Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 7 of 318
Found at i:1766938 original size:21 final size:21
Alignment explanation
Indices: 1766900--1766939 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1766890 CTTTCTCTAT
1766900 TAATCATTATAAACCTAAAAA
1 TAATCATTATAAACCTAAAAA
*
1766921 TAAT-ATTATTAACACTAAA
1 TAATCATTATAAAC-CTAAA
1766940 CTTAATGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATCATTATAAACCTAAAAA
Found at i:1766945 original size:21 final size:21
Alignment explanation
Indices: 1766898--1766945 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1766888 TACTTTCTCT
1766898 ATTAATCATTATAAACCTAAA
1 ATTAATCATTATAAACCTAAA
* *
1766919 AATAAT-ATTATTAACACTAAA
1 ATTAATCATTATAAAC-CTAAA
*
1766940 CTTAAT
1 ATTAAT
1766946 GAGCTTAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTAATCATTATAAACCTAAA
Found at i:1771559 original size:166 final size:162
Alignment explanation
Indices: 1771273--1771608 Score: 469
Period size: 166 Copynumber: 2.0 Consensus size: 162
1771263 GTATGAAATT
*
1771273 TTTAAATAATATTAAACATTTAGCTTATATGTAAATTTAATATTAGTTGAATAAAGTAAATTAAA
1 TTTAAA-AATATTAAACATTCAGCTTATATGTAAATTTAATATTAGTTGAATAAAGTAAATTAAA
* * * *
1771338 TTCCCATGTAAAGGCATAGTTAGGAGAGTTGGTAGGGGTTAGTCTCCTTTAAAATAGAAAATTTT
65 TTCCCATGTAAAGGCATAGTTAGGAGAGTTGGTAGGGGCTAGCCCCCTCTAAAATAGAAAATTTT
1771403 CCATTTACGTTTTAAAGGTAAAATAACATTTTGTCCC
130 CCA--TAC-TTTTAAAGGTAAAATAACATTTT-TCCC
* * *
1771440 TTTAAAAATATTAAACATTCAG-TTGATATGTAAATTTAGTATTAGTTGAATAAGGTAAATTGAA
1 TTTAAAAATATTAAACATTCAGCTT-ATATGTAAATTTAATATTAGTTGAATAAAGTAAATTAAA
* **
1771504 TTTCCATGTAGGGGCATAGTTA-GAGGAGTTGGTAGGGGCTAGCCCCCTCTAAAATAGAAAATTT
65 TTCCCATGTAAAGGCATAGTTAGGA-GAGTTGGTAGGGGCTAGCCCCCTCTAAAATAGAAAATTT
* *
1771568 TCCATGCTTTTGAAGGTAAAATAACATTTTTCCC
129 TCCATACTTTTAAAGGTAAAATAACATTTTTCCC
*
1771602 CTTAAAA
1 TTTAAAA
1771609 TTAATAAAAA
Statistics
Matches: 153, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
162 10 0.07
163 22 0.14
164 2 0.01
165 4 0.03
166 109 0.71
167 6 0.04
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.36
Consensus pattern (162 bp):
TTTAAAAATATTAAACATTCAGCTTATATGTAAATTTAATATTAGTTGAATAAAGTAAATTAAAT
TCCCATGTAAAGGCATAGTTAGGAGAGTTGGTAGGGGCTAGCCCCCTCTAAAATAGAAAATTTTC
CATACTTTTAAAGGTAAAATAACATTTTTCCC
Found at i:1773097 original size:29 final size:29
Alignment explanation
Indices: 1773060--1773140 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 29
1773050 ATTAATACAC
* *
1773060 GATAGAATTACATTTTTATTTCTTAAAAT
1 GATAAAATTACATTTTTATTTCTAAAAAT
*
1773089 GATAAAATTACAATTTAATATTTCTAAAAAT
1 GATAAAATTAC-ATTT-TTATTTCTAAAAAT
*
1773120 TATAAAAAAATTACATTTTTA
1 GAT---AAAATTACATTTTTA
1773141 AGTTTCTAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
29 10 0.24
30 4 0.10
31 14 0.33
32 2 0.05
33 4 0.10
34 8 0.19
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (29 bp):
GATAAAATTACATTTTTATTTCTAAAAAT
Found at i:1773147 original size:34 final size:30
Alignment explanation
Indices: 1773060--1773153 Score: 82
Period size: 34 Copynumber: 3.0 Consensus size: 30
1773050 ATTAATACAC
* *
1773060 GATAGAATTACATTTTT-ATTTCTTAAAAT
1 GATAAAATTACATTTTTAATTTCTAAAAAT
* *
1773089 GATAAAATTACAATTTAATATTTCTAAAAAT
1 GATAAAATTACATTTTTA-ATTTCTAAAAAT
*
1773120 TATAAAAAAATTACATTTTTAAGTTTCTAGAAAA
1 GAT---AAAATTACATTTTTAA-TTTCTA-AAAA
1773154 AATTAATTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.27
31 13 0.25
33 1 0.02
34 19 0.37
35 4 0.08
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.41
Consensus pattern (30 bp):
GATAAAATTACATTTTTAATTTCTAAAAAT
Found at i:1784017 original size:23 final size:23
Alignment explanation
Indices: 1783984--1784037 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1783974 CGAAAATAAT
*
1783984 AAATTATTATT-TTTATCATTTGAA
1 AAATT-TTATTATTTATAATTT-AA
1784008 AAATTTTATTATTTATAATTTAA
1 AAATTTTATTATTTATAATTTAA
*
1784031 AATTTTT
1 AAATTTT
1784038 CAAAGTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
AAATTTTATTATTTATAATTTAA
Found at i:1785086 original size:4 final size:4
Alignment explanation
Indices: 1785077--1785104 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1785067 TTTTCCCTCA
1785077 CCCT CCCT CCCT CCCT CCCT CCCT CCCT
1 CCCT CCCT CCCT CCCT CCCT CCCT CCCT
1785105 TACCCTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.75, G:0.00, T:0.25
Consensus pattern (4 bp):
CCCT
Found at i:1787342 original size:83 final size:83
Alignment explanation
Indices: 1787203--1787369 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 83
1787193 ATTCTTTATG
1787203 TGCACACAAAAAGATATTTAAGTGCATCAATCAAATTTATTTAACCAGCGTATGGGTCTCTTTAT
1 TGCACACAAAAAGATATTTAAGTGCATCAATCAAATTTATTTAACCAGCGTATGGGTCTCTTTAT
1787268 GTTTGGGGTATAATCCTC
66 GTTTGGGGTATAATCCTC
*
1787286 TGCACACAAAGAGATATTTAAGTGCATCAATCAAATTTATTTAACCAGCGTATGGGTCTCTTTAT
1 TGCACACAAAAAGATATTTAAGTGCATCAATCAAATTTATTTAACCAGCGTATGGGTCTCTTTAT
1787351 GTTTGGGGTATAATCCTC
66 GTTTGGGGTATAATCCTC
1787369 T
1 T
1787370 AAAGGTTCTA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (83 bp):
TGCACACAAAAAGATATTTAAGTGCATCAATCAAATTTATTTAACCAGCGTATGGGTCTCTTTAT
GTTTGGGGTATAATCCTC
Found at i:1792890 original size:36 final size:36
Alignment explanation
Indices: 1792844--1792915 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
1792834 AAACCTAACT
1792844 CTCTTCAAACGAGATAAGACTACAAATAGTAAGATA
1 CTCTTCAAACGAGATAAGACTACAAATAGTAAGATA
1792880 CTCTTCAAACGAGATAAGACTACAAATAGTAAGATA
1 CTCTTCAAACGAGATAAGACTACAAATAGTAAGATA
1792916 ACTGGTAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (36 bp):
CTCTTCAAACGAGATAAGACTACAAATAGTAAGATA
Found at i:1792916 original size:20 final size:20
Alignment explanation
Indices: 1792855--1792916 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
1792845 TCTTCAAACG
1792855 AGATAAGACTACAAATAGTA
1 AGATAAGACTACAAATAGTA
** * *
1792875 AGAT-ACTCTTCAAA-CG--
1 AGATAAGACTACAAATAGTA
1792891 AGATAAGACTACAAATAGTA
1 AGATAAGACTACAAATAGTA
1792911 AGATAA
1 AGATAA
1792917 CTGGTAACTG
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
16 4 0.13
17 7 0.23
18 2 0.07
19 7 0.23
20 10 0.33
ACGTcount: A:0.52, C:0.13, G:0.15, T:0.21
Consensus pattern (20 bp):
AGATAAGACTACAAATAGTA
Found at i:1794496 original size:27 final size:27
Alignment explanation
Indices: 1794458--1794514 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1794448 CAAGCCTACA
1794458 AAATGAAGGCATCAGCTACTAGATCCG
1 AAATGAAGGCATCAGCTACTAGATCCG
1794485 AAATGAAGGCATCAGCTACTAGATCCG
1 AAATGAAGGCATCAGCTACTAGATCCG
1794512 AAA
1 AAA
1794515 ACATCCGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (27 bp):
AAATGAAGGCATCAGCTACTAGATCCG
Found at i:1802185 original size:2 final size:2
Alignment explanation
Indices: 1802178--1802208 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1802168 GAAAAGGTAA
1802178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1802209 GGTTAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1812472 original size:53 final size:53
Alignment explanation
Indices: 1812384--1812534 Score: 196
Period size: 53 Copynumber: 2.8 Consensus size: 53
1812374 CTTACACGGT
* *
1812384 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCA-ACTATGGTCTTATACGGAATCACATTA
*
1812439 TCACATTATACCGATGCCATAGCCCAACTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAACTATGGTCTTATACGGAATCACATTA
** * * *
1812492 TCACATTGCACCAATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAACTATGGTCTTATACGG
1812535 GCGCACTTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 2 0.02
53 78 0.90
54 1 0.01
55 6 0.07
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAACTATGGTCTTATACGGAATCACATTA
Found at i:1816163 original size:27 final size:27
Alignment explanation
Indices: 1816128--1816210 Score: 101
Period size: 27 Copynumber: 3.4 Consensus size: 27
1816118 ATATTTAATG
*
1816128 TAAAATTCAAATTAGTATTTAAAGTTT
1 TAAAGTTCAAATTAGTATTTAAAGTTT
1816155 TAAAGTTCAAATTAG----T--A--TT
1 TAAAGTTCAAATTAGTATTTAAAGTTT
1816174 TAAAGTTCAAATTAGTATTTAAAGTTT
1 TAAAGTTCAAATTAGTATTTAAAGTTT
1816201 TAAAGTTCAA
1 TAAAGTTCAA
1816211 CACAATAAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
19 17 0.36
21 1 0.02
23 2 0.04
25 1 0.02
27 26 0.55
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (27 bp):
TAAAGTTCAAATTAGTATTTAAAGTTT
Found at i:1816177 original size:19 final size:19
Alignment explanation
Indices: 1816153--1816199 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
1816143 TATTTAAAGT
1816153 TTTAAAGTTCAAATTAGTA
1 TTTAAAGTTCAAATTAGTA
1816172 TTTAAAGTTCAAATTAGTA
1 TTTAAAGTTCAAATTAGTA
1816191 TTTAAAGTT
1 TTTAAAGTT
1816200 TTAAAGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTAAAGTTCAAATTAGTA
Found at i:1816750 original size:18 final size:17
Alignment explanation
Indices: 1816726--1816770 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1816716 ATTTTAGTTG
1816726 AATTTTTATATTTTTAA
1 AATTTTTATATTTTTAA
*
1816743 ATATTTTTGA-ATTTTTAC
1 A-ATTTTT-ATATTTTTAA
1816761 AATTTTTATA
1 AATTTTTATA
1816771 CAAAATTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 1 0.04
17 8 0.33
18 14 0.58
19 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
AATTTTTATATTTTTAA
Found at i:1832001 original size:25 final size:25
Alignment explanation
Indices: 1831987--1832055 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
1831977 CTTTTTTTTT
1831987 CTTTTTAAGTTTTTTTATTTATTTA
1 CTTTTTAAGTTTTTTTATTTATTTA
1832012 CTTTTTAAGTTTTTTTA-TT-TTTA
1 CTTTTTAAGTTTTTTTATTTATTTA
*
1832035 CTTTATTTA-TTTTATTTATTT
1 CTTT-TTAAGTTTT-TTTATTT
