Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 122 of 168
Found at i:35447711 original size:30 final size:31
Alignment explanation
Indices: 35447672--35447731 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
35447662 AGAGGTGGGA
* *
35447672 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGAGAACAAAAATTTTAGGGGAAAAG
* *
35447703 TGGG-AGAGAGCAAAAATTTTGGGGGAAAA
1 TGGGAAGAGAACAAAAATTTTAGGGGAAAA
35447732 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.43, C:0.02, G:0.37, T:0.18
Consensus pattern (31 bp):
TGGGAAGAGAACAAAAATTTTAGGGGAAAAG
Found at i:35447959 original size:9 final size:9
Alignment explanation
Indices: 35447945--35447981 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
35447935 TATAGTTTGA
35447945 TATTCGAAT
1 TATTCGAAT
35447954 TATTCGAAT
1 TATTCGAAT
*
35447963 TATTCGAGT
1 TATTCGAAT
35447972 TATTCGAAT
1 TATTCGAAT
35447981 T
1 T
35447982 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:35448051 original size:18 final size:18
Alignment explanation
Indices: 35448025--35448067 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
35448015 AAAAAAATAT
*
35448025 TCGAGTTAATTCGAATAAC
1 TCGA-TTAACTCGAATAAC
35448044 TCGATTAACTCGAATAAC
1 TCGATTAACTCGAATAAC
35448062 TCGATT
1 TCGATT
35448068 CGTTTAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (18 bp):
TCGATTAACTCGAATAAC
Found at i:35448052 original size:9 final size:9
Alignment explanation
Indices: 35448025--35448067 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
35448015 AAAAAAATAT
*
35448025 TCGAGTTAAT
1 TCGA-TTAAC
*
35448035 TCGAATAAC
1 TCGATTAAC
35448044 TCGATTAAC
1 TCGATTAAC
*
35448053 TCGAATAAC
1 TCGATTAAC
35448062 TCGATT
1 TCGATT
35448068 CGTTTAACTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 24 0.86
10 4 0.14
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (9 bp):
TCGATTAAC
Found at i:35461143 original size:13 final size:13
Alignment explanation
Indices: 35461125--35461155 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
35461115 TTCCAGCAAC
35461125 TATGAATTTATTT
1 TATGAATTTATTT
35461138 TATGAATTTATTT
1 TATGAATTTATTT
*
35461151 GATGA
1 TATGA
35461156 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:35461364 original size:50 final size:50
Alignment explanation
Indices: 35461250--35461491 Score: 286
Period size: 50 Copynumber: 4.7 Consensus size: 50
35461240 ATTTGGGTAA
* * *
35461250 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--G
*
35461306 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * * *
35461356 AGAGGTCCCTTGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
35461406 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
35461456 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
35461492 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 91 0.55
51 29 0.17
52 1 0.01
53 4 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:35461439 original size:100 final size:103
Alignment explanation
Indices: 35461250--35461499 Score: 353
Period size: 100 Copynumber: 2.4 Consensus size: 103
35461240 ATTTGGGTAA
35461250 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATAAGAGGTCCC
* *
35461315 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * * * *
35461356 AGAGGTCCCTTGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
*
35461418 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
35461456 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
35461500 GTTATTATCA
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
100 51 0.39
101 38 0.29
105 2 0.02
106 39 0.30
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:35468729 original size:110 final size:107
Alignment explanation
Indices: 35468537--35468732 Score: 293
Period size: 110 Copynumber: 1.8 Consensus size: 107
35468527 AAACTTGGCA
35468537 ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
1 ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* *
35468602 AATATTGCCTTATTTTGAAATTTTTATGAAGGATATTAAGCC
66 AATATTGCCTCAATTTGAAATTTTTATGAAGGATATTAAGCC
* * * * *
35468644 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAATG
1 ATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTCGAATTTCCAAACG
*
35468709 CTAAATATTGCCTCAATTTGAAAT
63 CAAAATATTGCCTCAATTTGAAAT
35468733 ATTCTCCCTT
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
107 14 0.18
109 26 0.33
110 38 0.49
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (107 bp):
ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
AATATTGCCTCAATTTGAAATTTTTATGAAGGATATTAAGCC
Found at i:35468993 original size:2 final size:2
Alignment explanation
Indices: 35468986--35469069 Score: 59
Period size: 2 Copynumber: 43.5 Consensus size: 2
35468976 CATATAAGAA
* * * *
35468986 AT AT AT AT AT AT AT AT AT AT AT GA- AG GT AT AC AT AT -T TT A-
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
* * * *
35469026 AT AC GT A- AT AT AT AT AT AA AT AT AT AA 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
35469067 AT A
1 AT A
35469070 AGTATGTATG
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
1 4 0.06
2 58 0.92
3 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (2 bp):
AT
Found at i:35469202 original size:2 final size:2
Alignment explanation
Indices: 35469195--35469226 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35469185 AAGTTACTAG
35469195 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
35469227 GCGTGTATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35469312 original size:17 final size:17
Alignment explanation
Indices: 35469290--35469322 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35469280 GAGTTTATAC
35469290 ATATAATGAT-TTAAAAT
1 ATATAAT-ATATTAAAAT
35469307 ATATAATATATTAAAA
1 ATATAATATATTAAAA
35469323 GAATTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATATAATATATTAAAAT
Found at i:35470643 original size:11 final size:10
Alignment explanation
Indices: 35470607--35470643 Score: 65
Period size: 10 Copynumber: 3.6 Consensus size: 10
35470597 CTTTGTAATT
35470607 TTTGGGTTTG
1 TTTGGGTTTG
35470617 TTTGGGTTTG
1 TTTGGGTTTG
35470627 TTTGGGTTTG
1 TTTGGGTTTG
35470637 ATTTGGG
1 -TTTGGG
35470644 CCCGGACGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 20 0.77
11 6 0.23
ACGTcount: A:0.03, C:0.00, G:0.41, T:0.57
Consensus pattern (10 bp):
TTTGGGTTTG
Found at i:35471212 original size:44 final size:44
Alignment explanation
Indices: 35471149--35471627 Score: 261
Period size: 44 Copynumber: 11.0 Consensus size: 44
35471139 AAGATAGTGT
* *
35471149 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGG
1 CTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGG
* * * * *
35471193 CTTCAATCTGTTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT-C
1 CTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT---CTGG
* * *
35471239 CTTCGGTCTGCTCCATTGTAATATCAGGGAGATAAGA--TCT-G
1 CTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGG
* * * * * **
35471280 ATGCGATCTACTCTACTGTAAAT-TCAGAGAGATAAGATC-CTTTA
1 CTTCGATCTGCTCCACTGT-AATCTCAGGGAGATAAGATCTC-TGG
* ** * * * ** *
35471324 TTTTAATCCGCTCCACTGTAA-CTTTAGGGAGATAGGAT-AGTGT
1 CTTCGATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTCTGG
* * * *
35471367 CTTCGATCTGCTCCGCTGTAAACTCAGGAAGATAAGATTTCTGG
1 CTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGG
* * * * * *
35471411 CTTCAATCTGCTCCACTATAACCTCAGGAAGATAAGATCTGAAAT-T
1 CTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT---CTGG
* * * *
35471457 CTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGA-CT-TGTAT
1 CTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTG--G
* * * * * *
35471501 ATTC-AACTTGCCCCACTGTAA-CTTCAGGGAGATAAGGTTTGTGG
1 CTTCGATC-TGCTCCACTGTAATC-TCAGGGAGATAAGATCTCTGG
* * * *
35471545 CTCCGATCTACTCCTCTGTAATCTCAGGGAGATAAGA-CT-T-A
1 CTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGG
* *
35471586 ATGCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCT
1 CTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCT
35471628 AATATTCACC
Statistics
Matches: 330, Mismatches: 78, Indels: 55
0.71 0.17 0.12
Matches are distributed among these distances:
41 61 0.18
42 7 0.02
43 36 0.11
44 153 0.46
45 6 0.02
46 65 0.20
47 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
CTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGG
Found at i:35471506 original size:90 final size:86
Alignment explanation
Indices: 35471150--35471625 Score: 347
Period size: 90 Copynumber: 5.5 Consensus size: 86
35471140 AGATAGTGTC
* * * * * ** *
35471150 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAAC
1 TTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGTGTCTTCGATCTACTCCACTGTAAA
**
35471215 CTCAGGGAGATAAGATCTGAAA
66 CTCAGGGAGATAAGA-CTTTAA
** * ** *
35471237 TCCTTCGGTCTGCTCCATTGTAATATCAGGGAGATAAGATCTGATG----CGATCTACTCTACTG
1 ---TTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTG-TGTCTTCGATCTACTCCACTG
* * *
35471298 TAAATTCAGAGAGATAAGATCCTTTAT
62 TAAACTCAGGGAGATAAGA--CTTTAA
* * * * * * * *
35471325 TTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGAT-AGTGTCTTCGATCTGCTCCGCTGTAAA
1 TTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGTGTCTTCGATCTACTCCACTGTAAA
* * **
35471389 CTCAGGAAGATAAGATTTCTGGC
66 CTCAGGGAGATAAGACTT-T-AA
* * *
35471412 TTCAATCTGCTCCACTATAACCTCAGGAAGATAAGATCTGAAAT-TCTTCGGTCTACTCCACTGT
1 TTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTG---TGTCTTCGATCTACTCCACTGT
*
35471476 AACCTCAGGGAGATAAGACTTGTATA
63 AAACTCAGGGAGATAAGACTT-TA-A
* * * * * * *
35471502 TTCAA-CTTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTCCGATCTACTCCTCTGTAA
1 TTCAATC-TGCTCCACTGTAACCTCAGGGAGATAAGATCTGTGTCTTCGATCTACTCCACTGTAA
*
35471566 TCTCAGGGAGATAAGAC-TTAA
65 ACTCAGGGAGATAAGACTTTAA
* * *
35471587 TGCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT
1 TTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT
35471626 CTAATATTCA
Statistics
Matches: 299, Mismatches: 71, Indels: 37
