Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold111
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: 1194829
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.25
Warning! 272571 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:154677 original size:120 final size:120
Alignment explanation
Indices: 154464--154693 Score: 316
Period size: 120 Copynumber: 1.9 Consensus size: 120
154454 TGATTGATAA
* * ** *** *
154464 AAGAAGTCTCTCGGGTATAAGCTGATAGGCAGATGATTGATAAAGGAAGTCTTTTGGGTCTAAGC
1 AAGAAGTCTCTCGAGTATAAGCTGATAGGCAGACGATTGATAAACAAAGTCTTTCAAGACTAAGC
* * *
154529 CGACGGGCAAATGGTGGATGAAGAAGTCTCCCGAGTCTAAGCCGAATGAAAGATG
66 CGACAGGCAAATAGTGGATGAAGAAGTCTCCCAAGTCTAAGCCGAATGAAAGATG
* * * *
154584 AAGAAGTCTCTCGAGTCTAAGCTGATGGGCAGACGGTTGATAAACAAAGTCTTTCAAGACTGAGC
1 AAGAAGTCTCTCGAGTATAAGCTGATAGGCAGACGATTGATAAACAAAGTCTTTCAAGACTAAGC
*
154649 CGATAGGCAAATAGTGGATGAAGAAGTCTCCCAAGTCTAAGCCGA
66 CGACAGGCAAATAGTGGATGAAGAAGTCTCCCAAGTCTAAGCCGA
154694 CAGGCAGACG
Statistics
Matches: 94, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
120 94 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.22
Consensus pattern (120 bp):
AAGAAGTCTCTCGAGTATAAGCTGATAGGCAGACGATTGATAAACAAAGTCTTTCAAGACTAAGC
CGACAGGCAAATAGTGGATGAAGAAGTCTCCCAAGTCTAAGCCGAATGAAAGATG
Found at i:154909 original size:43 final size:43
Alignment explanation
Indices: 154826--155250 Score: 460
Period size: 43 Copynumber: 9.9 Consensus size: 43
154816 GCCAATAGGG
* * * * * *
154826 AGACTTACGGGTGA-AAAGCCTCCAAGGTAAAAGCCAACAGGC
1 AGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAGGC
* * * *
154868 AGACTTAAGGGCGAGGAAGTCTCCAGGGTCAAAGTCGACAGGC
1 AGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAGGC
* * * *
154911 AGACTTAAGGGTAAAGAAGTCTCCAAGGTCAAAGCCGACAAGC
1 AGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAGGC
* * * *
154954 AGACTTAAGGGTGAAGAAGTCTCTAGGGTCAAAGCCGATATGC
1 AGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAGGC
* * * *
154997 AGACTTAAAGGTGAGGAAGTCTCCAAGGTCAAAGCTGACAGAC
1 AGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAGGC
* * **
155040 AGACTTAAGGGTGAGGAAGTCTCTAGGGTCAAAGTCGACAAAC
1 AGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAGGC
* * * * * * *
155083 AAACTTAAGGGTGAAGAA-TTTTTAGGGTCAAAACCCACAGGC
1 AGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAGGC
* * *
155125 AGACTTATA-GGTGAGGAAGTCTCCAAGGTCAAAGCCGAGAGTC
1 AGACTTA-AGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAGGC
* * *
155168 AGAATTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAAGA
1 AGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAGGC
*
155211 AGACTTAAGGGTGAAGAAGTCTCTAAGGTCAAAGCCGACA
1 AGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACA
155251 TGCATACTCA
Statistics
Matches: 319, Mismatches: 60, Indels: 7
0.83 0.16 0.02
Matches are distributed among these distances:
42 44 0.14
43 275 0.86
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.17
Consensus pattern (43 bp):
AGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAGGC
Found at i:155176 original size:128 final size:128
Alignment explanation
Indices: 154826--155243 Score: 520
Period size: 128 Copynumber: 3.3 Consensus size: 128
154816 GCCAATAGGG
* * * * * *
154826 AGACTTACGGGTGAA-AAGCCTCCAAGGT-AAAAGCCAACAGGCAGACTTAAGGGCGAGGAAGTC
1 AGACTTAAGGGTGAAGAAGTCTCTAGGGTCAAAA-CCCACAGGCAGACTTAA-GGTGAGGAAGTC
* * * * * * *
154889 TCCAGGGTCAAAGTCGACAGGCAGACTTAAGGGTAAAGAAGTCTCCAAGGTCAAAGCCGACAAGC
64 TCCAAGGTCAAAGCCGACAGACAGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAAAC
* * * *
154954 AGACTTAAGGGTGAAGAAGTCTCTAGGGTCAAAGCCGATATGCAGACTTAAAGGTGAGGAAGTCT
1 AGACTTAAGGGTGAAGAAGTCTCTAGGGTCAAAACCCACAGGCAGACTT-AAGGTGAGGAAGTCT
* * *
155019 CCAAGGTCAAAGCTGACAGACAGACTTAAGGGTGAGGAAGTCTCTAGGGTCAAAGTCGACAAAC
65 CCAAGGTCAAAGCCGACAGACAGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAAAC
* * *
155083 AAACTTAAGGGTGAAGAA-TTTTTAGGGTCAAAACCCACAGGCAGACTTATAGGTGAGGAAGTCT
1 AGACTTAAGGGTGAAGAAGTCTCTAGGGTCAAAACCCACAGGCAGACTTA-AGGTGAGGAAGTCT
* * *
155147 CCAAGGTCAAAGCCGAGAGTCAGAATTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAAGA-
65 CCAAGGTCAAAGCCGACAGACAGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAA-AC
*
155211 AGACTTAAGGGTGAAGAAGTCTCTAAGGTCAAA
1 AGACTTAAGGGTGAAGAAGTCTCTAGGGTCAAA
155244 GCCGACATGC
Statistics
Matches: 248, Mismatches: 36, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
127 1 0.00
128 125 0.50
129 117 0.47
130 5 0.02
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.17
Consensus pattern (128 bp):
AGACTTAAGGGTGAAGAAGTCTCTAGGGTCAAAACCCACAGGCAGACTTAAGGTGAGGAAGTCTC
CAAGGTCAAAGCCGACAGACAGACTTAAGGGTGAGGAAGTCTCTAAGGTCAAAGCCGACAAAC
Found at i:155520 original size:48 final size:48
Alignment explanation
Indices: 155467--155577 Score: 170
Period size: 48 Copynumber: 2.3 Consensus size: 48
155457 TAGGAAAAAG
*
155467 AAGAGTTTGACTAGGCCCTAACACCAATACT-GTCAAATGAGGGATGAA
1 AAGAGTTTGACTAGGCCCTAACACCAATA-TGGTCAAATGAGGGAAGAA
**
155515 AAGAGTTTGACTAGGCCCTAACACCAATATGGTTGAATGAGGGAAGAA
1 AAGAGTTTGACTAGGCCCTAACACCAATATGGTCAAATGAGGGAAGAA
*
155563 AAGAGTTTGGCTAGG
1 AAGAGTTTGACTAGG
155578 TACAACCAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
47 1 0.02
48 57 0.98
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (48 bp):
AAGAGTTTGACTAGGCCCTAACACCAATATGGTCAAATGAGGGAAGAA
Found at i:156515 original size:89 final size:87
Alignment explanation
Indices: 156377--156666 Score: 316
Period size: 89 Copynumber: 3.3 Consensus size: 87
156367 TGCAAAAACT
* * * * *
156377 AAATGCATATGAAATGAGGTAAAT-GCAAATGACATCTAATGGTGTAGATGCACATGAAATGATG
1 AAATGCATATGAAATGATGCAAATACCAAATG-CATCTAA-AGTGCAGATGCA-ATGAAATGATG
* *
156441 TAAATGCAAGCATCAGTA-AAATGGC
63 CAAATGCAAGCATCAATAGAAA-GGC
* * * * *
156466 AAATGCATATGAGATGATGCAAATACCAAACGTCATCTAAAGTGCAGATGTATGTGAAATAATGC
1 AAATGCATATGAAATGATGCAAATACCAAATG-CATCTAAAGTGCAGATGCA-ATGAAATGATGC
*
156531 AAATGCAAACATCAATAGAAAGGC
64 AAATGCAAGCATCAATAGAAAGGC
* * *
156555 AAATGCATATGGAATAATGCAAATACC-AATGCTATCTAAAATGCAGATGCAAGTGAAATGATGC
1 AAATGCATATGAAATGATGCAAATACCAAATGC-ATCTAAAGTGCAGATGCAA-TGAAATGATGC
*
156619 AAATGCAAGCATCAATAGGAAGGC
64 AAATGCAAGCATCAATAGAAAGGC
* *
156643 AAAAGCATATGAAAAGATGCAAAT
1 AAATGCATATGAAATGATGCAAAT
156667 GCTGATGTAG
Statistics
Matches: 168, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
87 1 0.01
88 71 0.42
89 81 0.48
90 15 0.09
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.21
Consensus pattern (87 bp):
AAATGCATATGAAATGATGCAAATACCAAATGCATCTAAAGTGCAGATGCAATGAAATGATGCAA
ATGCAAGCATCAATAGAAAGGC
Found at i:156571 original size:44 final size:43
Alignment explanation
Indices: 156424--156668 Score: 167
Period size: 44 Copynumber: 5.6 Consensus size: 43
156414 AATGGTGTAG
* * * *
156424 ATGCACATGAAATGATGTAAATGCAAGCATCAGTAAAATGGCAA
1 ATGCATATGAAATAATGCAAATGCAAGCATCAATAAAA-GGCAA
* * * * * * *
156468 ATGCATATGAGATGATGCAAATACCAAACGTC-ATCTAAAGTGCAG
1 ATGCATATGAAATAATGCAAAT-GCAAGCATCAAT-AAAAG-GCAA
* * *
156513 ATGTATGTGAAATAATGCAAATGCAAACATCAATAGAAAGGCAA
1 ATGCATATGAAATAATGCAAATGCAAGCATCAATA-AAAGGCAA
* * * *
156557 ATGCATATGGAATAATGCAAATACCAATGCTATC--TAAAATGCAG
1 ATGCATATGAAATAATGCAAAT-GCAA-GC-ATCAATAAAAGGCAA
* *
156601 ATGCA-AGTGAAATGATGCAAATGCAAGCATCAATAGGAAGGCAA
1 ATGCATA-TGAAATAATGCAAATGCAAGCATCAATA-AAAGGCAA
*
156645 AAGCATATGAAA-AGATGCAAATGC
1 ATGCATATGAAATA-ATGCAAATGC
156669 TGATGTAGTC
Statistics
Matches: 155, Mismatches: 32, Indels: 28
0.72 0.15 0.13
Matches are distributed among these distances:
41 3 0.02
42 2 0.01
43 6 0.04
44 98 0.63
45 42 0.27
46 1 0.01
47 3 0.02
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.20
Consensus pattern (43 bp):
ATGCATATGAAATAATGCAAATGCAAGCATCAATAAAAGGCAA
Found at i:156632 original size:88 final size:88
Alignment explanation
Indices: 156422--156666 Score: 300
Period size: 88 Copynumber: 2.8 Consensus size: 88
156412 CTAATGGTGT
* * *
156422 AGATGCACA-TGAAATGATGTAAATGCAAGCATCAGTA-AAATGGCAAATGCATATGAGATGATG
1 AGATGCA-AGTGAAATGATGCAAATGCAAGCATCAATAGAAA-GGCAAATGCATATGA-ATAATG
*
156485 CAAATACCAAACGTCATCTAAAGTGC
63 CAAATACCAAACGTCATCTAAAATGC
* * * *
156511 AGATGTATGTGAAATAATGCAAATGCAAACATCAATAGAAAGGCAAATGCATATGGAATAATGCA
1 AGATGCAAGTGAAATGATGCAAATGCAAGCATCAATAGAAAGGCAAATGCATAT-GAATAATGCA
*
156576 AATACC-AATG-CTATCTAAAATGC
65 AATACCAAACGTC-ATCTAAAATGC
* * *
156599 AGATGCAAGTGAAATGATGCAAATGCAAGCATCAATAGGAAGGCAAAAGCATATGAAAAGATGCA
1 AGATGCAAGTGAAATGATGCAAATGCAAGCATCAATAGAAAGGCAAATGCATATGAATA-ATGCA
156664 AAT
65 AAT
156667 GCTGATGTAG
Statistics
Matches: 135, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
87 5 0.04
88 69 0.51
89 56 0.41
90 5 0.04
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (88 bp):
AGATGCAAGTGAAATGATGCAAATGCAAGCATCAATAGAAAGGCAAATGCATATGAATAATGCAA
ATACCAAACGTCATCTAAAATGC
Found at i:157037 original size:21 final size:20
Alignment explanation
Indices: 157011--157049 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
157001 AGGTCAAAAC
157011 CCTAGAAAGTATCGATACACA
1 CCTAG-AAGTATCGATACACA
*
157032 CCTAGATGTATCGATACA
1 CCTAGAAGTATCGATACA
157050 TATTGCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
CCTAGAAGTATCGATACACA
Found at i:157079 original size:19 final size:19
Alignment explanation
Indices: 157039--157107 Score: 120
Period size: 19 Copynumber: 3.6 Consensus size: 19
157029 ACACCTAGAT
*
157039 GTATCGATACATATTGCTTA
1 GTATCGATACATGTT-CTTA
157059 GTATCGATACATGTTCTTA
1 GTATCGATACATGTTCTTA
157078 GTATCGATACATGTTCTTA
1 GTATCGATACATGTTCTTA
157097 GTATCGATACA
1 GTATCGATACA
157108 CACTGAATTG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 34 0.71
20 14 0.29
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (19 bp):
GTATCGATACATGTTCTTA
Found at i:157212 original size:20 final size:21
Alignment explanation
Indices: 157165--157218 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
157155 AATATCGATA
* *
157165 CATTGTATCGATGCATACTTG
1 CATTGTATCGATACATACGTG
*
157186 AATTGTATCGATACATA-GTG
1 CATTGTATCGATACATACGTG
157206 CATTGTATCGATA
1 CATTGTATCGATA
157219 TATTGAGCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (21 bp):
CATTGTATCGATACATACGTG
Found at i:160379 original size:21 final size:20
Alignment explanation
Indices: 160353--160407 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
160343 GTATCGATAC
*
160353 ATTGTATCGATACAAACTTGA
1 ATTGTATCGATACAAA-GTGA
* * *
160374 ATTGTATTGATACATAGTGC
1 ATTGTATCGATACAAAGTGA
160394 ATTGTATCGATACA
1 ATTGTATCGATACA
160408 TTGAGCCCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACAAAGTGA
Found at i:161478 original size:112 final size:110
Alignment explanation
Indices: 161295--161591 Score: 294
Period size: 112 Copynumber: 2.6 Consensus size: 110
161285 TGATAGGGTG
* * * *
161295 CATGCCCCATTTTCCTAGGCACGAATGGGTCAGAACGTATAAAATAT-AAGTTTCTTTCAAAATC
1 CATG-CCCATTTTCCTAGGCACGAATGGATCA-AATGTATAAACTATGAA-TTTCTTTGAAAAT-
* * * ** * * *
161359 CAACAAATTTGACGTTGCAGGGCTCATAGATTTCAAAATTGATAAGATA
62 CAACAAATTTGACGTTGCAAGGCTCAAAAAGATCAAAACTAACAAGATA
* * *
161408 CATGCTC-TATTTCCTAGGCACGAATGAATCGAAATGTATAAACTGTGAATTTCTTTGAAAATCA
1 CATGCCCAT-TTTCCTAGGCACGAATGGATC-AAATGTATAAACTATGAATTTCTTTGAAAATCA
* * *
161472 AGCAAATTTGATGTTGTAAGGCTCAAAAAGATCGAAACTAACAAGATA
64 A-CAAATTTGACGTTGCAAGGCTCAAAAAGATCAAAACTAACAAGATA
* * *
161520 CGTGCCCATTTTCCTAGGCACGGATGGATCAAGATGTATAAAAC-ATGAATTTCTTTGAAAATTA
1 CATGCCCATTTTCCTAGGCACGAATGGATCAA-ATGTAT-AAACTATGAATTTCTTTGAAAA-TC
161584 AACAAATT
63 AACAAATT
161592 CAATGTTCTT
Statistics
Matches: 152, Mismatches: 24, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
111 6 0.04
112 131 0.86
113 15 0.10
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (110 bp):
CATGCCCATTTTCCTAGGCACGAATGGATCAAATGTATAAACTATGAATTTCTTTGAAAATCAAC
AAATTTGACGTTGCAAGGCTCAAAAAGATCAAAACTAACAAGATA
Found at i:162390 original size:20 final size:20
Alignment explanation
Indices: 162365--162491 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 20
162355 TTTTACCTTC
162365 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
162385 ATGTATCGATACATTCTGTCTTTTACCCA
1 ATGTATCGATACA-----T-TTTT---CA
*
162414 GATTTATCGATACATTCTTT-A
1 -ATGTATCGATACATT-TTTCA
** * *
162435 ATGTATCGATACACATATGA
1 ATGTATCGATACATTTTTCA
*
162455 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
162475 ATGTATCGATAAATTTT
1 ATGTATCGATACATTTT
162492 GTCTTTTTAC
Statistics
Matches: 83, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
19 2 0.02
20 56 0.67
21 1 0.01
24 1 0.01
25 5 0.06
26 4 0.05
29 2 0.02
30 12 0.14
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:163986 original size:112 final size:111
Alignment explanation
Indices: 163803--164100 Score: 293
Period size: 112 Copynumber: 2.6 Consensus size: 111
163793 TGGTAGGGTG
* * * *
163803 CATGCCCCATTTTCCTAGGCACGAATGGGTCAGAACGTATGAAA-TAT-AAGTTTCTTTCAAAAT
1 CATG-CCCATTTTCCTAGGCACGAATGGATCA-AATGTATAAAACTATGAA-TTTCTTTGAAAA-
* * * ** * *
163866 TCAACAAATTTGACGTTGTAGGGCTCATAGATTTC-ATAACTGATAAGATA
62 TCAACAAATTTGACGTTGTAAGGCTCAAAAAGATCGA-AACTAACAAGATA
* *
163916 CATGCTC-TATTTCCTAGGCACGAATGGATCGAAATGTAT-AAACTGTGAATTTCTTTGAAAATC
1 CATGCCCAT-TTTCCTAGGCACGAATGGATC-AAATGTATAAAACTATGAATTTCTTTGAAAATC
* *