1832056 GTTTGTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
23 12 0.30
24 9 0.22
25 19 0.47
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.74
Consensus pattern (25 bp):
CTTTTTAAGTTTTTTTATTTATTTA
Found at i:1832145 original size:21 final size:22
Alignment explanation
Indices: 1832089--1832136 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
1832079 GTAAATAAAT
* *
1832089 AAAAAACTTAAAAAGAAAAACA
1 AAAAAAATGAAAAAGAAAAACA
1832111 AAAAAAATGAAAAA-AAAAACA
1 AAAAAAATGAAAAAGAAAAACA
1832132 AAAAA
1 AAAAA
1832137 TCAGAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.83, C:0.06, G:0.04, T:0.06
Consensus pattern (22 bp):
AAAAAAATGAAAAAGAAAAACA
Found at i:1832164 original size:7 final size:7
Alignment explanation
Indices: 1832072--1832168 Score: 54
Period size: 7 Copynumber: 13.3 Consensus size: 7
1832062 TATTGGTTTT
1832072 ATAAAAA
1 ATAAAAA
*
1832079 GTAAATAA
1 ATAAA-AA
1832087 ATAAAAA
1 ATAAAAA
*
1832094 ACTTAAAA
1 A-TAAAAA
*
1832102 AGAAAAA
1 ATAAAAA
*
1832109 CAAAAAAA
1 -ATAAAAA
*
1832117 AT-GAAA
1 ATAAAAA
1832123 A-AAAAA
1 ATAAAAA
*
1832129 ACAAAAA
1 ATAAAAA
1832136 ATCAGAAAA
1 AT-A-AAAA
**
1832145 AGTAACCA
1 A-TAAAAA
1832153 ATAAAAA
1 ATAAAAA
1832160 ATAAAAA
1 ATAAAAA
1832167 AT
1 AT
1832169 TTAGATTGTT
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
6 8 0.12
7 31 0.46
8 22 0.32
9 6 0.09
10 1 0.01
ACGTcount: A:0.76, C:0.06, G:0.05, T:0.12
Consensus pattern (7 bp):
ATAAAAA
Found at i:1832227 original size:19 final size:19
Alignment explanation
Indices: 1832203--1832239 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1832193 TACATAACAG
1832203 GCTAATATTTTGAAATTTA
1 GCTAATATTTTGAAATTTA
1832222 GCTAATATTTTGAAATTT
1 GCTAATATTTTGAAATTT
1832240 GGTGACGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (19 bp):
GCTAATATTTTGAAATTTA
Found at i:1832435 original size:34 final size:34
Alignment explanation
Indices: 1832392--1832459 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1832382 AAAAAATTAA
1832392 ATTTTTAATACAAATTGCTGACTTACTATGTTGG
1 ATTTTTAATACAAATTGCTGACTTACTATGTTGG
1832426 ATTTTTAATACAAATTGCTGACTTACTATGTTGG
1 ATTTTTAATACAAATTGCTGACTTACTATGTTGG
1832460 TAACGCCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (34 bp):
ATTTTTAATACAAATTGCTGACTTACTATGTTGG
Found at i:1841778 original size:18 final size:18
Alignment explanation
Indices: 1841757--1841856 Score: 69
Period size: 18 Copynumber: 5.2 Consensus size: 18
1841747 AAAGTTTTTT
1841757 AAAATTTTAAATATATTA
1 AAAATTTTAAATATATTA
*
1841775 AAAATTGTTAATTATAATTA
1 AAAATT-TTAAATAT-ATTA
* *
1841795 ATTTTAAATTTTTAATATATTT
1 A----AAATTTTAAATATATTA
*
1841817 AAAA-TTTAAA-AAACTTAA
1 AAAATTTTAAATATA-TT-A
*
1841835 AAAAATTTAAATATATTA
1 AAAATTTTAAATATATTA
1841853 AAAA
1 AAAA
1841857 AAGTGTTAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
16 2 0.03
17 7 0.11
18 18 0.28
19 15 0.23
20 7 0.11
22 4 0.06
23 6 0.09
24 5 0.08
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (18 bp):
AAAATTTTAAATATATTA
Found at i:1841857 original size:18 final size:18
Alignment explanation
Indices: 1841757--1841857 Score: 53
Period size: 19 Copynumber: 5.3 Consensus size: 18
1841747 AAAGTTTTTT
*
1841757 AAAATTTTAAATATATTA
1 AAAAATTTAAATATATTA
* *
1841775 AAAATTGTTAATTATAATTA
1 AAAAAT-TTAAATAT-ATTA
* *
1841795 ATTTTAAATTTTTAATATATT-
1 A----AAAATTTAAATATATTA
* *
1841816 TAAAATTTAAA-AAACTTAA
1 AAAAATTTAAATATA-TT-A
1841835 AAAAATTTAAATATATTA
1 AAAAATTTAAATATATTA
1841853 AAAAA
1 AAAAA
1841858 AGTGTTAAGT
Statistics
Matches: 64, Mismatches: 9, Indels: 20
0.69 0.10 0.22
Matches are distributed among these distances:
16 2 0.03
17 10 0.16
18 12 0.19
19 19 0.30
20 7 0.11
22 3 0.05
23 6 0.09
24 5 0.08
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (18 bp):
AAAAATTTAAATATATTA
Found at i:1841870 original size:21 final size:19
Alignment explanation
Indices: 1841817--1841858 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1841807 TAATATATTT
*
1841817 AAAATTTAAA-AAACTTAAA
1 AAAATTTAAATATA-TTAAA
1841836 AAAATTTAAATATATTAAA
1 AAAATTTAAATATATTAAA
1841855 AAAA
1 AAAA
1841859 GTGTTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATTTAAATATATTAAA
Found at i:1841931 original size:87 final size:80
Alignment explanation
Indices: 1841752--1841942 Score: 215
Period size: 80 Copynumber: 2.3 Consensus size: 80
1841742 CTTTTAAAGT
* * ** *
1841752 TTTTTAAAATTTTAAATATATT--AAAAATTGTTAATTATAATTAATTTTAAATTTTTAATATAT
1 TTTTTAAAATTTTAAATATATTAAAAAAAGTGTTAAGTATAACCAATTTTAAAATTTTAATATAT
1841815 TTAAAATTTAAAAAA
66 TTAAAATTTAAAAAA
* ** *
1841830 CTTAAAAAAATTTAAATATATTAAAAAAAGTGTTAAGTATAACCAATTTTAAAATTTTAATATAT
1 TTTTTAAAATTTTAAATATATTAAAAAAAGTGTTAAGTATAACCAATTTTAAAATTTTAATATAT
1841895 ATTCAATATACTTTTTAAAAAA
66 -TT-AA-A-A---TTTAAAAAA
*
1841917 TTTTTAAACTTTTAAATATATTAAAA
1 TTTTTAAAATTTTAAATATATTAAAA
1841943 TTTTAATATA
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
78 18 0.20
80 36 0.40
81 2 0.02
82 2 0.02
83 1 0.01
84 1 0.01
87 30 0.33
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (80 bp):
TTTTTAAAATTTTAAATATATTAAAAAAAGTGTTAAGTATAACCAATTTTAAAATTTTAATATAT
TTAAAATTTAAAAAA
Found at i:1841950 original size:16 final size:17
Alignment explanation
Indices: 1841920--1842049 Score: 57
Period size: 17 Copynumber: 6.9 Consensus size: 17
1841910 TAAAAAATTT
*
1841920 TTAAACTTTTAAATATA
1 TTAAAATTTTAAATATA
1841937 TTAAAATTTT-AATATA
1 TTAAAATTTTAAATATA
*
1841953 TTTAATATATTTTTTAATAGGTA
1 -TTAA-A-A-TTTTAAATA--TA
* *
1841976 -AAGAGAATTTTTTAATATA
1 TTA-A-AA-TTTTAAATATA
* * *
1841995 TTTACAATTTTAAAAAAAA
1 -TTAAAATTTT-AAATATA
1842014 TTAAAAATAATTTAAATATA
1 TT-AAAAT--TTTAAATATA
1842034 TTAAAATTTTAAATAT
1 TTAAAATTTTAAATAT
1842050 GTTGAAGAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
16 6 0.07
17 22 0.25
18 7 0.08
19 18 0.20
20 11 0.12
21 20 0.23
22 2 0.02
23 2 0.02
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAAATTTTAAATATA
Found at i:1842166 original size:81 final size:79
Alignment explanation
Indices: 1842019--1842186 Score: 198
Period size: 81 Copynumber: 2.1 Consensus size: 79
1842009 AAAAATTAAA
* * * * *
1842019 AATAATTTAAATATATTAAAATTTTAAATATGTTGAAGAAAATATTGAGTATAACCAATTTTAAT
1 AATAATTTAAATATATTAAAATTTGAAATA-GTTAAAAAAAATATTAAGCATAACCAATTTTAAT
1842084 TTTTTTAATATACTT
65 TTTTTTAATATACTT
*
1842099 AATACATTTAAATATATTAAAATTTGAACATA-TTAAAAAAAAT-TTAAGCATAACTAATTTTAA
1 AATA-ATTTAAATATATTAAAATTTGAA-ATAGTTAAAAAAAATATTAAGCATAACCAATTTTAA
** *
1842162 -AATTTTAATATATTT
64 TTTTTTTAATATACTT
1842177 AATATATTTA
1 AATA-ATTTA
1842187 CCTATCAGAA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
78 21 0.28
79 17 0.22
80 13 0.17
81 22 0.29
82 3 0.04
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (79 bp):
AATAATTTAAATATATTAAAATTTGAAATAGTTAAAAAAAATATTAAGCATAACCAATTTTAATT
TTTTTAATATACTT
Found at i:1842859 original size:6 final size:6
Alignment explanation
Indices: 1842850--1842889 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
1842840 TTATGAGACT
1842850 GAGGGC GAGGGC GAGGGC GAGGGC GAGGGC GAGGGC GAGG
1 GAGGGC GAGGGC GAGGGC GAGGGC GAGGGC GAGGGC GAGG
1842890 CAATTGCGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.15, G:0.68, T:0.00
Consensus pattern (6 bp):
GAGGGC
Found at i:1858971 original size:13 final size:13
Alignment explanation
Indices: 1858953--1858977 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1858943 TATCATTCAT
1858953 AATATAAATATAA
1 AATATAAATATAA
1858966 AATATAAATATA
1 AATATAAATATA
1858978 TAAGATCTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATATAAATATAA
Found at i:1859400 original size:7 final size:7
Alignment explanation
Indices: 1859382--1859415 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
1859372 CCAATTATGA
1859382 TCATGATT
1 TCATG-TT
1859390 TCATGTT
1 TCATGTT
1859397 TCATGTT
1 TCATGTT
1859404 TCATGTT
1 TCATGTT
1859411 TCATG
1 TCATG
1859416 ATCTATGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.81
8 5 0.19
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.53
Consensus pattern (7 bp):
TCATGTT
Found at i:1859407 original size:14 final size:15
Alignment explanation
Indices: 1859382--1859417 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
1859372 CCAATTATGA
1859382 TCATGATTTCATGTT
1 TCATGATTTCATGTT
1859397 TCATG-TTTCATGTT
1 TCATGATTTCATGTT
1859411 TCATGAT
1 TCATGAT
1859418 CTATGATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (15 bp):
TCATGATTTCATGTT
Found at i:1859890 original size:39 final size:38
Alignment explanation
Indices: 1859833--1859916 Score: 132
Period size: 39 Copynumber: 2.2 Consensus size: 38
1859823 TGAATTTGAA
*
1859833 AATTTGATTTAATTTTATTTTAAAAAGTCAATAACTAG
1 AATTTGATTTAAATTTATTTTAAAAAGTCAATAACTAG
* *
1859871 AATTTGTTTTAGAATTTATTTTAAAAAGTCAATAATTAG
1 AATTTGATTTA-AATTTATTTTAAAAAGTCAATAACTAG
1859910 AATTTGA
1 AATTTGA
1859917 CATTTAAAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 10 0.24
39 31 0.76
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.45
Consensus pattern (38 bp):
AATTTGATTTAAATTTATTTTAAAAAGTCAATAACTAG
Found at i:1866758 original size:15 final size:15
Alignment explanation
Indices: 1866738--1866767 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1866728 CCTAGTGCCG
*
1866738 CCGCCACCACCACCA
1 CCGCCACCACAACCA
1866753 CCGCCACCACAACCA
1 CCGCCACCACAACCA
1866768 GTTATAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.63, G:0.07, T:0.00
Consensus pattern (15 bp):
CCGCCACCACAACCA
Found at i:1867685 original size:31 final size:30
Alignment explanation