0.73 0.17 0.09
Matches are distributed among these distances:
83 2 0.01
84 1 0.00
85 61 0.20
86 4 0.01
87 87 0.29
88 38 0.13
89 1 0.00
90 102 0.34
91 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (86 bp):
TTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGTGTCTTCGATCTACTCCACTGTAAA
CTCAGGGAGATAAGACTTTAA
Found at i:35471546 original size:134 final size:129
Alignment explanation
Indices: 35471382--35471622 Score: 286
Period size: 134 Copynumber: 1.8 Consensus size: 129
35471372 ATCTGCTCCG
* *
35471382 CTGTAAACTCAGGAAGATAAGATTTCTGGCTTCAATCTGCTCCACTATAACCTCAGGAAGATAAG
1 CTGTAAACTCAGGAAGATAAGATTTCTGGCTCCAATCTACTCCACTATAACCTCAGGAAGATAAG
* *
35471447 ATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGTATATTCAACTTGC
66 A-CT-AAA---TGCGATCTACTCCACTGTAACCTCAGGGAGATAAGACTTGTATATTCAACTTGC
35471512 CCCA
126 CCCA
* * * * * * * *
35471516 CTGT-AACTTCAGGGAGATAAGGTTTGTGGCTCCGATCTACTCCTCTGTAATCTCAGGGAGATAA
1 CTGTAAAC-TCAGGAAGATAAGATTTCTGGCTCCAATCTACTCCACTATAACCTCAGGAAGATAA
* * *
35471580 GACTTAATGCGATCTGCTCCACTGTAATCTCAGGGAGATAAGA
65 GACTAAATGCGATCTACTCCACTGTAACCTCAGGGAGATAAGA
35471623 TCTCTAATAT
Statistics
Matches: 91, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
129 32 0.35
132 2 0.02
133 5 0.05
134 52 0.57
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (129 bp):
CTGTAAACTCAGGAAGATAAGATTTCTGGCTCCAATCTACTCCACTATAACCTCAGGAAGATAAG
ACTAAATGCGATCTACTCCACTGTAACCTCAGGGAGATAAGACTTGTATATTCAACTTGCCCCA
Found at i:35483647 original size:110 final size:107
Alignment explanation
Indices: 35483455--35483650 Score: 284
Period size: 110 Copynumber: 1.8 Consensus size: 107
35483445 AAACTTGGCA
35483455 ATTTGGTTAAACGAGAAATAGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
1 ATTTGGTTAAACGAGAAATAGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* *
35483520 AATATTGCCTTATTTTGAAATTTTTATGAAGGATATTAAGCC
66 AATATTGCCTCAATTTGAAATTTTTATGAAGGATATTAAGCC
* * * * * *
35483562 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAATG
1 ATTTGGTTAAACGAG--AAATAGAAACCCAGCACCTTAGGGCACG-TTCCTCGAATTTCCAAACG
*
35483627 CTAAATATTGCCTCAATTTGAAAT
63 CAAAATATTGCCTCAATTTGAAAT
35483651 ATTCTCCCTT
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
107 14 0.18
109 25 0.32
110 38 0.49
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (107 bp):
ATTTGGTTAAACGAGAAATAGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
AATATTGCCTCAATTTGAAATTTTTATGAAGGATATTAAGCC
Found at i:35484140 original size:17 final size:17
Alignment explanation
Indices: 35484118--35484150 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35484108 GAGTTTATAC
35484118 ATATAATGAT-TTAAAAT
1 ATATAAT-ATATTAAAAT
35484135 ATATAATATATTAAAA
1 ATATAATATATTAAAA
35484151 GAATTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATATAATATATTAAAAT
Found at i:35485441 original size:11 final size:11
Alignment explanation
Indices: 35485415--35485452 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
35485405 CTTTGTAATT
35485415 TTTGGGTTTG-
1 TTTGGGTTTGA
35485425 TTTGGGTTTGA
1 TTTGGGTTTGA
35485436 TTTGGGTTTGA
1 TTTGGGTTTGA
35485447 TTTGGG
1 TTTGGG
35485453 CCCGGACGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.05, C:0.00, G:0.39, T:0.55
Consensus pattern (11 bp):
TTTGGGTTTGA
Found at i:35485919 original size:88 final size:88
Alignment explanation
Indices: 35485765--35486138 Score: 536
Period size: 88 Copynumber: 4.3 Consensus size: 88
35485755 AAATTGAGTT
* *
35485765 GGAA-ACAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGAAGATAAGGTTGGTGTTTT
1 GGAAGACAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGAAGATAAGGCTGGTGTTTT
*
35485829 CGATCTACTTCACTGTCAGTACA
66 CGATCTACTTCACTGCCAGTACA
* * * * * *
35485852 GGAAGTCAAGATCTACAATCTTCAACTTACTCCACTGCTACTCAGGGAGATAACGTTGGTGTTTT
1 GGAAGACAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGAAGATAAGGCTGGTGTTTT
* * *
35485917 CGATCTACTTCATTGCTAGTACT
66 CGATCTACTTCACTGCCAGTACA
**
35485940 GG-AGTACAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAGGAAGATAAGGCTGGTGTTT
1 GGAAG-ACAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGAAGATAAGGCTGGTGTTT
*
35486004 TCAATCTACTTCACTGCCAGTACA
65 TCGATCTACTTCACTGCCAGTACA
* * *
35486028 GGAAGACAAGATCTACAATCTTCAACCTACTCCATTGCTGCTTAGGGAGATAAGGCTGGTGTTTT
1 GGAAGACAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGAAGATAAGGCTGGTGTTTT
*
35486093 CGATATACTTCACTGCCAGTACA
66 CGATCTACTTCACTGCCAGTACA
* *
35486116 AGAAGACAAGATCTAAAATCTTC
1 GGAAGACAAGATCTACAATCTTC
35486139 TTCAATCTAT
Statistics
Matches: 253, Mismatches: 31, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
87 6 0.02
88 245 0.97
89 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (88 bp):
GGAAGACAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGAAGATAAGGCTGGTGTTTT
CGATCTACTTCACTGCCAGTACA
Found at i:35486058 original size:45 final size:45
Alignment explanation
Indices: 35485833--35486058 Score: 115
Period size: 45 Copynumber: 5.1 Consensus size: 45
35485823 TGTTTTCGAT
* * *
35485833 CTACTTCACTGTCAGTACAGGAAGTCAAGATCTACAATCTTCAAC
1 CTACTTCACTGCCAGTACAGGAAGACAAGATCTGCAATCTTCAAC
* * * * * * *** * * *
35485878 TTACTCCACTGCTACT-CAGGGAGATAACG-T-TGGTGTTTTCGAT
1 CTACTTCACTGCCAGTACAGGAAGACAA-GATCTGCAATCTTCAAC
* * * *
35485921 CTACTTCATTGCTAGTACTGG-AGTACAAGATCTGTAATCTTCAAC
1 CTACTTCACTGCCAGTACAGGAAG-ACAAGATCTGCAATCTTCAAC
* * * * *** * *
35485966 CTACTCCACTG-CTGCT-CAGGAAGATAAG-GCTGGTGTTTTCAAT
1 CTACTTCACTGCCAG-TACAGGAAGACAAGATCTGCAATCTTCAAC
*
35486009 CTACTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAAC
1 CTACTTCACTGCCAGTACAGGAAGACAAGATCTGCAATCTTCAAC
35486054 CTACT
1 CTACT
35486059 CCATTGCTGC
Statistics
Matches: 122, Mismatches: 49, Indels: 20
0.64 0.26 0.10
Matches are distributed among these distances:
43 41 0.34
44 37 0.30
45 44 0.36
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (45 bp):
CTACTTCACTGCCAGTACAGGAAGACAAGATCTGCAATCTTCAAC
Found at i:35491223 original size:2 final size:2
Alignment explanation
Indices: 35491218--35491245 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35491208 CTAAAAAACC
35491218 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
35491246 GAAAGAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35512984 original size:41 final size:41
Alignment explanation
Indices: 35512939--35513018 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
35512929 AAAATTGGAG
* *
35512939 GCACATAGGCGTGTT-TCAGGTTGTCTGGGACACATGGGCAC
1 GCACACAGGCGT-TTGTCAGGTTGTCTGGGACACACGGGCAC
*
35512980 GCACACAGGCGTTTGTCAGGTTGTGTGGGACACACGGGC
1 GCACACAGGCGTTTGTCAGGTTGTCTGGGACACACGGGC
35513019 GTGTGCCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 2 0.06
41 33 0.94
ACGTcount: A:0.19, C:0.23, G:0.36, T:0.23
Consensus pattern (41 bp):
GCACACAGGCGTTTGTCAGGTTGTCTGGGACACACGGGCAC
Found at i:35515808 original size:21 final size:22
Alignment explanation
Indices: 35515784--35515826 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
35515774 GTATTTCTTA
* *
35515784 GTTATGTTTTA-ATTTTTAATG
1 GTTATATTTTACAATTTTAATG
35515805 GTTATATTTTACAATTTTAATG
1 GTTATATTTTACAATTTTAATG
35515827 AATCAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (22 bp):
GTTATATTTTACAATTTTAATG
Found at i:35516916 original size:13 final size:12
Alignment explanation
Indices: 35516882--35516920 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
35516872 ACTGGCAATC
* *
35516882 AAATTGACTGTA
1 AAATTTACTATA
35516894 AAATTTACTATA
1 AAATTTACTATA
35516906 AAATATTACTATA
1 AAAT-TTACTATA
35516919 AA
1 AA
35516921 CATTAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (12 bp):
AAATTTACTATA
Found at i:35535570 original size:15 final size:16
Alignment explanation
Indices: 35535545--35535585 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
35535535 ATTTATTTTC
*
35535545 TTTATTATTATGCATT
1 TTTATTATTATCCATT
35535561 TTTATT-TTATCCA-T
1 TTTATTATTATCCATT
35535575 TTTATTATTAT
1 TTTATTATTAT
35535586 TTCTATCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 10 0.43
16 6 0.26
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTATTATTATCCATT
Found at i:35535732 original size:12 final size:12
Alignment explanation
Indices: 35535717--35535741 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35535707 TCCTTTTTAT
35535717 TTTATTTATTCA
1 TTTATTTATTCA
35535729 TTTATTTATTCA
1 TTTATTTATTCA
35535741 T
1 T
35535742 CTACCATGTT
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTATTCA
Found at i:35539804 original size:3 final size:3
Alignment explanation
Indices: 35539789--35539839 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
35539779 CAATTATATG
* * * * *
35539789 TAT TAT TAG TAT TAT TAG TAT TAT TAT TAA TAT TAT TGT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35539837 TAT
1 TAT
35539840 ATTTTCATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:35539972 original size:7 final size:7
Alignment explanation
Indices: 35539960--35539993 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
35539950 CATATGTACG
35539960 TATATTT
1 TATATTT
35539967 TATATTT
1 TATATTT
35539974 TATATTT
1 TATATTT
35539981 TATATATT
1 TATAT-TT
35539989 TATAT
1 TATAT
35539994 GTACATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TATATTT
Found at i:35541596 original size:2 final size:2
Alignment explanation
Indices: 35541589--35541635 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
35541579 TATCTTATTT
35541589 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35541631 TA TA T
1 TA TA T
35541636 CTCTTTATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35542836 original size:20 final size:20
Alignment explanation
Indices: 35542786--35542836 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
35542776 TTTTCATAAA
*
35542786 TATATATACATGCTTATATT
1 TATATATATATGCTTATATT
* *
35542806 TTTTTATTATAT-CTTATAATT
1 TATATA-TATATGCTTAT-ATT
35542827 TATATATATA
1 TATATATATA
35542837 CACATACTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (20 bp):
