7 2 0.05
8 5 0.12
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (6 bp):
AAATAT
Found at i:54976180 original size:14 final size:13
Alignment explanation
Indices: 54976153--54976205 Score: 58
Period size: 12 Copynumber: 4.2 Consensus size: 13
54976143 TCGTGAGAAA
54976153 AAATATAA-ATAT
1 AAATATAATATAT
54976165 AAATATACATATAT
1 AAATATA-ATATAT
*
54976179 AAATAT-ATATCT
1 AAATATAATATAT
*
54976191 ATATAT-ATATAT
1 AAATATAATATAT
54976203 AAA
1 AAA
54976206 ATGAGTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
12 24 0.69
13 1 0.03
14 10 0.29
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATAATATAT
Found at i:54976180 original size:20 final size:20
Alignment explanation
Indices: 54976155--54976199 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
54976145 GTGAGAAAAA
54976155 ATATAAATATAAATATACAT
1 ATATAAATATAAATATACAT
* * *
54976175 ATATAAATATATATCTATAT
1 ATATAAATATAAATATACAT
54976195 ATATA
1 ATATA
54976200 TATAAAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATAAATATAAATATACAT
Found at i:54976246 original size:24 final size:25
Alignment explanation
Indices: 54976219--54976288 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 25
54976209 AGTATTTATG
54976219 TATGTATAAAAAAATATA-A-GTATA
1 TATGTATAAAAAAATATACACGT-TA
* *
54976243 TATGTACATATAAAAATATACACGTTT
1 TATGT--ATAAAAAAATATACACGTTA
*
54976270 TAATATATAAAAAAATATA
1 T-ATGTATAAAAAAATATA
54976289 TATGAATAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
24 5 0.14
26 24 0.65
27 3 0.08
28 5 0.14
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (25 bp):
TATGTATAAAAAAATATACACGTTA
Found at i:54976362 original size:18 final size:18
Alignment explanation
Indices: 54976335--54976369 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54976325 ATAAGAGAAA
* *
54976335 TAACAGTAATATTAATAC
1 TAACAATAATAGTAATAC
54976353 TAACAATAATAGTAATA
1 TAACAATAATAGTAATA
54976370 ATAATAACCA
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:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (18 bp):
TAACAATAATAGTAATAC
Found at i:54976371 original size:3 final size:3
Alignment explanation
Indices: 54976341--54976441 Score: 98
Period size: 3 Copynumber: 34.0 Consensus size: 3
54976331 GAAATAACAG
* * * * **
54976341 TAA TAT TAA TAC TAA CAA TAA TAG TAA TAA TAA TAA CCA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
54976389 TAA TAG TAA -AC TAA TAA TAA TAA TATT TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
54976433 TAA TAA TAA
1 TAA TAA TAA
54976442 CATAAAATTG
Statistics
Matches: 77, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
2 3 0.04
3 72 0.94
4 2 0.03
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54976478 original size:31 final size:30
Alignment explanation
Indices: 54976454--54976517 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
54976444 TAAAATTGCT
*
54976454 AAAATAT-GGGCTAAATCGAAATAAAAATG
1 AAAATATAGGGCGAAATCGAAATAAAAATG
* *
54976483 AAAATATAGGGCGAAATTGAAAGAAAAAT-
1 AAAATATAGGGCGAAATCGAAATAAAAATG
54976512 AAAATA
1 AAAATA
54976518 AAATGGACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.59, C:0.05, G:0.17, T:0.19
Consensus pattern (30 bp):
AAAATATAGGGCGAAATCGAAATAAAAATG
Found at i:54978143 original size:44 final size:44
Alignment explanation
Indices: 54977966--54978159 Score: 143
Period size: 44 Copynumber: 4.5 Consensus size: 44
54977956 AATCCGACCT
* * *
54977966 ACTGCAACTTCAGAG-GTATAGGATTGGTTTCTTCCGTCTGCTCC
1 ACTGCAACTTCAGAGAG-ATAAGATTGGATTCTTCTGTCTGCTCC
* * * * *
54978010 ACTGCAACTCCAGGGAGATAAGACTGGATGCAATCTG-CT-CT--
1 ACTGCAACTTCAGAGAGATAAGATTGGATTC-TTCTGTCTGCTCC
** * **
54978051 ACTGCAACTTCAGAGAGATAAGATCTGTGATT-TT-AATCCGCTTT
1 ACTGCAACTTCAGAGAGATAAGAT-TG-GATTCTTCTGTCTGCTCC
* * *
54978095 ACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTGTCTACTCC
1 ACTGCAACTTCAGAGAGATAAGATTGGATTCTTCTGTCTGCTCC
*
54978139 ACTGCAAC-TCAGGGAGATAAG
1 ACTGCAACTTCAGAGAGATAAG
54978160 GGTGGTACTT
Statistics
Matches: 114, Mismatches: 26, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
41 23 0.20
42 7 0.06
43 20 0.18
44 60 0.53
45 4 0.04
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (44 bp):
ACTGCAACTTCAGAGAGATAAGATTGGATTCTTCTGTCTGCTCC
Found at i:54978222 original size:46 final size:46
Alignment explanation
Indices: 54978183--54978991 Score: 1267
Period size: 46 Copynumber: 17.6 Consensus size: 46
54978173 ATCTGCTTGA
* *
54978183 CTGCCAAATACAGGAAGACAAGATCTGTTATCTTCGATCTCCTCCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
* * * *
54978229 CTACCAAATACAGGAAGACAAGATCTTCTATCTTCGATTTACTTCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
* * *
54978275 CTACCAAATACAAGAAGACAAGATCTGCTATCTTCGATCTCCTCCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
*
54978321 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
* * *
54978367 TTGCCAAATACAGGAAGACAAGATCCGCTATCTTTGATCTACTCCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
* *
54978413 CTGCCAAATACAGGAAGATAAGATCTACTATCTTCGATCTACTCCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
*
54978459 CTGCCAAATACAGGAAGATAAGATCTGCTATCTTCGATCTACTCCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
54978505 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
* * * *
54978551 CTGTCAAATACAGGAAGACAAGATCCGCTATCTTTGATCTACTCTG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
* *
54978597 CTGCCAAATACAGGAATACAAGATCTGCTATCTTCGATCTACTTCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
* *
54978643 CTGCCAAATACAGGAAGACAAGATCTACTATCTTCGATCTACTTCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