163979 AAGCAAATCTGATGTTGTAAGGCTCAAAAAGATCGAAACTAACAAGATA
64 AA-CAAATTTGACGTTGTAAGGCTCAAAAAGATCGAAACTAACAAGATA
* *
164028 CGTGCCCATTTTCCTAGGCACTGGATGGATCAAGATGTATAAAAC-ATGAATTTCTTTGAAAATT
1 CATGCCCATTTTCCTAGGCAC-GAATGGATCAA-ATGTATAAAACTATGAATTTCTTTGAAAA-T
*
164092 AAACAAATT
63 CAACAAATT
164101 CAATGTTCTT
Statistics
Matches: 154, Mismatches: 20, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
111 8 0.05
112 95 0.62
113 44 0.29
114 7 0.05
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (111 bp):
CATGCCCATTTTCCTAGGCACGAATGGATCAAATGTATAAAACTATGAATTTCTTTGAAAATCAA
CAAATTTGACGTTGTAAGGCTCAAAAAGATCGAAACTAACAAGATA
Found at i:164944 original size:20 final size:20
Alignment explanation
Indices: 164916--164990 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
164906 TATTACCCAG
* *
164916 ATGTGTCGATACATTCTTTA
1 ATGTATCGATACATTCTTCA
*
164936 ATGTATCGATACA--CGTATGA
1 ATGTATCGATACATTC-T-TCA
164956 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
164976 ATGTATCGATACATT
1 ATGTATCGATACATT
164991 TTGTCTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 44 0.92
21 1 0.02
22 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:165030 original size:91 final size:90
Alignment explanation
Indices: 164870--165039 Score: 234
Period size: 91 Copynumber: 1.9 Consensus size: 90
164860 ACCTAGATGA
* * * * *
164870 ATCGATACATTTTTCAGTTTATCGATACGTTCTGTCTATTACCCAGATGTGTCGATACATTCTTT
1 ATCGATACATTCTTCAATGTATCGATACATTCTGTCTATTACCCAGATGTATCGATACATTCTTT
*
164935 AATGTATCGATACACGTATGAATGT
66 AATGTACCGATACACGTATGAATGT
* * *
164960 ATCGATACATTCTTCAATGTATCGATACATTTTGTCTTTTTACCTAGATGTATCGATACATT-TT
1 ATCGATACATTCTTCAATGTATCGATACATTCTGTC-TATTACCCAGATGTATCGATACATTCTT
165024 TCAATGTACCGATACA
65 T-AATGTACCGATACA
165040 TCTAGTTAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
90 34 0.49
91 35 0.51
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (90 bp):
ATCGATACATTCTTCAATGTATCGATACATTCTGTCTATTACCCAGATGTATCGATACATTCTTT
AATGTACCGATACACGTATGAATGT
Found at i:179547 original size:28 final size:28
Alignment explanation
Indices: 179502--180110 Score: 532
Period size: 28 Copynumber: 21.4 Consensus size: 28
179492 TGCCAGTACA
179502 ACCCTTTTCAAAGCCCACAAGTCAGTGGC
1 ACCC-TTTCAAAGCCCACAAGTCAGTGGC
*
179531 ACCCTTGCAAAGCCCACAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
* * *
179559 ACACTTTCAAAGCCCATAAGTCAGTAGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
** *
179587 ACTATTTTCAAAGCCCACAAGTTAGTGGC
1 AC-CCTTTCAAAGCCCACAAGTCAGTGGC
** * *
179616 ACTATTTCGAGGCCCACAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
* *
179644 ACCATTTTCAAAACCCACAAGTCAGTGGC
1 ACC-CTTTCAAAGCCCACAAGTCAGTGGC
179673 ACCCTTTCAAAGCCCACAAGAT-AGTAGGC
1 ACCCTTTCAAAGCCCACAAG-TCAGT-GGC
*
179702 ACCCTTTTCAAAGCCCACAAGTTAGTGGC
1 ACCC-TTTCAAAGCCCACAAGTCAGTGGC
* * * * *
179731 AACATTTCGAAGCCCATAAGTCAGTGGT
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
* * *
179759 ATCCTTTCAAAGCTCACAAGTCAGCGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
* *
179787 ATCCTTTCAAAGCACC-CAAGTCAGCGGC
1 ACCCTTTCAAAGC-CCACAAGTCAGTGGC
* * * *
179815 ATCCTTTTAAAGCCCACAAATTAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
* *
179843 ATCCTTTCAAAGCTCACAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
* *
179871 ACCATTTCAAAGCCCACAAGTTAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
* * *
179899 ATCATTTCAAAGCCCACAAGTCAATGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
** * *
179927 ACTATTTCAAA-ACC-CAAGTCAATGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
* * * *
179953 ATCATTTCAAAGCCCATAAGTTAGTGG-
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
* *
179980 ---CTTTTAAAGCCCACAAGTCGGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
*
180005 ACTCTTTCAAAGCCCACACAAGTCAGTGGC
1 ACCCTTTCAAAG-CC-CACAAGTCAGTGGC
* *
180035 AACTCTTTTCAAAGCCCACACAAGTTAGTGGC
1 -AC-CCTTTCAAAG-CC-CACAAGTCAGTGGC
* * * *
180067 ACCTTTTTTTAAAGCCTACAATGTCGGTGGC
1 ACC--CTTTCAAAGCCCACAA-GTCAGTGGC
180098 AACCCTTTTCAAA
1 -ACCC-TTTCAAA
180111 TCTCCATTTT
Statistics
Matches: 482, Mismatches: 75, Indels: 44
0.80 0.12 0.07
Matches are distributed among these distances:
24 19 0.04
26 21 0.04
27 6 0.01
28 275 0.57
29 69 0.14
30 37 0.08
31 19 0.04
32 36 0.07
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (28 bp):
ACCCTTTCAAAGCCCACAAGTCAGTGGC
Found at i:181184 original size:20 final size:20
Alignment explanation
Indices: 181159--181215 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
181149 TTTTACCTAG
181159 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*
181179 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
181199 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
181216 GTCTTTTTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:187812 original size:23 final size:23
Alignment explanation
Indices: 187786--187836 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
187776 TGGTACGTTA
187786 TTGATTATATGTTAGTGTT-AAT-T
1 TTGATTATAT-TTAGT-TTCAATAT
*
187809 TTGATTTTATTTAGTTTCAATAT
1 TTGATTATATTTAGTTTCAATAT
187832 TTGAT
1 TTGAT
187837 ATTTAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 8 0.32
23 15 0.60
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (23 bp):
TTGATTATATTTAGTTTCAATAT
Found at i:188975 original size:155 final size:154
Alignment explanation
Indices: 188576--188968 Score: 477
Period size: 155 Copynumber: 2.5 Consensus size: 154
188566 AAGTACACGA
* * * * * * * * *
188576 TACCCCTAAAGGACATAAAAAGGACTATAAAAGGGATAAACCTATCCTAAAGACCCACCTTCGAC
1 TACCCCTAAAGAACTTAAAAAGGATTAGAAAAGGGATGAACCTATCCTAAATATCTACCTTCGGC
* * * * *
188641 GTAAAAACGAACTTAGTGATAACCTAGGACTCGATTCTAAAAAATACCAAAATGCCCATAGGGGG
66 ATAAAAGCGAACTTGGTGATAACCTAGGACTCGATTCTAAAAAATACCAAAATACCCAGAGGGGG
*
188706 TACCTTCAACATAAAAGTATCTAG
131 TACCTTCAACATAAAAGTACCTAG
* * * * *
188730 TACCCCCAAAGAACTTACAGAGGATTGGAAAAGAGATGAACCTATCCTAAATATCTACCTTCGGC
1 TACCCCTAAAGAACTTAAAAAGGATTAGAAAAGGGATGAACCTATCCTAAATATCTACCTTCGGC
** * *
188795 ATAAAAGC-AGACCCGGTGATAACCTAGGACTCGATTTTGAAAAATTACCAAAATACTCC-GAGG
66 ATAAAAGCGA-ACTTGGTGATAACCTAGGACTCGATTCT-AAAAAATACCAAAATAC-CCAGAGG
* * *
188858 GGGTACCTTCGACGTAAAAGTACCTGG
128 GGGTACCTTCAACATAAAAGTACCTAG
*
188885 TACCCCTAAAGAACTTAAAAAGGATTAGAAAAGGGATGAATCTAT-CTGAAATATCTACCTTCGG
1 TACCCCTAAAGAACTTAAAAAGGATTAGAAAAGGGATGAACCTATCCT-AAATATCTACCTTCGG
188949 CATAAAAGCGAACTTGGTGA
65 CATAAAAGCGAACTTGGTGA
188969 CGACCTAAGA
Statistics
Matches: 199, Mismatches: 35, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
153 1 0.01
154 83 0.42
155 112 0.56
156 3 0.02
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (154 bp):
TACCCCTAAAGAACTTAAAAAGGATTAGAAAAGGGATGAACCTATCCTAAATATCTACCTTCGGC
ATAAAAGCGAACTTGGTGATAACCTAGGACTCGATTCTAAAAAATACCAAAATACCCAGAGGGGG
TACCTTCAACATAAAAGTACCTAG
Found at i:189344 original size:13 final size:13
Alignment explanation
Indices: 189326--189382 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
189316 CATAAGTGCC
189326 GTATCGATACAAT
1 GTATCGATACAAT
189339 GTATCGATACATAAGTATT
1 GTATCGATAC---A--A-T
189358 GTATCGATACAAT
1 GTATCGATACAAT
*
189371 GTATCGCTACAA
1 GTATCGATACAA
189383 AGCTACTGCC
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.30
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:189345 original size:32 final size:32
Alignment explanation
Indices: 189304--189381 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
189294 ACAAACAGTA
*
189304 AATGTATCGATACATAAGTGCCGTATCGATAC
1 AATGTATCGATACATAAGTACCGTATCGATAC
**
189336 AATGTATCGATACATAAGTATTGTATCGATAC
1 AATGTATCGATACATAAGTACCGTATCGATAC
*
189368 AATGTATCGCTACA
1 AATGTATCGATACA
189382 AAGCTACTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (32 bp):
AATGTATCGATACATAAGTACCGTATCGATAC
Found at i:189362 original size:19 final size:19
Alignment explanation
Indices: 189284--189368 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 19
189274 TTTCAACAAT
*
189284 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACATA-AGT-A
* *
189305 ATGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTA
**
189324 CCGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
189338 -TGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
189356 TTGTATCGATACA
1 TTGTATCGATACA
189369 ATGTATCGCT
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
13 10 0.20
16 2 0.04
18 1 0.02
19 22 0.43
20 3 0.06
21 13 0.25
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:189423 original size:20 final size:20
Alignment explanation
Indices: 189398--189452 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
189388 CTGCCAAGGA
189398 AATGTATCGATACATT-ATTC
1 AATGTATCGATACATTGA-TC
189418 AATGTATCGATACATTGATC
1 AATGTATCGATACATTGATC
**
189438 TTTGTATCGATACAT
1 AATGTATCGATACAT
189453 CTGGGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:193057 original size:32 final size:35
Alignment explanation
Indices: 193016--193102 Score: 103
Period size: 36 Copynumber: 2.6 Consensus size: 35
193006 GCTATCTTTC
193016 AAGGCTAAGATAGAAACCT-T-CCTATCTTTT-CA
1 AAGGCTAAGATAGAAACCTCTCCCTATCTTTTCCA
**
193048 CGGGCTAAGATAG-AACCTTTCTCCCTATCTTTTCCA
1 AAGGCTAAGATAGAAACC--TCTCCCTATCTTTTCCA
193084 AAGGCTAAGATA-AAACCTC
1 AAGGCTAAGATAGAAACCTC
193103 ACAATCACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
31 4 0.09
32 11 0.24
33 1 0.02
34 3 0.07
35 10 0.22
36 16 0.36
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (35 bp):
AAGGCTAAGATAGAAACCTCTCCCTATCTTTTCCA
Found at i:193599 original size:24 final size:24
Alignment explanation
Indices: 193567--193638 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
193557 ACAGTGTATC
*
193567 GATACATGAATAGTGATAAATAGT
1 GATACATGAATAGTGATAAACAGT
*
193591 GATACATGAATAGTGATGAACAGT
1 GATACATGAATAGTGATAAACAGT
* *
193615 TATACATGAATAGTGATGAACAGT
1 GATACATGAATAGTGATAAACAGT
193639 AATGTATCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (24 bp):
GATACATGAATAGTGATAAACAGT
Found at i:193602 original size:14 final size:14
Alignment explanation
Indices: 193567--193631 Score: 56
Period size: 14 Copynumber: 5.2 Consensus size: 14
193557 ACAGTGTATC
193567 GATACATGAATAGT
1 GATACATGAATAGT
193581 GAT--A--AATAGT
1 GATACATGAATAGT
193591 GATACATGAATAGT
1 GATACATGAATAGT
*
193605 G----ATGAACAGT
1 GATACATGAATAGT
*
193615 TATACATGAATAGT
1 GATACATGAATAGT
193629 GAT
1 GAT
193632 GAACAGTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
10 17 0.44
12 2 0.05
14 20 0.51
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (14 bp):
GATACATGAATAGT
Found at i:195629 original size:23 final size:23
Alignment explanation
Indices: 195597--195675 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
195587 TGTTTGATGT
* *
195597 TTGCTGTTTGCTGTTGCTTTTGC
1 TTGCTATTTGCTGCTGCTTTTGC
* *
195620 TTGTTATTTGCTGCTGCTCTTGC
1 TTGCTATTTGCTGCTGCTTTTGC
* * *
195643 TTGCTCTTTCCTGCTGCTTTTTAC
1 TTGCTATTTGCTGCTGC-TTTTGC
195667 TTGCTATTT
1 TTGCTATTT
195676 TCTTGCTTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 33 0.73
24 12 0.27
ACGTcount: A:0.04, C:0.22, G:0.19, T:0.56
Consensus pattern (23 bp):
TTGCTATTTGCTGCTGCTTTTGC
Found at i:196824 original size:16 final size:16
Alignment explanation
Indices: 196805--196835 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
196795 TGTCACACAT
*
196805 AAAAAAATCAAAAATC
1 AAAAAAATAAAAAATC
196821 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
196836 AATTTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAAATAAAAAATC
Found at i:201858 original size:13 final size:13
Alignment explanation
Indices: 201840--201865 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
201830 CAATTTTTTG
201840 TGTATCGATACAT
1 TGTATCGATACAT
201853 TGTATCGATACAT
1 TGTATCGATACAT
201866 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:204233 original size:21 final size:21
Alignment explanation
Indices: 204209--204255 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
204199 TTTAATGCTG
204209 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
204229 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
204250 ATTTTG
1 ATTTTG
204256 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:204394 original size:13 final size:13
Alignment explanation
Indices: 204376--204414 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
204366 ATAATCACCC
*
204376 TGTATCGATACAG
1 TGTATCGATACAA
*
204389 TGTATCGTTACAA
1 TGTATCGATACAA
204402 TGTATCGATACAA
1 TGTATCGATACAA
204415 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:204425 original size:20 final size:20
Alignment explanation
Indices: 204400--204478 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
204390 GTATCGTTAC
204400 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
204420 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
204445 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
204465 CATGTATCGATACA
1 AATGTATCGATACA
204479 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:206515 original size:15 final size:15
Alignment explanation
Indices: 206495--206525 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
206485 ATTTCGTTTG
*
206495 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
206510 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