TATATATATATGCTTATATT
Found at i:35543348 original size:69 final size:70
Alignment explanation
Indices: 35543236--35543374 Score: 217
Period size: 69 Copynumber: 2.0 Consensus size: 70
35543226 TTTTCAAACC
* * *
35543236 CAAGTTTTAAACGATCTCAGGAATTAAGAAGAGATTGTATCCTAATTTACTGGGCATGAT-CCTT
1 CAAGTTTTAAACGATCTCAGGAATTAAGAAAAGATCGTATCCTAACTTACTGGGCATGATCCCTT
35543300 TTTTT
66 TTTTT
* * *
35543305 CAAGTTTTAAATGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCCTT
1 CAAGTTTTAAACGATCTCAGGAATTAAGAAAAGATCGTATCCTAACTTACTGGGCATGATCCCTT
35543370 TTTTT
66 TTTTT
35543375 AATCCAAGAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
69 54 0.86
70 9 0.14
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (70 bp):
CAAGTTTTAAACGATCTCAGGAATTAAGAAAAGATCGTATCCTAACTTACTGGGCATGATCCCTT
TTTTT
Found at i:35549060 original size:114 final size:115
Alignment explanation
Indices: 35548859--35549094 Score: 339
Period size: 114 Copynumber: 2.1 Consensus size: 115
35548849 CCTGACGTTG
* * * *
35548859 CAGTGGAGCAGACTAAAACCACAAATCTCGTCCCCCTAAAGTTGTTGCGAAGAAGTTTGAAGTTA
1 CAGTGGAGCAGACTAAAACCACAAATCTCGTCCCCCTAAAGTTGCTGCGAAGAAGATTAAAGCTA
* * *
35548924 CAAGTCATACCTTTCTGAAGTGCAGTAAAGTGGATTGAAGCAACGAGACA
66 CAACTCATACCTCTCTGAAGTGCAGTAAAGTGGATAGAAGCAACGAGACA
* * * *
35548974 CAGTGGAGTAGACTAAAACCATAAATCT-TTCCCCCTGAAGTTGCTGCGAAGAAGATTAAAGCTA
1 CAGTGGAGCAGACTAAAACCACAAATCTCGTCCCCCTAAAGTTGCTGCGAAGAAGATTAAAGCTA
* * *
35549038 CAACTCATATCTCTCTGAAGTGCAGTAGAGTGGATAGAAGCAATGAGACA
66 CAACTCATACCTCTCTGAAGTGCAGTAAAGTGGATAGAAGCAACGAGACA
35549088 CAGTGGA
1 CAGTGGA
35549095 CTGGAATGAG
Statistics
Matches: 107, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
114 81 0.76
115 26 0.24
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.22
Consensus pattern (115 bp):
CAGTGGAGCAGACTAAAACCACAAATCTCGTCCCCCTAAAGTTGCTGCGAAGAAGATTAAAGCTA
CAACTCATACCTCTCTGAAGTGCAGTAAAGTGGATAGAAGCAACGAGACA
Found at i:35549860 original size:3 final size:3
Alignment explanation
Indices: 35549845--35549895 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
35549835 CAATTATATG
* * * * *
35549845 TAT TAT TAG TAT TAT TAG TAT TAT TAT TAA TAT TAT TGT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35549893 TAT
1 TAT
35549896 ATTTTCATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:35550141 original size:22 final size:21
Alignment explanation
Indices: 35550077--35550142 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 21
35550067 AACTTCAATA
35550077 TATATATATATATGAATACATTTT
1 TATA-ATATATAT--ATACATTTT
35550101 TATAATATATATATGTACATATTT
1 TATAATATATATA--TACAT-TTT
35550125 TCATAA-ATATATATACAT
1 T-ATAATATATATATACAT
35550143 GCTTATATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
21 1 0.03
22 5 0.13
23 13 0.34
24 15 0.39
25 4 0.11
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (21 bp):
TATAATATATATATACATTTT
Found at i:35550680 original size:69 final size:69
Alignment explanation
Indices: 35550569--35550699 Score: 235
Period size: 69 Copynumber: 1.9 Consensus size: 69
35550559 TTTTCAAACC
* *
35550569 CAAGTTTTAAACGATCTCGGGAATTAAGAAGAGATGGTGTCCTAACTTACTGGGCATGATCCTTG
1 CAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCTTG
35550634 TTTT
66 TTTT
*
35550638 CAAGTTTTAAATGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCC
1 CAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCC
35550700 CTTTTTTTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (69 bp):
CAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCTTG
TTTT
Found at i:35557090 original size:21 final size:22
Alignment explanation
Indices: 35557052--35557092 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
35557042 TAATCTTATC
35557052 ATAATTATAAAAAAAAATATTG
1 ATAATTATAAAAAAAAATATTG
* *
35557074 ATAATT-TAAACACAAATAT
1 ATAATTATAAAAAAAAATAT
35557093 GAACTTAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (22 bp):
ATAATTATAAAAAAAAATATTG
Found at i:35558767 original size:13 final size:13
Alignment explanation
Indices: 35558749--35558778 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35558739 ACTAAATGTA
*
35558749 ATTTTACCACTAT
1 ATTTTAACACTAT
35558762 ATTTTAACACTAT
1 ATTTTAACACTAT
35558775 ATTT
1 ATTT
35558779 GATTTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTTAACACTAT
Found at i:35560783 original size:14 final size:14
Alignment explanation
Indices: 35560766--35560795 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35560756 CCTTTTGGTT
35560766 CCTTTCTTGCCTTC
1 CCTTTCTTGCCTTC
*
35560780 CCTTTCTTGCTTTC
1 CCTTTCTTGCCTTC
35560794 CC
1 CC
35560796 CCCTGCTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.43, G:0.07, T:0.50
Consensus pattern (14 bp):
CCTTTCTTGCCTTC
Found at i:35562389 original size:3 final size:3
Alignment explanation
Indices: 35562381--35562429 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
35562371 TTAATAAACG
* *
35562381 AAT AAT AAT AAT AAAT AGAT AAAT AAG AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
35562429 A
1 A
35562430 GTAGTAGTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 31 0.79
4 7 0.18
5 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:35564079 original size:45 final size:45
Alignment explanation
Indices: 35563979--35564105 Score: 150
Period size: 45 Copynumber: 2.8 Consensus size: 45
35563969 TTATGGTTTT
* *
35563979 AGTCTGCTCCACTGCAACGTCAGGGAGATAAGACTCG-TTGCTTC
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTGCTTC
* * * * * *
35564023 A-ACTTGCTCCACGGCGACTTCAGGGAAATAAGATTTGTTTTCTTC
1 AGTC-TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTGCTTC
*
35564068 AGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT
35564106 ATCTTTTTTT
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
43 1 0.02
44 28 0.42
45 36 0.55
46 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (45 bp):
AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTGCTTC
Found at i:35564627 original size:44 final size:44
Alignment explanation
Indices: 35564560--35564859 Score: 225
Period size: 44 Copynumber: 6.8 Consensus size: 44
35564550 AGATTCGCCG
* * * *
35564560 TCTTCGATCTGCTCTACTACTGCTTAGGGAGACAGGATCTACAA
1 TCTTCAATCTACTCCACTACTGCTTAGGGAGATAGGATCTACAA
* * * * * ****
35564604 TCTTCAACCTATTCCACTGCTGCTCAGGGAAATAGGA-CTGGTG
1 TCTTCAATCTACTCCACTACTGCTTAGGGAGATAGGATCTACAA
* * * * *
35564647 GCTTCAATCTGCTTCC-CTACTGCCTT-GGGAAGATAAGAT-TCGCCA
1 TCTTCAATCTAC-TCCACTACTG-CTTAGGG-AGATAGGATCT-ACAA
* * *
35564692 TCTTCGATCTGCTCCACTACTGCTTAGGAAGATAGGATCTACAA
1 TCTTCAATCTACTCCACTACTGCTTAGGGAGATAGGATCTACAA
* ****
35564736 TCTTCAATCTACTCCACTGCTGCTTAGGGAGATAGGA-CTGGTG
1 TCTTCAATCTACTCCACTACTGCTTAGGGAGATAGGATCTACAA
* * *
35564779 GCCTCAATCTGCTTCC-CTACTGCTTAGGGAGATAGGATCTACAA
1 TCTTCAATCTAC-TCCACTACTGCTTAGGGAGATAGGATCTACAA
* * *
35564823 TCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGA
1 TCTTCAATCTACTCCACTACTGCTTAGGGAGATAGGA
35564860 CTAGTGGCTT
Statistics
Matches: 193, Mismatches: 52, Indels: 22
0.72 0.19 0.08
Matches are distributed among these distances:
43 52 0.27
44 121 0.63
45 20 0.10
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.28
Consensus pattern (44 bp):
TCTTCAATCTACTCCACTACTGCTTAGGGAGATAGGATCTACAA
Found at i:35564801 original size:132 final size:132
Alignment explanation
Indices: 35564321--35564799 Score: 706
Period size: 132 Copynumber: 3.6 Consensus size: 132
35564311 CTGCCAGTAC
* * * * * *
35564321 AGGAAGACAAGATCTACAATCTTCATCCTACTTCATTGCTACTCAGAGAGATAGGACTAGTGGCT
1 AGGAAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAGGACTGGTGGCT
* * * *
35564386 TAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCGTCTTTGATTTTCTCCACTACTGC
66 TCAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
35564451 TT
131 TT
* * * *
35564453 AGGGAGACAGGATCTACAATCTTCAACCTACTCTATTGCTGCTCAGAGAGATAGGACTGGTGGTT
1 AGGAAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAGGACTGGTGGCT
* * *
35564518 TCAATCTGCTTCCCTACTACATTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCTACTACTGC
66 TCAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
35564583 TT
131 TT
* * * *
35564585 AGGGAGACAGGATCTACAATCTTCAACCTATTCCACTGCTGCTCAGGGAAATAGGACTGGTGGCT
1 AGGAAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAGGACTGGTGGCT
* *
35564650 TCAATCTGCTTCCCTACTGCCTTGGGAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
35564715 TT
131 TT
* * * * *
35564717 AGGAAGATAGGATCTACAATCTTCAATCTACTCCACTGCTGCTTAGGGAGATAGGACTGGTGGCC
1 AGGAAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAGGACTGGTGGCT
35564782 TCAATCTGCTTCCCTACT
66 TCAATCTGCTTCCCTACT
35564800 GCTTAGGGAG
Statistics
Matches: 314, Mismatches: 33, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 314 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (132 bp):
AGGAAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAGGACTGGTGGCT
TCAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
TT
Found at i:35564803 original size:87 final size:87
Alignment explanation
Indices: 35564698--35564900 Score: 309
Period size: 87 Copynumber: 2.3 Consensus size: 87
35564688 GCCATCTTCG
* *
35564698 ATCTGC-TCCACTACTGCTTAGGAAGATAGGATCTACAATCTTCAATCTACTCCACTGCTGCTTA
1 ATCTGCTTCC-CTACTGCTTAGGAAGATAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
*
35564762 GGGAGATAGGACTGGTGGCCTCA
65 GGGAGATAGGACTAGTGGCCTCA
*
35564785 ATCTGCTTCCCTACTGCTTAGGGAGATAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
1 ATCTGCTTCCCTACTGCTTAGGAAGATAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
* *
35564850 GGAGATAGGACTAGTGGCTTTA
66 GGAGATAGGACTAGTGGCCTCA
* *
35564872 ATCTGCTTCCCTACTACCTTGGGAAGATA
1 ATCTGCTTCCCTACT-GCTTAGGAAGATA
35564901 AGACTCACCA
Statistics
Matches: 105, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
87 92 0.88
88 13 0.12
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.29
Consensus pattern (87 bp):
ATCTGCTTCCCTACTGCTTAGGAAGATAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