* * *
54978689 CTGCCAAATACAGGAAGACAAGATCCGCTATCTTTGATCTACTCTG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
* * *
54978735 CTGCCAAATACAGGGAGACAAGATCTGCTATCTTCGATCTCCTCCA
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
* *
54978781 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCAATCTCCTCCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
*
54978827 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
*
54978873 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
* * * * *
54978919 CTACAAAATAGAGGAAGATAAGATCTGCTATCTTCGATCTCCTCCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
54978965 CTGCCAAATACAGGAAGACAAGATCTG
1 CTGCCAAATACAGGAAGACAAGATCTG
54978992 TAACTTCATT
Statistics
Matches: 702, Mismatches: 61, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 702 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (46 bp):
CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCG
Found at i:54980206 original size:16 final size:15
Alignment explanation
Indices: 54980179--54980223 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
54980169 TAGCCTCTCA
54980179 ATTTTC-ATTTTTTC
1 ATTTTCAATTTTTTC
54980193 ATTTTTCAATTTTTTTC
1 A-TTTTCAA-TTTTTTC
54980210 ATTTTCAATTTTTT
1 ATTTTCAATTTTTT
54980224 TTCATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.04
15 11 0.39
16 8 0.29
17 8 0.29
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTCAATTTTTTC
Found at i:54980208 original size:17 final size:18
Alignment explanation
Indices: 54980186--54980232 Score: 80
Period size: 17 Copynumber: 2.7 Consensus size: 18
54980176 TCAATTTTCA
54980186 TTTTTTCATTTTTCAA-T
1 TTTTTTCATTTTTCAATT
54980203 TTTTTTCA-TTTTCAATT
1 TTTTTTCATTTTTCAATT
54980220 TTTTTTCATTTTT
1 TTTTTTCATTTTT
54980233 TTGACTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.25
17 17 0.61
18 4 0.14
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTCATTTTTCAATT
Found at i:54980354 original size:55 final size:55
Alignment explanation
Indices: 54980288--54980398 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
54980278 CTTCTTTAAA
54980288 CGAAGTGTTTCTTAACTGGATCCGAGTTTATAGGATTGGCAATCTCACTCAAGAT
1 CGAAGTGTTTCTTAACTGGATCCGAGTTTATAGGATTGGCAATCTCACTCAAGAT
54980343 CGAAGTGTTTCTTAACTGGATCCGAGTTTATAGGATTGGCAATCTCACTCAAGAT
1 CGAAGTGTTTCTTAACTGGATCCGAGTTTATAGGATTGGCAATCTCACTCAAGAT
54980398 C
1 C
54980399 AGTGCTCCTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (55 bp):
CGAAGTGTTTCTTAACTGGATCCGAGTTTATAGGATTGGCAATCTCACTCAAGAT
Found at i:54981142 original size:18 final size:19
Alignment explanation
Indices: 54981119--54981156 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
54981109 CTTTGATTGA
54981119 TTGATTTTT-TTTTTGCTT
1 TTGATTTTTCTTTTTGCTT
*
54981137 TTGATTTTTCTTTTTTCTT
1 TTGATTTTTCTTTTTGCTT
54981156 T
1 T
54981157 CCCCCCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.05, C:0.08, G:0.08, T:0.79
Consensus pattern (19 bp):
TTGATTTTTCTTTTTGCTT
Found at i:54981152 original size:26 final size:25
Alignment explanation
Indices: 54981089--54981152 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 25
54981079 TCCTTTTTTC
54981089 TTTTTCTCTTTTTTTTTTTACTTTGA
1 TTTTTCT-TTTTTTTTTTTACTTTGA
* ** *
54981115 TTGATT-GATTTTTTTTTTGCTTTTGA
1 TT-TTTCTTTTTTTTTTTTAC-TTTGA
54981141 TTTTTCTTTTTT
1 TTTTTCTTTTTT
54981153 CTTTCCCCCC
Statistics
Matches: 28, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
25 13 0.46
26 13 0.46
27 2 0.07
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (25 bp):
TTTTTCTTTTTTTTTTTTACTTTGA
Found at i:54985165 original size:4 final size:4
Alignment explanation
Indices: 54985150--54985181 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
54985140 AATAATAGTG
*
54985150 TAAA TGAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
54985182 ATGAATAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:54985325 original size:2 final size:2
Alignment explanation
Indices: 54985318--54985348 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54985308 ATCCACATGA
54985318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54985349 CTTTGAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54985458 original size:2 final size:2
Alignment explanation
Indices: 54985441--54985479 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
54985431 GTGAGAAAAA
* * *
54985441 AT AT AA AT AT AC AT AT AT AA AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54985480 AAATGAGTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:54985647 original size:3 final size:3
Alignment explanation
Indices: 54985633--54985691 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
54985623 TAATACCAAC
* * * *
54985633 AAT AAT AGT AAT AAT AAT AAC CAT AAT AAT AAT AAT AGTT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
*
54985678 AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AA
54985692 CATAAAATTG
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:54985651 original size:15 final size:15
Alignment explanation
Indices: 54985633--54985684 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
54985623 TAATACCAAC
54985633 AATAATAGTAATAAT
1 AATAATAGTAATAAT
*
54985648 AATAACCA-TAATAAT
1 AATAA-TAGTAATAAT
54985663 AATAATAGTTAA-AAT
1 AATAATAG-TAATAAT
54985678 AATAATA
1 AATAATA
54985685 ACAATAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 1 0.03
15 27 0.84
16 4 0.12
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (15 bp):
AATAATAGTAATAAT
Found at i:54985690 original size:12 final size:12
Alignment explanation
Indices: 54985618--54985691 Score: 55