Indices: 1867628--1867706 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 30
1867618 TTGTGAATTG
1867628 ATTAGATTTTT--AAAATAAAATATATTA-
1 ATTAGATTTTTAAAAAATAAAATATATTAC
*
1867655 ATTAGATTTTTAAAAACATTAAAATTTATTAC
1 ATTAGATTTTTAAAAA-A-TAAAATATATTAC
*
1867687 ATT--ATTTTTAAACAATAAAA
1 ATTAGATTTTTAAAAAATAAAA
1867707 ATGAATATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
27 11 0.24
28 5 0.11
29 4 0.09
30 11 0.24
31 11 0.24
32 3 0.07
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (30 bp):
ATTAGATTTTTAAAAAATAAAATATATTAC
Found at i:1873347 original size:14 final size:13
Alignment explanation
Indices: 1873320--1873354 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1873310 ATTTTAATAT
1873320 TTTAAAATTATTA
1 TTTAAAATTATTA
*
1873333 TTTAAATATTTTTA
1 TTTAAA-ATTATTA
1873347 TTTAAAAT
1 TTTAAAAT
1873355 ACATTAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTAAAATTATTA
Found at i:1873848 original size:3 final size:3
Alignment explanation
Indices: 1873840--1873865 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1873830 TTTTTAAAAT
1873840 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1873866 CTTAGATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1876211 original size:51 final size:52
Alignment explanation
Indices: 1876156--1876259 Score: 156
Period size: 51 Copynumber: 2.0 Consensus size: 52
1876146 AAATTATAAA
* *
1876156 GATATTACCTAATACAATGATGAAATTACA-TTTAACTAGAGGCGAATATAG
1 GATATTACCTAATACAATGACGAAATTAAATTTTAACTAGAGGCGAATATAG
* * *
1876207 GATATTAGCTAATACAATGGCGAAATTAAATTTTAACTAGAGGCGAATCTAG
1 GATATTACCTAATACAATGACGAAATTAAATTTTAACTAGAGGCGAATATAG
1876259 G
1 G
1876260 GGCTGGCAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 26 0.55
52 21 0.45
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (52 bp):
GATATTACCTAATACAATGACGAAATTAAATTTTAACTAGAGGCGAATATAG
Found at i:1877289 original size:2 final size:2
Alignment explanation
Indices: 1877282--1877314 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1877272 ATTCAACGAC
1877282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1877315 GATAAAAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1878695 original size:20 final size:20
Alignment explanation
Indices: 1878672--1878731 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
1878662 TGTTAAAAAC
1878672 TAGAAAAAATTAATAAATTT
1 TAGAAAAAATTAATAAATTT
1878692 TAGAAAAAATTAATAAATTT
1 TAGAAAAAATTAATAAATTT
1878712 TA-ACAAAAATATAA-AAATTT
1 TAGA-AAAAAT-TAATAAATTT
1878732 AAAATTTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.03
20 34 0.89
21 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (20 bp):
TAGAAAAAATTAATAAATTT
Found at i:1878754 original size:19 final size:20
Alignment explanation
Indices: 1878720--1878768 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
1878710 TTTAACAAAA
*
1878720 ATATAAAAATTTAAAA-TTT
1 ATATAAAAATTGAAAATTTT
1878739 AT-TAAAAATTAGAAAATTTT
1 ATATAAAAATT-GAAAATTTT
1878759 ATATAAAAAT
1 ATATAAAAAT
1878769 CATAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.31
19 6 0.23
20 5 0.19
21 7 0.27
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATATAAAAATTGAAAATTTT
Found at i:1878794 original size:19 final size:19
Alignment explanation
Indices: 1878770--1878849 Score: 60
Period size: 19 Copynumber: 4.2 Consensus size: 19
1878760 TATAAAAATC
1878770 ATAAAAAATATAAAATTTT
1 ATAAAAAATATAAAATTTT
* **
1878789 AT-AAAAATCGTAAAAAATT
1 ATAAAAAAT-ATAAAATTTT
*
1878808 ATAAAATATATAGAAA---T
1 ATAAAAAATATA-AAATTTT
1878825 ATAAAAAAGTTATAAAATTTT
1 ATAAAAAA--TATAAAATTTT
1878846 ATAA
1 ATAA
1878850 TGTCGTAAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
17 8 0.17
18 9 0.19
19 17 0.36
20 8 0.17
21 5 0.11
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (19 bp):
ATAAAAAATATAAAATTTT
Found at i:1878802 original size:28 final size:29
Alignment explanation
Indices: 1878742--1878849 Score: 132
Period size: 28 Copynumber: 3.7 Consensus size: 29
1878732 AAAATTTATT
*
1878742 AAAAATTAGAAAATTTTATATAAAAATCATA
1 AAAAATTATAAAA-TTT-TATAAAAATCATA
*
1878773 AAAAA-TATAAAATTTTATAAAAATCGTA
1 AAAAATTATAAAATTTTATAAAAATCATA
* *
1878801 AAAAATTATAAAA-TATATAGAAAT-ATA
1 AAAAATTATAAAATTTTATAAAAATCATA
1878828 AAAAAGTTATAAAATTTTATAA
1 AAAAA-TTATAAAATTTTATAA
1878850 TGTCGTAAGA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
27 7 0.10
28 34 0.51
29 15 0.22
30 6 0.09
31 5 0.07
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAAATTATAAAATTTTATAAAAATCATA
Found at i:1878824 original size:10 final size:9
Alignment explanation
Indices: 1878758--1878842 Score: 50
Period size: 9 Copynumber: 9.1 Consensus size: 9
1878748 TAGAAAATTT
1878758 TATATAAAA
1 TATATAAAA
1878767 -ATCATAAAA
1 TAT-ATAAAA
*
1878776 AATATAAAA
1 TATATAAAA
*
1878785 TTTTATAAAA
1 -TATATAAAA
*
1878795 -ATCGTAAAA
1 TAT-ATAAAA
*
1878804 AATTATAAAA
1 TA-TATAAAA
1878814 TATATAGAAA
1 TATATA-AAA
*
1878824 TATAAAAAA
1 TATATAAAA
1878833 GT-TATAAAA
1 -TATATAAAA
1878842 T
1 T
1878843 TTTATAATGT
Statistics
Matches: 60, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
8 4 0.07
9 30 0.50
10 25 0.42
11 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
TATATAAAA
Found at i:1878898 original size:57 final size:56
Alignment explanation
Indices: 1878765--1878888 Score: 153
Period size: 57 Copynumber: 2.2 Consensus size: 56
1878755 TTTTATATAA
* *
1878765 AAATCATAAAAA-ATATAAAATTTTATAAAAATCGTAAAAAATTATAAAATATATAG
1 AAAT-ATAAAAAGTTATAAAATTTTATAAAAATCGTAAAAAATTATAAAATATAAAG
**
1878821 AAATATAAAAAAGTTATAAAATTTTAT-AATGTCGTAAGAAAATTATGCAAAATATAAAG
1 AAATAT-AAAAAGTTATAAAATTTTATAAAAATCGTAA-AAAATTAT--AAAATATAAAG
1878880 AAATATAAA
1 AAATATAAA
1878889 TTTTTTAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
55 2 0.03
56 17 0.29
57 21 0.36
58 3 0.05
59 16 0.27
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.30
Consensus pattern (56 bp):
AAATATAAAAAGTTATAAAATTTTATAAAAATCGTAAAAAATTATAAAATATAAAG
Found at i:1879116 original size:20 final size:19
Alignment explanation
Indices: 1879091--1879136 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
1879081 ATTTTTTAAT
1879091 ATTTTTATAAAAAATTTCTA
1 ATTTTT-TAAAAAATTTCTA
*
1879111 A-TTTTTAATAAATTTCTA
1 ATTTTTTAAAAAATTTCTA
1879129 ATTTTTTA
1 ATTTTTTA
1879137 TATTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 13 0.54
19 10 0.42
20 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTTTAAAAAATTTCTA
Found at i:1879149 original size:27 final size:29
Alignment explanation
Indices: 1879043--1879164 Score: 83
Period size: 29 Copynumber: 4.3 Consensus size: 29
1879033 TAGGGGTTTT
* *
1879043 TAATTTTTTATGATATTT-ATAAAATTTTA
1 TAATTTTTTAT-ATTTTTAATAAAATTTAA
* * ***
1879072 CATTTTTTTAT-TTTTTAATATTTTTATAA
1 TAATTTTTTATATTTTTAATAAAATT-TAA
* * * *
1879101 AAAATTTCTA-ATTTTTAAT-AAATTT-C
1 TAATTTTTTATATTTTTAATAAAATTTAA
*
1879127 TAATTTTTTATATTTTTATTAAAATTTAA
1 TAATTTTTTATATTTTTAATAAAATTTAA
1879156 TAATTTTTT
1 TAATTTTTT
1879165 TCTAAAATTT
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
26 7 0.10
27 13 0.19
28 13 0.19
29 34 0.51
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (29 bp):
TAATTTTTTATATTTTTAATAAAATTTAA
Found at i:1879181 original size:20 final size:19
Alignment explanation
Indices: 1879133--1879187 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1879123 TTTCTAATTT
1879133 TTTA-TATTTTTATTAAAA
1 TTTATTATTTTTATTAAAA
* *
1879151 TTTAATAATTTTTTTCTAAAA
1 TTT-ATTATTTTTAT-TAAAA
1879172 TTTATTATTTATTATT
1 TTTATTATTT-TTATT
1879188 TTTATACTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 3 0.10
19 1 0.03
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTATTTTTATTAAAA
Found at i:1879331 original size:92 final size:92
Alignment explanation
Indices: 1879214--1879417 Score: 250
Period size: 92 Copynumber: 2.2 Consensus size: 92
1879204 AATTTTTAAT
*
1879214 AAGAGCAGGGGCTTAATTGAATTTTT-GAAAAAATTTAAGGGTCTTTTTGATGCATTTTGAAAGT
1 AAGAGCAGGGGCTTAATTGAATTTTTGGAAAAAATTTAAGAG-CTTTTTGATGCATTTTGAAAGT
* * *
1879278 TTAAGTATCCAATTGAGTGGAAAAAAAA
65 TCAAGTATCCAACTGAGTGCAAAAAAAA
* * * * *
1879306 AAGAGCTGGGGCTTAATT-ACTTTTTTGGAAGAAGTTTGAGAGCTTTTTGATGCATTTTGAAAGT
1 AAGAGCAGGGGCTTAATTGA-ATTTTTGGAAAAAATTTAAGAGCTTTTTGATGCATTTTGAAAGT
* *
1879370 TCCAGTATTCAACTGAGTGCAAAAAAAAA
65 TCAAGTATCCAACTGAGTGC-AAAAAAAA
* *
1879399 AAAAGGAGGGGCTTAATTG
1 AAGAGCAGGGGCTTAATTG
1879418 TTTTTTTTTT
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
91 1 0.01
92 59 0.63
93 34 0.36
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (92 bp):
AAGAGCAGGGGCTTAATTGAATTTTTGGAAAAAATTTAAGAGCTTTTTGATGCATTTTGAAAGTT
CAAGTATCCAACTGAGTGCAAAAAAAA
Found at i:1882467 original size:2 final size:2
Alignment explanation
Indices: 1882460--1882485 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1882450 GATGTACGAC
1882460 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1882486 GTTTTCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1886235 original size:17 final size:17
Alignment explanation
Indices: 1886215--1886247 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1886205 CTAAAGTCAA
*
1886215 CTCAGAATGTCAGTCCG
1 CTCAAAATGTCAGTCCG
1886232 CTCAAAATGTCAGTCC
1 CTCAAAATGTCAGTCC
1886248 TAAAAGTAGT
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:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (17 bp):
CTCAAAATGTCAGTCCG
Found at i:1888046 original size:20 final size:21
Alignment explanation
Indices: 1888023--1888064 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1888013 AGCATAAGAA
1888023 AGTGAAGA-GAAAATAAATGT