GGAGATAGGACTAGTGGCCTCA
Found at i:35565594 original size:108 final size:108
Alignment explanation
Indices: 35565405--35565626 Score: 304
Period size: 108 Copynumber: 2.1 Consensus size: 108
35565395 GAAAAATGCT
* * * ** * *
35565405 TGAAAAAGATTATAACAATAGATAATATGAAATTTTGTTGAGAGCAAATCTCGAAATGGATAAAT
1 TGAAAAAGATTATAACAATAGACAAGATGAAATTTTATTGAGAGCAAAGATCAAAATGAATAAAT
* * *
35565470 TAATCGAGATTGCAAATTTTGCT-AGAATACGAAATGAGTAAGA
66 TAATCAAGATAGCAAATTTTGCTAAG-ATACGAAATGAATAAGA
* *
35565513 TGAAAAAGATTATCACAAT-GAACAAGATGGAATTTTATTGAGAGCAAAGATCAAAATGAATAAA
1 TGAAAAAGATTATAACAATAG-ACAAGATGAAATTTTATTGAGAGCAAAGATCAAAATGAATAAA
35565577 TTAATCAAGATAGCAAATTTTGCTAAGATACGAAATGAATAAGA
65 TTAATCAAGATAGCAAATTTTGCTAAGATACGAAATGAATAAGA
35565621 TGAAAA
1 TGAAAA
35565627 CAGGTGCCCC
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
107 1 0.01
108 97 0.97
109 2 0.02
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.27
Consensus pattern (108 bp):
TGAAAAAGATTATAACAATAGACAAGATGAAATTTTATTGAGAGCAAAGATCAAAATGAATAAAT
TAATCAAGATAGCAAATTTTGCTAAGATACGAAATGAATAAGA
Found at i:35567828 original size:2 final size:2
Alignment explanation
Indices: 35567821--35567860 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
35567811 AGATATTTTC
35567821 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
35567861 TCGTTTGGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35568074 original size:16 final size:17
Alignment explanation
Indices: 35568053--35568087 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
35568043 TACTTATTTT
35568053 TTATATATATAC-ATTA
1 TTATATATATACTATTA
*
35568069 TTATATATGTACTATTA
1 TTATATATATACTATTA
35568086 TT
1 TT
35568088 TTCATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (17 bp):
TTATATATATACTATTA
Found at i:35572673 original size:3 final size:3
Alignment explanation
Indices: 35572665--35572719 Score: 65
Period size: 3 Copynumber: 17.3 Consensus size: 3
35572655 TTAATAAACG
* *
35572665 AAT AAT AAT AAT AAAT AGAT AAAT AAG AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
35572713 AAT AAT A
1 AAT AAT A
35572720 GTAGTAGTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 37 0.82
4 7 0.16
5 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:35572686 original size:8 final size:7
Alignment explanation
Indices: 35572615--35572719 Score: 53
Period size: 6 Copynumber: 14.9 Consensus size: 7
35572605 ATACATGGTG
35572615 ATAAT-A
1 ATAATAA
35572621 ATAATAA
1 ATAATAA
*
35572628 ATAAGAA
1 ATAATAA
35572635 ATACAATAA
1 AT--AATAA
*
35572644 ATAAT-C
1 ATAATAA
*
35572650 ATACATTA
1 ATA-ATAA
35572658 ATAA-ACGA
1 ATAATA--A
35572666 ATAAT-A
1 ATAATAA
35572672 ATAATAA
1 ATAATAA
35572679 ATAGATAA
1 ATA-ATAA
*
35572687 ATAAGAGTA
1 ATAATA--A
35572696 ATAAT-A
1 ATAATAA
35572702 ATAAT-A
1 ATAATAA
35572708 ATAAT-A
1 ATAATAA
35572714 ATAATA
1 ATAATA
35572720 GTAGTAGTAG
Statistics
Matches: 79, Mismatches: 7, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
6 32 0.41
7 21 0.27
8 15 0.19
9 11 0.14
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.28
Consensus pattern (7 bp):
ATAATAA
Found at i:35579201 original size:14 final size:15
Alignment explanation
Indices: 35579173--35579203 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
35579163 AAGGTTTATA
35579173 GATTATGGAATTAGG
1 GATTATGGAATTAGG
35579188 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
35579202 GA
1 GA
35579204 CTCTGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:35579511 original size:15 final size:15
Alignment explanation
Indices: 35579488--35579517 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35579478 GGATTAAGAG
*
35579488 TTAGTGATTTAGGGT
1 TTAGAGATTTAGGGT
35579503 TTAGAGATTTAGGGT
1 TTAGAGATTTAGGGT
35579518 CGAGTTAGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.43
Consensus pattern (15 bp):
TTAGAGATTTAGGGT
Found at i:35579906 original size:18 final size:17
Alignment explanation
Indices: 35579871--35579906 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35579861 ATATTAGATT
*
35579871 TAAAAAAAATTAATAAA
1 TAAAAAAAATTAACAAA
35579888 TAAAAAAAATGTAACAAA
1 TAAAAAAAAT-TAACAAA
35579906 T
1 T
35579907 TGATACGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (17 bp):
TAAAAAAAATTAACAAA
Found at i:35580616 original size:115 final size:118
Alignment explanation
Indices: 35580413--35580629 Score: 368
Period size: 115 Copynumber: 1.9 Consensus size: 118
35580403 CATAGCAAAA
*
35580413 CATATAAAAACGCCGCAAAAGGTAAGCAACAGCGGCGTTTTTTTATAAAAACGCCACAAAAAATA
1 CATATAAAAACGCCGCAAAAGGTAAGCAACAGCGGCGTTTTTATATAAAAACGCCACAAAAAATA
* *
35580478 ATTTTACTTTTAAAAATAGTCATTTTATATAGCAAAACATTTAGCGGCGTTTT
66 ATTTTACTTTAAAAAATAATCATTTTATATAGCAAAACATTTAGCGGCGTTTT
* *
35580531 CATA-AAAAACGCCGCAAAAGGTCAGCAATAGCGGCGTTTTTATA-AAAAACGCCAC-AAAAATA
1 CATATAAAAACGCCGCAAAAGGTAAGCAACAGCGGCGTTTTTATATAAAAACGCCACAAAAAATA
35580593 ATTTTACTTTAAAAAATAATCATTTTATATAGCAAAA
66 ATTTTACTTTAAAAAATAATCATTTTATATAGCAAAA
35580630 TATTATAAAA
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
115 42 0.45
116 11 0.12
117 37 0.39
118 4 0.04
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (118 bp):
CATATAAAAACGCCGCAAAAGGTAAGCAACAGCGGCGTTTTTATATAAAAACGCCACAAAAAATA
ATTTTACTTTAAAAAATAATCATTTTATATAGCAAAACATTTAGCGGCGTTTT
Found at i:35580883 original size:21 final size:21
Alignment explanation
Indices: 35580839--35580887 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
35580829 ATAAAATCCC
35580839 TTCCCCCCAAAATCCCCAACT
1 TTCCCCCCAAAATCCCCAACT
* *
35580860 TTCCCTCCTAAAATCCCTAA-T
1 TTCCC-CCCAAAATCCCCAACT
35580881 TTCCCCC
1 TTCCCCC
35580888 TTGAAACCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 11 0.44
22 12 0.48
ACGTcount: A:0.24, C:0.49, G:0.00, T:0.27
Consensus pattern (21 bp):
TTCCCCCCAAAATCCCCAACT
Found at i:35582186 original size:24 final size:24
Alignment explanation
Indices: 35582146--35582203 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
35582136 GAGACTACTG
*
35582146 TATCTA-TTCTAAGTTGTTTAATT
1 TATCTATTTCTAAGTTGTTTAAGT
*
35582169 TATCTATTTCTAATTTGTTTAAGT
1 TATCTATTTCTAAGTTGTTTAAGT
35582193 TATCTATTTCT
1 TATCTATTTCT
35582204 GCCTTCAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 6 0.19
24 26 0.81
ACGTcount: A:0.24, C:0.10, G:0.07, T:0.59
Consensus pattern (24 bp):
TATCTATTTCTAAGTTGTTTAAGT
Found at i:35585278 original size:43 final size:43
Alignment explanation
Indices: 35585244--35585557 Score: 511
Period size: 43 Copynumber: 7.3 Consensus size: 43
35585234 GAATTGTACT
** * *
35585244 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
35585287 TTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
35585330 TTCAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
35585373 TTTAGCGACGTTTGTGGGAAAAGCGCCGTTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
35585416 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCATAGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
35585459 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
35585502 TTTAGCCGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
35585545 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
35585558 AGTTATAAAA
Statistics
Matches: 249, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 249 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:35587778 original size:21 final size:22
Alignment explanation
Indices: 35587737--35587779 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
35587727 TAAATTGATT
* *
35587737 CATTAAAATTGTAAAATATAAC
1 CATTAAAAATGTAAAACATAAC
35587759 CATTAAAAAT-TAAAACATAAC
1 CATTAAAAATGTAAAACATAAC
35587780 TAAAAAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (22 bp):
CATTAAAAATGTAAAACATAAC
Found at i:35588328 original size:2 final size:2
Alignment explanation
Indices: 35588317--35588359 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
35588307 AAATTGGTTT
35588317 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35588357 TA T
1 TA T
35588360 TGTTAAAGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35592628 original size:12 final size:12
Alignment explanation
Indices: 35592611--35592649 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
35592601 ATAATGGATA
*
35592611 AATAAATAAGTG
1 AATAAATAAATG
35592623 AATAAATAAATG
1 AATAAATAAATG
*
35592635 AATCAAACAAATG
1 AAT-AAATAAATG
35592648 AA
1 AA
35592650 ACTATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (12 bp):
AATAAATAAATG
Found at i:35594440 original size:44 final size:44
Alignment explanation
Indices: 35594373--35595833 Score: 402
Period size: 44 Copynumber: 32.9 Consensus size: 44
35594363 ATACATCTTG
* *** * *
35594373 TAGCTTCAATCCACTCTGTTGTAA-CTCCAGGGGGATAGGAT-TAC
1 TAGCTTCAATCTACTCCACTGTAATCT-CAGGGAGATAAGATCT-C
35594417 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTC
1 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTC
* * *
35594461 TGGCTTCAATCTAATGTGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTT
1 TAGCTTCAATC-----T-A-CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT-CTC
* * ** *
35594516 TA-TTTTAATCCGCTCCACTGTAATCTCAGAGAGATAAGAT-TAC
1 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-C
* *
35594559 TAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTC
1 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTC
* ** *
35594603 TGGCTTCAATCTGTTCCACTGTAA-CATCAGGGAGATAAGATCTGA
1 TAGCTTCAATCTACTCCACTGTAATC-TCAGGGAGATAAGATCT-C
* * ** * *
35594648 AATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGA-C-C
1 TA-GCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTC
* * * * ** * *
35594691 T-GATGCGATCCACTCTGCTGTAA-CTTCAGAGAGATAAGATCATT
1 TAGCTTCAATCTACTCCACTGTAATC-TCAGGGAGATAAGATC-TC
* * * *
35594735 TA-TTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGAT-TAC
1 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-C
* * * * *
35594778 TATCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGA
1 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-C
* * ** * *
35594823 AATTCTTCGGTCTACTCCACTATAACCTCAGGGAGATAAGA-C-C
1 TA-GCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTC
* * * * ** * *
35594866 T-GATGCGATCCACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTT
1 TAGCTTCAATCTACTCCACTGTAATC-TCAGGGAGATAAGAT-CTC
* * *** *
35594910 TA-TTTTAATCCGTTCCACTGTAATCTCAGGGAGATAGGATTACTATAGGATTAC
1 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGA-T-C--------T-C
* * * **
35594964 TAGTTTCAATCTGCTCCGCTGTAATCTCAAAGAGATAAGA-C-C
1 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTC
* * * * * *
35595006 T-GATACGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCATT
1 TAGCTTCAATCTACTCCACTGTAATC-TCAGGGAGATAAGATC-TC
* * ** * * *
35595050 TA-TTTTAATCCGCTCTACTGTAATCTTAGGGAGATAGGAT-TAC
1 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-C
* * *
35595093 TAGCTTCAATCTGCTCCTCTGTAATCTCAGGGAGATAAGATCTGA
1 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-C
* * ** ** *
35595138 AATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGA-C-C
1 TA-GCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTC
* * * *
35595181 T-GGTGT-GATCTACTCTACTGTAA-CTTCAGAGAGATAAGATC-C
1 TAGCT-TCAATCTACTCCACTGTAATC-TCAGGGAGATAAGATCTC
* * * *
35595223 TTCA-TTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGAT-TAC
1 -T-AGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-C
* * * *
35595268 TAACTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
1 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-C
* * ** ** * *
35595313 AATCTTTCGGTCTGTTCCCCTGTAATCTCAGAGAGATAAGA-C-C
1 TAGC-TTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTC
* * * ** *
35595356 T-GATGCGATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATC-C
1 TAGCTTCAATCTACTCCACTGTAATC-TCAGGGAGATAAGATCTC
* * * *
35595398 TTCA-TTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGAT-TAC
1 -T-AGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-C
* * * *
35595443 TATCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAATATCTGA
1 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-C
* ** ** ** * *
35595488 AATTATTCGGTCTGTTCCACTGTAGTCTCAGGGAAATAAGA-C-C
1 TA-GCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTC
* * * *** * *
35595531 T-GGTGCGATCTACTCTGTTGTAA-CTTCAGAGAGAAAAGATCAT-
1 TAGCTTCAATCTACTCCACTGTAATC-TCAGGGAGATAAGATC-TC
* * * ** *
35595574 TCA-TTTTAATCCACTCCACTGTAATCTCAAAGAGATAGGAT-TAC
1 T-AGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-C
* * *
35595618 TAACTTTAATCTGCT-CAGCTGTAATCTCAGGGAGATAAGATCTGAC
1 TAGCTTCAATCTACTCCA-CTGTAATCTCAGGGAGATAAGATCT--C
* * ** ** *
35595664 -ATTCTGCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGA-C-C
1 TA-GCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTC
* * ** * *
35595706 T-GACGT-GATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCATT
1 TAG-CTTCAATCTACTCCACTGTAATC-TCAGGGAGATAAGATC-TC
* * ** *
35595750 TA-TTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-TAC
1 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-C
* * *
35595793 TATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
1 TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGAT
35595834 TTGAAATCTT
Statistics
Matches: 1044, Mismatches: 264, Indels: 218
0.68 0.17 0.14
Matches are distributed among these distances:
40 7 0.01
41 186 0.18
42 18 0.02
43 20 0.02
44 517 0.50
45 34 0.03
46 186 0.18
47 5 0.00
49 1 0.00
50 1 0.00
51 2 0.00
52 2 0.00
53 3 0.00
54 29 0.03
55 33 0.03
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
TAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTC
Found at i:35595047 original size:315 final size:315
Alignment explanation
Indices: 35594662--35595269 Score: 1000
Period size: 315 Copynumber: 1.9 Consensus size: 315
35594652 CTTCGGTCTA
* * *
35594662 CTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGATCCACTCTGCTGTAACTTCAGAGAGATA
1 CTCCACTGTAACCTCAAAGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATA
*
35594727 AGATCATTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGC
66 AGATCATTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
35594792 TCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTATAACCTCAGGGA
131 TCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTATAACCTCAGGGA
* * * *
35594857 GATAAGACCTGATGCGATCCACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
196 AATAAGACCTGATGCGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCA
*
35594922 TTCCACTGTAATCTCAGGGAGATAGGATTACTATAGGATTACTAGTTTCAATCTG
261 CTCCACTGTAATCTCAGGGAGATAGGATTACTATAGGATTACTAGTTTCAATCTG
* * *
35594977 CTCCGCTGTAATCTCAAAGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
1 CTCCACTGTAACCTCAAAGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATA
* * *
35595042 AGATCATTTATTTTAATCCGCTCTACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGC
66 AGATCATTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
* * ** * *
35595107 TCCTCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGA
131 TCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTATAACCTCAGGGA
* * *
35595172 AATAAGACCTGGTGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCA
196 AATAAGACCTGATGCGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCA
35595237 CTCCACTGTAATCTCAGGGAGATAGGATTACTA
261 CTCCACTGTAATCTCAGGGAGATAGGATTACTA
35595270 ACTTCAATCT
Statistics
Matches: 269, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
315 269 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (315 bp):
CTCCACTGTAACCTCAAAGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATA
AGATCATTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
TCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTATAACCTCAGGGA
AATAAGACCTGATGCGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCA
CTCCACTGTAATCTCAGGGAGATAGGATTACTATAGGATTACTAGTTTCAATCTG
Found at i:35595180 original size:175 final size:174
Alignment explanation
Indices: 35594478--35595840 Score: 1367
Period size: 175 Copynumber: 7.7 Consensus size: 174
35594468 AATCTAATGT
* * *
35594478 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCACTCCACTGTAATCTC
* *
35594543 AGAGAGATAAGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT---CTG
66 AGAGAGATAGGATTACTA-CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT-
* ** * *
35594605 GCTTCAATCTGTTCCACTGTAA-CATCAGGGAGATAAGATCTGAAATTCTTC
129 TCTTCGGTCTGTTCCACTGTAATC-TCAGGGAGATAAGACCTG--A---TGC
* * * * * *** **
35594656 GGTCTACTCCACTGTAACCTCAGAGAGATAAGA-C-CTGA-TGCGATCCACTCTGCTGTAA-CTT
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCACTCCACTGTAATC-T
* * * * * ** * * *
35594717 CAGAGAGATAAGATCATTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGAT-T--ACT
65 CAGAGAGATAGGATTA-CTACTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
** * * * * *
35594779 ATCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTC
129 -TCTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG--A---TGC
* * * * * * * *** **
35594831 GGTCTACTCCACTATAACCTCAGGGAGATAAGA-C-CTGA-TGCGATCCACTCTGCTGTAA-CTT
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCACTCCACTGTAATC-T
* * * * * * * *
35594892 CAGAGAGATAAGATCCT-TTATTTTAATCCGTTCCACTGTAATCTCAGGGAGATAGGATTACT-A
65 CAGAGAGATAGGAT--TACTACTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA-T-CTGA
** * * ** *
35594955 TAGGATTACTAGTTTCAATCTGCTCCGCTGTAATCTCAAAGAGATAAGACCTGATAC
126 -A--ATT-C----TTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
* * * *
35595012 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCTACTGTAATCTT
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCACTCCACTGTAATCTC
* *
35595077 AGGGAGATAGGATTACTAGCTTCAATCTGCTCCTCTGTAATCTCAGGGAGATAAGATCTGAAATT
66 AGAGAGATAGGATTACTA-CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
* * *
35595142 CTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGT
130 CTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
*
35595187 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCACTCCACTGTAATCTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCACTCCACTGTAATCTC
*
35595252 AGGGAGATAGGATTACTAACTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAA-T
66 AGAGAGATAGGATTACT-ACTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
* *
35595316 CTTTCGGTCTGTTCCCCTGTAATCTCAGAGAGATAAGACCTGATGC
130 C-TTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
* *
35595362 GATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCACTCCACTGTAATCTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCACTCCACTGTAATCTC
* * *
35595427 AGGGAGATAGGATTACTATCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAATATCTGAAATT
66 AGAGAGATAGGATTACTA-CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
* * * *
35595492 ATTCGGTCTGTTCCACTGTAGTCTCAGGGAAATAAGACCTGGTGC
130 CTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
** *
35595537 GATCTACTCTGTTGTAACTTCAGAGAGAAAAGATCATTCATTTTAATCCACTCCACTGTAATCTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCACTCCACTGTAATCTC
* * * *
35595602 AAAGAGATAGGATTACTAACTTTAATCTGCTCAGCTGTAATCTCAGGGAGATAAGATCTGACATT
66 AGAGAGATAGGATTACT-ACTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
* * * *
35595667 CTGCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGACGT
130 CTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
* * *
35595712 GATCTACTCTGCTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCACTCCACTGTAATCTC
* *
35595777 AGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTGAAAT
66 AGAGAGATAGGATTACTA-CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
35595841 CTTTCAATCA
Statistics
Matches: 1042, Mismatches: 112, Indels: 65
0.85 0.09 0.05
Matches are distributed among these distances:
174 6 0.01
175 850 0.82
176 9 0.01
177 1 0.00
178 31 0.03
179 1 0.00
180 4 0.00
181 31 0.03
182 7 0.01
183 6 0.01
184 59 0.06
185 1 0.00
186 36 0.03
