Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 133 of 153
Found at i:41807471 original size:88 final size:88
Alignment explanation
Indices: 41807322--41807756 Score: 690
Period size: 88 Copynumber: 4.9 Consensus size: 88
41807312 AAGATTCGCC
* * * * * * *
41807322 GTCTTCGATCTGCTTCACAGTCGATACAGAAAGGCAAAATCTGCTATCCTCAACCAGCTCCATTA
1 GTCTTCGATCTACTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
* *
41807387 CAACTGAGGGAGGCAAGGTTTGT
66 CAACCGAGGGAGGCAAGGTTTAT
41807410 GTCTTCGATCTACTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
1 GTCTTCGATCTACTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
*
41807475 CAACCAAGGGAGGCAAGGTTTAT
66 CAACCGAGGGAGGCAAGGTTTAT
41807498 GTCTTCGATCTACTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
1 GTCTTCGATCTACTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
*
41807563 CAACCAAGGGAGGCAAGGTTTAT
66 CAACCGAGGGAGGCAAGGTTTAT
* * *
41807586 GTCTTCGATCTACTTCACTGTCGATACAGGAAGGCAAGATTTGCTATCTTCAACCAGTTCCACTA
1 GTCTTCGATCTACTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
* * *
41807651 CAACTGAGGGAGGTAAGGTTTGT
66 CAACCGAGGGAGGCAAGGTTTAT
* * *
41807674 GTCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCCACCAGCTCCACTA
1 GTCTTCGATCTACTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
41807739 CAACCGAGGGAGGCAAGG
66 CAACCGAGGGAGGCAAGG
41807757 ATCTTCACTG
Statistics
Matches: 322, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 322 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (88 bp):
GTCTTCGATCTACTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
CAACCGAGGGAGGCAAGGTTTAT
Found at i:41807489 original size:44 final size:43
Alignment explanation
Indices: 41807436--41807760 Score: 140
Period size: 44 Copynumber: 7.4 Consensus size: 43
41807426 ACTGTCGATG
*
41807436 CAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAAC
1 CAGGGAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAAC
* ** * * * * * **
41807479 CAAGGGAGGCAAGGT-TTATGTCTTCGATCTA-CTTCACTGTCGATG
1 C-AGGGAGGCAAGATCTGCTATCTTC-AACCAGCTCCACT-AC-AAC
*
41807524 CAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAAC
1 CAGGGAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAAC
* ** * * * * *
41807567 CAAGGGAGGCAAGGT-TTATGTCTTCGATCTA-CTTCACTGTCGATA-
1 C-AGGGAGGCAAGATCTGCTATCTTC-AACCAGCTCCACT-AC-A-AC
* * *
41807612 CAGGAAGGCAAGATTTGCTATCTTCAACCAGTTCCACTACAAC
1 CAGGGAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAAC
* * * * * * * * * * * **
41807655 TGAGGGAGGTAAGGTTTG-TGTCTTCGATCTGCTTCGCTGTCGATG
1 -CAGGGAGGCAAGATCTGCTATCTTCAACCAGCTCCACT-AC-AAC
* *
41807700 CAGGAAGGCAAGATCTGCTATCTTCCACCAGCTCCACTACAAC
1 CAGGGAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAAC
41807743 CGAGGGAGGCAAGGATCT
1 C-AGGGAGGCAA-GATCT
41807761 TCACTGATCT
Statistics
Matches: 192, Mismatches: 70, Indels: 38
0.64 0.23 0.13
Matches are distributed among these distances:
42 1 0.01
43 45 0.23
44 96 0.50
45 49 0.26
46 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.25
Consensus pattern (43 bp):
CAGGGAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAAC
Found at i:41808934 original size:6 final size:7
Alignment explanation
Indices: 41808918--41808951 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
41808908 TCGTCATTAC
41808918 TTTTCAT
1 TTTTCAT
41808925 TTTTCA-
1 TTTTCAT
41808931 TTTTCAT
1 TTTTCAT
41808938 TTTTCAT
1 TTTTCAT
41808945 TTTTCAT
1 TTTTCAT
41808952 CCTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:41808936 original size:13 final size:13
Alignment explanation
Indices: 41808918--41808947 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
41808908 TCGTCATTAC
41808918 TTTTCATTTTTCA
1 TTTTCATTTTTCA