Period size: 12 Copynumber: 6.4 Consensus size: 12
54985608 AAATAACAGT
* *
54985618 AATATTAATACC
1 AATAATAATAAC
* **
54985630 AACAATAATAGT
1 AATAATAATAAC
54985642 AATAATAATAAC
1 AATAATAATAAC
* *
54985654 CATAATAATAAT
1 AATAATAATAAC
*
54985666 AATAGT--TAA-
1 AATAATAATAAC
54985675 AATAATAATAAC
1 AATAATAATAAC
54985687 AATAA
1 AATAA
54985692 CATAAAATTG
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
9 5 0.11
10 3 0.06
11 3 0.06
12 36 0.77
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.28
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:54986544 original size:11 final size:11
Alignment explanation
Indices: 54986528--54986589 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 11
54986518 TATTTTTTAA
54986528 TTTTAAAATAC
1 TTTTAAAATAC
54986539 TTTTAAAATAC
1 TTTTAAAATAC
54986550 TTTTTAAAAT--
1 -TTTTAAAATAC
*
54986560 TTTT----TAA
1 TTTTAAAATAC
54986567 TTTTAAAATA-
1 TTTTAAAATAC
54986577 TTTTAAAATAC
1 TTTTAAAATAC
54986588 TT
1 TT
54986590 ATTTTAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
5 1 0.02
7 4 0.09
9 4 0.09
10 10 0.23
11 15 0.35
12 9 0.21
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:54986563 original size:38 final size:37
Alignment explanation
Indices: 54986519--54986655 Score: 211
Period size: 38 Copynumber: 3.5 Consensus size: 37
54986509 AAATATATTT
54986519 ATTTTTTAATTTTAAAATACTTTTAAAATACTTTTTAAA
1 ATTTTTTAATTTTAAAATA-TTTTAAAATACTTTTT-AA
*
54986558 ATTTTTTAATTTTAAAATATTTTAAAATACTTATTTTA
1 ATTTTTTAATTTTAAAATATTTTAAAATACTT-TTTAA
54986596 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
1 ATTTTTTAATTTTAAAATA-TTTTAAAATACTTTTTAA
54986634 ATTTTTTAAAATTTTAAAATAT
1 ATTTTTT--AATTTTAAAATAT
54986656 ATTTTTGTAT
Statistics
Matches: 92, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
38 44 0.48
39 36 0.39
40 12 0.13
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (37 bp):
ATTTTTTAATTTTAAAATATTTTAAAATACTTTTTAA
Found at i:54986572 original size:16 final size:16
Alignment explanation
Indices: 54986551--54986582 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54986541 TTAAAATACT
*
54986551 TTTTAAAATTTTTTAA
1 TTTTAAAATATTTTAA
54986567 TTTTAAAATATTTTAA
1 TTTTAAAATATTTTAA
54986583 AATACTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAAAATATTTTAA
Found at i:54986621 original size:11 final size:11
Alignment explanation
Indices: 54986605--54986645 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
54986595 AATTTTTTAA
54986605 TTTTAAAATAT
1 TTTTAAAATAT
54986616 TTTTAAAATACT
1 TTTTAAAATA-T
54986628 TTTT-AAAT-T
1 TTTTAAAATAT
54986637 TTTTAAAAT
1 TTTTAAAAT
54986646 TTTAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 5 0.18
10 4 0.14
11 14 0.50
12 5 0.18
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:54986673 original size:77 final size:76
Alignment explanation
Indices: 54986514--54986655 Score: 234
Period size: 77 Copynumber: 1.9 Consensus size: 76
54986504 ATAATAAATA
54986514 TATTT-ATTTTTTAATTTTAAAATACTTTTAAAATACTTTTTAAAATTTTTTAATTTTAAAATAT
1 TATTTAATTTTTTAATTTTAAAATACTTTTAAAATACTTTTTAAAATTTTTTAATTTTAAAATAT
54986578 TTTAAAATACT
66 TTTAAAATACT
*
54986589 TATTTTAATTTTTTAATTTTAAAATATTTTTAAAATACTTTTT-AAATTTTTTAAAATTTTAAAA
1 TA-TTTAATTTTTTAATTTTAAAATACTTTTAAAATACTTTTTAAAATTTTTT--AATTTTAAAA
54986653 TAT
63 TAT
54986656 ATTTTTGTAT
Statistics
Matches: 62, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
75 2 0.03
76 12 0.19
77 35 0.56
78 13 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (76 bp):
TATTTAATTTTTTAATTTTAAAATACTTTTAAAATACTTTTTAAAATTTTTTAATTTTAAAATAT
TTTAAAATACT
Found at i:54988646 original size:19 final size:20
Alignment explanation
Indices: 54988611--54988649 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
54988601 TTAAAATTTC
54988611 AAAAGAAATATATAAAATAT
1 AAAAGAAATATATAAAATAT
54988631 AAAA-AAATAGTA-AAAATAT
1 AAAAGAAATA-TATAAAATAT
54988650 TATGAAGCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAAGAAATATATAAAATAT
Found at i:54991101 original size:3 final size:3
Alignment explanation
Indices: 54991095--54991124 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
54991085 AGAAGAAGAA
*
54991095 GAG GAG GAG GAG GAG GAG GAA GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
54991125 AGAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:54996746 original size:40 final size:38
Alignment explanation
Indices: 54996685--54996799 Score: 106
Period size: 44 Copynumber: 2.8 Consensus size: 38
54996675 ACAAAAAAAA
*
54996685 CAATTGATTTCTAACCCTAAACCCTATTAATCAATT-TC
1 CAATAGATTTCTAA-CCTAAACCCTATTAATCAATTCTC
* * *
54996723 CTAATGGATTTTCTAACCTTAAACCAACCTTGTTAATCAGTTCTC
1 C-AATAGA-TTTCTAACC-TAAA-C--CC-TATTAATCAATTCTC
54996768 CAATAGATTTCTAACCTAGAACCCTATTAATC
1 CAATAGATTTCTAACCTA-AACCCTATTAATC
54996800 GAGTTTCTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
38 1 0.02
39 14 0.22
40 13 0.21
41 1 0.02
42 3 0.05
43 13 0.21
44 15 0.24
45 3 0.05
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (38 bp):
CAATAGATTTCTAACCTAAACCCTATTAATCAATTCTC
Found at i:54996953 original size:21 final size:21
Alignment explanation
Indices: 54996927--54996966 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
54996917 CCAACGTGCA
54996927 AGTTAA-TTGGCCACATCAGCT
1 AGTTAACTT-GCCACATCAGCT
54996948 AGTTAACTTGCCACATCAG
1 AGTTAACTTGCCACATCAG
54996967 TGGTCTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (21 bp):
AGTTAACTTGCCACATCAGCT
Found at i:55003088 original size:20 final size:20
Alignment explanation