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (174 bp):
GATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCACTCCACTGTAATCTC
AGAGAGATAGGATTACTACTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTC
TTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
Found at i:35595956 original size:87 final size:87
Alignment explanation
Indices: 35595839--35596098 Score: 342
Period size: 87 Copynumber: 3.0 Consensus size: 87
35595829 AAGATTTGAA
* * * *
35595839 ATCTTTCAATCAGCTTCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGTTGTT
1 ATCTTT-AATCAGCTCCACTACAACCGATGGAGACAAGGCTTTGTTTTCGATCTGCTTCGCTGTT
*
35595904 AACGCATGAAGGCAAGATCTACT
65 AACGCAGGAAGGCAAGATCTACT
* *
35595927 ATCTTTAATCAGCTCCACTACAACCGATGGAGACAAGGCTTTGTTTCCAATCTGCTTCGCTGTTA
1 ATCTTTAATCAGCTCCACTACAACCGATGGAGACAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
* *
35595992 ACGCAGGAAGGCCAGATCTGCT
66 ACGCAGGAAGGCAAGATCTACT
* * * * * *
35596014 ATCTTCAAACAGTTCCACCACAACCGATGGAGACAAAGC-TTGTATCTTCGATCTGCTTCACTGT
1 ATCTTTAATCAGCTCCACTACAACCGATGGAGACAAGGCTTTGT-T-TTCGATCTGCTTCGCTGT
*
35596078 TAAGGCAGGAAGGCAAGATCT
64 TAACGCAGGAAGGCAAGATCT
35596099 GTTGTCTTTG
Statistics
Matches: 151, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
86 4 0.03
87 107 0.71
88 40 0.26
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (87 bp):
ATCTTTAATCAGCTCCACTACAACCGATGGAGACAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
ACGCAGGAAGGCAAGATCTACT
Found at i:35597251 original size:21 final size:21
Alignment explanation
Indices: 35597225--35597271 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
35597215 GGTATAGCAG
35597225 GATCACCACATGCCCAAATCT
1 GATCACCACATGCCCAAATCT
** * *
35597246 GATCACTTCATGCCCTATTCT
1 GATCACCACATGCCCAAATCT
35597267 GATCA
1 GATCA
35597272 ATATTTGAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.34, G:0.11, T:0.28
Consensus pattern (21 bp):
GATCACCACATGCCCAAATCT
Found at i:35597414 original size:20 final size:20
Alignment explanation
Indices: 35597366--35597413 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
35597356 CATTTTTACG
35597366 TTTTCA-TTTTT--TTCATT
1 TTTTCATTTTTTCATTCATT
35597383 TTTTCATTTTTTCATTCATT
1 TTTTCATTTTTTCATTCATT
35597403 TTTT-ATTTTTT
1 TTTTCATTTTTT
35597414 TTGACTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.21
18 5 0.18
19 7 0.25
20 10 0.36
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTCATTTTTTCATTCATT
Found at i:35597415 original size:9 final size:9
Alignment explanation
Indices: 35597366--35597414 Score: 57
Period size: 8 Copynumber: 5.4 Consensus size: 9
35597356 CATTTTTACG
35597366 TTTTCATTT
1 TTTTCATTT
35597375 TTTTCA-TT
1 TTTTCATTT
35597383 TTTTCA-TT
1 TTTTCATTT
35597391 TTTTCATTCAT
1 TTTTCATT--T
*
35597402 TTTTTATTT
1 TTTTCATTT
35597411 TTTT
1 TTTT
35597415 TGACTCAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
8 16 0.44
9 12 0.33
11 8 0.22
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTCATTT
Found at i:35598298 original size:23 final size:21
Alignment explanation
Indices: 35598272--35598335 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 21
35598262 TTTTCTCTTA
35598272 TTTTTGACTTTGATTTTTTTGAT
1 TTTTTGA-TTTGATTTTTTT-AT
35598295 TTTTTGA-TTGATTTTTTTAT
1 TTTTTGATTTGATTTTTTTAT
35598315 TTGATTTGATTTGATTTTTTT
1 TT--TTTGATTTGATTTTTTT
35598336 TTGTTTTTCG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.11
21 11 0.29
22 5 0.13
23 18 0.47
ACGTcount: A:0.14, C:0.02, G:0.12, T:0.72
Consensus pattern (21 bp):
TTTTTGATTTGATTTTTTTAT
Found at i:35598302 original size:17 final size:17
Alignment explanation
Indices: 35598280--35598334 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
35598270 TATTTTTGAC
35598280 TTTGATTTTTTTGATTT
1 TTTGATTTTTTTGATTT
*
35598297 TTTGATTGATTTTT--TTA
1 TTTGATT--TTTTTGATTT
*
35598314 TTTGATTTGATTTGATTT
1 TTTGATTT-TTTTGATTT
35598332 TTT
1 TTT
35598335 TTTGTTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 16 0.53
18 5 0.17
19 5 0.17
ACGTcount: A:0.15, C:0.00, G:0.13, T:0.73
Consensus pattern (17 bp):
TTTGATTTTTTTGATTT
Found at i:35598305 original size:12 final size:13
Alignment explanation
Indices: 35598289--35598334 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
35598279 CTTTGATTTT
35598289 TTTGATTTTTTGA
1 TTTGATTTTTTGA
*
35598302 -TTGATTTTTTTA
1 TTTGATTTTTTGA
35598314 TTTGA---TTTGA
1 TTTGATTTTTTGA
35598324 TTTGATTTTTT
1 TTTGATTTTTT
35598335 TTTGTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
10 9 0.33
12 11 0.41
13 7 0.26
ACGTcount: A:0.15, C:0.00, G:0.13, T:0.72
Consensus pattern (13 bp):
TTTGATTTTTTGA
Found at i:35598305 original size:27 final size:26
Alignment explanation
Indices: 35598285--35598337 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
35598275 TTGACTTTGA
35598285 TTTT-TTTGATTT-TTTGATTGATTT
1 TTTTATTTGATTTATTTGATTGATTT
35598309 TTTTATTTGATTTGATTTGATT--TTT
1 TTTTATTTGATTT-ATTTGATTGATTT
35598334 TTTT
1 TTTT
35598338 GTTTTTCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.15
25 15 0.58
27 7 0.27
ACGTcount: A:0.13, C:0.00, G:0.11, T:0.75
Consensus pattern (26 bp):
TTTTATTTGATTTATTTGATTGATTT
Found at i:35598338 original size:21 final size:21
Alignment explanation
Indices: 35598274--35598338 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
35598264 TTCTCTTATT
*
35598274 TTTGACTTTGATTTTTTTGATT-T
1 TTTGA-TTTGATTTTTTT--TTGA
35598297 TTTGA-TTGATTTTTTTATTTGA
1 TTTGATTTGA-TTTTTT-TTTGA
35598319 TTTGATTTGATTTTTTTTTG
1 TTTGATTTGATTTTTTTTTG
35598339 TTTTTCGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
21 10 0.27
22 17 0.46
23 10 0.27
ACGTcount: A:0.14, C:0.02, G:0.14, T:0.71
Consensus pattern (21 bp):
TTTGATTTGATTTTTTTTTGA
Found at i:35598342 original size:10 final size:11
Alignment explanation
Indices: 35598285--35598343 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
35598275 TTGACTTTGA
35598285 TTTTTTTGATT
1 TTTTTTTGATT
*
35598296 TTTTGATTGATTT
1 TTTT-TTTGA-TT
35598309 TTTTATTTGA-T
1 TTTT-TTTGATT
**
35598320 TTGATTTGATT
1 TTTTTTTGATT
35598331 TTTTTTTG-TT
1 TTTTTTTGATT
35598341 TTT
1 TTT
35598344 CGTTTTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
10 10 0.26
11 14 0.37
12 4 0.11
13 10 0.26
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (11 bp):
TTTTTTTGATT
Found at i:35598700 original size:12 final size:12
Alignment explanation
Indices: 35598683--35598707 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35598673 CTGACATCAA
35598683 GCTGCTGTGCAG
1 GCTGCTGTGCAG
35598695 GCTGCTGTGCAG
1 GCTGCTGTGCAG
35598707 G
1 G
35598708 TTCTATTATA
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:0.08, C:0.24, G:0.44, T:0.24
Consensus pattern (12 bp):
GCTGCTGTGCAG
Found at i:35602599 original size:12 final size:12
Alignment explanation
Indices: 35602582--35602620 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
35602572 ATAATGGATA
*
35602582 AATAAATAAGTG
1 AATAAATAAATG
35602594 AATAAATAAATG
1 AATAAATAAATG
*
35602606 AATCAAACAAATG
1 AAT-AAATAAATG
35602619 AA
1 AA
35602621 ACTATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (12 bp):
AATAAATAAATG
Found at i:35604720 original size:12 final size:12
Alignment explanation
Indices: 35604703--35604727 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35604693 CAAAGACTAT
35604703 TAACAATATTTA
1 TAACAATATTTA
35604715 TAACAATATTTA
1 TAACAATATTTA
35604727 T
1 T
35604728 GTTATAAAAT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:35605134 original size:11 final size:11
Alignment explanation
Indices: 35605091--35605146 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
35605081 TTTTTTAAAC
35605091 TTTAAAATATT
1 TTTAAAATATT
*
35605102 TTTCAAATATT
1 TTTAAAATATT
* *
35605113 TTT---TTAAT
1 TTTAAAATATT
35605121 TTTAAAATATT
1 TTTAAAATATT
35605132 TTTAAAATACTT
1 TTTAAAATA-TT
35605144 TTT
1 TTT
35605147 TTAATTTCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
8 6 0.17
11 25 0.69
12 5 0.14
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTAAAATATT
Found at i:35605149 original size:14 final size:14
Alignment explanation
Indices: 35605130--35605219 Score: 55
Period size: 14 Copynumber: 6.5 Consensus size: 14
35605120 TTTTAAAATA
35605130 TTTTTAAAATACTT
1 TTTTTAAAATACTT
* *
35605144 TTTTT-AATTTCTT
1 TTTTTAAAATACTT
*
35605157 TATTTTAAAA-A-TA
1 T-TTTTAAAATACTT
*
35605170 TTTTTATAAAT-TTT
1 TTTTTA-AAATACTT
35605184 TATTTTAAAATA-TT
1 T-TTTTAAAATACTT
**
35605198 TTAAATAAAATACTT
1 TT-TTTAAAATACTT
35605213 TTTTTAA
1 TTTTTAA
35605220 NNNNNNNNNN
Statistics
Matches: 57, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
12 5 0.09
13 13 0.23
14 28 0.49
15 11 0.19
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTTAAAATACTT
Found at i:35605151 original size:31 final size:30
Alignment explanation
Indices: 35605079--35605153 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
35605069 TAAATATATT
* * *
35605079 TATTTTTTAAACTTTAAAATATTTTTCAAA
1 TATTTTTTTAATTTTAAAATATTTTTAAAA
35605109 TATTTTTTTAATTTTAAAATATTTTTAAAA
1 TATTTTTTTAATTTTAAAATATTTTTAAAA
35605139 TACTTTTTTTAATTT
1 TA-TTTTTTTAATTT
35605154 CTTTATTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 29 0.71
31 12 0.29
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (30 bp):
TATTTTTTTAATTTTAAAATATTTTTAAAA
Found at i:35605167 original size:29 final size:27
Alignment explanation
Indices: 35605128--35605199 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 27
35605118 AATTTTAAAA
* * *
35605128 TATTTTTAAAATACTTTTTTTAATTTCTT
1 TATTTTAAAAATA-TTTTTATAAATT-TT
35605157 TATTTTAAAAATATTTTTATAAATTTT
1 TATTTTAAAAATATTTTTATAAATTTT
35605184 TATTTT-AAAATATTTT
1 TATTTTAAAAATATTTT
35605200 AAATAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 10 0.25
27 8 0.20
28 10 0.25
29 12 0.30
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTTTAAAAATATTTTTATAAATTTT
Found at i:35605185 original size:27 final size:27
Alignment explanation