41808931 TTTTCATTTTTCA
1 TTTTCATTTTTCA
41808944 TTTT
1 TTTT
41808948 TCATCCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:41809952 original size:25 final size:25
Alignment explanation
Indices: 41809897--41809949 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
41809887 TTGATTTTGA
41809897 TTTTGATTTTTCTTCTTTTTTGTAT
1 TTTTGATTTTTCTTCTTTTTTGTAT
* *
41809922 TTTTGATTTTTGTT-TTTTTTTTAT
1 TTTTGATTTTTCTTCTTTTTTGTAT
41809946 TTTT
1 TTTT
41809950 TGAATTGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.08, C:0.04, G:0.08, T:0.81
Consensus pattern (25 bp):
TTTTGATTTTTCTTCTTTTTTGTAT
Found at i:41817833 original size:188 final size:187
Alignment explanation
Indices: 41817504--41817853 Score: 531
Period size: 188 Copynumber: 1.9 Consensus size: 187
41817494 AACGCAGAGT
* *
41817504 TTGGTCTTAAGGTACACTAGCATTAGTGGCGCTTATACGAAAACGCCGCTAAAGTATAGTATTAG
1 TTGGTCTTAAGGTACACTAACATTAATGGCGCTTATACGAAAACGCCGCTAAAGTATAGTATTAG
* * *
41817569 CAGCGAGTAGTGAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTTGTCTTGAGGTATAT
66 CAGCGAGTAGTAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACAT
*
41817634 TAGGATTAGTGGCGCTTAT-TGGAAAACACCGCAAAATATTAACCAAAACACTGCGCA
131 TACGATTAGTGGCGCTTATAT-GAAAACACCGCAAAATATTAACCAAAACACTGCGCA
* * * * *
41817691 TTGGTCTTAATGTATAGTAACATTAATGGCGCTTATGCTAAAACGCCGCTAAAGTATAGTATTAG
1 TTGGTCTTAAGGTACACTAACATTAATGGCGCTTATACGAAAACGCCGCTAAAGTATAGTATTAG
* * * *
41817756 CGGCGAGTACTTAAAAGCGCCGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACA
66 CAGCGAGTA-GTAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACA
*
41817821 TTACGATTAGTGGCGCTTATATGAAAACGCCGC
130 TTACGATTAGTGGCGCTTATATGAAAACACCGC
41817854 TAAAGCATAG
Statistics
Matches: 145, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
187 66 0.46
188 78 0.54
189 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (187 bp):
TTGGTCTTAAGGTACACTAACATTAATGGCGCTTATACGAAAACGCCGCTAAAGTATAGTATTAG
CAGCGAGTAGTAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACAT
TACGATTAGTGGCGCTTATATGAAAACACCGCAAAATATTAACCAAAACACTGCGCA
Found at i:41817959 original size:112 final size:113
Alignment explanation
Indices: 41817712--41817961 Score: 310
Period size: 112 Copynumber: 2.2 Consensus size: 113
41817702 GTATAGTAAC
* * *
41817712 ATTAATGGCGCTTA-TGCTAAAACGCCGCTAAAGTATAGTATTAGCGGCGAGTACTTAAAAGCGC
1 ATTAGTGGCGCTTATTG-GAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTACTTAAAAGCGC
* ** * *
41817776 CGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTACG
65 CACAA-CAATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACG
* * *
41817826 ATTAGTGGCGCTTATAT-GAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTA-TTGTAAAGTG
1 ATTAGTGGCGCTTAT-TGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTACTT-AAAAGCG
* * *
41817889 CCACAA-AATATTAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGG
64 CCACAACAATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACG
41817938 ATTAGTGGCGCTTATTGGAAAACG
1 ATTAGTGGCGCTTATTGGAAAACG
41817962 ACACAAAATA
Statistics
Matches: 118, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
111 1 0.01
112 58 0.49
113 2 0.02
114 56 0.47
116 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (113 bp):
ATTAGTGGCGCTTATTGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTACTTAAAAGCGCC
ACAACAATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACG
Found at i:41818030 original size:300 final size:299
Alignment explanation
Indices: 41817469--41818262 Score: 1159
Period size: 300 Copynumber: 2.6 Consensus size: 299
41817459 GTTTACTACC
* * * *
41817469 AAGCGCCGCAATAC-ATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTACACTAGCATTAGTGG
1 AAGCGCCGCAAT-CTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTAG-ATTAGTGG
* * * * * *
41817533 CGCTTATACGAAAACGCCGCTAAAGTATAGTATTAGCAGCGAGTAGTGAAAGCGCCGCAATATTT
64 CGCTTATATGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTATTGAAAGCGCCGCAA-A-AT
* *
41817598 CTTAACCAAAACGCAGAGTTTTGTCTTGAGGTATATTAGGATTAGTGGCGCTTATTGGAAAAC-A
127 ATTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATTGGAAAACGA
*
41817662 CCGCAAAATATTAACCAAAACACTGCGCATTGGTCTTAATGTATAGTAACATTAATGGCGCTTAT
192 CCACAAAATATTAACCAAAACACTGCGCATTGGTCTTAATGTATAGTAACATTAATGGCGCTTAT
*
41817727 GCTAAAACGCCGCTAAAGTATAGTATTAGCGGCGAGTACT-TAA
257 GCTAAAACGCCGCTAAAGTATAGTATTAGCGGCAAGTACTGT-A
41817770 AAGCGCCGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTACGATTAGTGGC
1 AAGCGCCGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTA-GATTAGTGGC
* *
41817835 GCTTATATGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTATTGTAAAGTGCCACAAAATAT
65 GCTTATATGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTATTG-AAAGCGCCGCAAAATAT
*
41817900 TAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGGATTAGTGGCGCTTATTGGAAAACGA-C
129 TAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATTGGAAAACGACC
** * * * *
41817964 ACAAAATATTAACCAAAACGTTGCGCTTTGGTCTTGATGTATAGTAGCATTAGTGGCGCTTATGC
194 ACAAAATATTAACCAAAACACTGCGCATTGGTCTTAATGTATAGTAACATTAATGGCGCTTATGC
41818029 TAAAACGCCGCTAAAGTATAGTATTAGCGGCAAGTACTGTA
259 TAAAACGCCGCTAAAGTATAGTATTAGCGGCAAGTACTGTA
*
41818070 AAGCGCCGCAATCTTTCTTAACCAAAACGAAGAGTTTGGTGTTGAGGTACATTAGGATTAGTGGC
1 AAGCGCCGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTA-GATTAGTGGC
* * *
41818135 GCTTATTTGAAAACGCCGCTAAAGGATAATATTAGCGGCGCGTATTGAAAAGCGCCGCAAAATAT
65 GCTTATATGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTATTG-AAAGCGCCGCAAAATAT
* * * *
41818200 TAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTAGCAATT-GTGGCGCTTA-TGGTAAAACG
129 TAACCAAAACGCAGAG-TTTGGTCTTGAGGTATATTAG-GATTAGTGGCGCTTATTGG-AAAACG
41818263 CCGCTAAAAC
Statistics
Matches: 449, Mismatches: 36, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
300 299 0.67
301 136 0.30
302 14 0.03
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (299 bp):
AAGCGCCGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTAGATTAGTGGCG
CTTATATGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTATTGAAAGCGCCGCAAAATATTA
ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATTGGAAAACGACCAC
AAAATATTAACCAAAACACTGCGCATTGGTCTTAATGTATAGTAACATTAATGGCGCTTATGCTA
AAACGCCGCTAAAGTATAGTATTAGCGGCAAGTACTGTA
Found at i:41818035 original size:74 final size:73
Alignment explanation
Indices: 41817890--41818026 Score: 202
Period size: 74 Copynumber: 1.9 Consensus size: 73
41817880 TGTAAAGTGC
* * *
41817890 CACAAAATATTAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGGATTAGTGGCGCTTATTG
1 CACAAAATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTATAGTAGCATTAGTGGCGCTTATTG
41817955 GAAAACGA
66 GAAAACGA
** * *
41817963 CACAAAATATTAACCAAAACGTTGCGCTTTGGTCTTGATGTATAGTAGCATTAGTGGCGCTTAT
1 CACAAAATATTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATAGTAGCATTAGTGGCGCTTAT
41818027 GCTAAAACGC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
73 23 0.41
74 33 0.59
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (73 bp):
CACAAAATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTATAGTAGCATTAGTGGCGCTTATTG
GAAAACGA
Found at i:41818281 original size:113 final size:113
Alignment explanation
Indices: 41817938--41818290 Score: 381
Period size: 114 Copynumber: 3.1 Consensus size: 113
41817928 GTATATTAGG
* * * * **
41817938 ATTAGTGGCGCTTATTGGAAAA-CGACACAAAATATTAACCAAAACGTTGCGCTTTGGTCTTGAT