206525 G
1 G
206526 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:208358 original size:21 final size:21
Alignment explanation
Indices: 208329--208373 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
208319 AAGTTTTCAT
*
208329 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
208349 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
208371 TTT
1 TTT
208374 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:210027 original size:13 final size:13
Alignment explanation
Indices: 210009--210035 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
209999 ACAATTTTTT
210009 TTGTATCGATACA
1 TTGTATCGATACA
210022 TTGTATCGATACA
1 TTGTATCGATACA
210035 T
1 T
210036 ACTTGCTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:212964 original size:6 final size:6
Alignment explanation
Indices: 212955--213010 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
212945 TTTATGCTTA
*
212955 TTAATT TTAATT TTAATT TT--TT TCTAATT TTAGATT TTTATT TT-ATT
1 TTAATT TTAATT TTAATT TTAATT T-TAATT TTA-ATT TTAATT TTAATT
*
213002 TTATTT TTA
1 TTAATT TTA
213011 CACTAGTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
4 3 0.07
5 6 0.14
6 26 0.60
7 8 0.19
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (6 bp):
TTAATT
Found at i:213924 original size:156 final size:155
Alignment explanation
Indices: 213629--213968 Score: 402
Period size: 156 Copynumber: 2.2 Consensus size: 155
213619 TTTCTAGTTG
* * *
213629 TTTTGC-AATTATAGAAAGTTCAGGGACTAAATTACAAAAAGTTTGAAATTTTTTTCTTTGAGTA
1 TTTTGCAAATTATAGAAAGTTCAAGGACTAAATTACAAAAAATTTGAAATTTTTTTCTTTGAATA
* * * * * * *
213693 TGCTTGCTTGGCGGAAAGTCCCTAGTGCCATAGGAGGATAGTTTCATGCATTTTTAAACACGTTT
66 TCCTTGCTTGGCCGAAAGTCCCTAATACCATAAGAGGATAGTTTCATGCATTTCTAAACACATTT
*
213758 TAGGCTTTTTAGCATG-TTAAGGACCT
131 TAGGCCTTTTA--ATGATTAAGGACCT
*
213784 TTTTGCAAATTTTAGAAAGTTCAAGGACTAAATTGTA-AAAAAATTT-AAATTTTTTTCTTTGAA
1 TTTTGCAAATTATAGAAAGTTCAAGGACTAAA-T-TACAAAAAATTTGAAATTTTTTTCTTTGAA
* *
213847 TATCCTTGCTTGGCCGAGAGTCCCTAATACCATAAGAGGACT-GTTTCATGCATTTCTAAACATA
64 TATCCTTGCTTGGCCGAAAGTCCCTAATACCATAAGAGGA-TAGTTTCATGCATTTCTAAACACA
* * *
213911 TTTTGGGCCTTTTAATGTATTAGGGACTT
128 TTTTAGGCCTTTTAATG-ATTAAGGACCT
* * * *
213940 TTTTACAAATTCTAAAAAGTTTAAGGACT
1 TTTTGCAAATTATAGAAAGTTCAAGGACT
213969 GACTTAAAAT
Statistics
Matches: 158, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
154 3 0.02
155 6 0.04
156 137 0.87
157 10 0.06
158 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (155 bp):
TTTTGCAAATTATAGAAAGTTCAAGGACTAAATTACAAAAAATTTGAAATTTTTTTCTTTGAATA
TCCTTGCTTGGCCGAAAGTCCCTAATACCATAAGAGGATAGTTTCATGCATTTCTAAACACATTT
TAGGCCTTTTAATGATTAAGGACCT
Found at i:215709 original size:50 final size:51
Alignment explanation
Indices: 215635--215779 Score: 213
Period size: 50 Copynumber: 2.9 Consensus size: 51
215625 AAACTCACAT
* *
215635 TTTTACCTAGATGTATCAATACATTTTTCAATATATCGATACCTTCTG-TA
1 TTTTACCTAGATGTATCGATACATTTTTCAATATATCGATACATTCTGTTA
* *
215685 TTTTACCTAGATGTATCGATACA-TTCTCTAATATATCGATACATTCTGTTT
1 TTTTACCTAGATGTATCGATACATTTTTC-AATATATCGATACATTCTGTTA
* *
215736 TTTTACCTAGATGTATCGATACATTTTTCAATGTATTGATACAT
1 TTTTACCTAGATGTATCGATACATTTTTCAATATATCGATACAT
215780 CTAGTTAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
49 4 0.05
50 40 0.47
51 37 0.44
52 4 0.05
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (51 bp):
TTTTACCTAGATGTATCGATACATTTTTCAATATATCGATACATTCTGTTA
Found at i:220650 original size:20 final size:20
Alignment explanation
Indices: 220625--220662 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
220615 GGTCCCAATT
220625 AGTGAATATATTGATACATA
1 AGTGAATATATTGATACATA
*
220645 AGTGAATGTATTGATACA
1 AGTGAATATATTGATACA
220663 GGTCTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.34
Consensus pattern (20 bp):
AGTGAATATATTGATACATA
Found at i:226054 original size:21 final size:21
Alignment explanation
Indices: 226030--226070 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
226020 TTTTGCCTAC
* *
226030 ATGTATTGATATATGCAAGGG
1 ATGTATCGATACATGCAAGGG
226051 ATGTATCGATACATGCAAGG
1 ATGTATCGATACATGCAAGG
226071 TCCCAACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGCAAGGG
Found at i:226155 original size:20 final size:20
Alignment explanation
Indices: 226105--226157 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
226095 TTCAGCAATT
*
226105 TGTATCGATAAATAAGGCAA
1 TGTATCGATACATAAGGCAA
226125 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAAG-GCAA
226145 TGTATCGATACAT
1 TGTATCGATACAT
226158 GCTTGAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATAAGGCAA
Found at i:226164 original size:20 final size:21
Alignment explanation
Indices: 226105--226177 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 21
226095 TTCAGCAATT
* *
226105 TGTATCGATAAATAAG-GCAA
1 TGTATCGATACATAAGTGAAA
226125 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAAGTGAAA
***
226145 TGTATCGATACATGCTTGAAA
1 TGTATCGATACATAAGTGAAA
*
226166 TATATCGATACA
1 TGTATCGATACA
226178 GGACCATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 32 0.70
21 14 0.30
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATAAGTGAAA
Found at i:226291 original size:52 final size:52
Alignment explanation
Indices: 226213--226352 Score: 192
Period size: 52 Copynumber: 2.7 Consensus size: 52
226203 TCTAGAAAGA
* * *
226213 AAATGTATCGATACATTTTTCATTGTATTGATACATTCTGGGTTTATGACAC-
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTATGAC-CT
* * *
226265 AAATGTATCAATACATTCTTCATTGTATCGATACATTCTATGTTTTTGACCT
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTATGACCT
* *
226317 AAATGTATCGATACATTCTTCAATCTATCGATACAT
1 AAATGTATCGATACATTCTTCATTGTATCGATACAT
226353 CCATTTAAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 1 0.01
52 77 0.99
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.41
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTATGACCT
Found at i:228689 original size:10 final size:10
Alignment explanation
Indices: 228674--228703 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
228664 TTCTTTATAA
228674 AAAATTTATC
1 AAAATTTATC
228684 AAAATTTATC
1 AAAATTTATC
228694 AAAATTTATC
1 AAAATTTATC
228704 GGGGATACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (10 bp):
AAAATTTATC
Found at i:228869 original size:97 final size:97
Alignment explanation
Indices: 228704--228939 Score: 316
Period size: 97 Copynumber: 2.4 Consensus size: 97
228694 AAAATTTATC
* *
228704 GGGGATACTCCAACCCAATTTTTCGAAGGGATACTCCAA-CCTCGTTTTTAAACTTGTCAAAATT
1 GGGGATACTCCAACCCCATTCTTCGAAGGGATACTCCAACCCTCGTTTTTAAACTTGTCAAAATT
228768 TAAATCTTATTTTC-ATATAAATTGTCATCGTT
66 TAAATCTTATTTTCGAT-TAAATTGTCATCGTT
* * * *
228800 GGGGATACTCCAACCCCATTCTTCTGAGGGGATACTCCAACCCT-TTTTTTTAACTTGTCAAGAT
1 GGGGATACTCCAACCCCATTCTTC-GAAGGGATACTCCAACCCTCGTTTTTAAACTTGTCAAAAT
* **
228864 TTAAATCTTATTTTCGCTTGGATTGTCATCGTT
65 TTAAATCTTATTTTCGATTAAATTGTCATCGTT
* * *
228897 GGGGACACTACAACCCCATTTCTTCGAAGGGATACTCTAACCC
1 GGGGATACTCCAACCCCA-TTCTTCGAAGGGATACTCCAACCC
228940 CATTTTCAAC
Statistics
Matches: 123, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
96 22 0.18
97 91 0.74
98 10 0.08
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (97 bp):
GGGGATACTCCAACCCCATTCTTCGAAGGGATACTCCAACCCTCGTTTTTAAACTTGTCAAAATT
TAAATCTTATTTTCGATTAAATTGTCATCGTT
Found at i:239474 original size:165 final size:164
Alignment explanation
Indices: 239255--239681 Score: 590
Period size: 165 Copynumber: 2.6 Consensus size: 164
239245 AATTACAGAG
* * * * * *
239255 TTTTCTTCTCTGTAAATTTTTTCGAGAGCATTTTACTT-GTTCTTTAAATTTTAAACTTCATAAA
1 TTTTCTACT-TGTAAATTTTTTCGGGAGGATTTTTCTTGGTT-TTTAATTTTTAAAATTCATAAA
*
239319 ATATTATTATTTATTTCATATTAATTGAATTTTCAAAAATTCATTCATTTCCATAAATTTTGAAT
64 ATATTATTATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTCCATAAATTTTGAAT
*
239384 TTTTCCTTGAAATACT-TTTTTTTCTAAAATATGAAA
129 TTTTCCTTGAAATACTCCTTTTTTC-AAAATATGAAA
*
239420 TTTTCTACTTCGTAAATTTTTTCGGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAA
1 TTTTCTACTT-GTAAATTTTTTCGGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAA
* *
239485 TATTATTATTTATTTCACATTAATTTAATTTTCAAAAATTCATTCATTTCCATAAATTTTGAATT
65 TATTATTATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTCCATAAATTTTGAATT
* * * * *
239550 TTTTCTTGAAATTCTCCTTTTTTCGAAATATGGAG
130 TTTCCTTGAAATACTCCTTTTTTCAAAATATGAAA
* * * *
239585 TTTTCTACTTGATAATTTTTTTGGAGGA-GATTTTTCTTGGTTTTTGATCTTTAAAATTCATAAA
1 TTTTCTACTTG-TAAATTTTTTCG-GGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAA
*
239649 ATATTATTATTTATTTCATATTAAATCAATTTT
64 ATATTATTATTTATTTCATATTAATTCAATTTT
239682 AACATGAGTT
Statistics
Matches: 234, Mismatches: 23, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
164 2 0.01
165 219 0.94
166 13 0.06
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (164 bp):
TTTTCTACTTGTAAATTTTTTCGGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAAT
ATTATTATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTCCATAAATTTTGAATTT
TTCCTTGAAATACTCCTTTTTTCAAAATATGAAA
Found at i:240205 original size:15 final size:15
Alignment explanation
Indices: 240182--240219 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
240172 AAGTTCAGCT
*
240182 GAAAGAAGAGAGAGA
1 GAAAAAAGAGAGAGA
240197 GAAAAAAGAGAGAGA
1 GAAAAAAGAGAGAGA
240212 -AAAAAAGA
1 GAAAAAAGA
240220 AGAAAATAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
GAAAAAAGAGAGAGA
Found at i:240208 original size:13 final size:13
Alignment explanation
Indices: 240190--240225 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
240180 CTGAAAGAAG
240190 AGAGAGAGAAAAA
1 AGAGAGAGAAAAA
240203 AGAGAGAGAAAAA
1 AGAGAGAGAAAAA
240216 A-AGA-AGAAAA
1 AGAGAGAGAAAA
240226 TAGGTAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 6 0.26
12 3 0.13
13 14 0.61
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AGAGAGAGAAAAA
Found at i:240247 original size:22 final size:21
Alignment explanation
Indices: 240196--240247 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
240186 GAAGAGAGAG
240196 AGAAAAAAGAGAGAGAAAAAA
1 AGAAAAAAGAGAGAGAAAAAA
* *
240217 AGAAGAAAATAG-GTAGAAAAATT
1 AGAA-AAAAGAGAG-AGAAAAA-A
240240 AGAAAAAA
1 AGAAAAAA
240248 CAAGGCTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.19
22 17 0.65
23 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (21 bp):
AGAAAAAAGAGAGAGAAAAAA
Found at i:241425 original size:162 final size:162
Alignment explanation
Indices: 241153--241455 Score: 430
Period size: 162 Copynumber: 1.9 Consensus size: 162
241143 AAAATCAAAC
* *
241153 AATATTTATTTTTTCTTATCTTTTATATTCCTATGGGCATTCGTAGGGGTATAAAAGATTTTAAA
1 AATATTTATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGGTATAAAAGATTTTAAA
* * * *
241218 AACCTTTTGTATTCTTTCAGGCTTTCATTAGGGTACGAAATGGTATTTACAAAAATAAATAAAAT
66 AACCTTTTGTATCCTTTCAGGCATCCATTAAGGTACGAAATGGTATTTACAAAAATAAATAAAAT
*
241283 TAAATTAAATTGGTATTATTAGGATAAATTCT
131 AAAATTAAATTGGTATTATTAGGATAAATTCT
241315 AATATTTATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGGTATAAAAG-TTTTCAA
1 AATATTTATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGGTATAAAAGATTTT-AA
** * * * ***
241379 AAA-CTTTTCGTATCCTTTTGGGCATCCATTAAGTTATGAGATGGTATTTTTGAAAATAAATAAA
65 AAACCTTTT-GTATCCTTTCAGGCATCCATTAAGGTACGAAATGGTATTTACAAAAATAAATAAA
*
241443 ATAAAATTGAATT
129 ATAAAATTAAATT
241456 AATACTTTCG
Statistics
Matches: 123, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
161 9 0.07
162 114 0.93
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (162 bp):
AATATTTATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGGTATAAAAGATTTTAAA
AACCTTTTGTATCCTTTCAGGCATCCATTAAGGTACGAAATGGTATTTACAAAAATAAATAAAAT
AAAATTAAATTGGTATTATTAGGATAAATTCT
Found at i:245351 original size:51 final size:51
Alignment explanation
Indices: 245293--245402 Score: 150
Period size: 51 Copynumber: 2.2 Consensus size: 51
245283 ACGGGGTCGG
* *
245293 AGTATCCCCGATTGT-GGAAGATTAATATTTTGGAAATAAAATCAGGGTTGA
1 AGTATCCCCGATTATGGGAA-ATCAATATTTTGGAAATAAAATCAGGGTTGA
* ** *
245344 AGTATCCCCGATTATGGGAAATCAATGTTTTGGAAATAAAATTGGGGTTGG
1 AGTATCCCCGATTATGGGAAATCAATATTTTGGAAATAAAATCAGGGTTGA
245395 AGTATCCC
1 AGTATCCC
245403 TTCGAAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 48 0.92
52 4 0.08
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
AGTATCCCCGATTATGGGAAATCAATATTTTGGAAATAAAATCAGGGTTGA
Found at i:245429 original size:79 final size:79
Alignment explanation
Indices: 245335--245729 Score: 391
Period size: 79 Copynumber: 5.0 Consensus size: 79
245325 GAAATAAAAT
* * ** ***
245335 CAGGGTTGAAGTATCCCCGATTATGGGAAATCAATGTTTTGGAAATAAAATTGGGGTTGGAGTAT
1 CAGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATTGGGGTTGGAGTAT
245400 CCCTTCGAAAATAA
66 CCCTTCGAAAATAA
* * * * * * * *
245414 CAGAGTTGGAGTATCCTCGATTGTGAAAAATCGGTGTTTTAGAAAAAAAACTGAGGTTGAAGTAT
1 CAGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATTGGGGTTGGAGTAT
*
245479 CCCCTCGAAAATAA
66 CCCTTCGAAAATAA
* * * * * *
245493 CAGGGATGGAATATCCCCAATTGTCAAAAATTGGTATTTTGGAAATAAAATCGGGGTTGGAGTAT
1 CAGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATTGGGGTTGGAGTAT
*
245558 CTCTTC-AGAAATAA
66 CCCTTCGA-AAATAA
* * * * * *
245572 CGGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGAAAATAAAATTTGGGTTAGAATAT