Indices: 55003063--55003119 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 20
55003053 CAACATTAAT
55003063 AATTAATAATTTTTAAAAAA
1 AATTAATAATTTTTAAAAAA
**
55003083 AATTAA-AA-TTCAAAAAAA
1 AATTAATAATTTTTAAAAAA
*
55003101 AATTACTAAATATTTTAAA
1 AATTAAT-AAT-TTTTAAA
55003120 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
18 13 0.46
19 2 0.07
20 8 0.29
22 5 0.18
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTAATAATTTTTAAAAAA
Found at i:55006898 original size:26 final size:26
Alignment explanation
Indices: 55006843--55006999 Score: 140
Period size: 26 Copynumber: 6.1 Consensus size: 26
55006833 CGGAAAAGCT
* *
55006843 GGCCTTGAGCCGGTGGTTA-TTAACA
1 GGCCTTGAGCCTGTGGTTATTTAGCA
* * *
55006868 GGCCTTAAGCATGTGTTTATTTAGCA
1 GGCCTTGAGCCTGTGGTTATTTAGCA
*
55006894 GGCCTTGAGCCCGTGGTTATTTAGCA
1 GGCCTTGAGCCTGTGGTTATTTAGCA
* * * *
55006920 GGCCTCGAGCCGGTGTTTATTTAGTA
1 GGCCTTGAGCCTGTGGTTATTTAGCA
*
55006946 GCCCTTGAG-CTAGTGGTTATTTAGCA
1 GGCCTTGAGCCT-GTGGTTATTTAGCA
* * * *
55006972 AGCTTTGAGCCAGT-GTATATTTAACA
1 GGCCTTGAGCCTGTGGT-TATTTAGCA
55006998 GG
1 GG
55007000 TACTATGTAC
Statistics
Matches: 104, Mismatches: 24, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
25 18 0.17
26 85 0.82
27 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.33
Consensus pattern (26 bp):
GGCCTTGAGCCTGTGGTTATTTAGCA
Found at i:55006952 original size:52 final size:52
Alignment explanation
Indices: 55006845--55006994 Score: 169
Period size: 52 Copynumber: 2.9 Consensus size: 52
55006835 GAAAAGCTGG
* * * *
55006845 CCTTGAGCCGGTGGTTA-TTAACAGGCCTTAAG-CATGTGTTTATTTAGCAGG
1 CCTTGAGCCAGTGGTTATTTAGCAGGCCTTGAGCCA-GTGTTTATTTAGCAGC
* * * *
55006896 CCTTGAGCCCGTGGTTATTTAGCAGGCCTCGAGCCGGTGTTTATTTAGTAGC
1 CCTTGAGCCAGTGGTTATTTAGCAGGCCTTGAGCCAGTGTTTATTTAGCAGC
* * * *
55006948 CCTTGAGCTAGTGGTTATTTAGCAAGCTTTGAGCCAGTGTATATTTA
1 CCTTGAGCCAGTGGTTATTTAGCAGGCCTTGAGCCAGTGTTTATTTA
55006995 ACAGGTACTA
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
51 16 0.19
52 66 0.80
53 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.35
Consensus pattern (52 bp):
CCTTGAGCCAGTGGTTATTTAGCAGGCCTTGAGCCAGTGTTTATTTAGCAGC
Found at i:55018132 original size:23 final size:24
Alignment explanation
Indices: 55018106--55018156 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
55018096 TGTATTTGTT
* *
55018106 TTTAAATCTAGCATCA-TTTAATA
1 TTTAAATCTAACATCATTTTAAAA
*
55018129 TTTAAATTTAACATCATTTTAAAA
1 TTTAAATCTAACATCATTTTAAAA
55018153 TTTA
1 TTTA
55018157 TCATTAGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTAAATCTAACATCATTTTAAAA
Found at i:55019680 original size:31 final size:30
Alignment explanation
Indices: 55019644--55019711 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
55019634 ATTTAACGGA
* *
55019644 GAGTGATCAAAATAGAAACAATCTAAAGTGT
1 GAGTGACCAAAATAGAAACAATATAAA-TGT
*
55019675 GAGTGACCAAAATAGAAATAATATAAATGT
1 GAGTGACCAAAATAGAAACAATATAAATGT
*
55019705 AAGTGAC
1 GAGTGAC
55019712 TAGATTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 9 0.27
31 24 0.73
ACGTcount: A:0.50, C:0.09, G:0.19, T:0.22
Consensus pattern (30 bp):
GAGTGACCAAAATAGAAACAATATAAATGT
Found at i:55023799 original size:82 final size:83
Alignment explanation
Indices: 55023657--55023857 Score: 235
Period size: 82 Copynumber: 2.4 Consensus size: 83
55023647 CTTACCTTTC
* * * *
55023657 GGGGCTTTAGCGACGTTTCTGAGAAAGCGCCGCTAATGTTGGGGGATTTAGCGTCATTTTTTAG-
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGTTGGGGGATTTAGAGTCATTTTTTAGA
55023721 AAAGCGCCGCTAATGATG
66 AAAGCGCCGCTAATGATG
** * * * *
55023739 GGGGCTTTAGCGGCGTTTTTGAAAAAGTTCCGCTAATGTTGTGGGCTTTAGTAG-CGTTTTTTGG
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGTTGGGGGATTTAG-AGTCATTTTTTAG
*
55023803 AAAAGCGCCGCTAATGCTG
65 AAAAGCGCCGCTAATGATG
* * * * *
55023822 TGGGCTTTAGCAGCGTTTTTGGAAAGGCGCTGCTAA
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
55023858 AAACATTTTA
Statistics
Matches: 99, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
82 52 0.53
83 47 0.47
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.31
Consensus pattern (83 bp):
GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGTTGGGGGATTTAGAGTCATTTTTTAGA
AAAGCGCCGCTAATGATG
Found at i:55023814 original size:42 final size:41
Alignment explanation
Indices: 55023657--55023857 Score: 194
Period size: 41 Copynumber: 4.9 Consensus size: 41
55023647 CTTACCTTTC
*
55023657 GGGGCTTTAGC-GACGTTTCT-GAGAAAGCGCCGCTAATGTTG
1 GGGGCTTTAGCAG-CGTTTTTGGA-AAAGCGCCGCTAATGTTG
* * * *
55023698 GGGGATTTAGC-GTCATTTTT-TAGAAAGCGCCGCTAATGATG
1 GGGGCTTTAGCAG-CGTTTTTGGA-AAAGCGCCGCTAATGTTG
* * **
55023739 GGGGCTTTAGCGGCGTTTTTGAAAAAGTTCCGCTAATGTTG
1 GGGGCTTTAGCAGCGTTTTTGGAAAAGCGCCGCTAATGTTG
* * *
55023780 TGGGCTTTAGTAGCGTTTTTTGGAAAAGCGCCGCTAATGCTG
1 GGGGCTTTAGCAGCG-TTTTTGGAAAAGCGCCGCTAATGTTG
* * *
55023822 TGGGCTTTAGCAGCGTTTTTGGAAAGGCGCTGCTAA
1 GGGGCTTTAGCAGCGTTTTTGGAAAAGCGCCGCTAA
55023858 AAACATTTTA
Statistics
Matches: 135, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
41 97 0.72
42 38 0.28
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.31
Consensus pattern (41 bp):
GGGGCTTTAGCAGCGTTTTTGGAAAAGCGCCGCTAATGTTG
Found at i:55024249 original size:14 final size:15
Alignment explanation
Indices: 55024210--55024256 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
55024200 TATTTTAAGG
* *
55024210 TTTAGGGAGTATGAA
1 TTTAGGGATTATGGA
*
55024225 TTTAAGGATTATGGA
1 TTTAGGGATTATGGA
55024240 -TTAGGGATTATGG-
1 TTTAGGGATTATGGA
55024253 TTTA
1 TTTA
55024257 AAGGTTGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:55024285 original size:7 final size:7