1 ATTAGCGGCGCGTATT-GAAAAGCGCCGCAAAATATTAACCAAAACGAAGCGCTTTGGTCTTGAT
* * *
41818002 GTATAGTAGCATTAGTGGCGCTTATGCTAAAACGCCGCTAAAGTATAGT
65 GTATACTAGCATTAGTGGCGCTTATGCTAAAACGCCGCTAAAGCATAAT
** * * ** * * *
41818051 ATTAGCGGCAAGTACTGTAAAGCGCCGCAATCTTTCTTAACCAAAACGAAGAG-TTTGGTGTTGA
1 ATTAGCGGCGCGTATTGAAAAGCGCCGCAA--AATATTAACCAAAACGAAGCGCTTTGGTCTTGA
* * * * * *
41818115 GGTACATTAGGATTAGTGGCGCTTAT-TTGAAAACGCCGCTAAAGGATAAT
64 TGTATACTAGCATTAGTGGCGCTTATGCT-AAAACGCCGCTAAAGCATAAT
*
41818165 ATTAGCGGCGCGTATTGAAAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
1 ATTAGCGGCGCGTATTGAAAAGCGCCGCAAAATATTAACCAAAACGAAGCGCTTTGGTCTTGATG
* * *
41818230 TATACTAGCAATT-GTGGCGCTTATGGTAAAACGCCGCTAAAACATATT
66 TATACTAGC-ATTAGTGGCGCTTATGCTAAAACGCCGCTAAAGCATAAT
41818278 ATTAGCGGCGCGT
1 ATTAGCGGCGCGT
41818291 TGTGGGAAAC
Statistics
Matches: 193, Mismatches: 40, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
112 20 0.10
113 77 0.40
114 81 0.42
115 15 0.08
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (113 bp):
ATTAGCGGCGCGTATTGAAAAGCGCCGCAAAATATTAACCAAAACGAAGCGCTTTGGTCTTGATG
TATACTAGCATTAGTGGCGCTTATGCTAAAACGCCGCTAAAGCATAAT
Found at i:41818344 original size:16 final size:16
Alignment explanation
Indices: 41818310--41818367 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
41818300 CGCCACTAGA
41818310 TTATTATATAATGTAGT
1 TTATTATAT-ATGTAGT
*
41818327 TTATTATATATTTAGT
1 TTATTATATATGTAGT
41818343 TTATTATATATGTAGT
1 TTATTATATATGTAGT
41818359 TTATTATAT
1 TTATTATAT
41818368 TATATAATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
16 30 0.77
17 9 0.23
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
TTATTATATATGTAGT
Found at i:41818379 original size:19 final size:19
Alignment explanation
Indices: 41818311--41818384 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 19
41818301 GCCACTAGAT
41818311 TATTATATAATG--TAGTT-
1 TATTATATAATGTTTA-TTA
*
41818328 TATTATATATTTAGTTTATTA
1 TATTATATA-AT-GTTTATTA
*
41818349 TA-TATGT-A-GTTTATTA
1 TATTATATAATGTTTATTA
41818365 TATTATATAATGTTTATTA
1 TATTATATAATGTTTATTA
41818384 T
1 T
41818385 TTTTGAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
16 10 0.22
17 13 0.29
18 2 0.04
19 10 0.22
20 6 0.13
21 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
TATTATATAATGTTTATTA
Found at i:41818380 original size:35 final size:33
Alignment explanation
Indices: 41818310--41818384 Score: 107
Period size: 32 Copynumber: 2.2 Consensus size: 33
41818300 CGCCACTAGA
*
41818310 TTATTATATAATGTAGTTTATTATATATTTAGT
1 TTATTATATAATGTAGTTTATTATATATTAAGT
41818343 TTATTATAT-ATGTAGTTTATTATATTATATAATGT
1 TTATTATATAATGTAGTTTATTATA-TAT-TAA-GT
41818378 TTATTAT
1 TTATTAT
41818385 TTTTGAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
32 15 0.39
33 12 0.32
34 2 0.05
35 9 0.24
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (33 bp):
TTATTATATAATGTAGTTTATTATATATTAAGT
Found at i:41819206 original size:72 final size:72
Alignment explanation
Indices: 41819129--41819277 Score: 280
Period size: 72 Copynumber: 2.1 Consensus size: 72
41819119 TTTTTTAAAA
*
41819129 ATTTCCATGTTCTTAGTGGCGTTTTACGAAAAAACGCCGCAAAATTATCCTAATTATTAGGAAAA
1 ATTTCCATGTTCTTAGTGGCGTTTTACGAAAAAACGCCGCAAAATTATCCTAATTATCAGGAAAA
41819194 CGACTGC
66 CGACTGC
*
41819201 GTTTCCATGTTCTTAGTGGCGTTTTACGAAAAAACGCCGCAAAATTATCCTAATTATCAGGAAAA
1 ATTTCCATGTTCTTAGTGGCGTTTTACGAAAAAACGCCGCAAAATTATCCTAATTATCAGGAAAA
41819266 CGACTGC
66 CGACTGC
41819273 ATTTC
1 ATTTC
41819278 GTTTATATTT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (72 bp):
ATTTCCATGTTCTTAGTGGCGTTTTACGAAAAAACGCCGCAAAATTATCCTAATTATCAGGAAAA
CGACTGC
Found at i:41820603 original size:3 final size:3
Alignment explanation