1 AGTGAAGATGAAAATAAATGT
* *
1888043 AGTGAATATGTAAATAAATGT
1 AGTGAAGATGAAAATAAATGT
1888064 A
1 A
1888065 TGTTAGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.26
Consensus pattern (21 bp):
AGTGAAGATGAAAATAAATGT
Found at i:1893158 original size:26 final size:24
Alignment explanation
Indices: 1893113--1893161 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
1893103 GTATTATTTT
*
1893113 TATTTGTTTTTATGTTTTTAAATA
1 TATTTGTTTTTATATTTTTAAATA
1893137 TATTTGATTTATTATATTTTTAAAT
1 TATTTG-TTT-TTATATTTTTAAAT
1893162 TTTTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 3 0.14
26 13 0.59
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (24 bp):
TATTTGTTTTTATATTTTTAAATA
Found at i:1894441 original size:2 final size:2
Alignment explanation
Indices: 1894434--1894460 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1894424 TCACTACCTT
1894434 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1894461 TTTCAACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1896820 original size:2 final size:2
Alignment explanation
Indices: 1896813--1896853 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1896803 AAGAAGATAG
1896813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1896854 GGGGTATCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1900507 original size:108 final size:108
Alignment explanation
Indices: 1900311--1900528 Score: 274
Period size: 108 Copynumber: 2.0 Consensus size: 108
1900301 TTGTTTGGAG
* * * *
1900311 TAGCCATAGTAAATCAGCTAACTCGGAGAAGATTGTTCATAATAGTAAATCAATGAACTTAAACT
1 TAGCAATAGTAAATCAACTAACTCAGAGAAGATTGTTCATAACAGTAAATCAATGAACTTAAACT
* * * * * *
1900376 GTGATCGTAAATCAGCAAACCTTAATAGTATCAGTTGTGATCA
66 CTGATCATAAATCAACAAACCTTAATAATATCAGCTGTAATCA
* * ***
1900419 TAGCAATAGTAAATCAACTAACTCAGAGAAGATTGTTTATGACAGTAAATCAATGAACTTAGGTT
1 TAGCAATAGTAAATCAACTAACTCAGAGAAGATTGTTCATAACAGTAAATCAATGAACTTAAACT
** *
1900484 CTGATCATAAATCAATGACCCTTAATAATATCAGCTGTAATCA
66 CTGATCATAAATCAACAAACCTTAATAATATCAGCTGTAATCA
1900527 TA
1 TA
1900529 AATCGGTGAT
Statistics
Matches: 92, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
108 92 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (108 bp):
TAGCAATAGTAAATCAACTAACTCAGAGAAGATTGTTCATAACAGTAAATCAATGAACTTAAACT
CTGATCATAAATCAACAAACCTTAATAATATCAGCTGTAATCA
Found at i:1900899 original size:259 final size:260
Alignment explanation
Indices: 1900419--1900903 Score: 630
Period size: 259 Copynumber: 1.9 Consensus size: 260
1900409 GTTGTGATCA
* * *
1900419 TAGCAATAGTAAATCAACTAACTCAGAGAAGATTGTTTATGACAGTAAATCAATGAACTTAGGTT
1 TAGCAATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGACAGTAAATCAAAGAACTTAGATT
* * * ** * *
1900484 CTGATCATAAATCAATGACCCTTAATAATATCAGCTGTAATCATAAATCGGTGATCTGTTTGGAA
66 CTGATCATAAATCAATAAACCTTAATAATATCAACTGTAATCATAAATCAATAAGCTGTTTGGAA
* * * *
1900549 TAAAGATAGTAAATCAACTAACTTAGAGGAGATTGTTTATGATAGTAAATAAATGAACTTAGGTT
131 TAAAGATAGTAAATCAACTAACTCAGAGAAGATTGCTCATGATAGTAAATAAATGAACTTAGGTT
* * *** *
1900614 GTGATCATAAATTGGTGAATCTTAATAATATTAGCTATAATCGTAAATTGGCGAGCTGTTTGGAG
196 GTAATCACAAATCAATGAACCTTAATAATATTAGCTATAATCGTAAATTGGCGAGCTGTTTGGAG
* * *
1900679 TAGCGATAGT-AATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAAAGAACTTAGATT
1 TAGCAATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGACAGTAAATCAAAGAACTTAGATT
* * * * * * * *
1900743 GTTATCGTAAATCAGTAAACTTTAATAATATCAACTGTGATCGTAAATCAATAAGCTGTTTGGAG
66 CTGATCATAAATCAATAAACCTTAATAATATCAACTGTAATCATAAATCAATAAGCTGTTTGGAA
** * * *
1900808 TAGCGATCGTAAATCAACTAACTCAGAGAAGATTGCTCATGATAGTAAATTAATGAACTTGGGTT
131 TAAAGATAGTAAATCAACTAACTCAGAGAAGATTGCTCATGATAGTAAATAAATGAACTTAGGTT
*
1900873 GTAATCGCAAATCAATGAACCTTAATAATAT
196 GTAATCACAAATCAATGAACCTTAATAATAT
1900904 CAACTTTGAT
Statistics
Matches: 188, Mismatches: 37, Indels: 1
0.83 0.16 0.00
Matches are distributed among these distances:
259 179 0.95
260 9 0.05
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (260 bp):
TAGCAATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGACAGTAAATCAAAGAACTTAGATT
CTGATCATAAATCAATAAACCTTAATAATATCAACTGTAATCATAAATCAATAAGCTGTTTGGAA
TAAAGATAGTAAATCAACTAACTCAGAGAAGATTGCTCATGATAGTAAATAAATGAACTTAGGTT
GTAATCACAAATCAATGAACCTTAATAATATTAGCTATAATCGTAAATTGGCGAGCTGTTTGGAG
Found at i:1900906 original size:130 final size:130
Alignment explanation
Indices: 1900419--1900933 Score: 573
Period size: 130 Copynumber: 4.0 Consensus size: 130
1900409 GTTGTGATCA
* * *
1900419 TAGCAATAGTAAATCAACTAACTCAGAGAAGATTGTTTATGACAGTAAATCAATGAACTTAGGTT
1 TAGCGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTT
* * * * ** * *
1900484 CTGATCATAAATCAATGACCCTTAATAATATCAGCTGTAATCATAAATCGGTGATCTGTTTGGAA
66 GTGATCATAAATCAATGAACCTTAATAATATCAACTGTAATCGTAAATCAATGAGCTGTTTGGAG
** * * * *
1900549 TAAAGATAGTAAATCAACTAACTTAGAGGAGATTGTTTATGATAGTAAATAAATGAACTTAGGTT
1 TAGCGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTT
*** * * * * ****
1900614 GTGATCATAAATTGGTGAATCTTAATAATATTAGCTATAATCGTAAATTGGCGAGCTGTTTGGAG
66 GTGATCATAAATCAATGAACCTTAATAATATCAACTGTAATCGTAAATCAATGAGCTGTTTGGAG
* * *
1900679 TAGCGATAGT-AATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAAAGAACTTAGATT
1 TAGCGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTT
* * * * * * *
1900743 GTTATCGTAAATCAGTAAACTTTAATAATATCAACTGTGATCGTAAATCAATAAGCTGTTTGGAG
66 GTGATCATAAATCAATGAACCTTAATAATATCAACTGTAATCGTAAATCAATGAGCTGTTTGGAG
* * * *
1900808 TAGCGATCGTAAATCAACTAACTCAGAGAAGATTGCTCATGATAGTAAATTAATGAACTTGGGTT
1 TAGCGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTT
* ** * * * * *
1900873 GTAATCGCAAATCAATGAACCTTAATAATATCAACTTTGATTGTAAATCAACGAGTTGTTT
66 GTGATCATAAATCAATGAACCTTAATAATATCAACTGTAATCGTAAATCAATGAGCTGTTT
1900934 CATATATTTT
Statistics
Matches: 322, Mismatches: 62, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
129 105 0.33
130 217 0.67
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (130 bp):
TAGCGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTT
GTGATCATAAATCAATGAACCTTAATAATATCAACTGTAATCGTAAATCAATGAGCTGTTTGGAG
Found at i:1901468 original size:20 final size:18
Alignment explanation
Indices: 1901426--1901462 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1901416 ATATATATAC
**
1901426 AGAATGCAGTTATTGCCA
1 AGAATGCAACTATTGCCA
1901444 AGAATGCAACTATTGCCA
1 AGAATGCAACTATTGCCA
1901462 A
1 A
1901463 AAGAATTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (18 bp):
AGAATGCAACTATTGCCA
Found at i:1903264 original size:14 final size:15
Alignment explanation
Indices: 1903245--1903274 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1903235 TGTGTTATTG
1903245 TTCTTTTTTT-CTTT
1 TTCTTTTTTTACTTT
1903259 TTCTTTTTTTACTTT
1 TTCTTTTTTTACTTT
1903274 T
1 T
1903275 CTATTTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (15 bp):
TTCTTTTTTTACTTT
Found at i:1912107 original size:25 final size:24
Alignment explanation
Indices: 1912079--1912134 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
1912069 TTCAAAGCTT
* **
1912079 AATTTTTTTTAAATATATTTTTTAA
1 AATTTTTTTTAAA-AAATTTCATAA
1912104 AATTATTTTTTAAAAAATTTCATAA
1 AATT-TTTTTTAAAAAATTTCATAA
1912129 AATTTT
1 AATTTT
1912135 AAAACATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.07
25 16 0.59
26 9 0.33
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTTTTTTTAAAAAATTTCATAA
Found at i:1912122 original size:15 final size:13
Alignment explanation
Indices: 1912079--1912118 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1912069 TTCAAAGCTT
1912079 AATT-TTTTTT-A
1 AATTATTTTTTAA
1912090 AATATATTTTTTAA
1 AAT-TATTTTTTAA
1912104 AATTATTTTTTAA
1 AATTATTTTTTAA
1912117 AA
1 AA
1912119 AATTTCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.12
12 1 0.04
13 18 0.69
14 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATTATTTTTTAA
Found at i:1912123 original size:12 final size:12
Alignment explanation
Indices: 1912083--1912123 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
1912073 AAGCTTAATT
1912083 TTTTTTAAATATA
1 TTTTTTAAA-ATA
1912096 TTTTTTAAAATTA
1 TTTTTTAAAA-TA
*
1912109 TTTTTTAAAAAA
1 TTTTTTAAAATA
1912121 TTT
1 TTT
1912124 CATAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTTTTAAAATA
Found at i:1912148 original size:19 final size:18
Alignment explanation
Indices: 1912112--1912167 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
1912102 AAAATTATTT
1912112 TTTA-AAAAATTTCATAAAA
1 TTTATAAAAATTT--TAAAA
1912131 TTT-TAAAACATTATTAAAA
1 TTTATAAAA-ATT-TTAAAA
1912150 TTTATAAAAATTTTAAAA
1 TTTATAAAAATTTTAAAA
1912168 AAATTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
18 6 0.18
19 18 0.55
20 8 0.24
21 1 0.03
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTATAAAAATTTTAAAA
Found at i:1912169 original size:10 final size:10
Alignment explanation
Indices: 1912111--1912179 Score: 56
Period size: 10 Copynumber: 7.1 Consensus size: 10
1912101 TAAAATTATT
1912111 TTTTAAAAAA
1 TTTTAAAAAA
* *
1912121 TTTCATAAAA
1 TTTTAAAAAA
*
1912131 TTTTAAAACA
1 TTTTAAAAAA
1912141 TTATT--AAAA
1 TT-TTAAAAAA
1912150 -TTTATAAAAA
1 TTTTA-AAAAA
1912160 TTTTAAAAAA
1 TTTTAAAAAA
*
1912170 -ATTAAAAAA
1 TTTTAAAAAA
1912179 T
1 T
1912180 AAAATCTATA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 11 0.24
10 26 0.57
11 6 0.13
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:1912169 original size:20 final size:19
Alignment explanation
Indices: 1912111--1912179 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
1912101 TAAAATTATT
1912111 TTTTAAAAAATTTCATAAAA
1 TTTTAAAAAATTT-ATAAAA
*