1 CAGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATTGGGGTTGGAGTAT
*
245637 CCCCTCG-AAATAA
66 CCCTTCGAAAATAA
* * * * * *** *
245650 CAGGGTTAGAGTATCCTCGATTATGAAAAATTAGTATTTTGGAAATAAAGCCGGGGTGGGAGTAT
1 CAGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATTGGGGTTGGAGTAT
*
245715 CTCCTTAG-AAATAA
66 C-CCTTCGAAAATAA
245729 C
1 C
245730 GGGGAGGTAG
Statistics
Matches: 254, Mismatches: 59, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
78 58 0.23
79 196 0.77
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (79 bp):
CAGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATTGGGGTTGGAGTAT
CCCTTCGAAAATAA
Found at i:245472 original size:130 final size:129
Alignment explanation
Indices: 245233--245482 Score: 313
Period size: 130 Copynumber: 1.9 Consensus size: 129
245223 CAATGGTAAA
* * *
245233 AAATCGATGTTTTGGAAATAAAACTGGGTTAAAGTATCCCCTCGAAAATAACGGGGTCGGAGTAT
1 AAATCAATGTTTTGGAAATAAAACTGGGTTAAAGTATCCCCTCGAAAATAACAGAGTCGGAGTAT
* * * * *
245298 CCCCGATTGTGGAAGATTAATATTTTGGAAATAAAATCAGGGTTGAAGTATCCCCGATTATGGG
66 CCCCGATTGTGAAAAATCAATATTTTAGAAAAAAAATCAGGGTTGAAGTATCCCCGATTATGGG
* ** * *
245362 AAATCAATGTTTTGGAAATAAAATTGGGGTTGGAGTATCCCTTCGAAAATAACAGAGTTGGAGTA
1 AAATCAATGTTTTGGAAATAAAACT-GGGTTAAAGTATCCCCTCGAAAATAACAGAGTCGGAGTA
* ** * *
245427 TCCTCGATTGTGAAAAATCGGTGTTTTAGAAAAAAAA-CTGAGGTTGAAGTATCCCC
65 TCCCCGATTGTGAAAAATCAATATTTTAGAAAAAAAATCAG-GGTTGAAGTATCCCC
245483 TCGAAAATAA
Statistics
Matches: 101, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
129 25 0.25
130 76 0.75
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (129 bp):
AAATCAATGTTTTGGAAATAAAACTGGGTTAAAGTATCCCCTCGAAAATAACAGAGTCGGAGTAT
CCCCGATTGTGAAAAATCAATATTTTAGAAAAAAAATCAGGGTTGAAGTATCCCCGATTATGGG
Found at i:245716 original size:157 final size:157
Alignment explanation
Indices: 245335--245733 Score: 477
Period size: 158 Copynumber: 2.5 Consensus size: 157
245325 GAAATAAAAT
** * * * *
245335 CAGGGTTGAAGTATCCCCGATTATGGGAAATCAATGTTTTGGAAATAAAATTGGGGTTGGAGTAT
1 CAGGGTTG-AGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAATCGGGGTTGGAGTAT
* * * * *
245400 CCCTTC-GAAAATAACAGAGTTGGAGTATCCTCGATTGTGAAAAATCGGTGTTTTAGAAAAAAAA
65 CTCTTCAG-AAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGGTGTTTTAGAAAAAAAA
245464 CTGAGGTTGAAGTATCCCCTCGAAAATAA
129 CTGAGGTTGAAGTATCCCCTCGAAAATAA
* * * * * *
245493 CAGGGATGGAATATCCCCAATTGTCAAAAATTGGTATTTTGGAAATAAAATCGGGGTTGGAGTAT
1 CAGGG-TTGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAATCGGGGTTGGAGTAT
*
245558 CTCTTCAGAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTT-GAAAATAAAA
65 CTCTTCAGAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGGTGTTTTAGAAAA-AAAA
*
245622 TTTG-GGTTAGAA-TATCCCCTCG-AAATAA
129 -CTGAGGTT-GAAGTATCCCCTCGAAAATAA
* ** *
245650 CAGGGTTAGAGTATCCTCGATTATGAAAAATTAGTATTTTGGAAATAAAGCCGGGGTGGGAGTAT
1 CAGGGTT-GAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAATCGGGGTTGGAGTAT
245715 CTCCTT-AGAAATAACGGGG
65 CT-CTTCAGAAATAACGGGG
245734 AGGTAGCATG
Statistics
Matches: 205, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
156 1 0.00
157 79 0.39
158 117 0.57
159 8 0.04
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (157 bp):
CAGGGTTGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAATCGGGGTTGGAGTATC
TCTTCAGAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGGTGTTTTAGAAAAAAAACT
GAGGTTGAAGTATCCCCTCGAAAATAA
Found at i:247147 original size:50 final size:50
Alignment explanation
Indices: 247093--247195 Score: 134
Period size: 50 Copynumber: 2.1 Consensus size: 50
247083 ATATAGCGAC
* * *
247093 ACATCTGGGTAAAACCTAGAATGTATCGATACAACGAACAATGTATCGAT
1 ACATCTAGGTAAAACCCAGAATGTATCGATACAACGAACAATGTATCAAT
* * * * *
247143 ACATCTAGGTGAAACCCAGAATGTATCTATATAATGAAGAATGTATCAAT
1 ACATCTAGGTAAAACCCAGAATGTATCGATACAACGAACAATGTATCAAT
247193 ACA
1 ACA
247196 GATTATGCAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (50 bp):
ACATCTAGGTAAAACCCAGAATGTATCGATACAACGAACAATGTATCAAT
Found at i:247837 original size:43 final size:42
Alignment explanation
Indices: 247752--247867 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 42
247742 AGGAGTATGC
* * *
247752 CCTGC-CCTTCGAAGACAAAGGAAAAGA-G-AATGAAATGGGT
1 CCTGCTCCTT-GAAGACATAGGAAAAAAGGAAATTAAATGGGT
*
247792 CCTGCTCCTT-AAGGACATAGGAAAAAAAGGAAATTAAATGTGT
1 CCTGCTCCTTGAA-GACATAGG-AAAAAAGGAAATTAAATGGGT
*
247835 CCTGCTCCTTGAAGACATAGGAGAAAAGGAAAT
1 CCTGCTCCTTGAAGACATAGGAAAAAAGGAAAT
247868 AAAGTGCGTC
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
39 2 0.03
40 12 0.18
41 9 0.14
42 12 0.18
43 28 0.43
44 2 0.03
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (42 bp):
CCTGCTCCTTGAAGACATAGGAAAAAAGGAAATTAAATGGGT
Found at i:248056 original size:62 final size:61
Alignment explanation
Indices: 247909--248142 Score: 278
Period size: 62 Copynumber: 3.8 Consensus size: 61
247899 AAAAGGAAAT
* * * * * *
247909 AAAGTGCATCTTGCTCCTTGGGGACTAGAA-GGTGCCACCAACT--TATGGGCTTTGAAAAGA
1 AAAG-GCATCCTGCTCTTTGAGGACTA-AAGGGTGCCACCAACTCGTGTGGACTTTGAAAAAA
* *
247969 AAAGGCATCCTACTCTTTGATGACTAAAGGGTGCCACCAACTCGTGTGGAC-TTGAAATGAAA
1 AAAGGCATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGACTTTGAAA--AAA
** * *
248031 AAAGGTGTCCTGCTCTTTGGGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAGAAAAA
1 AAAGGCATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGACTTTGA-AAAAA
*
248093 AAAGGCATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGA
1 AAAGGCATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGA
248143 AAATGATTTT
Statistics
Matches: 148, Mismatches: 19, Indels: 12
0.83 0.11 0.07
Matches are distributed among these distances:
58 2 0.01
59 30 0.20
60 10 0.07
61 5 0.03
62 95 0.64
63 4 0.03
64 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (61 bp):
AAAGGCATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGACTTTGAAAAAA
Found at i:248140 original size:124 final size:121
Alignment explanation
Indices: 247920--248142 Score: 349
Period size: 124 Copynumber: 1.8 Consensus size: 121
247910 AAGTGCATCT
*
247920 TGCTCCTTGGGGACTAGAAGGTGCCACCAACTTATGGGCTTTGAAAAGAAAAGGCATCCTACTCT
1 TGCTCCTTGGGGACTAGAAGGTGCCACCAACTTATGGGCTTTGAAAAAAAAAGGCATCCTACTCT
*
247985 TTGATGACTAAAGGGTGCCACCAACTCGTGTGGACTTGAAATGAAAAAAGGTGTCC
66 TTGAGGACTAAAGGGTGCCACCAACTCGTGTGGACTTGAAATGAAAAAAGGTGTCC
* * *
248041 TGCTCTTTGGGGACTA-AAGGGTGCCACCAACTCGTGTGGGCTTTGAGAAAAAAAAGGCATCCTG
1 TGCTCCTTGGGGACTAGAA-GGTGCCACCAACT--TATGGGCTTTGA-AAAAAAAAGGCATCCTA
*
248105 CTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGA
62 CTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGA
248143 AAATGATTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
120 2 0.02
121 28 0.30
123 11 0.12
124 51 0.55
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (121 bp):
TGCTCCTTGGGGACTAGAAGGTGCCACCAACTTATGGGCTTTGAAAAAAAAAGGCATCCTACTCT
TTGAGGACTAAAGGGTGCCACCAACTCGTGTGGACTTGAAATGAAAAAAGGTGTCC
Found at i:248406 original size:50 final size:50
Alignment explanation
Indices: 248324--248487 Score: 238
Period size: 50 Copynumber: 3.3 Consensus size: 50
248314 AAAATGCCTG
* * * * *
248324 AATGTATCGATATATCTAGGTAAAACCTAGAATGTATCGATACAATGAAC
1 AATGTATCGATACATCTGGGTGAAACCTAGAATATATCAATACAATGAAC
* * *
248374 AATGTATCAATACATCTGGGTGAAACCCAGAATATATCAATACAACGAAC
1 AATGTATCGATACATCTGGGTGAAACCTAGAATATATCAATACAATGAAC
* *
248424 AATGTATCGATACACCTGGGTGAAACCTAGAATATATCAATACAATGAAG
1 AATGTATCGATACATCTGGGTGAAACCTAGAATATATCAATACAATGAAC
248474 AATGTATCGATACA
1 AATGTATCGATACA
248488 AATTGTGAAA
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 101 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (50 bp):
AATGTATCGATACATCTGGGTGAAACCTAGAATATATCAATACAATGAAC
Found at i:252780 original size:21 final size:21
Alignment explanation
Indices: 252733--252787 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
252723 TATAAACAGT
252733 AAATGTATCGATACGTAAGTG
1 AAATGTATCGATACGTAAGTG
***
252754 -AATGTATCGATACGTGCTTG
1 AAATGTATCGATACGTAAGTG
252774 AAATGTATCGATAC
1 AAATGTATCGATAC
252788 AAAATCACCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (21 bp):
AAATGTATCGATACGTAAGTG
Found at i:255318 original size:26 final size:26
Alignment explanation
Indices: 255269--255319 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
255259 TTTGATTGTC
*
255269 GGGGATACTCAACCCCGCTCTTTTAA
1 GGGGATACTCAACCCCACTCTTTTAA
255295 GGGGATACTCCAACCCCACT-TTTTA
1 GGGGATACT-CAACCCCACTCTTTTA
255320 TCAAACTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (26 bp):
GGGGATACTCAACCCCACTCTTTTAA
Found at i:266519 original size:46 final size:46
Alignment explanation
Indices: 266448--266536 Score: 137
Period size: 46 Copynumber: 1.9 Consensus size: 46
266438 TTTTGTCCAA
*
266448 ATGTATTGATACATTTAAGGATGTATCGATATAAGGTCCCAACAGG
1 ATGTATTGATACATTTAAGGATGTATCAATATAAGGTCCCAACAGG
266494 ATGTATCT-ATACATTTAA-GACTGTATCAATATAAGGTCCCAAC
1 ATGTAT-TGATACATTTAAGGA-TGTATCAATATAAGGTCCCAAC
266537 GGTCAAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
45 2 0.05
46 37 0.93
47 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (46 bp):
ATGTATTGATACATTTAAGGATGTATCAATATAAGGTCCCAACAGG
Found at i:267639 original size:13 final size:13
Alignment explanation
Indices: 267621--267646 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
267611 TACAGCAAGT
267621 ATGTATCGATACA
1 ATGTATCGATACA
267634 ATGTATCGATACA
1 ATGTATCGATACA
267647 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:269890 original size:21 final size:21
Alignment explanation
Indices: 269857--269901 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
269847 TTGCAAGTTG
*
269857 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
269879 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
269899 AAA
1 AAA
269902 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:271725 original size:15 final size:15
Alignment explanation
Indices: 271705--271735 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
271695 TAAAAATGTC
*
271705 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
271720 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
271735 C
1 C
271736 CAAGCGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:273875 original size:21 final size:20
Alignment explanation
Indices: 273851--273897 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
273841 AAATCTTTTG
*
273851 CAAAATACTT-GTTTTTCACTT
1 CAAAATACTTCATTTTTCA--T
*
273872 CAAATTACTTCATTTTTCAT
1 CAAAATACTTCATTTTTCAT
273892 CAAAAT
1 CAAAAT
273898 CAGCATCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 9 0.41
22 7 0.32
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.45
Consensus pattern (20 bp):
CAAAATACTTCATTTTTCAT
Found at i:279574 original size:46 final size:46
Alignment explanation
Indices: 279503--279591 Score: 137
Period size: 46 Copynumber: 1.9 Consensus size: 46
279493 TTTTGTCCAA
*
279503 ATGTATTGATACATTTAAGGATGTATCGATATAAGGTCCCAACAGG
1 ATGTATTGATACATTTAAGGATGTATCAATATAAGGTCCCAACAGG
279549 ATGTATCT-ATACATTTAA-GACTGTATCAATATAAGGTCCCAAC
1 ATGTAT-TGATACATTTAAGGA-TGTATCAATATAAGGTCCCAAC
279592 GGTCAAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
45 2 0.05
46 37 0.93
47 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (46 bp):
ATGTATTGATACATTTAAGGATGTATCAATATAAGGTCCCAACAGG
Found at i:280694 original size:13 final size:13
Alignment explanation
Indices: 280676--280701 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
280666 TACAGCAAGT
280676 ATGTATCGATACA
1 ATGTATCGATACA
280689 ATGTATCGATACA
1 ATGTATCGATACA
280702 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:282446 original size:71 final size:72
Alignment explanation
Indices: 282358--282502 Score: 274
Period size: 71 Copynumber: 2.0 Consensus size: 72
282348 TTTATAACGG
*
282358 TATCTTATTTTCCCTTGGATCATTTTGGATGAATGAGTTATGATTTTTCGAACCTAAGCTGTCCA
1 TATCTTATTTTCCCTTGGATCATTCTGGATGAATGAGTTATGATTTTTCGAACCTAAGCTGTCCA
282423 GAACCCC
66 GAACCCC
282430 TATCTTA-TTTCCCTTGGATCATTCTGGATGAATGAGTTATGATTTTTCGAACCTAAGCTGTCCA
1 TATCTTATTTTCCCTTGGATCATTCTGGATGAATGAGTTATGATTTTTCGAACCTAAGCTGTCCA
282494 GAACCCC
66 GAACCCC
282501 TA
1 TA
282503 GAATCAGCAA
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
71 65 0.90
72 7 0.10
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (72 bp):
TATCTTATTTTCCCTTGGATCATTCTGGATGAATGAGTTATGATTTTTCGAACCTAAGCTGTCCA
GAACCCC
Found at i:289138 original size:11 final size:10
Alignment explanation
Indices: 289119--289159 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
289109 TAATATGTCT
*
289119 AAAAGAAAAC
1 AAAAAAAAAC
289129 AAAAACAAAAC
1 AAAAA-AAAAC
289140 AAAAAAATAAC
1 AAAAAAA-AAC
289151 AAAAAAAAA
1 AAAAAAAAA
289160 AATAGAGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 8 0.29
11 20 0.71
ACGTcount: A:0.85, C:0.10, G:0.02, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:289138 original size:16 final size:15
Alignment explanation
Indices: 289119--289163 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
289109 TAATATGTCT
289119 AAAAGAAAACAAA-AAC
1 AAAA-AAAA-AAATAAC
289135 AAAACAAAAAAATAAC
1 AAAA-AAAAAAATAAC
289151 AAAAAAAAAAATA
1 AAAAAAAAAAATA
289164 GAGGTGTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.84, C:0.09, G:0.02, T:0.04