Indices: 35605131--35605199 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 27
35605121 TTTAAAATAT
* *
35605131 TTTTAAAATACTTTTTTTAATTTCTTTA
1 TTTTAAAATA-TTTTTATAAATTCTTTA
35605159 TTTTAAAAATATTTTTATAAATT-TTTA
1 TTTT-AAAATATTTTTATAAATTCTTTA
35605186 TTTTAAAATATTTT
1 TTTTAAAATATTTT
35605200 AAATAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 10 0.26
27 8 0.21
28 14 0.37
29 6 0.16
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTTAAAATATTTTTATAAATTCTTTA
Found at i:35605205 original size:27 final size:27
Alignment explanation
Indices: 35605128--35605206 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
35605118 AATTTTAAAA
* ** *
35605128 TATTTTTAAAATACTTTTTTTAATTTCTT
1 TATTTTAAAAATA-TTTTAATAAATT-TT
*
35605157 TATTTTAAAAATATTTTTATAAATTTT
1 TATTTTAAAAATATTTTAATAAATTTT
35605184 TATTTT-AAAATATTTTAAATAAA
1 TATTTTAAAAATATTTT-AATAAA
35605207 ATACTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.22
27 13 0.29
28 10 0.22
29 12 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (27 bp):
TATTTTAAAAATATTTTAATAAATTTT
Found at i:35607088 original size:20 final size:20
Alignment explanation
Indices: 35607061--35607107 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
35607051 GTGTTCATCG
35607061 TTTATTTCTGTTCATTTT-T
1 TTTATTTCTGTTCATTTTCT
* *
35607080 TTATATTTCTTTTTATTTTCT
1 TT-TATTTCTGTTCATTTTCT
35607101 TTTATTT
1 TTTATTT
35607108 TCATTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTATTTCTGTTCATTTTCT
Found at i:35607099 original size:11 final size:11
Alignment explanation
Indices: 35607077--35607114 Score: 51
Period size: 10 Copynumber: 3.4 Consensus size: 11
35607067 TCTGTTCATT
35607077 TTTTTATATTTC
1 TTTTTAT-TTTC
35607089 TTTTTATTTTC
1 TTTTTATTTTC
35607100 -TTTTATTTTC
1 TTTTTATTTTC
35607110 ATTTT
1 -TTTT
35607115 GTTTCACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.42
11 4 0.17
12 10 0.42
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATTTTC
Found at i:35608032 original size:21 final size:21
Alignment explanation
Indices: 35607970--35608036 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
35607960 TGTACACACA
*
35607970 TTTATATATATATATTTACA-T
1 TTTATAT-TATATATATACATT
* *
35607991 TTTATAATTCA-AAATACACATT
1 TTTAT-ATT-ATATATATACATT
35608013 TTTATATTATATATATACATT
1 TTTATATTATATATATACATT
35608034 TTT
1 TTT
35608037 TGATATTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
20 1 0.03
21 27 0.73
22 9 0.24
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTATATTATATATATACATT
Found at i:35610396 original size:3 final size:3
Alignment explanation
Indices: 35610388--35610446 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
35610378 AAAGGATAGA
35610388 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35610436 AAT AAT AAT AA
1 AAT AAT AAT AA
35610447 AAGGGATAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:35611490 original size:18 final size:18
Alignment explanation
Indices: 35611469--35611506 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
35611459 AACCTATTAT
35611469 GTATGCAAAACCCCATAA
1 GTATGCAAAACCCCATAA
*
35611487 GTATGCCAAACCCCATAA
1 GTATGCAAAACCCCATAA
35611505 GT
1 GT
35611507 TTGGGTTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.18
Consensus pattern (18 bp):
GTATGCAAAACCCCATAA
Found at i:35614266 original size:13 final size:15
Alignment explanation
Indices: 35614244--35614275 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
35614234 TTCTATTTTC
35614244 TTTTCTCTC-AATTT
1 TTTTCTCTCAAATTT
35614258 TTTTC-CTCAAATTT
1 TTTTCTCTCAAATTT
35614272 TTTT
1 TTTT
35614276 TTTCATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTCTCTCAAATTT
Found at i:35625152 original size:18 final size:19
Alignment explanation
Indices: 35625131--35625166 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35625121 TTAAATAGTA
35625131 TTAAAA-ATAATTTTATAT
1 TTAAAAGATAATTTTATAT
*
35625149 TTAAAAGATATTTTTATA
1 TTAAAAGATAATTTTATA
35625167 AGAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TTAAAAGATAATTTTATAT
Found at i:35626685 original size:27 final size:28
Alignment explanation
Indices: 35626650--35626711 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
35626640 AAAATCAAAC
*
35626650 TTAACAACCTAGG-TTTTGAAATCTGTTT
1 TTAA-AACCTAGGTTTTTGAAACCTGTTT
*
35626678 TTAAAACCTTGGTTTTTGAAACCTGTTT
1 TTAAAACCTAGGTTTTTGAAACCTGTTT
35626706 TTAAAA
1 TTAAAA
35626712 ATCAACCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 7 0.23
28 24 0.77
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (28 bp):
TTAAAACCTAGGTTTTTGAAACCTGTTT
Found at i:35626694 original size:15 final size:13
Alignment explanation
Indices: 35626672--35626711 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
35626662 GTTTTGAAAT
35626672 CTGTTTTTAAAAC
1 CTGTTTTTAAAAC
*
35626685 CTTGGTTTTTGAAAC
1 C-T-GTTTTTAAAAC
35626700 CTGTTTTTAAAA
1 CTGTTTTTAAAA
35626712 ATCAACCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 10 0.43
14 2 0.09
15 11 0.48
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (13 bp):
CTGTTTTTAAAAC
Found at i:35628525 original size:21 final size:21
Alignment explanation
Indices: 35628499--35628542 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
35628489 CTTCAGCAAA
35628499 AACCCAGAAAAAAGATTTTTT
1 AACCCAGAAAAAAGATTTTTT
*
35628520 AACCCAGAATAAAGATTTTTT
1 AACCCAGAAAAAAGATTTTTT
35628541 AA
1 AA
35628543 TCTTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.30
Consensus pattern (21 bp):
AACCCAGAAAAAAGATTTTTT
Found at i:35632621 original size:28 final size:27
Alignment explanation
Indices: 35632568--35632627 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
35632558 ACATCTATAC
*
35632568 ATTTTCATAATACATATATGTACATAT
1 ATTTTCATAATACATATATATACATAT
*
35632595 ATTTT-ATAATATATATATATACACATAT
1 ATTTTCATAATACATATATAT--ACATAT
35632623 ATTTT
1 ATTTT
35632628 TTGTTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 13 0.45
27 5 0.17
28 11 0.38
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTTTCATAATACATATATATACATAT
Found at i:35633533 original size:16 final size:16
Alignment explanation
Indices: 35633512--35633545 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
35633502 ACCAAGACAT
35633512 TAAGTAATCAACTAGG
1 TAAGTAATCAACTAGG
35633528 TAAGTAATCAACTAGG
1 TAAGTAATCAACTAGG
35633544 TA
1 TA
35633546 CCAATTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (16 bp):
TAAGTAATCAACTAGG
Found at i:35640735 original size:24 final size:24
Alignment explanation
Indices: 35640694--35640762 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
35640684 AAATGAAAAA
*
35640694 AATAATAATATAGT-ATAACTTTTA-
1 AATAATAATACA-TAATAA-TTTTAG
*
35640718 AGTAATAATACATAATAATTTTAG
1 AATAATAATACATAATAATTTTAG
* *
35640742 AATAATAATACACAATGATTT
1 AATAATAATACATAATAATTT
35640763 CGAAAACATG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 6 0.16
24 32 0.84
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
AATAATAATACATAATAATTTTAG
Found at i:35640865 original size:3 final size:3
Alignment explanation
Indices: 35640857--35640918 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
35640847 ATAGTACATA
*
35640857 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35640905 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
35640919 AAGGTTTAGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:35645938 original size:2 final size:2
Alignment explanation
Indices: 35645931--35645974 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
35645921 TATTGAAAAG
35645931 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
35645973 AT
1 AT
35645975 TGAAGGAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35647700 original size:17 final size:17
Alignment explanation
Indices: 35647678--35647718 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
35647668 TATTGTACTT
*
35647678 TTTTTTCTT-CACTTTGA
1 TTTTTTCTTCCAC-TAGA
35647695 TTTTTT-TTCCACTAGA
1 TTTTTTCTTCCACTAGA
35647711 TTTTTTCT
1 TTTTTTCT
35647719 AGTAAGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.12, C:0.17, G:0.05, T:0.66
Consensus pattern (17 bp):
TTTTTTCTTCCACTAGA
Found at i:35655223 original size:34 final size:34
Alignment explanation
Indices: 35655180--35655249 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
35655170 ACGATAAGTC
35655180 TGGCAATACCTCAATTGACTCAACTAATATAACA
1 TGGCAATACCTCAATTGACTCAACTAATATAACA
35655214 TGGCAATACCTCAATTGACTCAACTAATATAACA
1 TGGCAATACCTCAATTGACTCAACTAATATAACA
35655248 TG
1 TG
35655250 AAACATGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (34 bp):
TGGCAATACCTCAATTGACTCAACTAATATAACA
Found at i:35658698 original size:20 final size:20
Alignment explanation
Indices: 35658673--35658711 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35658663 AATTTTTTTT
35658673 TTTAAAAATACATAAAAATA
1 TTTAAAAATACATAAAAATA
* *
35658693 TTTAAAAGTTCATAAAAAT
1 TTTAAAAATACATAAAAAT
35658712 CTTAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
TTTAAAAATACATAAAAATA
Found at i:35658719 original size:20 final size:19
Alignment explanation
Indices: 35658674--35658719 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
35658664 ATTTTTTTTT
35658674 TTAAAAATACATAAAAATA
1 TTAAAAATACATAAAAATA
* * *
35658693 TTTAAAAGTTCATAAAAATC
1 -TTAAAAATACATAAAAATA
35658713 TTAAAAA
1 TTAAAAA
35658720 AAATATCTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (19 bp):
TTAAAAATACATAAAAATA
Found at i:35661190 original size:26 final size:26
Alignment explanation
Indices: 35661138--35661188 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
35661128 CACTAATCCA
* *
35661138 TATTTAATATATTTATTAATTCAAAT
1 TATTTAAAATATTTATCAATTCAAAT
*
35661164 TATTTAAAATATTTCTCACATTCAA
1 TATTTAAAATATTTATCA-ATTCAA
35661189 TTTAATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (26 bp):
TATTTAAAATATTTATCAATTCAAAT
Found at i:35672089 original size:16 final size:17
Alignment explanation
Indices: 35672068--35672100 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