1912131 TTTTAAAACA-TTATTAAAA
1 TTTTAAAAAATTTA-TAAAA
*
1912150 TTTATAAAAATTTTA-AAAA
1 TTT-TAAAAAATTTATAAAA
**
1912169 AATTAAAAAAT
1 TTTTAAAAAAT
1912180 AAAATCTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 8 0.20
19 15 0.38
20 14 0.35
21 3 0.08
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTTAAAAAATTTATAAAA
Found at i:1919097 original size:23 final size:24
Alignment explanation
Indices: 1919041--1919099 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
1919031 AAATTAATTA
*
1919041 TTTTATTACAAGTGTACATATATC
1 TTTTATTACAAATGTACATATATC
1919065 TATTTATTACAAATGTACCA-ATAT-
1 T-TTTATTACAAATGTA-CATATATC
1919089 TTTTATTACAA
1 TTTTATTACAA
1919100 TTGTCATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 10 0.31
24 2 0.06
25 18 0.56
26 2 0.06
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (24 bp):
TTTTATTACAAATGTACATATATC
Found at i:1922306 original size:6 final size:6
Alignment explanation
Indices: 1922288--1922323 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1922278 TAAGAAAATT
*
1922288 AAAT-A AAAGAA AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A
1922324 TAAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
5 3 0.11
6 25 0.89
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:1929056 original size:26 final size:26
Alignment explanation
Indices: 1929025--1929076 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1929015 AAAATTTCAC
*
1929025 TTTAATC-TCTAAAAATGATACAAAAT
1 TTTAATCTTATAAAAATGATA-AAAAT
*
1929051 TTTAATCTTATAAAAATTATAAAAAT
1 TTTAATCTTATAAAAATGATAAAAAT
1929077 ATAAATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (26 bp):
TTTAATCTTATAAAAATGATAAAAAT
Found at i:1931083 original size:13 final size:13
Alignment explanation
Indices: 1931065--1931138 Score: 89
Period size: 13 Copynumber: 5.8 Consensus size: 13
1931055 TTCTTCATTA
1931065 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
1931078 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
1931091 C-TGTGAAGAAGTG
1 CTTTTGAA-AAGTG
* *
1931104 CTTTTGAGAAGTA
1 CTTTTGAAAAGTG
*
1931117 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
1931130 C-TTTGAAAA
1 CTTTTGAAAA
1931139 AATTTAAGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
12 12 0.23
13 37 0.70
14 4 0.08
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:1941146 original size:25 final size:27
Alignment explanation
Indices: 1941118--1941180 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 27
1941108 AAAATTTACA
*
1941118 ACAATAATATAAAATA-ATA-ATATGT
1 ACAAAAATATAAAATATATACATATGT
*
1941143 ACAAAAATAT-ATATATATACATATGT
1 ACAAAAATATAAAATATATACATATGT
1941169 ACATAAAATATA
1 ACA-AAAATATA
1941181 CACTAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 4 0.12
25 12 0.38
26 9 0.28
27 7 0.22
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (27 bp):
ACAAAAATATAAAATATATACATATGT
Found at i:1941324 original size:2 final size:2
Alignment explanation
Indices: 1941261--1941305 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1941251 TGGTATTTAA
*
1941261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1941303 AT A
1 AT A
1941306 ATAGTATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1941587 original size:10 final size:10
Alignment explanation
Indices: 1941554--1941589 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1941544 ATATATAAAG
1941554 AAAGAAAAAA
1 AAAGAAAAAA
*
1941564 AAACACAAAAA
1 AAAGA-AAAAA
1941575 AAAGAAAAAA
1 AAAGAAAAAA
1941585 AAAGA
1 AAAGA
1941590 TTCGAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:1941892 original size:28 final size:28
Alignment explanation
Indices: 1941851--1941917 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
1941841 AGGTGGCTAG
* *
1941851 GGTTTCTTTGTTTTTTTTGGGGGGGTTA
1 GGTTTTTTTTTTTTTTTTGGGGGGGTTA
****
1941879 GGTTTTTTTTTTTTTTTTTTTTGGGTTA
1 GGTTTTTTTTTTTTTTTTGGGGGGGTTA
1941907 GGTTTTTTTTT
1 GGTTTTTTTTT
1941918 GGGGGGGCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.03, C:0.01, G:0.25, T:0.70
Consensus pattern (28 bp):
GGTTTTTTTTTTTTTTTTGGGGGGGTTA
Found at i:1943045 original size:74 final size:76
Alignment explanation
Indices: 1942927--1943165 Score: 313
Period size: 74 Copynumber: 3.1 Consensus size: 76
1942917 AAAACAGATT
** * * *
1942927 TTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTT
1 TTGAAAATACCTC-ACGCGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1942992 GAAAGACAGAAA
65 GAAAGACAGAAA
*
1943004 TTG-AAATACCTCA-GCGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 TTGAAAATACCTCACGCGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1943066 GAAAGACAGAAA
65 GAAAGACAGAAA
* *
1943078 TTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 TTGAAAATACCTCA-CGCGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTT
*
1943143 TTTTGAAAGGCAGAAA
61 TTTTGAAAGACAGAAA
1943159 TTGAAAA
1 TTGAAAA
1943166 ACGCAAATTG
Statistics
Matches: 144, Mismatches: 9, Indels: 14
0.86 0.05 0.08
Matches are distributed among these distances:
73 2 0.01
74 56 0.39
75 10 0.07
76 9 0.06
77 40 0.28
78 2 0.01
81 25 0.17
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (76 bp):
TTGAAAATACCTCACGCGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
AAAGACAGAAA
Found at i:1943131 original size:77 final size:75
Alignment explanation
Indices: 1942953--1943508 Score: 318
Period size: 77 Copynumber: 7.2 Consensus size: 75
1942943 ATGTGACCCG
* *
1942953 AGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAGACAGAAATTG-AAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
* *
1943017 GCGTGTCCTG
66 GCGTGGCCTA
*
1943027 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
1943092 GCGCGTGAGCC-A
66 --GCGTG-GCCTA
*
1943104 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAGGCAGAAATTGAAAA-AC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTTGAAAGACAGAAATTGAAAATAC
* * * * *
1943168 GCAAATTGAAAATACCTCGGCGTG
62 -C----T---CA-GCGT-GGCCTA
* * * * * * ** * * * ** ****
1943192 TGACCTGAGGCTCAACTCGC-CTCTCA-CAATACGAGTTGATTTTTTTGACAACAGAAATTGAAA
1 AG-GCTCA-ACTCACCTCTCGCAAT-ATGAGT-TGA-TTTTTTTGAAAGACA---GAAATTGAAA
* * *
1943255 TTACCTCAGCGTGTCCTG
58 ATACCTCAGCGTGGCCTA
* * *
1943273 AGGCTCAACTCACCTCTCCCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAACACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
* * * *
1943338 GCATGTCTTG
66 GCGTGGCCTA
** * * *
1943348 AGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTTTAAAAAACAGAAATTGAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAGACAGAAATTGAAAATACCT
* * * *
1943413 CAGCATGTCTTG
64 CAGCGTGGCCTA
* ** * *
1943425 AGGCTCAACTAATTTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
* * *
1943487 GCGTGTCTTG
66 GCGTGGCCTA
1943497 AGGCTCAACTCA
1 AGGCTCAACTCA
1943509 TTTTGAACAG
Statistics
Matches: 380, Mismatches: 72, Indels: 62
0.74 0.14 0.12
Matches are distributed among these distances:
72 40 0.11
73 7 0.02
74 52 0.14
75 62 0.16
77 108 0.28
78 10 0.03
79 11 0.03
80 8 0.02
81 31 0.08
82 2 0.01
83 1 0.00
85 1 0.00
86 1 0.00
87 12 0.03
88 3 0.01
89 7 0.02
90 22 0.06
91 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (75 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
GCGTGGCCTA
Found at i:1943263 original size:246 final size:245
Alignment explanation
Indices: 1942787--1943388 Score: 787
Period size: 246 Copynumber: 2.5 Consensus size: 245
1942777 ATTAAAAAGT
*
1942787 TCAACTCACCTCTCGCAATATGAGTTAAATTTTTTTGAAAAAAAAACAGAAATTGAAAATAGCTC
1 TCAACTCACCTCTCGCAATATGAGTT-GATTTTTTTG----AAAAACAGAAATTGAAAATAGCTC
* * *
1942852 AGCACGCGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGA------TTTTTGAAAATAGA
61 AGCGCGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAACAGA
** *
1942911 ATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATCTCGCAAT
126 ATCTGAAAAACAGAAATTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATCTCACAAT
**
1942976 GTGAGTTGATTTTTTTGAAAGACAGAAATTGAAATACCTCAGCGTGTCCTGAGGC
191 ACGAGTTGATTTTTTTGAAAGACAGAAATTGAAATACCTCAGCGTGTCCTGAGGC
*
1943031 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTCAGCGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATAGCTCAGCGC
* *
1943096 GTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAGGCAGAAAT-
66 GTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTTGAAA-ACAG-AATC
* * * * *
1943160 TGAAAAAC-GCAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATAC
129 TGAAAAACAG-AAATTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATCTCACAATAC
*
1943224 GAGTTGATTTTTTTGACA-ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGC
193 GAGTTGATTTTTTTGAAAGACAGAAATTGAAA-TACCTCAGCGTGTCCTGAGGC
* * *
1943277 TCAACTCACCTCTCCCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAACACCTCA--GC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATAGCTCAGCGC
* * ** * *
1943340 ATG-TCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTTT
66 GTGAGC-CAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTT
1943389 AAAAAACAGA
Statistics
Matches: 318, Mismatches: 29, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
239 65 0.20
243 10 0.03
244 68 0.21
245 23 0.07
246 149 0.47
247 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (245 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATAGCTCAGCGC
GTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAACAGAATCTG
AAAAACAGAAATTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATCTCACAATACGAG
TTGATTTTTTTGAAAGACAGAAATTGAAATACCTCAGCGTGTCCTGAGGC
Found at i:1943354 original size:75 final size:75
Alignment explanation