Alignment explanation
Indices: 55024275--55024333 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
55024265 AATTTAAGGT
55024275 TTAGGGG
1 TTAGGGG
55024282 TTAGGGG
1 TTAGGGG
*
55024289 TTAAGGG
1 TTAGGGG
*
55024296 TTAGAGG
1 TTAGGGG
55024303 TTATGGGG
1 TTA-GGGG
* *
55024311 TTAAGAG
1 TTAGGGG
*
55024318 TTAGGGA
1 TTAGGGG
55024325 TTCAGGGG
1 TT-AGGGG
55024333 T
1 T
55024334 CGGTTAGGTT
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
7 29 0.73
8 11 0.28
ACGTcount: A:0.22, C:0.02, G:0.46, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:55024298 original size:14 final size:14
Alignment explanation
Indices: 55024268--55024323 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
55024258 AGGTTGGAAT
*
55024268 TTAAGGTTTAGGGG
1 TTAAGGGTTAGGGG
* *
55024282 TTAGGGGTTAAGGG
1 TTAAGGGTTAGGGG
55024296 TT-AGAGGTTATGGGG
1 TTAAG-GGTTA-GGGG
*
55024311 TTAAGAGTTAGGG
1 TTAAGGGTTAGGG
55024324 ATTCAGGGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
13 1 0.03
14 21 0.64
15 9 0.27
16 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.45, T:0.32
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:55024304 original size:42 final size:42
Alignment explanation
Indices: 55024222--55024304 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
55024212 TAGGGAGTAT
* * *
55024222 GAATTTAAGGATTATGGATTAGGGATTATGGTTTAAAGGTTG
1 GAATTTAAGGATTAGGGATTAGGGATTAAGGGTTAAAGGTTG
* * * *
55024264 GAATTTAAGGTTTAGGGGTTAGGGGTTAAGGGTTAGAGGTT
1 GAATTTAAGGATTAGGGATTAGGGATTAAGGGTTAAAGGTT
55024305 ATGGGGTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.36, T:0.36
Consensus pattern (42 bp):
GAATTTAAGGATTAGGGATTAGGGATTAAGGGTTAAAGGTTG
Found at i:55024310 original size:22 final size:21
Alignment explanation
Indices: 55024268--55024321 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
55024258 AGGTTGGAAT
* *
55024268 TTAAGGTTTAGGGGTTAGGGG
1 TTAAGGGTTAGAGGTTAGGGG
55024289 TTAAGGGTTAGAGGTTATGGGG
1 TTAAGGGTTAGAGGTTA-GGGG
*
55024311 TTAAGAGTTAG
1 TTAAGGGTTAG
55024322 GGATTCAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (21 bp):
TTAAGGGTTAGAGGTTAGGGG
Found at i:55024540 original size:14 final size:15
Alignment explanation
Indices: 55024505--55024541 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
55024495 TATTTTAAGG
55024505 TTTAGGGAGTATGGA
1 TTTAGGGAGTATGGA
*
55024520 TTTAGGGATTATGGA
1 TTTAGGGAGTATGGA
55024535 -TTAGGGA
1 TTTAGGGA
55024542 ACATGGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.27, C:0.00, G:0.38, T:0.35
Consensus pattern (15 bp):
TTTAGGGAGTATGGA
Found at i:55025661 original size:115 final size:117
Alignment explanation
Indices: 55025524--55025755 Score: 353
Period size: 117 Copynumber: 2.0 Consensus size: 117
55025514 ATAAATCGCC
55025524 GCAAAAAATAAATAAATTTATAAAAACAATAA-AAAAA-TTAGC-ATAGCAAAACGACGTCATTT
1 GCAAAAAATAAATAAATTTATAAAAACAATAACAAAAATTTAGCAAT-GCAAAACGACGTCATTT
* *
55025586 TGTTCAAAAGAAATAATTGTTTGCGGCGTTTCTACGAAAAACGCCGCAAAAGA
65 TGTTCAAAAGAAATAATTGTTTGCAGCATTTCTACGAAAAACGCCGCAAAAGA
* *
55025639 GCAAAAAATAAATAAATTTATAAAAAGAATAACAAAAATTTAGCAATGCAAAACGGCGTCATTTT
1 GCAAAAAATAAATAAATTTATAAAAACAATAACAAAAATTTAGCAATGCAAAACGACGTCATTTT
* * ** *
55025704 GTTCAAAAGAAATAATTTTTTGCAGCATTTTTGTGAAAATCGCCGCAAAAGA
66 GTTCAAAAGAAATAATTGTTTGCAGCATTTCTACGAAAAACGCCGCAAAAGA
55025756 TAAGCAATAG
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
115 31 0.30
116 5 0.05
117 67 0.64
118 2 0.02
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.25
Consensus pattern (117 bp):
GCAAAAAATAAATAAATTTATAAAAACAATAACAAAAATTTAGCAATGCAAAACGACGTCATTTT
GTTCAAAAGAAATAATTGTTTGCAGCATTTCTACGAAAAACGCCGCAAAAGA
Found at i:55025670 original size:21 final size:21
Alignment explanation
Indices: 55025641--55025680 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
55025631 GCAAAAGAGC
*
55025641 AAAAAATAA-ATAAATTTATA
1 AAAAAATAACAAAAATTTATA
55025661 AAAAGAATAACAAAAATTTA
1 AAAA-AATAACAAAAATTTA
55025681 GCAATGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 5 0.29
22 8 0.47
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (21 bp):
AAAAAATAACAAAAATTTATA
Found at i:55025797 original size:21 final size:21
Alignment explanation
Indices: 55025780--55025818 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
55025770 GTTTTTATGC
55025780 AAAA-AATAAAAAAATTTATA
1 AAAAGAATAAAAAAATTTATA
55025800 AAAAGAATAAAAAAATTTA
1 AAAAGAATAAAAAAATTTA
55025819 GCATAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAAGAATAAAAAAATTTATA
Found at i:55025833 original size:138 final size:134
Alignment explanation
Indices: 55025639--55026041 Score: 530
Period size: 130 Copynumber: 3.0 Consensus size: 134
55025629 CCGCAAAAGA
*
55025639 GCAAAAAATAAATAAATTTATAAAAAGAATAACAAAAATTTAGCA-ATGCAAAACGGCGTCATTT
1 GCAAAAAATAAATAAATTTATAAAAAGAATAA-AAAAATTTAGCATA-GCAAAACGGCATCATTT
* * *
55025703 TGTTCAAAAGAAATAATTTTTTGCAGCATTTTTGTGAAAATCGCCGCAAAAGATAAGCAATAGCG
64 TGTTCAAAAGAAATAATTTTTTGCAGCGTTTTTGTGAAAATCGCCGCAAAAGATAAGTAATAAC-
*
55025768 GCGTTTTTAT
128 GCG--TTT-C
* *
55025778 GCAAAAAATAAAAAAATTTATAAAAAGAATAAAAAAATTTAGCATAACAAAACGGCATCATTTTG
1 GCAAAAAATAAATAAATTTATAAAAAGAATAAAAAAATTTAGCATAGCAAAACGGCATCATTTTG
* * *
55025843 TTCAAAAGAAATAATTGTTTGCGGCGTTTTTGTGAAAATCGCCGCAAAAGATAAGTAAAAACGC-
66 TTCAAAAGAAATAATTTTTTGCAGCGTTTTTGTGAAAATCGCCGCAAAAGATAAGTAATAACGCG
55025907 ---C
131 TTTC
* * * *
55025908 GCAAAAAGTAAATAAATTTATAAAAAGAATAAAAAATTTTAGCATAGCAAAATGGCTTCATTTTG
1 GCAAAAAATAAATAAATTTATAAAAAGAATAAAAAAATTTAGCATAGCAAAACGGCATCATTTTG
* * * *
55025973 TTCAAAAGAAATAATTTTTTGCCGTGTTTTTATGAAAAAT-GCCGCAAAAAATAAGTAATAACAG