Indices: 41820595--41820629 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
41820585 CTATTGTTAA
41820595 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41820630 CACTACATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41821635 original size:9 final size:9
Alignment explanation
Indices: 41821603--41822213 Score: 500
Period size: 9 Copynumber: 70.2 Consensus size: 9
41821593 TATCTTAGAC
41821603 AACTTACAT
1 AACTTACAT
41821612 AA--TACAT
1 AACTTACAT
* *
41821619 AGCATACAT
1 AACTTACAT
41821628 AACTTACAT
1 AACTTACAT
*
41821637 AA--TACAA
1 AACTTACAT
41821644 AACTTACAT
1 AACTTACAT
*
41821653 AACTTAAAT
1 AACTTACAT
* *
41821662 ATCTTACAC
1 AACTTACAT
41821671 AACTTACAT
1 AACTTACAT
* *
41821680 AACCTATAT
1 AACTTACAT
41821689 AA--TACATTT
1 AACTTACA--T
*
41821698 AACTTACGT
1 AACTTACAT
41821707 AACTTACAT
1 AACTTACAT
41821716 AACTTACAT
1 AACTTACAT
*
41821725 AA--TACAA
1 AACTTACAT
41821732 AACTTACAT
1 AACTTACAT
*
41821741 AACTTAAAT
1 AACTTACAT
* *
41821750 ATCTTACAC
1 AACTTACAT
41821759 AACTTACAT
1 AACTTACAT
*
41821768 AACCTACAT
1 AACTTACAT
41821777 AA--TACATTT
1 AACTTACA--T
41821786 AACTTACAT
1 AACTTACAT
41821795 AACTTACAT
1 AACTTACAT
41821804 AACTTACAT
1 AACTTACAT
*
41821813 AA--TACAA
1 AACTTACAT
41821820 AAC-TACAT
1 AACTTACAT
*
41821828 AACTTAAAT
1 AACTTACAT
* *
41821837 ATCTTACAC
1 AACTTACAT
41821846 AACTTACAT
1 AACTTACAT
*
41821855 AACCTACAT
1 AACTTACAT
41821864 AA--TACATTT
1 AACTTACA--T
41821873 AACTTACAT
1 AACTTACAT
41821882 AACTTACAT
1 AACTTACAT
*
41821891 AA--TACAA
1 AACTTACAT
41821898 AAC-TACAT
1 AACTTACAT
*
41821906 AACTTAAAT
1 AACTTACAT
* *
41821915 ATCTTACAC
1 AACTTACAT
41821924 AACTTACAT
1 AACTTACAT
*
41821933 AACCTACAT
1 AACTTACAT
41821942 AA--TACATTT
1 AACTTACA--T
41821951 AACTTACAT
1 AACTTACAT
41821960 AACTTACAT
1 AACTTACAT
*
41821969 AA--TACAA
1 AACTTACAT
41821976 AAC-TACAT
1 AACTTACAT
*
41821984 AACTTAAAT
1 AACTTACAT
* *
41821993 ATCTTACAC
1 AACTTACAT
41822002 AACTTACAT
1 AACTTACAT
*
41822011 AACCTACAT
1 AACTTACAT
41822020 AA--TACATTT
1 AACTTACA--T
41822029 AACTTACAT
1 AACTTACAT
41822038 AACTTACAT
1 AACTTACAT
*
41822047 AA--TACAA
1 AACTTACAT
41822054 AAC-TACAT
1 AACTTACAT
*
41822062 AACTTAAAT
1 AACTTACAT
* *
41822071 ATCTTACAC
1 AACTTACAT
41822080 AACTTACAT
1 AACTTACAT
*
41822089 AACCTACAT
1 AACTTACAT
41822098 AA--TACATTT
1 AACTTACA--T
41822107 AACTTACAT
1 AACTTACAT
41822116 AACTTACAT
1 AACTTACAT
*
41822125 AA--TACAA
1 AACTTACAT
41822132 AAC-TACAT
1 AACTTACAT
*
41822140 AACTTAAAT
1 AACTTACAT
* *
41822149 ATCTTACAC
1 AACTTACAT
41822158 AACTTACAT
1 AACTTACAT
*
41822167 AACCTACAT
1 AACTTACAT
41822176 AA--TACATTT
1 AACTTACA--T
41822185 AACTTACAT
1 AACTTACAT
41822194 AACTTACAT
1 AACTTACAT
41822203 AACTTACAT
1 AACTTACAT
41822212 AA
1 AA
41822214 TAACTTATAC
Statistics
Matches: 488, Mismatches: 70, Indels: 88
0.76 0.11 0.14
Matches are distributed among these distances:
7 75 0.15
8 35 0.07
9 351 0.72
11 27 0.06
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:41821765 original size:156 final size:155
Alignment explanation
Indices: 41821596--41822204 Score: 842
Period size: 156 Copynumber: 3.8 Consensus size: 155
41821586 TACGAAATAT
* * *
41821596 CTTAGACAACTTACATAATACA-TAGCATACATAACTTACATAATACAAAACTTACATAACTTAA
1 CTTACACAACCTACATAATACATTAACATACATAACTTACATAATACAAAAC-TACATAACTTAA
*
41821660 ATATCTTACACAACTTACATAACCTATATAATACATTTAACTTACGTAACTTACATAACTTACAT
65 ATATCTTACACAACTTACATAACCTACATAATAC-----A-TT---TAACTTACATAACTTACAT
* * *
41821725 AATACAAAACTTACATAACTTAAATATCTTACACAA
121 AATACAAAAC-TACAAAACTTAAATAACTTAAACAA
*
41821761 CTTACATAACCTACATAATACATTTAACTTACATAACTTACATAACTTACATAATACAAAACTAC
1 CTTACACAACCTACATAATACA-TT-A---AC---A--TACATAACTTACATAATACAAAACTAC
41821826 ATAACTTAAATATCTTACACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACAT
56 ATAACTTAAATATCTTACACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACAT
* * *
41821891 AATACAAAACTACATAACTTAAATATCTTACACAA
121 AATACAAAACTACAAAACTTAAATAACTTAAACAA
* *
41821926 CTTACATAACCTACATAATACATTTAACTTACATAACTTACATAATACAAAACTACATAACTTAA
1 CTTACACAACCTACATAATACA-TTAACATACATAACTTACATAATACAAAACTACATAACTTAA
41821991 ATATCTTACACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAATACAAAA
65 ATATCTTACACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAATACAAAA
* * *
41822056 CTACATAACTTAAATATCTTACACAA
130 CTACAAAACTTAAATAACTTAAACAA
* *
41822082 CTTACATAACCTACATAATACATTTAACTTACATAACTTACATAATACAAAACTACATAACTTAA
1 CTTACACAACCTACATAATACA-TTAACATACATAACTTACATAATACAAAACTACATAACTTAA
41822147 ATATCTTACACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAA
65 ATATCTTACACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAA
41822205 CTTACATAAT
Statistics
Matches: 427, Mismatches: 6, Indels: 31
0.92 0.01 0.07
Matches are distributed among these distances:
156 250 0.59
161 2 0.00
164 1 0.00
165 69 0.16
166 29 0.07
167 1 0.00
168 1 0.00
169 2 0.00
170 1 0.00
171 1 0.00
174 1 0.00
175 45 0.11
176 24 0.06
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (155 bp):
CTTACACAACCTACATAATACATTAACATACATAACTTACATAATACAAAACTACATAACTTAAA
TATCTTACACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAATACAAAAC
TACAAAACTTAAATAACTTAAACAA
Found at i:41821879 original size:78 final size:78
Alignment explanation
Indices: 41821794--41822204 Score: 822
Period size: 78 Copynumber: 5.3 Consensus size: 78
41821784 TTAACTTACA
41821794 TAACTTACATAACTTACATAATACAAAACTACATAACTTAAATATCTTACACAACTTACATAACC
1 TAACTTACATAACTTACATAATACAAAACTACATAACTTAAATATCTTACACAACTTACATAACC
41821859 TACATAATACATT
66 TACATAATACATT
41821872 TAACTTACATAACTTACATAATACAAAACTACATAACTTAAATATCTTACACAACTTACATAACC
1 TAACTTACATAACTTACATAATACAAAACTACATAACTTAAATATCTTACACAACTTACATAACC
41821937 TACATAATACATT
66 TACATAATACATT
41821950 TAACTTACATAACTTACATAATACAAAACTACATAACTTAAATATCTTACACAACTTACATAACC
1 TAACTTACATAACTTACATAATACAAAACTACATAACTTAAATATCTTACACAACTTACATAACC
41822015 TACATAATACATT
66 TACATAATACATT
41822028 TAACTTACATAACTTACATAATACAAAACTACATAACTTAAATATCTTACACAACTTACATAACC
1 TAACTTACATAACTTACATAATACAAAACTACATAACTTAAATATCTTACACAACTTACATAACC
41822093 TACATAATACATT
66 TACATAATACATT
41822106 TAACTTACATAACTTACATAATACAAAACTACATAACTTAAATATCTTACACAACTTACATAACC
1 TAACTTACATAACTTACATAATACAAAACTACATAACTTAAATATCTTACACAACTTACATAACC
41822171 TACATAATACATT
66 TACATAATACATT
41822184 TAACTTACATAACTTACATAA
1 TAACTTACATAACTTACATAA
41822205 CTTACATAAT
Statistics
Matches: 333, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 333 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (78 bp):
TAACTTACATAACTTACATAATACAAAACTACATAACTTAAATATCTTACACAACTTACATAACC
TACATAATACATT
Found at i:41827714 original size:21 final size:21
Alignment explanation
Indices: 41827688--41827758 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
41827678 CTACAACTTA
*
41827688 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
41827709 AAGCAGCGGTTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
41827730 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
41827751 AAGCAGAG
1 AAGCAGAG
41827759 TAGAGCAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.32, C:0.18, G:0.45, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:41828134 original size:42 final size:42
Alignment explanation
Indices: 41828077--41828278 Score: 293
Period size: 42 Copynumber: 4.8 Consensus size: 42
41828067 GTTTTTGTAT
*