Consensus pattern (15 bp):
AAAAAAAAAAATAAC
Found at i:290474 original size:40 final size:40
Alignment explanation
Indices: 290413--290594 Score: 244
Period size: 40 Copynumber: 4.5 Consensus size: 40
290403 ATTTTATCCC
*
290413 CTTTTCCCTTTGTCCTTAAGGAGTAGGACTCACTTCATCT
1 CTTTTCCCTTTGTCCTCAAGGAGTAGGACTCACTTCATCT
*
290453 CATTTT-CCTTTGTCCTCAAGGAGTAGGAC-CTATTTCATCCT
1 C-TTTTCCCTTTGTCCTCAAGGAGTAGGACTC-ACTTCAT-CT
290494 CTTTTCCCTTTGTCCTCAAGGAGTAGGACTCACTTCATCTT
1 CTTTTCCCTTTGTCCTCAAGGAGTAGGACTCACTTCATC-T
* *
290535 CTTTT-CCTTTGTCCTCAAGGAGTAGGACCCATTTCATTCT
1 CTTTTCCCTTTGTCCTCAAGGAGTAGGACTCACTTCA-TCT
* *
290575 TTTTTCCCTTTATCCTCAAG
1 CTTTTCCCTTTGTCCTCAAG
290595 AAACATGACG
Statistics
Matches: 127, Mismatches: 7, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
39 1 0.01
40 68 0.54
41 57 0.45
42 1 0.01
ACGTcount: A:0.18, C:0.28, G:0.14, T:0.41
Consensus pattern (40 bp):
CTTTTCCCTTTGTCCTCAAGGAGTAGGACTCACTTCATCT
Found at i:290498 original size:81 final size:81
Alignment explanation
Indices: 290395--290594 Score: 321
Period size: 81 Copynumber: 2.5 Consensus size: 81
290385 CTTCAAAAAA
* * *
290395 TAGGACCCATTTTATCCCCTTTTCCCTTTGTCCTTAAGGAGTAGGACTCACTTCATC-TCATTTT
1 TAGGACCCATTTCATCCTCTTTTCCCTTTGTCCTCAAGGAGTAGGACTCACTTCATCTTC-TTTT
290459 CCTTTGTCCTCAAGGAG
65 CCTTTGTCCTCAAGGAG
*
290476 TAGGACCTATTTCATCCTCTTTTCCCTTTGTCCTCAAGGAGTAGGACTCACTTCATCTTCTTTTC
1 TAGGACCCATTTCATCCTCTTTTCCCTTTGTCCTCAAGGAGTAGGACTCACTTCATCTTCTTTTC
290541 CTTTGTCCTCAAGGAG
66 CTTTGTCCTCAAGGAG
* * *
290557 TAGGACCCATTTCATTCTTTTTTCCCTTTATCCTCAAG
1 TAGGACCCATTTCATCCTCTTTTCCCTTTGTCCTCAAG
290595 AAACATGACG
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
81 108 0.98
82 2 0.02
ACGTcount: A:0.18, C:0.28, G:0.14, T:0.40
Consensus pattern (81 bp):
TAGGACCCATTTCATCCTCTTTTCCCTTTGTCCTCAAGGAGTAGGACTCACTTCATCTTCTTTTC
CTTTGTCCTCAAGGAG
Found at i:290631 original size:44 final size:43
Alignment explanation
Indices: 290574--290712 Score: 133
Period size: 44 Copynumber: 3.2 Consensus size: 43
290564 CATTTCATTC
290574 TTTTTTCCCTTTATCCTCAAGAAACATGACGCATTCCTTTTCTT
1 TTTTTTCCCTTTATCCTCAAGAAACATGAC-CATTCCTTTTCTT
* * * * * *
290618 TTTTTTTCCTTTATCCTTAAGAAATAGGACCTATTTC-ATTC-T
1 TTTTTTCCCTTTATCCTCAAGAAACATGACC-ATTCCTTTTCTT
*
290660 TTTTTTCCCTTTATCCTCAA-AAAGC-TGGATACATTCCTTTTCTCT
1 TTTTTTCCCTTTATCCTCAAGAAA-CAT-GA-CCATTCCTTTTCT-T
290705 TTTTTTCC
1 TTTTTTCC
290713 TTTGTCTTTA
Statistics
Matches: 75, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
41 3 0.04
42 25 0.33
43 8 0.11
44 30 0.40
45 9 0.12
ACGTcount: A:0.20, C:0.24, G:0.06, T:0.49
Consensus pattern (43 bp):
TTTTTTCCCTTTATCCTCAAGAAACATGACCATTCCTTTTCTT
Found at i:290753 original size:86 final size:85
Alignment explanation
Indices: 290455--290741 Score: 302
Period size: 86 Copynumber: 3.4 Consensus size: 85
290445 CTTCATCTCA
* * * * * ** *
290455 TTTTCCTTTGTCCTCAAGGAGTAGGACCTATTTCATCCTCTTTTCCCTTTGTCCTCAAGGAGTAG
1 TTTTCCTTTGTCCTTAAGGAGTAGGACCTATTTCATTCTTTTTTCCCTTTATCCTCAAGAAACAT
* *
290520 GACTCA---C--TTCATCTTC
66 GACACATTCCTTTTC-TCTTT
* *
290536 TTTTCCTTTGTCCTCAAGGAGTAGGACCCATTTCATTCTTTTTTCCCTTTATCCTCAAGAAACAT
1 TTTTCCTTTGTCCTTAAGGAGTAGGACCTATTTCATTCTTTTTTCCCTTTATCCTCAAGAAACAT
* *
290601 GACGCATTCCTTTTCTTTTT
66 GACACATTCCTTTTCTCTTT
* * *
290621 TTTTCCTTTATCCTTAAGAAATAGGACCTATTTCATTCTTTTTTTCCCTTTATCCTCAA-AAAGC
1 TTTTCCTTTGTCCTTAAGGAGTAGGACCTATTTCATTC-TTTTTTCCCTTTATCCTCAAGAAA-C
*
290685 -TGGATACATTCCTTTTCTCTTT
64 AT-GACACATTCCTTTTCTCTTT
*
290707 TTTTCCTTTGTCTTTAAGGAGGT-GGACCTATTTCA
1 TTTTCCTTTGTCCTTAAGGA-GTAGGACCTATTTCA
290742 CTCACCTTTT
Statistics
Matches: 174, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
81 62 0.36
84 1 0.01
85 40 0.23
86 70 0.40
87 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.44
Consensus pattern (85 bp):
TTTTCCTTTGTCCTTAAGGAGTAGGACCTATTTCATTCTTTTTTCCCTTTATCCTCAAGAAACAT
GACACATTCCTTTTCTCTTT
Found at i:290972 original size:31 final size:31
Alignment explanation
Indices: 290934--291012 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
290924 GCCTTAGAAT
* **
290934 GTCAAAGCCCGCACGAGTCGGTGGCACCCTA
1 GTCAAAGCCCGCACGAGTCAGTGGCACCAAA
* *
290965 GTCAAAGCCCTGCACAAGTTAGTGGCACCAAA
1 GTCAAAGCCC-GCACGAGTCAGTGGCACCAAA
*
290997 GTCTAAGCCCGCACGA
1 GTCAAAGCCCGCACGA
291013 ATTGATAGCA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 15 0.38
32 25 0.62
ACGTcount: A:0.28, C:0.33, G:0.25, T:0.14
Consensus pattern (31 bp):
GTCAAAGCCCGCACGAGTCAGTGGCACCAAA
Found at i:291824 original size:20 final size:21
Alignment explanation
Indices: 291785--291837 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
291775 TTTTATAATT
*
291785 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAACTGAAA
**
291805 TGTATCGATACATGCCTGAAA
1 TGTATCGATACATAACTGAAA
*
291826 TATATCGATACA
1 TGTATCGATACA
291838 AAACCACCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATAACTGAAA
Found at i:291930 original size:20 final size:21
Alignment explanation
Indices: 291885--291940 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
291875 CGTAAGTAAA
*
291885 TGTATCGATACATTTACTATT
1 TGTATCGATACATTTACGATT
291906 TGTATCGATACA-TTATCGA-T
1 TGTATCGATACATTTA-CGATT
291926 TGTATCGATACATTT
1 TGTATCGATACATTT
291941 TGGGTTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATTTACGATT
Found at i:293606 original size:51 final size:52
Alignment explanation
Indices: 293542--293660 Score: 170
Period size: 52 Copynumber: 2.3 Consensus size: 52
293532 GAAAATAACA
*
293542 AGGTTGGAGTATCCCTAA-TTATAGAAAATCGGTATTTTAAAAATAAAATCG
1 AGGTTGGAGTATCCCCAATTTATAGAAAATCGGTATTTTAAAAATAAAATCG
* * * *
293593 -GAGTTGGAGTATCCCCAATTTGTGGAAAATTGGTATTTTAGAAATAAAATCG
1 AG-GTTGGAGTATCCCCAATTTATAGAAAATCGGTATTTTAAAAATAAAATCG
293645 AGGTTGGAGTATCCCC
1 AGGTTGGAGTATCCCC
293661 TCAGAAATAA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
50 1 0.02
51 15 0.25
52 43 0.72
53 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (52 bp):
AGGTTGGAGTATCCCCAATTTATAGAAAATCGGTATTTTAAAAATAAAATCG
Found at i:293682 original size:28 final size:29
Alignment explanation
Indices: 293651--293716 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 29
293641 ATCGAGGTTG
293651 GAGTATCCCCTCA-GAAATAACGGGATTA
1 GAGTATCCCCTCATGAAATAACGGGATTA
* * *
293679 GAGTATCCCC-GATGAAATAACGGGGTTG
1 GAGTATCCCCTCATGAAATAACGGGATTA
293707 GAGTA-CCCCT
1 GAGTATCCCCT
293717 GATTATGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 5 0.15
28 28 0.85
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (29 bp):
GAGTATCCCCTCATGAAATAACGGGATTA
Found at i:293796 original size:28 final size:28
Alignment explanation
Indices: 293753--293826 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 28
293743 GATATAAAGC
293753 CGGGGTTGGAGTATCCTCTC-A-GAAATAA
1 CGGGGTTGGAGTATCC-C-CGATGAAATAA
*
293781 CGGGGTTGGAGCATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
293809 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
293827 AATTGTGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.02
27 2 0.05
28 39 0.93
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:293894 original size:109 final size:109
Alignment explanation
Indices: 293595--293907 Score: 386
Period size: 110 Copynumber: 2.9 Consensus size: 109
293585 TAAAATCGGA
* ** * * *
293595 GTTGGAGTATCCCCAATTTGTGGAAAAT-TGGTA-TTTTAGAAATAAA-ATCGAGGTTGGAGTAT
1 GTTGGAGTATCCCCAA-TTGTGAAAAATATAATATTTTTAGATATAAAGCT-GGGGTTGGAGTAT
* * *
293657 CCCCTCAGAAATAACGGGATTAGAGTATCCCCGATGAAATAACGGG
64 TCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGGG
* * * *
293703 GTTGGAGTA-CCCCTGATTATGAAAAAAAATAATATTTTTAGATATAAAGCCGGGGTTGGAGTA-
1 GTTGGAGTATCCCC-AATTGTG-AAAAATATAATATTTTTAGATATAAAGCTGGGGTTGGAGTAT
*
293766 TCCTCTCAGAAATAACGGGGTTGGAGCATCCCCGATGAAATAACGGG
64 TCC-CTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGGG
*
293813 GTTGGAGTATCCCCAATTGTGAAAAATACAATATTTTTAGATATAAAGCTGGGGTTGGAGTATTC
1 GTTGGAGTATCCCCAATTGTGAAAAATATAATATTTTTAGATATAAAGCTGGGGTTGGAGTATTC
*
293878 CC-GATGAAATAACGGGGTTGGAGTATCCCC
66 CCTCA-GAAATAACGGGGTTGGAGTATCCCC
293908 AATTGTGAAA
Statistics
Matches: 175, Mismatches: 21, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
107 8 0.05
108 15 0.09
109 68 0.39
110 80 0.46
111 4 0.02
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (109 bp):
GTTGGAGTATCCCCAATTGTGAAAAATATAATATTTTTAGATATAAAGCTGGGGTTGGAGTATTC
CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGGG
Found at i:293917 original size:81 final size:81
Alignment explanation
Indices: 293781--293988 Score: 348
Period size: 81 Copynumber: 2.6 Consensus size: 81
293771 TCAGAAATAA
* *
293781 CGGGGTTGGAGCATCCCCGATGAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATACAATA
1 CGGGGTTGGAGTATTCCCGATGAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATACAATA
293846 TTTTTAGATATAAAGC
66 TTTTTAGATATAAAGC
*
293862 TGGGGTTGGAGTATTCCCGATGAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATACAATA
1 CGGGGTTGGAGTATTCCCGATGAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATACAATA
293927 TTTTTAGATATAAAGC
66 TTTTTAGATATAAAGC
*
293943 CGGGGTTGGAGTA-TCCC-CTCGAAAATAACGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATTCCCGAT-G-AAATAACGGGGTTGGAGTATCCCC
293989 GATGAAATAA
Statistics
Matches: 120, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
79 1 0.01
80 5 0.04
81 114 0.95
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (81 bp):
CGGGGTTGGAGTATTCCCGATGAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATACAATA
TTTTTAGATATAAAGC
Found at i:293948 original size:190 final size:191
Alignment explanation
Indices: 293679--294029 Score: 564
Period size: 190 Copynumber: 1.8 Consensus size: 191
293669 AACGGGATTA
* *
293679 GAGTATCCCCGATGAAATAACGGGGTTGGAGTACCCCTGATTATGAAAAAAAATAATATTTTTAG
1 GAGTATCCCCGATGAAATAACGGGGTTGGAGTACCCCTAATTATGAAAAAAAACAATATTTTTAG
*
293744 ATATAAAGCCGGGGTTGGAGTATCCTCTC-AGAAATAACGGGGTTGGAGCATCCCCGATGAAATA
66 ATATAAAGCCGGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGCATCCCCGATGAAATA
* *
293808 ACGGGGTTGGAGTATCCCCAATTGTGAAAAATACAATATTTTTAGATATAAAGCTGGGGTTG
130 ACGAGGTTGGAGTACCCCCAATTGTGAAAAATACAATATTTTTAGATATAAAGCTGGGGTTG
* * *
293870 GAGTATTCCCGATGAAATAACGGGGTTGGAGTATCCCC-AATTGTG-AAAAATACAATATTTTTA
1 GAGTATCCCCGATGAAATAACGGGGTTGGAGTA-CCCCTAATTATGAAAAAAAACAATATTTTTA
*
293933 GATATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATA
65 GATATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGCATCCCCGATGAAATA
* *
293998 ACGAGGTTGGAGTACCCCCGATTTTGAAAAAT
130 ACGAGGTTGGAGTACCCCCAATTGTGAAAAAT
294030 TGGTGTTTTG
Statistics
Matches: 147, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
190 105 0.71
191 38 0.26
192 4 0.03
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (191 bp):
GAGTATCCCCGATGAAATAACGGGGTTGGAGTACCCCTAATTATGAAAAAAAACAATATTTTTAG
ATATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGCATCCCCGATGAAATAA
CGAGGTTGGAGTACCCCCAATTGTGAAAAATACAATATTTTTAGATATAAAGCTGGGGTTG
Found at i:293983 original size:28 final size:28
Alignment explanation
Indices: 293943--294018 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
293933 GATATAAAGC
293943 CGGGGTTGGAGTATCCCCTCGA-AAATAA
1 CGGGGTTGGAGTATCCCC-CGAGAAATAA
293971 CGGGGTTGGAGTAT-CCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCCGA-GAAATAA
*
293999 CGAGGTTGGAGTA-CCCCCGA
1 CGGGGTTGGAGTATCCCCCGA
294019 TTTTGAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
26 3 0.07
27 3 0.07
28 38 0.86
ACGTcount: A:0.26, C:0.22, G:0.32, T:0.20
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCGAGAAATAA
Found at i:294146 original size:51 final size:51
Alignment explanation
Indices: 294003--294171 Score: 173
Period size: 51 Copynumber: 3.3 Consensus size: 51
293993 AAATAACGAG
* * * *
294003 GTTGGAGTACCCCCGATTTTGAAAAATTGGTGTTTTGGCAATAAAATCGGA
1 GTTGGAGTATCCCCGATTTAGAAAAATTGATGTTTTGGAAATAAAATCGGA
* * * * *
294054 GTTGGAGTATCCCCAATTGTAG-TAAATCGATGCTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATT-TAGAAAAATTGATGTTTTGGAAATAAAATCGGA
* * * *
294105 GTTGGAGTATCCCCGATTAAGAAAAATTGACGTTTTGGAAATGGAACTAC-GA
1 GTTGGAGTATCCCCGATTTAGAAAAATTGATGTTTTGGAAAT-AAAAT-CGGA
294157 -TTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
294172 GATGAAAAAT
Statistics
Matches: 96, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
50 2 0.02
51 86 0.90
52 7 0.07
53 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTTAGAAAAATTGATGTTTTGGAAATAAAATCGGA
Found at i:295987 original size:21 final size:18
Alignment explanation
Indices: 295938--295979 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
295928 GAGCTACGGG
295938 AATGGAGTGTTGAAGGCC
1 AATGGAGTGTTGAAGGCC
*
295956 AATGGAGTGTTGGAGGCC
1 AATGGAGTGTTGAAGGCC
295974 AATGGA
1 AATGGA
295980 ATAGTGTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.10, G:0.40, T:0.21
Consensus pattern (18 bp):
AATGGAGTGTTGAAGGCC
Found at i:296499 original size:20 final size:21
Alignment explanation
Indices: 296474--296532 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
296464 AAAATGCCTG
*
296474 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATGTAGA
*
296494 AATGTATCGATACAATG-AGC
1 AATGTATCGATACAATGTAGA
296514 AATGTATCGATACAATGTA