66 TTCAAAAGAAATAATTTTTTGCAGCGTTTTTGTG-AAAATCGCCGCAAAAGATAAGTAATAAC-G
55026037 CGTTT
129 CGTTT
55026042 GTATAAAAAA
Statistics
Matches: 235, Mismatches: 22, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
130 109 0.46
131 7 0.03
137 2 0.01
138 85 0.36
139 32 0.14
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.28
Consensus pattern (134 bp):
GCAAAAAATAAATAAATTTATAAAAAGAATAAAAAAATTTAGCATAGCAAAACGGCATCATTTTG
TTCAAAAGAAATAATTTTTTGCAGCGTTTTTGTGAAAATCGCCGCAAAAGATAAGTAATAACGCG
TTTC
Found at i:55025923 original size:22 final size:22
Alignment explanation
Indices: 55025877--55025923 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
55025867 CGTTTTTGTG
* *
55025877 AAAATCGCCGCAAAAGATAAGT
1 AAAAACGCCGCAAAAGATAAAT
55025899 AAAAACGCCGCAAAA-AGTAAAT
1 AAAAACGCCGCAAAAGA-TAAAT
55025921 AAA
1 AAA
55025924 TTTATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.57, C:0.17, G:0.15, T:0.11
Consensus pattern (22 bp):
AAAAACGCCGCAAAAGATAAAT
Found at i:55029873 original size:43 final size:43
Alignment explanation
Indices: 55029806--55030133 Score: 417
Period size: 43 Copynumber: 7.6 Consensus size: 43
55029796 AAATATTTTT
* *
55029806 TAAAGGTTATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGC
* * *
55029849 AAAAGGTCATGTTCTATAGTGGCGTTTGTGGAAAAAGCGCCGC
1 TAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGC
** * *
55029892 TAAAGGTTTTGTTCTTTAGTGGCGTTTGT-GGAAAAGGCGCCGC
1 TAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAA-GCGCCGC
* * * * *
55029935 TAAAGGTCTTATTCTTTAGCGGCGTTTGTAGAAAAAGCGCCGC
1 TAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGC
* * * * *
55029978 TAAAGCTAATGTTCTATAGCGGCGATTGTGGAAAAAGAGCCGC
1 TAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGC
* *
55030021 TAAAGCTCATGTTCTATAGCGGCGTTTTTGGGAAAAGCGCCGC
1 TAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGC
*
55030064 TAAAGGTCTTGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGC
*
55030107 TAAAGGTC-TAGTTCTTTAGCGGCGTTT
1 TAAAGGTCAT-GTTCTATAGCGGCGTTT
55030134 ATTTCTAAAA
Statistics
Matches: 251, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
42 6 0.02
43 240 0.96
44 5 0.02
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (43 bp):
TAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGC
Found at i:55034301 original size:6 final size:6
Alignment explanation
Indices: 55034292--55034319 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
55034282 AAACAAAACG
55034292 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
55034320 GTCCAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:55035673 original size:3 final size:3
Alignment explanation
Indices: 55035665--55035707 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
55035655 TTCTTGACTT
*
55035665 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
55035708 GTTTTCATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:55043954 original size:2 final size:2
Alignment explanation
Indices: 55043947--55043983 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
55043937 TGCTTATTCT
55043947 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55043984 GATGTAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55054086 original size:26 final size:26
Alignment explanation
Indices: 55054049--55054100 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
55054039 GAATCAGCAA
55054049 ACACACACATATCTGCACATATAGAC
1 ACACACACATATCTGCACATATAGAC
*
55054075 ACACACATATATCTGCACATATAGAC
1 ACACACACATATCTGCACATATAGAC
55054101 TACTAGGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.29, G:0.08, T:0.21
Consensus pattern (26 bp):
ACACACACATATCTGCACATATAGAC
Found at i:55059981 original size:12 final size:13
Alignment explanation
Indices: 55059948--55059997 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 13
55059938 ATGCAATTTG
55059948 TAATAA-AATACA
1 TAATAATAATACA
55059960 TTAATAAATAATA-A
1 -TAAT-AATAATACA
55059974 TAATAATAATAGACA
1 TAATAATAAT--ACA
55059989 TAATAATAA
1 TAATAATAA
55059998 ATATAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 6 0.19
13 8 0.25
14 4 0.12
15 14 0.44
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (13 bp):
TAATAATAATACA
Found at i:55061910 original size:44 final size:43
Alignment explanation
Indices: 55061861--55062838 Score: 277
Period size: 44 Copynumber: 21.6 Consensus size: 43
55061851 TTTAATCCGC
*
55061861 TCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTG
1 TCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAATCTG
* * * * * * *
55061904 TGCCACTGTAACTTTAGGAAGATAAGGTTGGGTATTTTCAGTCTTC
1 T-CCACTGCAACTTCAGGGAGATAAGATT-GGTATCTTCAATC-TG
* * * ** *
55061950 TCCACTGCAACTTCAAGGAGATAAGGCTTGATATGATCTA-C--
1 TCCACTGCAACTTCAGGGAGATAA-GATTGGTATCTTCAATCTG
* * *
55061991 TCTACTGCAAC-TCTAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTG
1 TCCACTGCAACTTC-AGGGAGATAAGAT-TG----GTAT--CTTCAATCTG
** * * *
55062041 TTCCACTATAACTTTAGGGAAATAAGATTGGTATCTTCAACCTG
1 -TCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAATCTG
* * * * *
55062085 CTCTACTGTAACTTTAGGGAGATAAGGTTGGTTATCTTCAGTCTG
1 -TCCACTGCAACTTCAGGGAGATAAGATTGG-TATCTTCAATCTG
* *
55062130 CTCCACTGCAACTTTAGGGAGATAAGACTTATTATGGTAGACTT-AATCTG
1 -TCCACTGCAACTTCAGGGAGATAAG----A-T-TGGTA-TCTTCAATCTG
* * * * * * *
55062180 ACCTACTGCAACTTCAGAGG-TATAGGATTCGT-TGTTTTAATCCG
1 TCC-ACTGCAACTTCAG-GGAGATAAGATTGGTAT-CTTCAATCTG
* * ** * * *
55062224 CTCCACTGCAACCTCAGGGAGATAGGATTAATAGCTTTAATCTAC
1 -TCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAATCT-G
* *