Indices: 1943159--1943508 Score: 440
Period size: 77 Copynumber: 4.7 Consensus size: 75
1943149 AAGGCAGAAA
* * *
1943159 TTGAAAAAC-GCAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATA
1 TTGAAAAACAG-AAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCACCTCTCACAATA
*
1943223 CGAGTTGATTTTT
63 TGAGTTGATTTTT
* * * *
1943236 TTG-ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCCCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGA
1943300 GTTGATTTTT
66 GTTGATTTTT
* * **
1943310 TTGAAAAACAGAAATTGAAAACACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGA
1943375 GTTGATTTTTTT
66 GTTGA--TTTTT
* * * ** *
1943387 TTAAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTAATTTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGA
*
1943452 GTTGA--ATT
66 GTTGATTTTT
*
1943460 TTG-AAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCA
1943509 TTTTGAACAG
Statistics
Matches: 246, Mismatches: 23, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
72 43 0.17
73 4 0.02
74 41 0.17
75 58 0.24
76 25 0.10
77 75 0.30
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (75 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGA
GTTGATTTTT
Found at i:1943485 original size:149 final size:148
Alignment explanation
Indices: 1943159--1943511 Score: 451
Period size: 149 Copynumber: 2.4 Consensus size: 148
1943149 AAGGCAGAAA
* * ***
1943159 TTGAAAAAC-GCAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATA
1 TTGAAAAACAG-AAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCATTTCTCACAATA
* * * * *
1943223 CGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCT
63 CGAGTTGATTTTTTTAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTAACCT
*
1943288 CTCCCAATATGAGTTGATTTTT
128 CTCCCAATATGAGTTGA-TATT
* * *
1943310 TTGAAAAACAGAAATTGAAAACACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATACGA
* **
1943375 GTTGATTTTTTTTTAAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTAATTT
66 GTTGA--TTTTTTT-AAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTAACCT
*
1943440 CTCGCAATATGAGTTGA-ATT
128 CTCCCAATATGAGTTGATATT
*
1943460 TTG-AAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTT
1943512 TGAACAGAAA
Statistics
Matches: 177, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
149 77 0.44
150 5 0.03
151 36 0.20
152 59 0.33
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (148 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATACGA
GTTGATTTTTTTAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTAACCTCTC
CCAATATGAGTTGATATT
Found at i:1943541 original size:49 final size:49
Alignment explanation
Indices: 1943465--1943560 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
1943455 GAATTTTGAA
*
1943465 AACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
*
1943514 AACAGAAATTGAAATTAGCTCAACGTGTCTTGAGGCTCAACTCATTT
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
1943561 CTCGCAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (49 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:1943594 original size:72 final size:72
Alignment explanation
Indices: 1943514--1943654 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 72
1943504 ACTCATTTTG
*
1943514 AACAGAAATTGAAATTAGCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1943579 TTTTGAA
66 TTTTGAA
1943586 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1943651 TTTT
66 TTTT
1943655 TTTTTTTGAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (72 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
TTTTGAA
Found at i:1943607 original size:121 final size:121
Alignment explanation
Indices: 1943393--1943632 Score: 426
Period size: 121 Copynumber: 2.0 Consensus size: 121
1943383 TTTTTTAAAA
*
1943393 AACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
*
1943458 TTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
* * * *
1943514 AACAGAAATTGAAATTAGCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
1943579 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
1943633 CTCGCAATAT
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 113 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (121 bp):
AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:1943724 original size:82 final size:78
Alignment explanation
Indices: 1943514--1943735 Score: 206
Period size: 72 Copynumber: 2.9 Consensus size: 78
1943504 ACTCATTTTG
* * * * ** *
1943514 AACAGAAATTGAAATTAGCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-
1 AACAGAAATTGAAAATACCTCAACGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
*
1943578 -----ATTTTGAA
66 TTTTTTTTTTGAA
* * * ** *
1943586 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAAATACCTCAACGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGCTG-A
1943651 TTTTTTTTTTTGAA
65 TTTTTTTTTTTGAA
* *
1943665 AGACAGAAATTGAAAATACCTCAGCATGTGAAC-CGAGGCTCAACTCACCTCTCGTAATATGAGC
1 A-ACAGAAATTGAAAATACCTCA--ACGTG-ACTCGAGGCTCAACTCACCTCTCGCAATATGAGC
1943729 TGATTTT
62 TGATTTT
1943736 GAAAAAGTAG
Statistics
Matches: 129, Mismatches: 10, Indels: 13
0.85 0.07 0.09
Matches are distributed among these distances:
72 62 0.48
73 1 0.01
79 8 0.06
80 20 0.16
81 5 0.04
82 32 0.25
83 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (78 bp):
AACAGAAATTGAAAATACCTCAACGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
TTTTTTTTTTGAA
Found at i:1943804 original size:54 final size:55
Alignment explanation
Indices: 1943704--1943809 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 55
1943694 GAACCGAGGC
* * *
1943704 TCAACTCACCTCTCGTAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
* * *
1943758 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAA-CATAAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAAAAAGCAGAAATTGAAAA
1943810 CAGAAATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
54 33 0.75
55 11 0.25
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (55 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
Found at i:1943816 original size:13 final size:13
Alignment explanation
Indices: 1943789--1943822 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1943779 GAGTTGATTC
*
1943789 TTGAACAACATAAA
1 TTGAA-AACAGAAA
1943803 TTGAAAACAGAAA
1 TTGAAAACAGAAA
1943816 TTGAAAA
1 TTGAAAA
1943823 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TTGAAAACAGAAA
Found at i:1944052 original size:62 final size:63
Alignment explanation
Indices: 1943947--1944141 Score: 212
Period size: 72 Copynumber: 3.0 Consensus size: 63
1943937 ACAGAAATTG
* ** *
1943947 AAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTTTA
1 AAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTA
* *
1944010 AAA-TACCTCAGCGCGTCCTGAGACTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACA
1 AAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-ATTTT-------
***
1944074 GAAATTA
58 -TTTTTA
*
1944081 AAATTACCTCAGCGTGTCCTAAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTT
1 AAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTT
1944142 AACAACAGAA
Statistics
Matches: 107, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
62 42 0.39
63 9 0.08
71 11 0.10
72 45 0.42
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (63 bp):
AAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTA
Found at i:1944111 original size:134 final size:137
Alignment explanation
Indices: 1943898--1944288 Score: 484
Period size: 134 Copynumber: 2.8 Consensus size: 137
1943888 ATTAAAAGGT
* * *
1943898 TCAACCCACTTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCATG
1 TCAACTCACTTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
** *
1943963 TCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTT-TT-AAAA-TACCTCAGCGCG
64 TCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTATTGAAAATTACCTCAGCGCG
1944025 TCC-TGAGAC
129 -CCTTGAGAC
* * *
1944034 TCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTAAAATTACCTCAGCGTGTC
1 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTC
*
1944099 CTAAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAAATTAC
66 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTTTT----------ATTGAAAATTAC
* *
1944164 CTCAGCGTGCCTTGAGGC
120 CTCAGCGCGCCTTGAGAC
* *
1944182 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTTAGCGTGT
1 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGA-AAACAGAAATTGAAATTACCTCAGCGTGT
*
1944247 CCTGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTT
65 CCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTT
1944289 GAAAAATAGA
Statistics
Matches: 220, Mismatches: 19, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
134 64 0.29
135 7 0.03
136 26 0.12
146 2 0.01
147 6 0.03
148 54 0.25
149 61 0.28
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (137 bp):
TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTC
CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTATTGAAAATTACCTCAGCGCGCC
TTGAGAC
Found at i:1944130 original size:72 final size:73
Alignment explanation
Indices: 1944007--1944293 Score: 411
Period size: 73 Copynumber: 3.9 Consensus size: 73
1943997 TGATTTTTTT
* * *
1944007 TTAAAA-TACCTCAGCGCGTCCTGAGACTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAA
1 TTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTGAA
1944070 AACAGAAA
66 AACAGAAA
* *
1944078 TTAAAATTACCTCAGCGTGTCCTAAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTA
1 TTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTTTGA
1944143 ACAACAGAAA
65 A-AACAGAAA