1 AATGTATCGATACAATGTA
296533 TCGATACATG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.31
Consensus pattern (21 bp):
AATGTATCGATACAATGTAGA
Found at i:296529 original size:13 final size:13
Alignment explanation
Indices: 296513--296540 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
296503 ATACAATGAG
296513 CAATGTATCGATA
1 CAATGTATCGATA
296526 CAATGTATCGATA
1 CAATGTATCGATA
296539 CA
1 CA
296541 TGCCCTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:305590 original size:22 final size:22
Alignment explanation
Indices: 305549--305590 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
305539 ATGGAAAAGA
* *
305549 CAACTTTTGTCACCATGTGAGG
1 CAACTTTTGTCACAAAGTGAGG
*
305571 CAACTTTTGTTACAAAGTGA
1 CAACTTTTGTCACAAAGTGA
305591 TGCCGTTTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (22 bp):
CAACTTTTGTCACAAAGTGAGG
Found at i:308322 original size:9 final size:9
Alignment explanation
Indices: 308308--308357 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
308298 TGCTTGAAAG
308308 AAAAACAAA
1 AAAAACAAA
*
308317 AAAAACAAC
1 AAAAACAAA
*
308326 AAAAA-GAA
1 AAAAACAAA
308334 AAAAACAATA
1 AAAAACAA-A
308344 AAAAACATAA
1 AAAAACA-AA
308354 AAAA
1 AAAA
308358 TGAAATAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
8 6 0.18
9 14 0.41
10 13 0.38
11 1 0.03
ACGTcount: A:0.84, C:0.10, G:0.02, T:0.04
Consensus pattern (9 bp):
AAAAACAAA
Found at i:308335 original size:17 final size:17
Alignment explanation
Indices: 308315--308347 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
308305 AAGAAAAACA
308315 AAAAAAACAACAAAAAG
1 AAAAAAACAACAAAAAG
*
308332 AAAAAAACAATAAAAA
1 AAAAAAACAACAAAAA
308348 ACATAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.03
Consensus pattern (17 bp):
AAAAAAACAACAAAAAG
Found at i:309707 original size:89 final size:89
Alignment explanation
Indices: 309570--309998 Score: 502
Period size: 89 Copynumber: 4.8 Consensus size: 89
309560 TTCCTTTATG
* ** *
309570 TTTGACGTATGGTTACCACTATGGTCAAACTCTTCTCATTTCAAGTCTGATGTATGGCTACCACC
1 TTTGACGTATGGTTATCACCCTGGTCAAACTCTTCTCATTTCAAGTCTGACGTATGGCTACCACC
*
309635 CTAGTCAAATTCTTTCCATCTTGA
66 CTAGTCAAATTCTTTCCATTTTGA
* * * * *
309659 TTTGACGTATGGTTATCGCCTTTGCCAAACTCTTTTCATTTCAAGTCTGACGTATGGCTACCACC
1 TTTGACGTATGGTTATCACCCTGGTCAAACTCTTCTCATTTCAAGTCTGACGTATGGCTACCACC
* *
309724 CTGGTCAAATTCTTTCCATTTTGG
66 CTAGTCAAATTCTTTCCATTTTGA
* * * ** * *
309748 TTTGACGTATGGTTATCACCCTGGTCAAACTCTTCCCATTTTAGGTCTGGTGTCTGGTTACCACC
1 TTTGACGTATGGTTATCACCCTGGTCAAACTCTTCTCATTTCAAGTCTGACGTATGGCTACCACC
* *
309813 CTAATCAGATT-TTTCCATTTTGA
66 CTAGTCAAATTCTTTCCATTTTGA
* * * * *
309836 TTTGACGTATGGTTACCACCCTAGTCAAACTCTTCTTATTTCAGGTCTGACGTATGGTTACCACC
1 TTTGACGTATGGTTATCACCCTGGTCAAACTCTTCTCATTTCAAGTCTGACGTATGGCTACCACC
* *
309901 CTGGTCAGATTCTTTCCATTTTGA
66 CTAGTCAAATTCTTTCCATTTTGA
* * * * * * * * *
309925 TTTGATGTATGGTTACCACCCTGGTCAGATTCTTTTCATTCCAA-TTTGACGTATGGTTACCATC
1 TTTGACGTATGGTTATCACCCTGGTCAAACTCTTCTCATTTCAAGTCTGACGTATGGCTACCACC
*
309989 GTAGTCAAAT
66 CTAGTCAAAT
309999 CTGCTTTCTT
Statistics
Matches: 289, Mismatches: 50, Indels: 3
0.85 0.15 0.01
Matches are distributed among these distances:
88 102 0.35
89 187 0.65
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.39
Consensus pattern (89 bp):
TTTGACGTATGGTTATCACCCTGGTCAAACTCTTCTCATTTCAAGTCTGACGTATGGCTACCACC
CTAGTCAAATTCTTTCCATTTTGA
Found at i:309769 original size:44 final size:44
Alignment explanation
Indices: 309569--309986 Score: 338
Period size: 44 Copynumber: 9.4 Consensus size: 44
309559 TTTCCTTTAT
** * **
309569 GTTTGACGTATGGTTACCACTATGGTCAAACTC-TTCTCATTTCAA
1 GTTTGACGTATGGTTACCACCCTGGTCAAATTCTTTC-CATTT-TG
* * * * *
309614 GTCTGATGTATGGCTACCACCCTAGTCAAATTCTTTCCATCTTG
1 GTTTGACGTATGGTTACCACCCTGGTCAAATTCTTTCCATTTTG
* * * * * * * * **
309658 ATTTGACGTATGGTTATCGCCTTTGCCAAACTCTTTTCATTTCAA
1 GTTTGACGTATGGTTACCACCCTGGTCAAATTCTTTCCATTT-TG
* *
309703 GTCTGACGTATGGCTACCACCCTGGTCAAATTCTTTCCATTTTG
1 GTTTGACGTATGGTTACCACCCTGGTCAAATTCTTTCCATTTTG
* * *
309747 GTTTGACGTATGGTTATCACCCTGGTCAAACTCTTCCCATTTTAG
1 GTTTGACGTATGGTTACCACCCTGGTCAAATTCTTTCCATTTT-G
* ** * ** *
309792 GTCTGGTGTCTGGTTACCACCCTAATCAGATT-TTTCCATTTTG
1 GTTTGACGTATGGTTACCACCCTGGTCAAATTCTTTCCATTTTG
* * * * *
309835 ATTTGACGTATGGTTACCACCCTAGTCAAACTC-TTCTTATTTCAG
1 GTTTGACGTATGGTTACCACCCTGGTCAAATTCTTTC-CATTT-TG
* *
309880 GTCTGACGTATGGTTACCACCCTGGTCAGATTCTTTCCATTTTG
1 GTTTGACGTATGGTTACCACCCTGGTCAAATTCTTTCCATTTTG
* * * * ***
309924 ATTTGATGTATGGTTACCACCCTGGTCAGATTCTTTTCATTCCA
1 GTTTGACGTATGGTTACCACCCTGGTCAAATTCTTTCCATTTTG
*
309968 ATTTGACGTATGGTTACCA
1 GTTTGACGTATGGTTACCA
309987 TCGTAGTCAA
Statistics
Matches: 290, Mismatches: 76, Indels: 15
0.76 0.20 0.04
Matches are distributed among these distances:
43 28 0.10
44 137 0.47
45 119 0.41
46 6 0.02
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.39
Consensus pattern (44 bp):
GTTTGACGTATGGTTACCACCCTGGTCAAATTCTTTCCATTTTG
Found at i:309886 original size:177 final size:178
Alignment explanation
Indices: 309569--309951 Score: 545
Period size: 177 Copynumber: 2.2 Consensus size: 178
309559 TTTCCTTTAT
** *
309569 GTTTGACGTATGGTTACCACTATGGTCAAACTCTTCTCATTTCAAGTCTGATGTATGGCTACCAC
1 GTTTGACGTATGGTTACCACCCTGGTCAAACTCTTCCCATTTCAAGTCTGATGTATGGCTACCAC
* * * * *
309634 CCTAGTCAAATTCTTTCCATCTTGATTTGACGTATGGTTATCGCCTTTGCCAAACTCTTTTCATT
66 CCTAATCAAATTCTTTCCATCTTGATTTGACGTATGGTTACCACCCTAGCCAAACTCTTTTCATT
309699 TCAAGTCTGACGTATGGCTACCACCCTGGTCAAATTCTTTCCATTTTG
131 TCAAGTCTGACGTATGGCTACCACCCTGGTCAAATTCTTTCCATTTTG
* * * * * *
309747 GTTTGACGTATGGTTATCACCCTGGTCAAACTCTTCCCATTTTAGGTCTGGTGTCTGGTTACCAC
1 GTTTGACGTATGGTTACCACCCTGGTCAAACTCTTCCCATTTCAAGTCTGATGTATGGCTACCAC
* * *
309812 CCTAATCAGATT-TTTCCATTTTGATTTGACGTATGGTTACCACCCTAGTCAAACTCTTCTT-AT
66 CCTAATCAAATTCTTTCCATCTTGATTTGACGTATGGTTACCACCCTAGCCAAACTCTT-TTCAT
* * *
309875 TTCAGGTCTGACGTATGGTTACCACCCTGGTCAGATTCTTTCCATTTTG
130 TTCAAGTCTGACGTATGGCTACCACCCTGGTCAAATTCTTTCCATTTTG
* *
309924 ATTTGATGTATGGTTACCACCCTGGTCA
1 GTTTGACGTATGGTTACCACCCTGGTCA
309952 GATTCTTTTC
Statistics
Matches: 181, Mismatches: 23, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
177 113 0.62
178 68 0.38
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.38
Consensus pattern (178 bp):
GTTTGACGTATGGTTACCACCCTGGTCAAACTCTTCCCATTTCAAGTCTGATGTATGGCTACCAC
CCTAATCAAATTCTTTCCATCTTGATTTGACGTATGGTTACCACCCTAGCCAAACTCTTTTCATT
TCAAGTCTGACGTATGGCTACCACCCTGGTCAAATTCTTTCCATTTTG
Found at i:310026 original size:177 final size:177
Alignment explanation
Indices: 309570--310026 Score: 537
Period size: 177 Copynumber: 2.6 Consensus size: 177
309560 TTCCTTTATG
** *
309570 TTTGACGTATGGTTACCACTATGGTCAAACTCTTCTCATTTCAAGTCTGATGTATGGCTACCACC
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTCAA-TCTGATGTATGGTTACCACC
* * * * *
309635 CTAGTCAAATTCTTTCCATCTTGATTTGACGTATGGTTATCGCCTTTGCCAAACTCTTTTCATTT
65 CTAGTCAAATTCTTTCCTTCTTGATTTGACGTATGGTTACCACCCTAGCCAAACTCTTTTCATTT
*
309700 CAAGTCTGACGTATGGCTACCACCCTGGTCAAATTCTTTCCATTTTGG
130 CAAGTCTGACGTATGGCTACCACCCTGGTCAAATTCTTTCCATTTTGA
* * * * * *
309748 TTTGACGTATGGTTATCACCCTGGTCAAACTCTTCCCATTTTAGGTCTGGTGTCTGGTTACCACC
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTCA-ATCTGATGTATGGTTACCACC
* * *
309813 CTAATCAGATT-TTTCCATT-TTGATTTGACGTATGGTTACCACCCTAGTCAAACTCTTCTT-AT
65 CTAGTCAAATTCTTTCC-TTCTTGATTTGACGTATGGTTACCACCCTAGCCAAACTCTT-TTCAT
* * *
309875 TTCAGGTCTGACGTATGGTTACCACCCTGGTCAGATTCTTTCCATTTTGA
128 TTCAAGTCTGACGTATGGCTACCACCCTGGTCAAATTCTTTCCATTTTGA
* * * * * * * * *
309925 TTTGATGTATGGTTACCACCCTGGTCAGATTCTTTTCATTCCAATTTGACGTATGGTTACCATCG
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTCAATCTGATGTATGGTTACCACCC
* *
309990 TAGTCAAATCTGCTTT-CTTCCTG-TTTGACATATGGTT
66 TAGTCAAAT-T-CTTTCCTTCTTGATTTGACGTATGGTT
310027 TTTACCTTGG
Statistics
Matches: 232, Mismatches: 40, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
176 22 0.09
177 137 0.59
178 70 0.30
179 3 0.01
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (177 bp):
TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTCAATCTGATGTATGGTTACCACCC
TAGTCAAATTCTTTCCTTCTTGATTTGACGTATGGTTACCACCCTAGCCAAACTCTTTTCATTTC
AAGTCTGACGTATGGCTACCACCCTGGTCAAATTCTTTCCATTTTGA
Found at i:310206 original size:43 final size:43
Alignment explanation
Indices: 310150--310270 Score: 122
Period size: 42 Copynumber: 2.8 Consensus size: 43
310140 AATCTCTAGT
* * * *
310150 AAACTTCTTATCCCCTCAATGACTTGTCGGCTTAGTCCCTA-A
1 AAACCTCTTATCCCCTCAATGACCTATCGGCTTAGTCCCCAGA
* * * *
310192 ACAACC-CTTCAT-CCCTTATTTACCTATCGGCTTAGTCCCCAGT
1 A-AACCTCTT-ATCCCCTCAATGACCTATCGGCTTAGTCCCCAGA
*
310235 AAACCTCTTATCCCCTCAATGACCTATCAGCTTAGT
1 AAACCTCTTATCCCCTCAATGACCTATCGGCTTAGT
310271 TCCTGGTCAA
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
42 33 0.53
43 29 0.47
ACGTcount: A:0.24, C:0.34, G:0.10, T:0.32
Consensus pattern (43 bp):
AAACCTCTTATCCCCTCAATGACCTATCGGCTTAGTCCCCAGA
Found at i:310248 original size:42 final size:42
Alignment explanation
Indices: 310125--310270 Score: 116
Period size: 43 Copynumber: 3.4 Consensus size: 42
310115 CATCTCATTG
* * * *
310125 TTTACCTATCGGCTCAATCTCTAGTAAACTTCTTATCCCCTCA
1 TTTACCTATCGGCTTAGTCCCTAGTAAACCTCTTAT-CCCTCA
* * * * * *
310168 ATGACTTGTCGGCTTAGTCCCTA-AACAACC-CTTCATCCCTTA
1 TTTACCTATCGGCTTAGTCCCTAGTA-AACCTCTT-ATCCCTCA
*
310210 TTTACCTATCGGCTTAGTCCCCAGTAAACCTCTTATCCCCTCA
1 TTTACCTATCGGCTTAGTCCCTAGTAAACCTCTTAT-CCCTCA
* * *
310253 ATGACCTATCAGCTTAGT
1 TTTACCTATCGGCTTAGT
310271 TCCTGGTCAA
Statistics
Matches: 78, Mismatches: 20, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
42 33 0.42
43 45 0.58
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.34
Consensus pattern (42 bp):
TTTACCTATCGGCTTAGTCCCTAGTAAACCTCTTATCCCTCA
Found at i:310288 original size:85 final size:86
Alignment explanation
Indices: 310125--310314 Score: 211
Period size: 85 Copynumber: 2.2 Consensus size: 86
310115 CATCTCATTG
* * * * * * * *
310125 TTTACCTATCGGCTCAATCTCTAGTAAACTTCTTATCCCCTCAATGACTTGTCGGCTTAGTCCCT
1 TTTACCTATCGGCTTAGTCCCCAGTAAACCTCTTATCCCCTCAATGACCTATCAGCTTAGTCCCT
* *
310190 AAACAACCCTTCAT-CCCTTA
66 AAACAAACCTTCATCCCCGTA
*
310210 TTTACCTATCGGCTTAGTCCCCAGTAAACCTCTTATCCCCTCAATGACCTATCAGCTTAGTTCCT
1 TTTACCTATCGGCTTAGTCCCCAGTAAACCTCTTATCCCCTCAATGACCTATCAGCTTAGTCCCT
*** * *
310275 GGTCAAACTTTCATCCCCGTG
66 AAACAAACCTTCATCCCCGTA
**
310296 TTTACCTATCAACTTAGTC
1 TTTACCTATCGGCTTAGTC
310315 TCGAGTAGAT
Statistics
Matches: 86, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
85 65 0.76
86 21 0.24
ACGTcount: A:0.23, C:0.33, G:0.11, T:0.34
Consensus pattern (86 bp):
TTTACCTATCGGCTTAGTCCCCAGTAAACCTCTTATCCCCTCAATGACCTATCAGCTTAGTCCCT
AAACAAACCTTCATCCCCGTA
Found at i:310607 original size:43 final size:43
Alignment explanation
Indices: 310559--310757 Score: 199
Period size: 43 Copynumber: 4.6 Consensus size: 43
310549 TTTTGTTTGT
*
310559 GAGAGACTTTCGTTATCTTTCGTCTGCTTGTCAGCTTAGACCC
1 GAGAGACTTTCTTTATCTTTCGTCTGCTTGTCAGCTTAGACCC
* * * *
310602 GAGAGACTTCCTTTATCTTTCGTCTGCTTATCGGCTTA-AACC
1 GAGAGACTTTCTTTATCTTTCGTCTGCTTGTCAGCTTAGACCC
* * *
310644 TAG-GATATTTCCTTTATCTTTCGTCTGCCTGTCAGCTTAGACCC
1 GAGAGA-CTTT-CTTTATCTTTCGTCTGCTTGTCAGCTTAGACCC
* * * * * *
310688 GAAAGAC-TTCTTTTACCTTTCGTCT-TTTCCTTAGCTTAGACTC
1 GAGAGACTTTC-TTTATCTTTCGTCTGCTT-GTCAGCTTAGACCC
*
310731 GAGAGACTTTCTTTATCTTTCATCTGC
1 GAGAGACTTTCTTTATCTTTCGTCTGC
310758 CCATTGGCTT
Statistics
Matches: 123, Mismatches: 25, Indels: 15
0.75 0.15 0.09
Matches are distributed among these distances:
41 2 0.02
42 9 0.07
43 103 0.84
44 7 0.06
45 2 0.02
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.41
Consensus pattern (43 bp):
GAGAGACTTTCTTTATCTTTCGTCTGCTTGTCAGCTTAGACCC
Found at i:310745 original size:86 final size:85
Alignment explanation
Indices: 310559--310758 Score: 233
Period size: 86 Copynumber: 2.3 Consensus size: 85
310549 TTTTGTTTGT
* * * *
310559 GAGAGACTTTCGTTATCTTTCGTCTGCTTGTCAGCTTAGACCCGAGAGACTTCCTTTATCTTTCG
1 GAGAGACTTTCTTTATCTTTCGTCTGCCTGTCAGCTTAGACCCGAAAGACTTCCTTTACCTTTCG
*
310624 TCTGCTTATCGGCTTAAACC
66 TCTGCTTATCAGCTTAAACC
* * *
310644 TAG-GATATTTCCTTTATCTTTCGTCTGCCTGTCAGCTTAGACCCGAAAGACTTCTTTTACCTTT
1 GAGAGA-CTTT-CTTTATCTTTCGTCTGCCTGTCAGCTTAGACCCGAAAGACTTCCTTTACCTTT
* * * *
310708 CGTCT-TTTCCTTAGCTTAGACTC
64 CGTCTGCTT-ATCAGCTTAAAC-C
*
310731 GAGAGACTTTCTTTATCTTTCATCTGCC
1 GAGAGACTTTCTTTATCTTTCGTCTGCC
310759 CATTGGCTTA
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
84 2 0.02
85 7 0.07
86 78 0.82
87 6 0.06
88 2 0.02
ACGTcount: A:0.17, C:0.26, G:0.16, T:0.41
Consensus pattern (85 bp):
GAGAGACTTTCTTTATCTTTCGTCTGCCTGTCAGCTTAGACCCGAAAGACTTCCTTTACCTTTCG
TCTGCTTATCAGCTTAAACC
Found at i:312271 original size:330 final size:333
Alignment explanation
Indices: 311834--312510 Score: 873
Period size: 330 Copynumber: 2.0 Consensus size: 333
311824 TTTCTTTCTG
* * *
311834 AATTCCTCCTATTTTCAAATTACAAGGTTTTCATCTCCATAAATTTTTTTCAAGAGGATTTTTCT
1 AATT-CTCCTTTTTTCAAAATACAAGGTTTTCATCTCCATAAATTATTTTCAAGAGGATTTTTCT
* * *
311899 TAGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTTAGTTTTCAAAA
65 TAGTTTTTAATTTTTAAAATACATAAAATATTATTATTTATTTCACATTAATTTAGTTTTCAAAA
* * * * *