41828077 AAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
*
41828119 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-A
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
41828160 AAAAACGCCGCTAAAG-TCCATGTTCTTTAGCGGCGCTTA-ATA
1 AAAAACGCCGCTAAAGAT-CATGTTCTTTAGCGGCGCTTAGA-A
* * * *
41828202 AAAAACGCCGCTAAAGACCTTGTTCTTTAGAGGCGCTTAGAT
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
* *
41828244 AAAAACGTCGTTAAAGATCATGTTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
41828279 TTTAATATTA
Statistics
Matches: 143, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
41 38 0.27
42 104 0.73
43 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
Found at i:41828174 original size:83 final size:84
Alignment explanation
Indices: 41828075--41828320 Score: 336
Period size: 83 Copynumber: 2.9 Consensus size: 84
41828065 GCGTTTTTGT
*
41828075 ATAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGA-AAAAAACGCCGCTAAAGACCA
1 ATAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-ATAAAAAACGCCGCTAAAGACCA
*
41828139 TGTTCTTTAGCGGCGCTTAG
65 TGTTCTTTAGAGGCGCTTAG
*
41828159 A-AAAAACGCCGCTAAAG-TCCATGTTCTTTAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCT
1 ATAAAAACGCCGCTAAAGAT-CATGTTCTTTAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCA
41828222 TGTTCTTTAGAGGCGCTTAG
65 TGTTCTTTAGAGGCGCTTAG
* * * ** ** *
41828242 ATAAAAACGTCGTTAAAGATCATGTTCTTTAGCGGCGTTTAATATTAAGTGCCGCTAAAGAACAT
1 ATAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCAT
* *
41828307 GGTATTTAGAGGCG
66 GTTCTTTAGAGGCG
41828321 TTTTTTATTA
Statistics
Matches: 144, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
82 2 0.01
83 76 0.53
84 65 0.45
85 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (84 bp):
ATAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCAT
GTTCTTTAGAGGCGCTTAG
Found at i:41828315 original size:42 final size:42
Alignment explanation
Indices: 41828084--41828365 Score: 142
Period size: 42 Copynumber: 6.7 Consensus size: 42
41828074 TATAAAAACA
* * * * ** *
41828084 CCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGA-AAAAAACG
1 CCGCTAAAGAACATGGTATTTAGCGGCGTTTA-ATATTAAGCG
* * * * * *
41828126 CCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGA-A-AAAACG
1 CCGCTAAAGAACATGGTATTTAGCGGCGTTTA-ATATTAAGCG
** * * * ** *
41828167 CCGCTAAAGTCCATGTTCTTTAGCGGCGCTTAATAAAAAACG
1 CCGCTAAAGAACATGGTATTTAGCGGCGTTTAATATTAAGCG
* * * * * * * *
41828209 CCGCTAAAGACCTTGTTCTTTAGAGGCGCTTAGATA-AAAACG
1 CCGCTAAAGAACATGGTATTTAGCGGCGTTTA-ATATTAAGCG
* * * * * *
41828251 TCGTTAAAGATCATGTTCTTTAGCGGCGTTTAATATTAAGTG
1 CCGCTAAAGAACATGGTATTTAGCGGCGTTTAATATTAAGCG
* **
41828293 CCGCTAAAGAACATGGTATTTAGAGGCGTTTTTTATTAAGCG
1 CCGCTAAAGAACATGGTATTTAGCGGCGTTTAATATTAAGCG
*
41828335 CTGCTAAAGAACATGG-ACTTTAGCGGCGTTT
1 CCGCTAAAGAACATGGTA-TTTAGCGGCGTTT
41828366 TTTCTAAGCG
Statistics
Matches: 210, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
40 1 0.00
41 42 0.20
42 164 0.78
43 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (42 bp):
CCGCTAAAGAACATGGTATTTAGCGGCGTTTAATATTAAGCG
Found at i:41828366 original size:42 final size:41
Alignment explanation
Indices: 41828268--41828505 Score: 183
Period size: 42 Copynumber: 5.4 Consensus size: 41
41828258 AGATCATGTT
* *
41828268 CTTTAGCGGCGTTTAATAT-TAAGTGCCGCTAAAGAACATGGTA
1 CTTTAGCGGCGTTT--TTTCTAAGCGCCGCTAAAGAACATGG-A
* * *
41828311 -TTTAGAGGCGTTTTTTATTAAGCGCTGCTAAAGAACATGGA
1 CTTTAGCGGCGTTTTTT-CTAAGCGCCGCTAAAGAACATGGA
* *
41828352 CTTTAGCGGCGTTTTTTCTAAGCGCTGCTACTAAGAGCCACTGAAGAACATGGC
1 CTTTAGCGGCGTTTTTTCTAA--GC-GC--C-----G---CTAAAGAACATGGA
* *
41828406 CTTTAGCGGCGCTTATTTCTAAGCGCCGCTAAAGAACATGGC
1 CTTTAGCGGCG-TTTTTTCTAAGCGCCGCTAAAGAACATGGA