55062269 TCCACTGCAACTTCAGGGAGATAAGATTAGTATCTTCAACCTG
1 TCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAATCTG
* * ** * *
55062312 CTCCACTGCAGCTTCAGGGAGATAAGGTTTGG-GGCTTCAATATAC
1 -TCCACTGCAACTTCAGGGAGATAA-GATTGGTATCTTCAATCT-G
* * * ** *
55062357 TCCACTGCAATTTCAGGGAGATAAAACTTGCTATGGT-AGATTTG
1 TCCACTGCAACTTCAGGGAGATAAGA-TTGGTATCTTCA-ATCTG
* * * * *
55062401 ATTCGACCTACTGCAACTTCAGAGG-TATAGGATTTGTTGTCTT-TATCCTG
1 --T---CC-ACTGCAACTTCAG-GGAGATAAGA-TTGGTATCTTCAAT-CTG
* * * * *
55062451 CTCCACTACAACTTCAGGGAGATAAGGTTTG-AT-GT-GATCTG
1 -TCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAATCTG
* * * * *
55062492 CTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTGAATATG
1 -TCCACTGCAACTTCAGGGAGATAAGAT-TG----GTAT--CTTCAATCTG
* * * * * *
55062543 TTCCACTACAACTTTAGGGAAATAAGATTCGCTATATTCAGTCTG
1 -TCCACTGCAACTTCAGGGAGATAAGATT-GGTATCTTCAATCTG
* * * * * *
55062588 CTCTACTGTAATTTCAGGGAGATAAGACCT-GTAACTTCAACCTG
1 -TCCACTGCAACTTCAGGGAGATAAGA-TTGGTATCTTCAATCTG
* * * *
55062632 CTCCACTGCAACTTCAAGGAGATAAGGTTTG-AT-GT-AATCTG
1 -TCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAATCTG
* * * * *
55062673 CTCTATTGCAACTTCAGAGAGATAAGATCT-ATAATTTTTAGCTTTAATCTG
1 -TCCACTGCAACTTCAGGGAGATAAGAT-TGGT-A----T--CTTCAATCTG
* * * *
55062724 TTCCATTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAATTTG
1 -TCCACTGCAACTTCAGGGAGATAAGATT-GGTATCTTCAATCTG
* * *
55062769 CTCCACTGCAACTTCAGGGAGATAAGACCT-GTAACTTCAACCTG
1 -TCCACTGCAACTTCAGGGAGATAAGA-TTGGTATCTTCAATCTG
*
55062813 CTCCACTGCAACTTCAAGGAGATAAG
1 -TCCACTGCAACTTCAGGGAGATAAG
55062839 GTTTGATATG
Statistics
Matches: 685, Mismatches: 175, Indels: 149
0.68 0.17 0.15
Matches are distributed among these distances:
40 4 0.01
41 75 0.11
42 6 0.01
43 9 0.01
44 258 0.38
45 158 0.23
46 14 0.02
47 10 0.01
48 1 0.00
49 7 0.01
50 54 0.08
51 87 0.13
52 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (43 bp):
TCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAATCTG
Found at i:55061962 original size:45 final size:44
Alignment explanation
Indices: 55061860--55062155 Score: 119
Period size: 45 Copynumber: 6.6 Consensus size: 44
55061850 TTTTAATCCG
* *
55061860 CTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGT
1 CTCCACTGCAACTT-AAGGAGATAAGGTTGGTATCTTCAACCTGT
* * * * **
55061905 -GCCACTGTAACTTTAGGAAGATAAGGTTGGGTATTTTCAGTCT-T
1 CTCCACTGCAACTTAAGG-AGATAAGGTT-GGTATCTTCAACCTGT
* ** *
55061949 CTCCACTGCAACTTCAAGGAGATAAGGCTTGATATGATCTA-C--T
1 CTCCACTGCAACTT-AAGGAGATAAGG-TTGGTATCTTCAACCTGT
* * *
55061992 CT--ACTGCAACTCT-AGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGT
1 CTCCACTGCAACT-TAAG-GAGATAAGGT-TG----GTAT--CTTCAACCTGT
** * * *
55062042 -TCCACTATAACTTTAGGGAAATAAGATTGGTATCTTCAACCTG-
1 CTCCACTGCAAC-TTAAGGAGATAAGGTTGGTATCTTCAACCTGT
* * * **
55062085 CTCTACTGTAACTTTAGGGAGATAAGGTTGGTTATCTTCAGTCTG-
1 CTCCACTGCAAC-TTAAGGAGATAAGGTTGG-TATCTTCAACCTGT
*
55062130 CTCCACTGCAACTTTAGGGAGATAAG
1 CTCCACTGCAAC-TTAAGGAGATAAG
55062156 ACTTATTATG
Statistics
Matches: 193, Mismatches: 35, Indels: 46
0.70 0.13 0.17
Matches are distributed among these distances:
40 3 0.02
41 19 0.10
42 1 0.01
43 5 0.03
44 57 0.30
45 74 0.38
46 8 0.04
47 3 0.02
48 1 0.01
49 1 0.01
50 3 0.02
51 16 0.08
52 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (44 bp):
CTCCACTGCAACTTAAGGAGATAAGGTTGGTATCTTCAACCTGT
Found at i:55061970 original size:89 final size:88
Alignment explanation
Indices: 55061860--55062156 Score: 271
Period size: 89 Copynumber: 3.3 Consensus size: 88
55061850 TTTTAATCCG
*
55061860 CTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGTGCCACTGTAACTTTAGGAAG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGT-CTACTGTAACTTTAGGAAG
* *
55061925 ATAAGGTTGGGTATTTTCAGTCTT
65 ATAAGGTTGGTTATCTTCAGTCTT
* * * ** * * *
55061949 CTCCACTGCAACTTCAAGGAGATAAGGCTTGATATGATCTA-C--TCTACTGCAACTCTA-GAGA
1 CTCCACTGCAACTTCAGGGAGATAA-GATTGGTATCTTCAACCTGTCTACTGTAACTTTAGGA-A
* * *
55062010 GATAAGATCTGTAATTTATAGCTTCAATCTGT
64 GATAAGGT-TG---GTTAT--CTTCAGTCT-T
** * * *
55062042 -TCCACTATAACTTTAGGGAAATAAGATTGGTATCTTCAACCTGCTCTACTGTAACTTTAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTG-TCTACTGTAACTTTAGGAAG
*
55062106 ATAAGGTTGGTTATCTTCAGTCTG
65 ATAAGGTTGGTTATCTTCAGTCTT
*
55062130 CTCCACTGCAACTTTAGGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
55062157 CTTATTATGG
Statistics
Matches: 159, Mismatches: 34, Indels: 30
0.71 0.15 0.13
Matches are distributed among these distances:
85 2 0.01
86 19 0.12
87 3 0.02
89 56 0.35
90 13 0.08
91 14 0.09
92 27 0.17
93 1 0.01
94 2 0.01
95 21 0.13
96 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (88 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGTCTACTGTAACTTTAGGAAGA
TAAGGTTGGTTATCTTCAGTCTT
Found at i:55062306 original size:227 final size:227
Alignment explanation
Indices: 55062027--55062474 Score: 591
Period size: 227 Copynumber: 2.0 Consensus size: 227
55062017 TCTGTAATTT
** * * * *
55062027 ATAGCTTCAATCTGTTCCACTATAACTTTAGGGAAATAAGATTGGTATCTTCAACCTGCTCTACT
1 ATAGCTTCAATCTACTCCACTACAACTTCAGGGAAATAAGATTAGTATCTTCAACCTGCTCCACT
* * * * * *
55062092 GTAACTTTAGGGAGATAAGG-TTGGTTATCTTCAGTCTGCTCCACTGCAACTTT-AGGGAGATAA
66 GCAACTTCAGGGAGATAAGGTTTGG--AGCTTCAATATACTCCACTGCAA-TTTCAGGGAGATAA
* *
55062155 GACTTATTATGGTAGACTTAA-TCTGACCTACTGCAACTTCAGAGGTATAGGATTCGTTGT-TTT
128 AACTTACTATGGTAGACTTAATTC-GACCTACTGCAACTTCAGAGGTATAGGATTCGTTGTCTTT
*
55062218 AATCC-GCTCCACTGCAACCTCAGGGAGATAGGATTA
192 -ATCCTGCTCCACTACAACCTCAGGGAGATAGGATTA
* * *
55062254 ATAGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTAGTATCTTCAACCTGCTCCACT
1 ATAGCTTCAATCTACTCCACTACAACTTCAGGGAAATAAGATTAGTATCTTCAACCTGCTCCACT
* *
55062319 GCAGCTTCAGGGAGATAAGGTTTGGGGCTTCAATATACTCCACTGCAATTTCAGGGAGATAAAAC
66 GCAACTTCAGGGAGATAAGGTTTGGAGCTTCAATATACTCCACTGCAATTTCAGGGAGATAAAAC
* * * *
55062384 TTGCTATGGTAGATTTGATTCGACCTACTGCAACTTCAGAGGTATAGGATTTGTTGTCTTTATCC
131 TTACTATGGTAGACTTAATTCGACCTACTGCAACTTCAGAGGTATAGGATTCGTTGTCTTTATCC
*
55062449 TGCTCCACTACAACTTCAGGGAGATA
196 TGCTCCACTACAACCTCAGGGAGATA
55062475 AGGTTTGATG
Statistics
Matches: 191, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
225 3 0.02
226 83 0.43
227 101 0.53
228 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (227 bp):
ATAGCTTCAATCTACTCCACTACAACTTCAGGGAAATAAGATTAGTATCTTCAACCTGCTCCACT
GCAACTTCAGGGAGATAAGGTTTGGAGCTTCAATATACTCCACTGCAATTTCAGGGAGATAAAAC
TTACTATGGTAGACTTAATTCGACCTACTGCAACTTCAGAGGTATAGGATTCGTTGTCTTTATCC
TGCTCCACTACAACCTCAGGGAGATAGGATTA
Found at i:55062612 original size:96 final size:95
Alignment explanation
Indices: 55062487--55062901 Score: 348
Period size: 89 Copynumber: 4.6 Consensus size: 95
55062477 GTTTGATGTG
* * * *
55062487 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTGAATATGTTCCACTAC
1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGACCTGTAATTTATAGCTTCAATCTGTTCCACTGC
*
55062552 AACTTTAGGGAAATAAGATTCGCTATATTCA
66 AACTTCAGGGAAATAAGATTCGCTAT-TTCA
* * * * * *
55062583 GTCTGCTCTACTGTAATTTCAGGGAGATAAGACCTG-----TA-A-CTTCAACCTGCTCCACTGC
1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGACCTGTAATTTATAGCTTCAATCTGTTCCACTGC
* * * * *
55062641 AACTTCAAGGAGATAAGGTTTG--ATGT-A
66 AACTTCAGGGAAATAAGATTCGCTATTTCA
* * * * * *
55062668 ATCTGCTCTATTGCAACTTCAGAGAGATAAGATCTATAATTTTTAGCTTTAATCTGTTCCATTGC
1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGACCTGTAATTTATAGCTTCAATCTGTTCCACTGC
55062733 AACTTCAGGGAAATAAGATTCGCTATCTTCA
66 AACTTCAGGGAAATAAGATTCGCTAT-TTCA
* * * * *
55062764 ATTTGCTCCACTGCAACTTCAGGGAGATAAGACCTG-----TA-A-CTTCAACCTGCTCCACTGC
1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGACCTGTAATTTATAGCTTCAATCTGTTCCACTGC
* * * * * *
55062822 AACTTCAAGGAGATAAGGTTTG--ATAT-G
66 AACTTCAGGGAAATAAGATTCGCTATTTCA
* **
55062849 ATTTGCTCTACTGCAACTTCAGAGAGATAAGTTCTGTAATTTATAGCTTCAAT
1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGACCTGTAATTTATAGCTTCAAT
55062902 TTGACTTGAG
Statistics
Matches: 246, Mismatches: 55, Indels: 40
0.72 0.16 0.12
Matches are distributed among these distances:
85 62 0.25
86 2 0.01
87 4 0.02
89 64 0.26
90 5 0.02
91 5 0.02
92 39 0.16
94 2 0.01
95 1 0.00
96 62 0.25
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (95 bp):
ATCTGCTCTACTGCAACTTCAGAGAGATAAGACCTGTAATTTATAGCTTCAATCTGTTCCACTGC
AACTTCAGGGAAATAAGATTCGCTATTTCA
Found at i:55062655 original size:181 final size:181
Alignment explanation
Indices: 55062447--55062897 Score: 722
Period size: 181 Copynumber: 2.5 Consensus size: 181
55062437 TTGTCTTTAT
* *
55062447 CCTGCTCCACTACAACTTCAGGGAGATAAGGTTTGATGTGATCTGCTCTACTGCAACTTCAGAGA
1 CCTGCTCCACTGCAACTTCAAGGAGATAAGGTTTGATGTGATCTGCTCTACTGCAACTTCAGAGA
*
55062512 GATAAGATCTGTAATTTATAGCTTGAATATGTTCCACTACAACTTTAGGGAAATAAGATTCGCTA
66 GATAAGATCTGTAATTTATAGCTTGAATATGTTCCACTACAACTTCAGGGAAATAAGATTCGCTA
* * * *
55062577 TATTCAGTCTGCTCTACTGTAATTTCAGGGAGATAAGACCTGTAACTTCAA
131 TATTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGTAACTTCAA
* *
55062628 CCTGCTCCACTGCAACTTCAAGGAGATAAGGTTTGATGTAATCTGCTCTATTGCAACTTCAGAGA
1 CCTGCTCCACTGCAACTTCAAGGAGATAAGGTTTGATGTGATCTGCTCTACTGCAACTTCAGAGA
* * * * * *
55062693 GATAAGATCTATAATTTTTAGCTTTAATCTGTTCCATTGCAACTTCAGGGAAATAAGATTCGCTA
66 GATAAGATCTGTAATTTATAGCTTGAATATGTTCCACTACAACTTCAGGGAAATAAGATTCGCTA
* *
55062758 TCTTCAATTTGCTCCACTGCAACTTCAGGGAGATAAGACCTGTAACTTCAA
131 TATTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGTAACTTCAA
* *
55062809 CCTGCTCCACTGCAACTTCAAGGAGATAAGGTTTGATATGATTTGCTCTACTGCAACTTCAGAGA
1 CCTGCTCCACTGCAACTTCAAGGAGATAAGGTTTGATGTGATCTGCTCTACTGCAACTTCAGAGA
*
55062874 GATAAGTTCTGTAATTTATAGCTT
66 GATAAGATCTGTAATTTATAGCTT
55062898 CAATTTGACT
Statistics
Matches: 246, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
181 246 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (181 bp):
CCTGCTCCACTGCAACTTCAAGGAGATAAGGTTTGATGTGATCTGCTCTACTGCAACTTCAGAGA
GATAAGATCTGTAATTTATAGCTTGAATATGTTCCACTACAACTTCAGGGAAATAAGATTCGCTA
TATTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGTAACTTCAA
Found at i:55063853 original size:16 final size:15
Alignment explanation
Indices: 55063828--55063873 Score: 67
Period size: 16 Copynumber: 3.0 Consensus size: 15
55063818 CTGGCCTCTC
55063828 CTTTTT-TTTTCTTTT
1 CTTTTTCTTTT-TTTT
55063843 CTTTTTCTTTTTTTT
1 CTTTTTCTTTTTTTT
55063858 CTATTTTCTTTTTTTT
1 CT-TTTTCTTTTTTTT
55063874 AAACTGAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (15 bp):
CTTTTTCTTTTTTTT
Found at i:55063857 original size:22 final size:22
Alignment explanation
Indices: 55063828--55063870 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
55063818 CTGGCCTCTC
*
55063828 CTTTTTTTT-TCTTTTCTTTTT
1 CTTTTTTTTCTATTTTCTTTTT
55063849 CTTTTTTTTCTATTTTCTTTTT
1 CTTTTTTTTCTATTTTCTTTTT
55063871 TTTAAACTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (22 bp):
CTTTTTTTTCTATTTTCTTTTT
Found at i:55064279 original size:13 final size:13
Alignment explanation
Indices: 55064261--55064285 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55064251 CAGTAGAGTT
55064261 TTTTTATTTTTTA
1 TTTTTATTTTTTA
55064274 TTTTTATTTTTT
1 TTTTTATTTTTT
55064286 TGCCTCCACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Done.