311964 ATTCATTTATTTCCATAAAATTTGAATTTTTCCTTGAATTTTTCTTTTTTTCAAAATACGAAGTT
130 ATTCATTCATTTCCATAAAATTTGAATTTTTCCTTAAAATTTCCCTTTTTTCAAAATACGAAGTT
* * * *
312029 TTCTACTTTGTAACTTTTTTCGAGAGG-ATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAAT
195 TTCTACTCTGTAACTTTTTTAG-GAGGAATGTTTCTTGGTTTTTAATTTTTAAAATTCATAAAAT
* * * * *
312093 ATTATTATTTATTTGAAATTAATTCAGTTTTCAAAAATTCATTCATTTCCATAAATGTTGAA-TT
259 ATTATTATTTATTTCAAATTAAATCAGTTTTAAAAAATTAATTCATTTCCATAAATGTTAAAGTT
312157 TTTTCCTTGA
324 TTTTCCTTGA
**
312167 AATTCTCCTTTTTTCAAAATAC-AGAGTTTTC-TACTCCATAAA-TATTTT-GGGAGGATTTTTC
1 AATTCTCCTTTTTTCAAAATACAAG-GTTTTCAT-CTCCATAAATTATTTTCAAGAGGATTTTTC
* * **
312228 TTTGTTTTTAATTTTTAAAATACATAAAATATTATTATTTATTTCACATTATTTTTTTTTTCAAA
64 TTAGTTTTTAATTTTTAAAATACATAAAATATTATTATTTATTTCACATTAATTTAGTTTTCAAA
* * * *
312293 AATTCATTCATTTTCATAAATTTTGAATTTTTTCTTAAAATTTCCCTTTTTTCGAAATACGAAGT
129 AATTCATTCATTTCCATAAAATTTGAATTTTTCCTTAAAATTTCCCTTTTTTCAAAATACGAAGT
* * * ** *
312358 TTTTTACTCTGTAATTTTTTTAGGGGGAATGTTTCTTGGTTTTTGTTTTTTGAAATTCATAAAAT
194 TTTCTACTCTGTAACTTTTTTAGGAGGAATGTTTCTTGGTTTTTAATTTTTAAAATTCATAAAAT
* * * * * *
312423 ATTATTATTTATTTCATATTAAATCAGTTTTAAAAAATTAATTTATTTTCATGAGTTTTAAAGTT
259 ATTATTATTTATTTCAAATTAAATCAGTTTTAAAAAATTAATTCATTTCCATAAATGTTAAAGTT
*
312488 TTTTCTTTGA
324 TTTTCCTTGA
*
312498 AAATC-CCTTTTTT
1 AATTCTCCTTTTTT
312511 TCGAGAAACC
Statistics
Matches: 296, Mismatches: 44, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
329 3 0.01
330 235 0.79
331 23 0.08
332 31 0.10
333 4 0.01
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.52
Consensus pattern (333 bp):
AATTCTCCTTTTTTCAAAATACAAGGTTTTCATCTCCATAAATTATTTTCAAGAGGATTTTTCTT
AGTTTTTAATTTTTAAAATACATAAAATATTATTATTTATTTCACATTAATTTAGTTTTCAAAAA
TTCATTCATTTCCATAAAATTTGAATTTTTCCTTAAAATTTCCCTTTTTTCAAAATACGAAGTTT
TCTACTCTGTAACTTTTTTAGGAGGAATGTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATAT
TATTATTTATTTCAAATTAAATCAGTTTTAAAAAATTAATTCATTTCCATAAATGTTAAAGTTTT
TTCCTTGA
Found at i:312473 original size:165 final size:163
Alignment explanation
Indices: 311845--312584 Score: 745
Period size: 165 Copynumber: 4.5 Consensus size: 163
311835 ATTCCTCCTA
* * * *
311845 TTTTCAAATTAC-AAGGTTTTC-ATCTCCATAAATTTTTTTCAAGAGGATTTTTCTTAGTTTTTA
1 TTTTCAAAATACGAA-GTTTTCTA-CTCCGTAAA-TTTTTT-AGGGGGATTTTTCTTAGTTTTTA
* * *
311908 ATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTTAGTTTTCAAAAATTCATTTA
62 ATTTTTAAAATTCATAAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCA
* * ** * *
311973 TTTCCATAAAATTTGAATTTTTCCTTGAATTTTTCTTT
127 TTTCCATAAATTTTGAATTTTTTCTT-AAAATTCCCTT
** * * * *
312011 TTTTCAAAATACGAAGTTTTCTACTTTGTAACTTTTTTCGAGAGGATTTTTCTTGGTTTTTAATT
1 TTTTCAAAATACGAAGTTTTCTACTCCGTAAATTTTTTAG-GGGGATTTTTCTTAGTTTTTAATT
* * *
312076 TTTAAAATTCATCAAATATTATTATTTATTTGAAATTAATTCAGTTTTCAAAAATTCATTCATTT
65 TTTAAAATTCATAAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTT
* *
312141 CCATAAATGTTGAATTTTTTCCTTGAAATTCTCCTT
130 CCATAAATTTTGAATTTTTT-CTTAAAATTC-CCTT
* * *
312177 TTTTCAAAATAC-AGAGTTTTCTACTCCATAAATATTTT-GGGAGGATTTTTCTTTGTTTTTAAT
1 TTTTCAAAATACGA-AGTTTTCTACTCCGTAAATTTTTTAGGG-GGATTTTTCTTAGTTTTTAAT
* * * ***
312240 TTTTAAAATACATAAAATATTATTATTTATTTCACATTATTTTTTTTTTCAAAAATTCATTCATT
64 TTTTAAAATTCATAAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATT
*
312305 TTCATAAATTTTGAATTTTTTCTTAAAATTTCCCTT
129 TCCATAAATTTTGAATTTTTTCTTAAAA-TTCCCTT
* * * * * * **
312341 TTTTCGAAATACGAAGTTTTTTACTCTGTAATTTTTTTAGGGGGAATGTTTCTTGGTTTTTGTTT
1 TTTTCAAAATACGAAGTTTTCTACTCCGTAAATTTTTTAGGGGG-ATTTTTCTTAGTTTTTAATT
* * * * *
312406 TTTGAAATTCATAAAATATTATTATTTATTTCATATTAAATCAGTTTTAAAAAATTAATTTATTT
65 TTTAAAATTCATAAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTT
* * * *
312471 TCATGAGTTTTAAAGTTTTTTCTTTGAAAA-TCCCTTT
130 CCATAAATTTTGAA-TTTTTTC-TT-AAAATTCCC-TT
* * * * * **
312508 TTTTCGAGAA-ACCAAATTTTCTTCTCCGTAAATTTTTTAGGGGAAATTTTTCTTAGTTTAAAAT
1 TTTTC-AAAATACGAAGTTTTCTACTCCGTAAATTTTTTAGGGG-GATTTTTCTTAGTTTTTAAT
*
312572 TTTTAGAATTCAT
64 TTTTAAAATTCAT
312585 CTAATATTGT
Statistics
Matches: 478, Mismatches: 79, Indels: 33
0.81 0.13 0.06
Matches are distributed among these distances:
164 43 0.09
165 296 0.62
166 70 0.15
167 63 0.13
168 6 0.01
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (163 bp):
TTTTCAAAATACGAAGTTTTCTACTCCGTAAATTTTTTAGGGGGATTTTTCTTAGTTTTTAATTT
TTAAAATTCATAAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTC
CATAAATTTTGAATTTTTTCTTAAAATTCCCTT
Found at i:314106 original size:162 final size:162
Alignment explanation
Indices: 313928--314398 Score: 667
Period size: 167 Copynumber: 2.9 Consensus size: 162
313918 AAAATTAAAA
* * *
313928 AATATTTATTTTTTCTAATCTTTTATATTCCCATGGGCATCTGTAAGGGTATAAGAGATTTCAAA
1 AATATTTATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAAGGGTATAAAAGATTTCAAA
* *
313993 AACCTTTCATATTCTTTCGGGCTTCTATTAGGGTACAAAATAGTATTTTCAAAAATAAATAAAAT
66 AACCTTTCATATTCTTTCGGGCTTCCATTAGGGTATAAAATAGTATTTTCAAAAATAAATAAAAT
*
314058 TAACTTAAATTAGTATTATTGGAATAAATTCT
131 TAAATTAAATTAGTATTATTGGAATAAATTCT
314090 AATATTTATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGT-AGAGGTATAAAAGATTTCAA
1 AATATTTATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAAG-GGTATAAAAGATTTCAA
* * * *
314154 AAACCTATCGAAATT-TTTTGGGCTTCCATTAGGGTATAAAATAGTATTTACAAAAATAAATTAA
65 AAACCTTTC-ATATTCTTTCGGGCTTCCATTAGGGTATAAAATAGTATTTTCAAAAATAAA-T--
* *
314218 ATTAAATTAAATTAAATTGGTATTATTGGGATAAATTCT
126 A--AAATTAAATTAAATTAGTATTATTGGAATAAATTCT
*
314257 AATATTTATTTTTTCTAATTTTTTATATTCCTATGGGCATCCGTAAGGGTATAAAAGATTTCAAA
1 AATATTTATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAAGGGTATAAAAGATTTCAAA
* * * * * * * *
314322 AACCTTTCGTATCCTTTCGAGCTTCCATTAAGGTATGAGATGGTATTTTCAAAAATAAATAAAAC
66 AACCTTTCATATTCTTTCGGGCTTCCATTAGGGTATAAAATAGTATTTTCAAAAATAAATAAAAT
*
314387 TAAATTGAATTA
131 TAAATTAAATTA
314399 ATACTTTCAT
Statistics
Matches: 273, Mismatches: 27, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
161 2 0.01
162 120 0.44
163 5 0.02
164 1 0.00
165 1 0.00
166 3 0.01
167 139 0.51
168 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (162 bp):
AATATTTATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAAGGGTATAAAAGATTTCAAA
AACCTTTCATATTCTTTCGGGCTTCCATTAGGGTATAAAATAGTATTTTCAAAAATAAATAAAAT
TAAATTAAATTAGTATTATTGGAATAAATTCT
Found at i:314220 original size:5 final size:5
Alignment explanation
Indices: 314210--314235 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
314200 TTTACAAAAA
314210 TAAAT TAAAT TAAAT TAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT T
314236 GGTATTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAAAT
Found at i:317243 original size:18 final size:15
Alignment explanation
Indices: 317222--317262 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 15
317212 TAAAATAATA
317222 TTTATTTTAGTACTTTAT
1 TTTATTTTA-TA-TTT-T
317240 TTTATTTTATATTTT
1 TTTATTTTATATTTT
317255 TTTATTTT
1 TTTATTTT
317263 CGAAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.39
16 3 0.13
17 2 0.09
18 9 0.39
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTATTTTATATTTT
Found at i:319804 original size:140 final size:141
Alignment explanation
Indices: 319641--320046 Score: 471
Period size: 147 Copynumber: 2.8 Consensus size: 141
319631 TGAAAATCTT
* *
319641 ATTTTGTACCTTAA-GGAATAACTGAAAAGATACGAAAAGTTTTAAAGATTACTATA-TCCCTAC
1 ATTTCGTACCTTAATGG-AGAACTGAAAAGATACGAAAAGTTTTAAAGATT-CTATACT-CCTAC
* ** **
319704 GAAAAATTATAACAATATTAGAAATCTT-AAAAAAAAAGATAATAATTTTTATTTAA-TTTTTAA
63 GAAAAATCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTAATTTTTTAA
* **
319767 TTTTTGAAATTTTC
128 TTTTTAAAAAATTC
* * *
319781 ATTTCGTACCTTAATGGTGAACTGCAAAGATACGAAAAGTTTTAAAGATGTCTATACTCCTACAA
1 ATTTCGTACCTTAATGGAGAACTGAAAAGATACGAAAAGTTTTAAAGAT-TCTATACTCCTACGA
* *
319846 AAAATCATTGGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTTTTTAATTTTAATTTTTT
65 AAAATCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAA--TTTTT-A-TTTAA-TTTTT
319911 TAATTTTTAAAAAATTC
125 TAATTTTTAAAAAATTC
** * * *
319928 ATTTCGTACCTTAATGGAGAA-TCGAAAAGATATAAAAAGTTTTGAAGATTTCTATACTCTTATG
1 ATTTCGTACCTTAATGGAGAACT-GAAAAGATACGAAAAGTTTTAAAGA-TTCTATACTCCTACG
* * *
319992 GAAAACCATAGGAATATTAGAAATCTTGAAAAATTAAGAAAATAATTTTTATTTA
64 AAAAATCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTA
320047 GTGATAAAAT
Statistics
Matches: 226, Mismatches: 28, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
140 74 0.33
141 19 0.08
143 9 0.04
144 2 0.01
145 10 0.04
146 1 0.00
147 110 0.49
148 1 0.00
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.37
Consensus pattern (141 bp):
ATTTCGTACCTTAATGGAGAACTGAAAAGATACGAAAAGTTTTAAAGATTCTATACTCCTACGAA
AAATCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTAATTTTTTAATTT
TTAAAAAATTC
Found at i:319907 original size:15 final size:15
Alignment explanation
Indices: 319887--319917 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
319877 ATTAAGATAA
319887 TAATTTTTTTAATTT
1 TAATTTTTTTAATTT
319902 TAATTTTTTTAATTT
1 TAATTTTTTTAATTT
319917 T
1 T
319918 TAAAAAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TAATTTTTTTAATTT
Found at i:321634 original size:163 final size:163
Alignment explanation
Indices: 321287--321850 Score: 602
Period size: 164 Copynumber: 3.4 Consensus size: 163
321277 TAATAATCAC
* * * * * * *
321287 AAAAATTCAAAATTTATG-AAATAATTTGAAATTTTCAAAACTAATTTAATATGAATTTAAT-GT
1 AAAAATTCAAAACTCATGAAAATAA-ATGAATTTTTGAAAACTAATTTAATATGAATTAAATAAT
** * * * **
321350 CAATATTAGATGAATTTTAAAAATTTTAAA-TGGAGGAAAGTCCTCCCGAAAACATTTATGGAAC
65 -AATATT-GATGAATTTTAAAAATTAAAAACT-GAGAAAAATCATCCCGAAAACATTTATGGAGT
*
321414 A-AAAATTTTGATTTTTCGATAACAGGAAAATTTCAAAG
127 AGAAAA-TTTGA-TTTTCAATAACAGGAAAATTTCAAAG
* * *
321452 AAAAATTTAAAACTCATGAAAATAAATGAATTTTTGAAAACTAACTTAAAATGAATTAAATAATA
1 AAAAATTCAAAACTCATGAAAATAAATGAATTTTTGAAAACTAATTTAATATGAATTAAATAATA
* * * *
321517 ATATTGATGAATTTTAAAAATTAAAAACTAAGAAAAATCTTCCCAAAAACATTTACGGAGTAGAA
66 ATATTGATGAATTTTAAAAATTAAAAACTGAGAAAAATCATCCCGAAAACATTTATGGAGTAGAA
* *
321582 AATTTGATTTTCAATAACAGGGACATTTCAAAG
131 AATTTGATTTTCAATAACAGGAAAATTTCAAAG
* *
321615 AAAAATTCAAAACTCATGAAAATAGATGAATTTTTGAAAACTGAA-TTAATATAAATTAAATAAT
1 AAAAATTCAAAACTCATGAAAATAAATGAATTTTTGAAAACT-AATTTAATATGAATTAAATAAT
* *
321679 AATATTTGATGAATTTTAAAAATTAAAAACCGAGAAAAATCATCCTGAAAACATTTATGGAGTAG
65 AATA-TTGATGAATTTTAAAAATTAAAAACTGAGAAAAATCATCCCGAAAACATTTATGGAGTAG
* ** * * *
321744 AAAACTCCATATTTCAAAAATAGGAAAAATTTCAAGAA
129 AAAATTTGAT-TTTCAATAACAGG-AAAATTTCAA-AG
** * * * * *
321782 AAAAATGAAAAACTCATAAAAATGAATG-ATTTTTTAAAACTAATTTAATGGTG-ATTAAATGAT
1 AAAAATTCAAAACTCATGAAAATAAATGAATTTTTGAAAACTAATTTAAT-ATGAATTAAATAAT
321845 AATATT
65 AATATT
321851 TGAAGAACTT
Statistics
Matches: 338, Mismatches: 50, Indels: 22
0.82 0.12 0.05
Matches are distributed among these distances:
163 84 0.25
164 113 0.33
165 71 0.21
166 45 0.13
167 25 0.07
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (163 bp):
AAAAATTCAAAACTCATGAAAATAAATGAATTTTTGAAAACTAATTTAATATGAATTAAATAATA
ATATTGATGAATTTTAAAAATTAAAAACTGAGAAAAATCATCCCGAAAACATTTATGGAGTAGAA
AATTTGATTTTCAATAACAGGAAAATTTCAAAG
Found at i:323959 original size:35 final size:35
Alignment explanation
Indices: 323913--324694 Score: 665
Period size: 35 Copynumber: 22.3 Consensus size: 35
323903 TCTTACCAAA
*
323913 CAAACTCTTTTCATCATCATTTGGCTGTATCTGGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
* *
323948 CAAACTTTTTTCATCAATCATTTGGCTGCATCTGCT
1 CAAACTCTTTTCATC-ATCATTTGGCTGCATCTGGT
**
323984 CAAACTCTTTTCATCATTGTTTGGCTGCATCTGGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
* * *
324019 CAAACTCTTTTCGTCATCGTTTGGCTGCATTTGGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
* * * *
324054 TAAACTCTTTTCATCATCATTTGGTTGTATCTAGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
* * ** *
324089 CGAACTCCTTTCATCATCATTTGGCTATATCTAGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
* * * *
324124 CAAAATCTTTTCATCATTATTTGGTTGTATCTGGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
* * * *
324159 CAAACTCCTTTCATCATCGTTTGGTTGTATCTGGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
* * * *
324194 CAAACTCCTTTCATCATCGTTTGGCTACATCGGGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
** * * *
324229 CAAACTCCGTTCATCATCGTTTGGTTGCATCTAGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
* * * * ** *
324264 TAAACTCCTTTCACCATCGTTTGGCTATATTTGGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
* * *
324299 CAAACTTTTTTCGTCATCATTTGGCTACATCTGGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
* *
324334 CAAACTCTTTTCGTCATCATTTGGTTGCATCTGGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
* ** * *
324369 CAAACTTTTTTCATTGTCAGTTGGCTGTATCTGGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
** ** * *
324404 CAAACTCTTTTTGTTGTCGA-TTGGTTGTATCTGGT
1 CAAACTCTTTTCATCATC-ATTTGGCTGCATCTGGT
* * * * *
324439 CAAATTCTTTTCCTTATCATTTGGTTGCATCCGGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
* * * * * * *
324474 GAAACTCCTTCCGTTATCATTTGGTTGCAT-TCGAT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCT-GGT
* * *
324509 GAAACTCTTTTCATCAT-TTGTTGGCTGTATCTGGT
1 CAAACTCTTTTCATCATCAT-TTGGCTGCATCTGGT
* * *
324544 CAAACT-TCTTTCGTCATCATTTGGCTTCATCCGGT