**
1944153 TTGAAAATTACCTCAGCGTG-CCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG
1 TT-AAAATTACCTCAGCGTGTCC-TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTG
1944216 ACAAACAGAAA
64 A-AAACAGAAA
* * *
1944227 TTGAAATTACCTTAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTTGAA
1 TTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTGAA
1944292 AA
66 AA
1944294 ATAGATTGAA
Statistics
Matches: 193, Mismatches: 14, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
71 6 0.03
72 46 0.24
73 49 0.25
74 31 0.16
75 13 0.07
76 48 0.25
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (73 bp):
TTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTGAA
AACAGAAA
Found at i:1944282 original size:149 final size:147
Alignment explanation
Indices: 1944009--1944288 Score: 445
Period size: 149 Copynumber: 1.9 Consensus size: 147
1943999 ATTTTTTTTT
**
1944009 AAAATACCTCAGCGCGTCCTGAGACTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACA
1 AAAATACCTCAGCGCGTCCTGAGACTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACA
1944074 GAAATTAAAATTACCTCAGCGTGTCCTAAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
66 GAAATTAAAATTACCTCAGCGTGTCCTAAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
1944139 TTTAACAACAGAAATTG
131 TTTAACAACAGAAATTG
* * *
1944156 AAAATTACCTCAGCGTG-CCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAA
1 AAAA-TACCTCAGCGCGTCC-TGAGACTCAACTCACCTCTCGCAATATGAGTTGAATTTTGA-AA
* * * *
1944220 ACAGAAATTGAAATTACCTTAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATGAGTTGATT
63 ACAGAAATTAAAATTACCTCAGCGTGTCCTAAGGCTCAACTCATTTCTCGCAATATGAGTTGATT
1944285 TTTT
128 TTTT
1944289 GAAAAATAGA
Statistics
Matches: 121, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
147 6 0.05
148 48 0.40
149 67 0.55
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (147 bp):
AAAATACCTCAGCGCGTCCTGAGACTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACA
GAAATTAAAATTACCTCAGCGTGTCCTAAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
TTTAACAACAGAAATTG
Found at i:1952682 original size:12 final size:12
Alignment explanation
Indices: 1952662--1952716 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
1952652 TGGGATATGC
*
1952662 AATGTATGAATG
1 AATGCATGAATG
1952674 AATGCATGAATG
1 AATGCATGAATG
1952686 AATGCATGAATG
1 AATGCATGAATG
1952698 --T-C--GAATG
1 AATGCATGAATG
1952705 AATGCATGAATG
1 AATGCATGAATG
1952717 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
7 5 0.14
9 2 0.05
10 2 0.05
12 28 0.76
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.27
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:1952705 original size:19 final size:19
Alignment explanation
Indices: 1952681--1952727 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1952671 ATGAATGCAT
1952681 GAATGAATGCATGAATGTC
1 GAATGAATGCATGAATGTC
1952700 GAATGAATGCATGAATGTC
1 GAATGAATGCATGAATGTC
*
1952719 AAATGAATG
1 GAATGAATG
1952728 TCAGTCATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (19 bp):
GAATGAATGCATGAATGTC
Found at i:1952707 original size:11 final size:10
Alignment explanation
Indices: 1952682--1952730 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 10
1952672 TGAATGCATG
1952682 AATGAATG-C
1 AATGAATGTC
1952691 -ATGAATGTC
1 AATGAATGTC
1952700 GAATGAATG-C
1 -AATGAATGTC
1952710 -ATGAATGTC
1 AATGAATGTC
1952719 AAATGAATGTC
1 -AATGAATGTC
1952730 A
1 A
1952731 GTCATGAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
8 14 0.41
9 2 0.06
10 2 0.06
11 16 0.47
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (10 bp):
AATGAATGTC
Found at i:1952726 original size:23 final size:21
Alignment explanation
Indices: 1952662--1952727 Score: 79
Period size: 19 Copynumber: 3.4 Consensus size: 21
1952652 TGGGATATGC
* *
1952662 AATGTATGAATGAATG-CATG
1 AATGAATGCATGAATGTCATG
1952682 AATGAATGCATGAATGTC--G
1 AATGAATGCATGAATGTCATG
1952701 AATGAATGCATGAATGTCA--
1 AATGAATGCATGAATGTCATG
1952720 AATGAATG
1 AATGAATG
1952728 TCAGTCATGA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
19 27 0.64
20 14 0.33
21 1 0.02
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (21 bp):
AATGAATGCATGAATGTCATG
Found at i:1952727 original size:4 final size:4
Alignment explanation
Indices: 1952662--1952716 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
1952652 TGGGATATGC
* * *
1952662 AATG TATG AATG AATG CATG AATG AATG CATG AATG --TCG AATG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AAT-G AATG AATG
*
1952709 CATG AATG
1 AATG AATG
1952717 TCAAATGAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
2 1 0.03
3 1 0.03
4 37 0.93
5 1 0.03
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.27
Consensus pattern (4 bp):
AATG
Found at i:1954773 original size:39 final size:39
Alignment explanation
Indices: 1954672--1954778 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 39
1954662 TATGGTATTT
* * * * *
1954672 AAAATATATATATATATATATGTATATATAATAGTATTTA
1 AAAATATATACATA-ATATATATATAAATAATAGCATTAA
* * * * *
1954712 AGAATATATACATAAGAAATATATAACTAATGGCATTAA
1 AAAATATATACATAATATATATATAAATAATAGCATTAA
1954751 AAAATATATACATAATATATATA-AAATA
1 AAAATATATACATAATATATATATAAATA
1954779 CTTAAAAAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
38 4 0.08
39 37 0.70
40 12 0.23
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.36
Consensus pattern (39 bp):
AAAATATATACATAATATATATATAAATAATAGCATTAA
Found at i:1955272 original size:27 final size:27
Alignment explanation
Indices: 1955240--1955300 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
1955230 GTGGCTAGGG
1955240 TTTCTTGGTTTTTTTGGGGGTTAGGTT
1 TTTCTTGGTTTTTTTGGGGGTTAGGTT
* ***
1955267 TTTCTT-TTTTTTTTTTTGGTTAGGTT
1 TTTCTTGGTTTTTTTGGGGGTTAGGTT
*
1955293 TTTTTTGG
1 TTTCTTGG
1955301 GAGGGCTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.03, C:0.03, G:0.25, T:0.69
Consensus pattern (27 bp):
TTTCTTGGTTTTTTTGGGGGTTAGGTT
Found at i:1955928 original size:18 final size:19
Alignment explanation
Indices: 1955893--1955931 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1955883 AAAACAAATT
1955893 TAAAAATTCAAAATATTTA
1 TAAAAATTCAAAATATTTA
*
1955912 TAAAAATTCCAAA-ATTTA
1 TAAAAATTCAAAATATTTA
1955930 TA
1 TA
1955932 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAATTCAAAATATTTA
Found at i:1955949 original size:24 final size:24
Alignment explanation
Indices: 1955905--1955956 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1955895 AAAATTCAAA
* * *
1955905 ATATTTATAAAAATTCCAAAATTT
1 ATATTTAAAAAAATTCAAAAATAT
1955929 ATATTTAAAAAAA-TCTAAAAATAT
1 ATATTTAAAAAAATTC-AAAAATAT
1955953 ATAT
1 ATAT
1955957 AAAGAAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATTTAAAAAAATTCAAAAATAT
Found at i:1961128 original size:2 final size:2
Alignment explanation
Indices: 1961121--1961146 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1961111 ATTAAAATTC
1961121 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1961147 GCTTTAGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1961129 original size:29 final size:31
Alignment explanation
Indices: 1961064--1961129 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1961054 AAAGTTTAAG
*
1961064 TATATATTTGAACCACAATTAAAATTTCATA
1 TATATAATTGAACCACAATTAAAATTTCATA
* *
1961095 TGTATAATTGCACCA-AATTAAAA-TTCATA
1 TATATAATTGAACCACAATTAAAATTTCATA
1961124 TATATA
1 TATATA
1961130 TATATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 11 0.35
30 8 0.26
31 12 0.39
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (31 bp):
TATATAATTGAACCACAATTAAAATTTCATA
Found at i:1962146 original size:38 final size:38
Alignment explanation
Indices: 1962104--1962179 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1962094 ATTTAATTTT
1962104 TTATCTCTCATATTTATAAATTTATTAGAAAATCGAAA
1 TTATCTCTCATATTTATAAATTTATTAGAAAATCGAAA
1962142 TTATCTCTCATATTTATAAATTTATTAGAAAATCGAAA
1 TTATCTCTCATATTTATAAATTTATTAGAAAATCGAAA
1962180 AAGAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (38 bp):
TTATCTCTCATATTTATAAATTTATTAGAAAATCGAAA
Found at i:1966418 original size:13 final size:14
Alignment explanation
Indices: 1966389--1966427 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
1966379 CTATTTCATT
*
1966389 AAAAATAGTTTTCG
1 AAAAATAATTTTCG
1966403 AAAAATAATTTT-G
1 AAAAATAATTTTCG
1966416 AAAAATAATTTT
1 AAAAATAATTTT
1966428 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (14 bp):
AAAAATAATTTTCG
Found at i:1966435 original size:16 final size:18
Alignment explanation
Indices: 1966411--1966449 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1966401 CGAAAAATAA
1966411 TTTTGAAAAA-TAAT-TT
1 TTTTGAAAAATTAATATT
*
1966427 TTTTTAAAAATTAATATT
1 TTTTGAAAAATTAATATT
1966445 TTTTG
1 TTTTG
1966450 GTGTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 9 0.47
17 4 0.21
18 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TTTTGAAAAATTAATATT
Found at i:1966436 original size:17 final size:18
Alignment explanation
Indices: 1966411--1966448 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1966401 CGAAAAATAA
*
1966411 TTTTGAAAAATAAT-TTT
1 TTTTAAAAAATAATATTT
*
1966428 TTTTAAAAATTAATATTT
1 TTTTAAAAAATAATATTT
1966446 TTT
1 TTT
1966449 GGTGTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTAAAAAATAATATTT
Found at i:1966596 original size:13 final size:14
Alignment explanation
Indices: 1966568--1966596 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1966558 TCGAGTTTAT
1966568 TTTATATTTGTAGA
1 TTTATATTTGTAGA
1966582 TTTATATTT-TAGA
1 TTTATATTTGTAGA
1966595 TT
1 TT