35672058 ATTTTCTTTA
35672068 TTATTAAATT-AGTATT
1 TTATTAAATTAAGTATT
*
35672084 TTATTAATTTAAGTATT
1 TTATTAAATTAAGTATT
35672101 GAATATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
TTATTAAATTAAGTATT
Found at i:35678507 original size:85 final size:85
Alignment explanation
Indices: 35678407--35678579 Score: 346
Period size: 85 Copynumber: 2.0 Consensus size: 85
35678397 TTTAAATTCA
35678407 AAAGCAAGTAGGTCAACTAAGTGCCGTCTCCCTCTCAAGAAATATTAGTTTGATCTCAATGGTTT
1 AAAGCAAGTAGGTCAACTAAGTGCCGTCTCCCTCTCAAGAAATATTAGTTTGATCTCAATGGTTT
35678472 CTGTTTGGTCTTGCTAAATC
66 CTGTTTGGTCTTGCTAAATC
35678492 AAAGCAAGTAGGTCAACTAAGTGCCGTCTCCCTCTCAAGAAATATTAGTTTGATCTCAATGGTTT
1 AAAGCAAGTAGGTCAACTAAGTGCCGTCTCCCTCTCAAGAAATATTAGTTTGATCTCAATGGTTT
35678557 CTGTTTGGTCTTGCTAAATC
66 CTGTTTGGTCTTGCTAAATC
35678577 AAA
1 AAA
35678580 ACAGCAATAG
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 88 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (85 bp):
AAAGCAAGTAGGTCAACTAAGTGCCGTCTCCCTCTCAAGAAATATTAGTTTGATCTCAATGGTTT
CTGTTTGGTCTTGCTAAATC
Found at i:35682872 original size:14 final size:13
Alignment explanation
Indices: 35682853--35682898 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
35682843 TTTCTTGTTC
35682853 TTATTTTGTTTTAT
1 TTATTTT-TTTTAT
35682867 TTATTTATTTTTAT
1 TTATTT-TTTTTAT
*
35682881 TTATTTTATTT-T
1 TTATTTTTTTTAT
35682893 TTATTT
1 TTATTT
35682899 CGAAATAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 7 0.23
13 4 0.13
14 18 0.60
15 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTTAT
Found at i:35683712 original size:3 final size:3
Alignment explanation
Indices: 35683704--35683749 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
35683694 TTTAACCTTG
35683704 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
35683750 TACTCATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:35683960 original size:23 final size:23
Alignment explanation
Indices: 35683934--35683978 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
35683924 ATTCTTGTAT
*
35683934 TTTTATAAT-TTTGTTCACGTTTC
1 TTTTA-AATATTTATTCACGTTTC
*
35683957 TTTTAATTATTTATTCACGTTT
1 TTTTAAATATTTATTCACGTTT
35683979 TCATCATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.62
Consensus pattern (23 bp):
TTTTAAATATTTATTCACGTTTC
Found at i:35690076 original size:24 final size:23
Alignment explanation
Indices: 35690044--35690089 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
35690034 ATATGATTTT
*
35690044 TTTTATTTTATATGTTCAATTAC
1 TTTTATTTTATATATTCAATTAC
*
35690067 TTTTAGTTTTATATATTTAATTA
1 TTTTA-TTTTATATATTCAATTA
35690090 AAGATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTTATTTTATATATTCAATTAC
Found at i:35691273 original size:2 final size:2
Alignment explanation
Indices: 35691266--35691294 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35691256 ACAAGTGATA
35691266 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 A
35691295 AATTTATTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35710258 original size:89 final size:87
Alignment explanation
Indices: 35710052--35710264 Score: 214
Period size: 89 Copynumber: 2.4 Consensus size: 87
35710042 CATGTGAATA
** * * *
35710052 GTGAACATTGAAATTGAGGGAAACCATGTTTGTGGGGAAGTAATTCAGTGGTGGAAACCATAAAA
1 GTGAACATTGAAA-TGAGGGAAACCATGTTTGTGGGGAAGTAACACACTGGTAGAAACAATAAAA
* *
35710117 GGCGATTCAGGAACATGTCAATG
65 GGCAATTCAGGAACATATCAATG
* * * * ** *
35710140 GTTAACATTGAAATCAAAGAAAATTATGTTTATGGGGAAGTAACACAACT-GTAGAAACAATAGA
1 GTGAACATTGAAAT-GAGGGAAACCATGTTTGTGGGGAAGTAACAC-ACTGGTAGAAACAATA-A
*
35710204 AAGGCAATTCAGGAGCATATCAATG
63 AAGGCAATTCAGGAACATATCAATG
*
35710229 GTGAACATTAAAACTGAGGGGAAA-CATGTTTGTGGG
1 GTGAACATTGAAA-TGA-GGGAAACCATGTTTGTGGG
35710265 TTAACTCAGT
Statistics
Matches: 98, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
87 1 0.01
88 45 0.46
89 47 0.48
90 5 0.05
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (87 bp):
GTGAACATTGAAATGAGGGAAACCATGTTTGTGGGGAAGTAACACACTGGTAGAAACAATAAAAG
GCAATTCAGGAACATATCAATG
Found at i:35711144 original size:7 final size:7
Alignment explanation
Indices: 35711134--35711173 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
35711124 GTTTTTGAGT
35711134 TTTAAGG
1 TTTAAGG
*
35711141 TTTAGGG
1 TTTAAGG
*
35711148 TTTAGGG
1 TTTAAGG
35711155 TTTAAGG
1 TTTAAGG
35711162 TTTTAAGG
1 -TTTAAGG
35711170 TTTA
1 TTTA
35711174 GAGTTTGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (7 bp):
TTTAAGG
Found at i:35711156 original size:14 final size:14
Alignment explanation
Indices: 35711134--35711179 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
35711124 GTTTTTGAGT
35711134 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
* *
35711148 TTTAGGGTTTAAGGT
1 TTTAAGGTTT-AGGG
*
35711163 TTTAAGGTTTAGAG
1 TTTAAGGTTTAGGG
35711177 TTT
1 TTT
35711180 GGGGTATAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:35711192 original size:29 final size:29
Alignment explanation
Indices: 35711132--35711192 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
35711122 CTGTTTTTGA
* *
35711132 GTTTTAAGGTTTAGGGTTTAGGGTTTAAG
1 GTTTTAAGGTTTAGAGTTTAGGGTATAAG
* *
35711161 GTTTTAAGGTTTAGAGTTTGGGGTATAGG
1 GTTTTAAGGTTTAGAGTTTAGGGTATAAG
35711190 GTT
1 GTT
35711193 AAAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (29 bp):
GTTTTAAGGTTTAGAGTTTAGGGTATAAG
Found at i:35711466 original size:39 final size:36
Alignment explanation
Indices: 35711422--35711495 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
35711412 TAAACACCAA
35711422 AAAAATATTTTAAAAATAAAAAGAATAAAAAAGTATTTT
1 AAAAATATTTT-AAAAT-AAAAGAATAAAAAA-TATTTT
*
35711461 AAAAATATTTTAAAATTAAAGAATAAAAAATATTT
1 AAAAATATTTTAAAATAAAAGAATAAAAAATATTT
35711496 ATTTATTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 5 0.15
37 13 0.38
38 5 0.15
39 11 0.32
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (36 bp):
AAAAATATTTTAAAATAAAAGAATAAAAAATATTTT
Found at i:35712335 original size:21 final size:21
Alignment explanation
Indices: 35712311--35712357 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
35712301 TTGTCCAGCT
* * *
35712311 TCCGGCGGGGGTTGTGGTTGC
1 TCCGGCGGGGATTCTGGTTCC
35712332 TCCGGCGGGGATTCTGGTTCC
1 TCCGGCGGGGATTCTGGTTCC
35712353 TCCGG
1 TCCGG
35712358 TAGGGTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.26, G:0.45, T:0.28
Consensus pattern (21 bp):
TCCGGCGGGGATTCTGGTTCC
Found at i:35714488 original size:11 final size:11
Alignment explanation
Indices: 35714469--35714597 Score: 126
Period size: 11 Copynumber: 12.0 Consensus size: 11
35714459 GGATTTAAGA
35714469 GAAATTTGAGAG
1 GAAA-TTGAGAG
35714481 GAAATTGAGAG
1 GAAATTGAGAG
* *
35714492 CAAATTGAGAT
1 GAAATTGAGAG
*
35714503 TAAA-T-AG-G
1 GAAATTGAGAG
*
35714511 G-ATTTGAGA-
1 GAAATTGAGAG
35714520 GAAATTTG-GAAG
1 GAAA-TTGAG-AG
* *
35714532 GCAATTAAGAG
1 GAAATTGAGAG
*
35714543 CAAATTGAGAG
1 GAAATTGAGAG
35714554 GAAATTGAGAG
1 GAAATTGAGAG
35714565 GAAATTGAGAG
1 GAAATTGAGAG
35714576 GAAATTGAGAG
1 GAAATTGAGAG
35714587 GAAATTGAGAG
1 GAAATTGAGAG
35714598 AATAATAGAA
Statistics
Matches: 96, Mismatches: 13, Indels: 17
0.76 0.10 0.13
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 5 0.05
10 3 0.03
11 78 0.81
12 8 0.08
ACGTcount: A:0.44, C:0.02, G:0.32, T:0.22
Consensus pattern (11 bp):
GAAATTGAGAG
Found at i:35714510 original size:51 final size:51
Alignment explanation
Indices: 35714453--35714597 Score: 168
Period size: 51 Copynumber: 2.8 Consensus size: 51
35714443 AATAATTAAA
* **
35714453 AAATAGGGATTTAAGAGAAATTTGAGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTGAGAGAAATTTGAGAGGAAATTGAGAGCAAATTGAGAGG
* *
35714504 AAATAGGGATTTGAGAGAAATTTG-GAAGGCAATTAAGAGCAAATTGAGAGG
1 AAATAGGGATTTGAGAGAAATTTGAG-AGGAAATTGAGAGCAAATTGAGAGG
*
35714555 AAATTGAGAGGAAATTGAGAGGAAA-TTGAGAGGAAATTGAGAG
1 AAA-T-AG-GG-ATTTGAGA-GAAATTTGAGAGGAAATTGAGAG
35714598 AATAATAGAA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
50 1 0.01
51 47 0.59
52 1 0.01
53 2 0.03
54 2 0.03
55 21 0.27
56 5 0.06
ACGTcount: A:0.45, C:0.02, G:0.31, T:0.22
Consensus pattern (51 bp):
AAATAGGGATTTGAGAGAAATTTGAGAGGAAATTGAGAGCAAATTGAGAGG
Found at i:35714971 original size:2 final size:2
Alignment explanation
Indices: 35714964--35714991 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35714954 CCAAGAGATG
35714964 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
35714992 TTACATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35717803 original size:4 final size:4
Alignment explanation
Indices: 35717794--35717825 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
35717784 CCTGTGAAGT
35717794 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
35717826 AATTTTTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:35723724 original size:9 final size:9
Alignment explanation
Indices: 35723710--35723740 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
35723700 GTTAAACGAA
35723710 TCGAGTTAT
1 TCGAGTTAT
*
35723719 TCGAGTTAA
1 TCGAGTTAT
35723728 TCGAGTTAT
1 TCGAGTTAT
35723737 TCGA
1 TCGA
35723741 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:35728106 original size:3 final size:3
Alignment explanation
Indices: 35728098--35728137 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
35728088 ATTTTAGTGA
*
35728098 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
35728138 GCTTTTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:35728489 original size:27 final size:26
Alignment explanation
Indices: 35728459--35728511 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
35728449 ATGTACGTAC
35728459 ATATTTTTC-ATATTTTATAATTTTCAT
1 ATATTTTTCTATATTTT-T-ATTTTCAT
*
35728486 ATATTTTTCTTTATTTTTATTTTCAT
1 ATATTTTTCTATATTTTTATTTTCAT
35728512 TTATGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 8 0.33
27 10 0.42
28 6 0.25
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.68
Consensus pattern (26 bp):
ATATTTTTCTATATTTTTATTTTCAT
Done.