1 CAAACTCT-TTTCATCATCATTTGGCTGCATCTGGT
* * * * *
324579 CAAACT-TCTTTCGTCATCGTTTGGTTACATCCGGT
1 CAAACTCT-TTTCATCATCATTTGGCTGCATCTGGT
* ** *
324614 CAAACTCTTTTCGTCATTGTTTGGCTACATCTGGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
* * ** *
324649 TAAACTCTTTTCATCACCATTTGGCTATATCTAGT
1 CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
*
324684 CAAACCCTTTT
1 CAAACTCTTTT
324695 TTTCTTGTTT
Statistics
Matches: 624, Mismatches: 114, Indels: 18
0.83 0.15 0.02
Matches are distributed among these distances:
34 3 0.00
35 585 0.94
36 36 0.06
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.43
Consensus pattern (35 bp):
CAAACTCTTTTCATCATCATTTGGCTGCATCTGGT
Found at i:326001 original size:166 final size:164
Alignment explanation
Indices: 325795--326294 Score: 494
Period size: 166 Copynumber: 3.0 Consensus size: 164
325785 TTCAAGCACC
* * * * *
325795 AAAATTCTTTAAATATTATCATTTAA-TCATTGTTAAATCAGTTTTGAAAAATTACTTTTATTTT
1 AAAATTCATCAAATATTATTATTTAATTCA-TATTAAATCAGTTTT-AAAAATT-CATTTATTTT
** * **
325859 ATGAGTTACTG-ATTTTCT-TTTAAAATTTTTCTTCTTTCTGAAATACGAAGTTTTTTACTCTAT
63 ATGAGTT-CTGAATTTTCTCTTTAAAA-TTCGCTTATTTCTGAAATACGAAGTTTCCTACTCTAT
* * * * *
325922 AAATATTTTTGGGGGGATTTTTCTTGGTTTTTAACTTTTT
126 AAATATTTTCGAGAGGATTTTTCTAGGTTCTTAA-TTTTT
* * *
325962 -AAATTTATCAAATTTTATTATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTCATTTTCA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTT-AAAAATTCATTTATTTT-A
* * * * *
326026 TGAGTTTTGAATTTTTTCTTTAAAATTCGCTTATTTTTGAAATATGTAGTTTCCTACTCTATAAA
64 TGAGTTCTGAATTTTCTCTTTAAAATTCGCTTATTTCTGAAATACGAAGTTTCCTACTCTATAAA
*
326091 TGTTTTCGAGAGGATTTTTCTAGGTTCTTAATTTTT
129 TATTTTCGAGAGGATTTTTCTAGGTTCTTAATTTTT
* * *
326127 AAAATTCATCAAATATTATTATTTAATTCATATGAAATCAGTTTTCAAATTTCATTTATTTTTAT
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTTAAAAATTCATTTA-TTTTAT
* * * * * *
326192 GAGTTTTGAATTTTTTCTTGAAAATTCTCATGT-TTTCT-AAATA-TAGAGTTTTCTACTAC-AT
65 GAGTTCTGAATTTTCTCTTTAAAATTCGC-T-TATTTCTGAAATACGA-AGTTTCCTACT-CTAT
* * * *
326253 AAATGTTTTCAAGGGGATTTTTCTGGGTTCTTAATTTTT
126 AAATATTTTCGAGAGGATTTTTCTAGGTTCTTAATTTTT
326292 AAA
1 AAA
326295 TTATTATTTA
Statistics
Matches: 283, Mismatches: 40, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
165 110 0.39
166 162 0.57
167 11 0.04
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.51
Consensus pattern (164 bp):
AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTTAAAAATTCATTTATTTTATG
AGTTCTGAATTTTCTCTTTAAAATTCGCTTATTTCTGAAATACGAAGTTTCCTACTCTATAAATA
TTTTCGAGAGGATTTTTCTAGGTTCTTAATTTTT
Found at i:326258 original size:165 final size:166
Alignment explanation
Indices: 325936--326361 Score: 526
Period size: 165 Copynumber: 2.6 Consensus size: 166
325926 ATTTTTGGGG
* * * * *
325936 GGATTTTTCTTGGTTTTTAACTTTTT-AAATTTATCAAATTTTATTATTTAATTCATATTAAATC
1 GGATTTTTCTAGGTTCTTAA-TTTTTAAAATTCATCAAATATTATTATTTAATTCATATGAAATC
* *
326000 AGTTTTCAAAAATTCATTCATTTTCATGAGTTTTGAATTTTTTCTTTAAAATTCGCTTATTTTTG
65 AGTTTTCAAAAATTCATTCATTTTCATGAGTTTTGAATTTTTTCTTGAAAATTCGCATATTTTTG
*
326065 AAATATGTAGTTTCCTACTCTATAAATGTTTTCGAGA
130 AAATATGTAGTTTCCTACTCTATAAATGTTTTCAAGA
326102 GGATTTTTCTAGGTTCTTAATTTTTAAAATTCATCAAATATTATTATTTAATTCATATGAAATCA
1 GGATTTTTCTAGGTTCTTAATTTTTAAAATTCATCAAATATTATTATTTAATTCATATGAAATCA
* * * * *
326167 GTTTTC-AAATTTCATTTATTTTTATGAGTTTTGAATTTTTTCTTGAAAATTCTCATGTTTTCT-
66 GTTTTCAAAAATTCATTCATTTTCATGAGTTTTGAATTTTTTCTTGAAAATTCGCATATTTT-TG
* *
326230 AAATATAG-AGTTTTCTACTAC-ATAAATGTTTTCAAGG
130 AAATAT-GTAGTTTCCTACT-CTATAAATGTTTTCAAGA
* * *
326267 GGATTTTTCTGGGTTCTTAA---TT----TT--T--AA-ATTATTATTTAATTCATATTAAATTA
1 GGATTTTTCTAGGTTCTTAATTTTTAAAATTCATCAAATATTATTATTTAATTCATATGAAATCA
*
326320 GTTTTCAAAAATTCATTCATTTTCTTGAGTTTTGAATTTTTT
66 GTTTTCAAAAATTCATTCATTTTCATGAGTTTTGAATTTTTT
326362 TTAGAAATTT
Statistics
Matches: 233, Mismatches: 22, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
153 30 0.13
154 33 0.14
156 1 0.00
158 2 0.01
162 2 0.01
165 102 0.44
166 63 0.27
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.52
Consensus pattern (166 bp):
GGATTTTTCTAGGTTCTTAATTTTTAAAATTCATCAAATATTATTATTTAATTCATATGAAATCA
GTTTTCAAAAATTCATTCATTTTCATGAGTTTTGAATTTTTTCTTGAAAATTCGCATATTTTTGA
AATATGTAGTTTCCTACTCTATAAATGTTTTCAAGA
Found at i:328700 original size:21 final size:20
Alignment explanation
Indices: 328667--328707 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
328657 GAGGTGTTGG
328667 ACATACTAAAAATGCATGAA
1 ACATACTAAAAATGCATGAA
* *
328687 ACATAGCTCAAAATGTATGAA
1 ACATA-CTAAAAATGCATGAA
328708 CATGGGTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (20 bp):
ACATACTAAAAATGCATGAA
Found at i:329753 original size:50 final size:51
Alignment explanation
Indices: 329611--329744 Score: 198
Period size: 51 Copynumber: 2.6 Consensus size: 51
329601 ATTTGCCTGC
* * * * *
329611 ATGTATCGATACATTGAATAATGTATTGATACATCTGGGT-AAAATCTAGA
1 ATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAAACCCAAA
*
329661 ATGTATCGATACAATGAAGAATGTATCGATACATCTGGGTAAAAACCCAAA
1 ATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAAACCCAAA
*
329712 ATGTATCAATACAATGAATAATGTATCGATACA
1 ATGTATCGATACAATGAATAATGTATCGATACA
329745 AATAGTAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 37 0.49
51 38 0.51
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (51 bp):
ATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAAACCCAAA
Found at i:332089 original size:166 final size:165
Alignment explanation
Indices: 331811--332367 Score: 653
Period size: 166 Copynumber: 3.4 Consensus size: 165
331801 TAATATATAC
* * * *
331811 AAAAAATTCAAAACTCATG-AAATTAATTGAATTTCTTG-AAATTGATTT--TATGAGAGTTTAA
1 AAAAAATTCAAAACTCATGAAAATGAA-TGAATTT-TTGAAAACTAATTTAATATGA-A-TTAAA
* ** * * *
331872 TAACAATATTAT-ATGAATTTTAAAAATTTTAAACCAAGTAAAATCCCCCCGAAAACATTTATAG
62 TAATAATATT-TGATGAATTTTAAAAATTAAAAACCAAGAAAAAT-CCCCCGAAAATATTTATGG
* * * **
331936 AATAGAAAACTC-GATTTTTCAAAAACAAAGAAATTTCAAAG
125 AGTAGAAAACTCTG-TTTTTCGAAAACAAAGGAATTTTTAAG
* * * * *
331977 AAAAAATTCAAAACTCATGAAAATAAATTAATTTTTTAAAAATAATTTAATATTAATTAAATAAT
1 AAAAAATTCAAAACTCATGAAAATGAATGAATTTTTGAAAACTAATTTAATATGAATTAAATAAT
*
332042 AATATTTGATGAATTTTAAAAATAAAAAAACCAAGAAAAATCCCCCGAAAAATATTTATGGAGTA
66 AATATTTGATGAATTTTAAAAAT-TAAAAACCAAGAAAAATCCCCCG-AAAATATTTATGGAGTA
* *
332107 GAAAACTCTGTATTTT-GAAAATAAAGGAATTTTTAAT
129 GAAAACTCTGT-TTTTCGAAAACAAAGGAATTTTTAAG
*
332144 AAAAAATTCAAAACTCATGAAAATGAATGAATTTTTGAAAACTGATTTAATATGAATTAAATAAT
1 AAAAAATTCAAAACTCATGAAAATGAATGAATTTTTGAAAACTAATTTAATATGAATTAAATAAT
* * *
332209 AATATTTGATGAATTTAAAAAATTAAGAACCAAGAAAAATCCCTTCGAAAATATTTATGGAGTAG
66 AATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCC-CCGAAAATATTTATGGAGTAG
* * *
332274 AAAACTCTGTATTTCGAAAAC-ATGTGAATTTTTAGG
130 AAAACTCTGTTTTTCGAAAACAAAG-GAATTTTTAAG
* * *
332310 AAAAAATTAAAAACTCATAAAAATGAATGAATTTTTGAAAACTAATTTAAGATGAATT
1 AAAAAATTCAAAACTCATGAAAATGAATGAATTTTTGAAAACTAATTTAATATGAATT
332368 TTAAAAATTA
Statistics
Matches: 339, Mismatches: 40, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
165 8 0.02
166 181 0.53
167 141 0.42
168 9 0.03
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.32
Consensus pattern (165 bp):
AAAAAATTCAAAACTCATGAAAATGAATGAATTTTTGAAAACTAATTTAATATGAATTAAATAAT
AATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCGAAAATATTTATGGAGTAGA
AAACTCTGTTTTTCGAAAACAAAGGAATTTTTAAG
Found at i:332375 original size:144 final size:142
Alignment explanation
Indices: 332216--332501 Score: 398
Period size: 144 Copynumber: 2.0 Consensus size: 142
332206 AATAATATTT
* *
332216 GATGAATTTAAAAAATTAAGAACCAAGAAAAATCCCTTCGAAAATATTTAT-GGAGTAGAAAACT
1 GATGAATTTAAAAAATTAAGAACCAAGAAAAATCCCCTCGAAAACATTTATAGG-GTAGAAAACT
* * * *
332280 CTGTATTTC-GAAA-ACATGTGAATTTTTAGGAAAAAATTAAAAACTCATAAAAATGAATGAATT
65 CTATATTTCAGAAATA-A-GAGAA-TTTCA-AAAAAAATTAAAAACTCATAAAAATGAATGAATT
332343 TTTGAAAACTAATTTAA
126 TTTGAAAACTAATTTAA
* * * *
332360 GATGAATTTTAAAAATTAAGAACTAAGAAAAATCCCCTCGAAAACATTTATAGGGTAGGAAACTT
1 GATGAATTTAAAAAATTAAGAACCAAGAAAAATCCCCTCGAAAACATTTATAGGGTAGAAAACTC
* *
332425 TATATTTCAGAAATAAGAGAATTTCAAAAAAAATTCAAAACTCATGAAAATGAATGAATTTTTGA
66 TATATTTCAGAAATAAGAGAATTTCAAAAAAAATTAAAAACTCATAAAAATGAATGAATTTTTGA
332490 AAACTAATTTAA
131 AAACTAATTTAA
332502 TATAAATTAA
Statistics
Matches: 127, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
142 48 0.38
143 4 0.03
144 67 0.53
145 7 0.06
146 1 0.01
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.29
Consensus pattern (142 bp):
GATGAATTTAAAAAATTAAGAACCAAGAAAAATCCCCTCGAAAACATTTATAGGGTAGAAAACTC
TATATTTCAGAAATAAGAGAATTTCAAAAAAAATTAAAAACTCATAAAAATGAATGAATTTTTGA
AAACTAATTTAA
Found at i:332484 original size:308 final size:311
Alignment explanation
Indices: 332049--332667 Score: 862
Period size: 308 Copynumber: 2.0 Consensus size: 311
332039 AATAATATTT
*
332049 GATGAATTTTAAAAATAAAAAAACCAAGAAAAATCCCCCGAAAAATATTTATGGAGTAGAAAACT
1 GATGAATTTTAAAAATAAAAAAACCAAGAAAAATCCCCCGAAAAACATTTATGGAGTAGAAAACT
* *
332114 CTGTATTTTGAAAATAAAGGAATTTTTAATAAAAAATTCAAAACTCATGAAAATGAATGAATTTT
66 CTGTATTTTCAAAATAAAGGAATTTTCAATAAAAAATTCAAAACTCATGAAAATGAATGAATTTT
* * * *
332179 TGAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTAAAAAATTAAGAACCAAGA
131 TGAAAACTAATTTAATATAAATTAAATAACAATATTTGATGAATTTAAAAAATTAAAAACCAAGA
* * * * * * **
332244 AAAATCCCT-TCGAAAATATTTATGGAGTAGAAAACTCTGTATTTCGAAAACATG-TGAATTTTT
196 AAAAT-CCTACCAAAAACATTTATGGAGTAGAAAACTCTATATTTCGAAAAC-GGAAGAATTTCC
*
332307 AGGAAAAAATTAAAAACTCATAAAAATGAATGAATTTTTGAAAACTAATTTAA
259 AAGAAAAAATTAAAAACTCATAAAAATGAATGAATTTTTGAAAACTAATTTAA
* * * *
332360 GATGAATTTTAAAAAT-TAAGAACTAAGAAAAATCCCCTCG-AAAACATTTATAGG-GTAGGAAA
1 GATGAATTTTAAAAATAAAAAAACCAAGAAAAATCCCC-CGAAAAACATTTAT-GGAGTAGAAAA
332422 CT-T-TATATTTCAGAAAT-AAGAGAA-TTTCAA-AAAAAATTCAAAACTCATGAAAATGAATGA
64 CTCTGTAT-TTTCA-AAATAAAG-GAATTTTCAATAAAAAATTCAAAACTCATGAAAATGAATGA
* *
332482 ATTTTTGAAAACTAATTTAATATAAATTAAGTAACAATATTTGATGAATTTTAAAAATTAAAAAC
126 ATTTTTGAAAACTAATTTAATATAAATTAAATAACAATATTTGATGAATTTAAAAAATTAAAAAC
* * *
332547 CAAGAAAAATTCTACCAAAAACATTTGTGGAGTCGAAAACTCTATATTTCGAAAACGGAAGAATT
191 CAAGAAAAATCCTACCAAAAACATTTATGGAGTAGAAAACTCTATATTTCGAAAACGGAAGAATT
* *
332612 TCCAAGAAAAAATTTAAAACTCATAAAAATGAATGAATTTTTTAAAACTAATTTAA
256 TCCAAGAAAAAATTAAAAACTCATAAAAATGAATGAATTTTTGAAAACTAATTTAA
332668 TATTGATTAA
Statistics
Matches: 274, Mismatches: 27, Indels: 17
0.86 0.08 0.05
Matches are distributed among these distances:
307 3 0.01
308 194 0.71
309 13 0.05
310 44 0.16
311 20 0.07
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (311 bp):
GATGAATTTTAAAAATAAAAAAACCAAGAAAAATCCCCCGAAAAACATTTATGGAGTAGAAAACT
CTGTATTTTCAAAATAAAGGAATTTTCAATAAAAAATTCAAAACTCATGAAAATGAATGAATTTT
TGAAAACTAATTTAATATAAATTAAATAACAATATTTGATGAATTTAAAAAATTAAAAACCAAGA
AAAATCCTACCAAAAACATTTATGGAGTAGAAAACTCTATATTTCGAAAACGGAAGAATTTCCAA
GAAAAAATTAAAAACTCATAAAAATGAATGAATTTTTGAAAACTAATTTAA
Found at i:332689 original size:166 final size:164
Alignment explanation
Indices: 332360--332864 Score: 569
Period size: 165 Copynumber: 3.1 Consensus size: 164
332350 ACTAATTTAA
* * *
332360 GATGAATTTTAAAAATTAAGAACTAAGAAAAATCCCCTCGAAAACATTTATAGG-GTAGGAAACT
1 GATGAATTTTAAAAATTAAAAACTAAGAAAAATCCCCTCAAAAACATTTAT-GGAGTAGAAAACT
* * *
332424 TTATATTTCAGAAATA-AG-AGAATTT-CAAAAAAAATTCAAAACTCATGAAAATGAATGAATTT
65 CTATATTTC-GAAA-ACGGAAGAATTTCCAAAAAAAATTTAAAACTCAT-AAAATGAATGAATTT
* ** * *
332486 TTGAAAACTAATTTAATATAAATTAAGTAACAATATTT
127 TTTAAAACTAATTTAATATTGATTAAATAATAATATTT
* ** * *
332524 GATGAATTTTAAAAATTAAAAACCAAGAAAAATTCTAC-CAAAAACATTTGTGGAGTCGAAAACT
1 GATGAATTTTAAAAATTAAAAACTAAGAAAAA-TCCCCTCAAAAACATTTATGGAGTAGAAAACT
332588 CTATATTTCGAAAACGGAAGAATTTCCAAGAAAAAATTTAAAACTCATAAAAATGAATGAATTTT
65 CTATATTTCGAAAACGGAAGAATTTCCAA-AAAAAATTTAAAACTCAT-AAAATGAATGAATTTT
332653 TTAAAACTAATTTAATATTGATTAAATAATAATATTT
128 TTAAAACTAATTTAATATTGATTAAATAATAATATTT
* *
332690 GATAAATTTTAAAAATT-AAAACTAAGAAAAATCCCCTCAAAAACATTTATGGACTAGAAAACTC
1 GATGAATTTTAAAAATTAAAAACTAAGAAAAATCCCCTCAAAAACATTTATGGAGTAGAAAACTC
* * * * * *
332754 TGTATTTCGGACACAGAGAA-AA-TTCTAAAAGAAAA-TTAATAACTCATAAAATAAAAAGAATT
66 TATATTTCGAAAAC-G-GAAGAATTTCCAAAA-AAAATTTAA-AACTCATAAAAT-GAATGAATT
* ** *
332816 TTTTAAAACTTATTTAATGGTGATTAAATCATAATATTT
126 TTTTAAAACTAATTTAATATTGATTAAATAATAATATTT
* *
332855 AAAGAATTTT
1 GATGAATTTT
332865 GATGCTTGAA
Statistics
Matches: 292, Mismatches: 37, Indels: 23
0.83 0.11 0.07
Matches are distributed among these distances:
162 1 0.00
163 7 0.02
164 78 0.27
165 119 0.41
166 84 0.29
167 3 0.01
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (164 bp):
GATGAATTTTAAAAATTAAAAACTAAGAAAAATCCCCTCAAAAACATTTATGGAGTAGAAAACTC
TATATTTCGAAAACGGAAGAATTTCCAAAAAAAATTTAAAACTCATAAAATGAATGAATTTTTTA
AAACTAATTTAATATTGATTAAATAATAATATTT
Found at i:338969 original size:22 final size:19
Alignment explanation
Indices: 338929--338971 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
338919 TTTAAAAATA
338929 TATAAAATGTGTATTTTAT
1 TATAAAATGTGTATTTTAT
* *
338948 TATAATAATTTGTA-TATAT
1 TATAA-AATGTGTATTTTAT
338967 TATAA
1 TATAA
338972 TATCTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (19 bp):
TATAAAATGTGTATTTTAT
Done.