1966597 GTTCTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (14 bp):
TTTATATTTGTAGA
Found at i:1966700 original size:18 final size:20
Alignment explanation
Indices: 1966665--1966713 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
1966655 ATTTTCCTTT
1966665 TAATAATCAAAATTTATTTTA
1 TAATAATCAAAA-TTATTTTA
*
1966686 TAATAAT-AAAA-TATTTTG
1 TAATAATCAAAATTATTTTA
1966704 TAATAATCAA
1 TAATAATCAA
1966714 TGTCATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 13 0.50
19 2 0.08
20 4 0.15
21 7 0.27
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (20 bp):
TAATAATCAAAATTATTTTA
Found at i:1967293 original size:15 final size:15
Alignment explanation
Indices: 1967273--1967324 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
1967263 ACTACAAAAC
1967273 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
1967288 ATTTATAATTATAATAAAT
1 ATTTATTA-T-TAAT--AT
*
1967307 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
1967322 ATT
1 ATT
1967325 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:1967310 original size:19 final size:19
Alignment explanation
Indices: 1967286--1967322 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1967276 TATTATTAAT
*
1967286 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
1967305 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
1967323 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:1973894 original size:16 final size:16
Alignment explanation
Indices: 1973873--1973910 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1973863 TTTTATGGGA
1973873 TAAGTGCGTTAAAACC
1 TAAGTGCGTTAAAACC
1973889 TAAGTGCGTTAAAACC
1 TAAGTGCGTTAAAACC
1973905 TAAGTG
1 TAAGTG
1973911 TCTTTATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (16 bp):
TAAGTGCGTTAAAACC
Found at i:1974658 original size:15 final size:15
Alignment explanation
Indices: 1974638--1974687 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
1974628 AAATAAGTCT
1974638 AAGAAAATAAAAATA
1 AAGAAAATAAAAATA
*
1974653 AAGAAACTAAAAAATTTA
1 AAGAAAAT-AAAAA--TA
*
1974671 AAAAAAATAAAAATA
1 AAGAAAATAAAAATA
1974686 AA
1 AA
1974688 AATAAAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 11 0.38
16 5 0.17
17 5 0.17
18 8 0.28
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (15 bp):
AAGAAAATAAAAATA
Found at i:1974794 original size:19 final size:18
Alignment explanation
Indices: 1974772--1974811 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1974762 AAAAAACTAA
*
1974772 AAATAATAGAAATATAATT
1 AAATAACAGAAATA-AATT
*
1974791 AAATAGCAGAAATAAATT
1 AAATAACAGAAATAAATT
1974809 AAA
1 AAA
1974812 ATAAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (18 bp):
AAATAACAGAAATAAATT
Found at i:1974909 original size:32 final size:31
Alignment explanation
Indices: 1974864--1974941 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
1974854 AATAGATCAG
* *
1974864 TAAAAT-AA-AAATAAATAATATAACA-AAAA
1 TAAAATAAAGAAATAAAGAA-ATAAAATAAAA
1974893 TAATAATAAAGAAATAAAGAAATAAAATAAAA
1 TAA-AATAAAGAAATAAAGAAATAAAATAAAA
1974925 TAAAATAAAGAAA-AAAG
1 TAAAATAAAGAAATAAAG
1974942 GTAAAAGGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 3 0.07
30 7 0.16
31 17 0.40
32 16 0.37
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (31 bp):
TAAAATAAAGAAATAAAGAAATAAAATAAAA
Found at i:1974947 original size:23 final size:23
Alignment explanation
Indices: 1974866--1974937 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
1974856 TAGATCAGTA
* *
1974866 AAATAAAA-ATAAATAATATAACAA
1 AAATAAAATA-AAATAAAATAA-AG
*
1974890 AAATAATAAT-AAA-GAAATAAAG
1 AAATAA-AATAAAATAAAATAAAG
1974912 AAATAAAATAAAATAAAATAAAG
1 AAATAAAATAAAATAAAATAAAG
1974935 AAA
1 AAA
1974938 AAAGGTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 3 0.08
22 10 0.25
23 16 0.40
24 9 0.22
25 2 0.05
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (23 bp):
AAATAAAATAAAATAAAATAAAG
Found at i:1975741 original size:18 final size:18
Alignment explanation
Indices: 1975718--1975756 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1975708 CTCTCCCTCA
1975718 TTTTTTCTCA-ACTTTTGG
1 TTTTTT-TCAGACTTTTGG
*
1975736 TTTTTTTTAGACTTTTGG
1 TTTTTTTCAGACTTTTGG
1975754 TTT
1 TTT
1975757 CTGCACACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.10, C:0.10, G:0.13, T:0.67
Consensus pattern (18 bp):
TTTTTTTCAGACTTTTGG
Found at i:1978461 original size:35 final size:37
Alignment explanation
Indices: 1978405--1978476 Score: 121
Period size: 35 Copynumber: 2.0 Consensus size: 37
1978395 AATTATATCT
1978405 TCTAAGATTGCATATCATATCTAAGATTGCA-ATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTGCATATCATA
1978442 TCTAAGATTG-TATCATATCTAAGATTGCATATCAT
1 TCTAAGATTGATATCATATCTAAGATTGCATATCAT
1978477 TGAAGATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 19 0.56
36 5 0.15
37 10 0.29
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (37 bp):
TCTAAGATTGATATCATATCTAAGATTGCATATCATA
Found at i:1978474 original size:14 final size:15
Alignment explanation
Indices: 1978419--1978474 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
1978409 AGATTGCATA
1978419 TCATATCTAAGATTG
1 TCATATCTAAGATTG
1978434 CAATCATATCTAAGATTG
1 ---TCATATCTAAGATTG
1978452 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
1978469 -CATATC
1 TCATATC
1978475 ATTGAAGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 6 0.16
17 16 0.43
18 15 0.41
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:1978484 original size:17 final size:19
Alignment explanation
Indices: 1978405--1978476 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
1978395 AATTATATCT
1978405 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
1978424 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
1978442 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
1978459 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
1978477 TGAAGATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1978887 original size:45 final size:45
Alignment explanation
Indices: 1978825--1979098 Score: 286
Period size: 45 Copynumber: 6.1 Consensus size: 45
1978815 AGAAGGCGAT
* * *
1978825 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * *
1978870 ATCTGTTATATTCGATCTACTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * *
1978915 ATCTGCT-TCTTCAATCTGCTCCCCGTCCAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* *
1978959 ATCTGTTATCTCCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * * * * *
1979004 ATTTGTCATCTTGGATCTGCT--TCGATGTAAATACATGA-AGGTCAG
1 ATCTGTTATCTTCGATCTGCTCCCCG-TCT-AATACA-GAGATGCCAA
* *
1979049 ATCTGCTATGTCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAA
1 ATCTG-T-TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
1979096 ATC
1 ATC
1979099 ATCTTGGATC
Statistics
Matches: 186, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
43 2 0.01
44 40 0.22
45 110 0.59
46 5 0.03
47 25 0.13
48 2 0.01
49 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.31
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
Found at i:1978990 original size:89 final size:90
Alignment explanation
Indices: 1978825--1979005 Score: 274
Period size: 89 Copynumber: 2.0 Consensus size: 90
1978815 AGAAGGCGAT
** * *
1978825 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATATTCGATCTAC
1 ATCTGCTATCTTCAATCTGCTCCCCGTCCAATACAGAGACGCCAAATCTGTTATATCCGATCTAC
1978890 TCCCCGTCTAATACAGAGACGCCAA
66 TCCCCGTCTAATACAGAGACGCCAA
* * * *
1978915 ATCTGCT-TCTTCAATCTGCTCCCCGTCCAATACAGAGATGCCAAATCTGTTATCTCCGATTTGC
1 ATCTGCTATCTTCAATCTGCTCCCCGTCCAATACAGAGACGCCAAATCTGTTATATCCGATCTAC
*
1978979 TCCCCGTCTAATACAGAGATGCCAA
66 TCCCCGTCTAATACAGAGACGCCAA
1979004 AT
1 AT
1979006 TTGTCATCTT
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
89 75 0.91
90 7 0.09
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.29
Consensus pattern (90 bp):
ATCTGCTATCTTCAATCTGCTCCCCGTCCAATACAGAGACGCCAAATCTGTTATATCCGATCTAC
TCCCCGTCTAATACAGAGACGCCAA
Found at i:1979171 original size:78 final size:78
Alignment explanation
Indices: 1979038--1979332 Score: 439
Period size: 78 Copynumber: 3.8 Consensus size: 78
1979028 ATGTAAATAC
*
1979038 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1979103 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * * * *
1979116 ATAAAGGTCCA-ATCTGTTATGTCTTCAATCTGCTCCCCATCTAATACAGAAATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1979180 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* * * *
1979194 ATGAAGGTCAGATCTGTTGTGTCTTCGATCTGCTCCCTGTCTAATACAGAGATTCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1979259 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * * **
1979272 ATGAAGGTCAGATCTGCTATGTCTTCGATTTGCTCTCCGTCGAATATGGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
1979333 TGTTTCTTCG
Statistics
Matches: 193, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
77 2 0.01
78 189 0.98
79 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:1991650 original size:18 final size:19
Alignment explanation
Indices: 1991614--1991693 Score: 90
Period size: 19 Copynumber: 3.9 Consensus size: 19
1991604 AATTATATCT
1991614 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
1991633 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
1991651 TCTAAGATTGTATGATTGTATCATA
1 TCTAAGATTG---CA---TATCATA
1991676 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
1991694 TGAAGATTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
18 16 0.31
19 18 0.35
21 1 0.02
22 1 0.02
25 16 0.31
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Done.