* * *
41828448 CTTTAGCGGCGCTTATTTCTAAGCGCCGCTAAAGAATATGGT
1 CTTTAGCGGCG-TTTTTTCTAAGCGCCGCTAAAGAACATGGA
41828490 CTTTAGCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
41828506 GTTTGTAAAC
Statistics
Matches: 164, Mismatches: 14, Indels: 36
0.77 0.07 0.17
Matches are distributed among these distances:
40 2 0.01
41 8 0.05
42 111 0.68
43 2 0.01
44 2 0.01
45 1 0.01
50 1 0.01
51 1 0.01
52 2 0.01
53 2 0.01
54 23 0.14
55 9 0.05
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTTCTAAGCGCCGCTAAAGAACATGGA
Found at i:41831062 original size:12 final size:11
Alignment explanation
Indices: 41831027--41831090 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 11
41831017 ATAAAAAAAT
41831027 TAAAAAATTAAA
1 TAAAAAA-TAAA
41831039 -AACAAAATTAAA
1 TAA-AAAA-TAAA
41831051 -AATAAAGATAAA
1 TAA-AAA-ATAAA
41831063 TAAAAAATAAA
1 TAAAAAATAAA
41831074 TAAAAAAATAAAA
1 T-AAAAAAT-AAA
41831087 TAAA
1 TAAA
41831091 CAACAACAAC
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
11 8 0.17
12 31 0.67
13 7 0.15
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:41831089 original size:28 final size:28
Alignment explanation
Indices: 41831014--41831099 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 28
41831004 TAAGTTTAAG
*
41831014 AAAATAAAAAAATTAAAA-AATTAAAAAC
1 AAAATAAAAAAA-TAAAATAAATAAAAAC
*
41831042 AAAAT-TAAAAATAAAGATAAATAAAAA-
1 AAAATAAAAAAATAAA-ATAAATAAAAAC
* *
41831069 ATAAATAAAAAAATAAAATAAACAACAAC
1 A-AAATAAAAAAATAAAATAAATAAAAAC
41831098 AA
1 AA
41831100 CAACAATAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
26 4 0.08
27 7 0.15
28 27 0.56
29 10 0.21
ACGTcount: A:0.78, C:0.05, G:0.01, T:0.16
Consensus pattern (28 bp):
AAAATAAAAAAATAAAATAAATAAAAAC
Found at i:41831243 original size:10 final size:11
Alignment explanation
Indices: 41831230--41831271 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
41831220 AAAATTAGTA
*
41831230 AAATAAA-AAT
1 AAATAAATAAC
41831240 AAATAATATAAC
1 AAATAA-ATAAC
41831252 AAAT-AATAAC
1 AAATAAATAAC
41831262 AAATAAATAA
1 AAATAAATAA
41831272 AATAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 15 0.54
11 7 0.25
12 6 0.21
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (11 bp):
AAATAAATAAC
Found at i:41831274 original size:19 final size:20
Alignment explanation
Indices: 41831228--41831278 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
41831218 GAAAAATTAG
*
41831228 TAAAATAAAAATAAATAATA
1 TAAAATAAAAACAAATAATA
*
41831248 TAACAAATAATAACAAATAA-A
1 T-A-AAATAAAAACAAATAATA
41831269 TAAAATAAAA
1 TAAAATAAAA
41831279 TGGGTGGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 7 0.27
20 2 0.08
21 3 0.12
22 14 0.54
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAAATAAAAACAAATAATA
Found at i:41831542 original size:18 final size:17
Alignment explanation
Indices: 41831509--41831543 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
41831499 TTTTAAGATT
*
41831509 TTTTGAAAATTAATTAA
1 TTTTGAAAATAAATTAA
41831526 TTTTGAAAATAACATTAA
1 TTTTGAAAATAA-ATTAA
41831544 ATAAGATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (17 bp):
TTTTGAAAATAAATTAA
Found at i:41834374 original size:14 final size:14
Alignment explanation
Indices: 41834355--41834381 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41834345 AAAAGCAAAT
41834355 AAAACAAAAATTAG
1 AAAACAAAAATTAG
41834369 AAAACAAAAATTA
1 AAAACAAAAATTA
41834382 AACTAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.07, G:0.04, T:0.15
Consensus pattern (14 bp):
AAAACAAAAATTAG
Found at i:41834395 original size:18 final size:18
Alignment explanation
Indices: 41834369--41834414 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
41834359 CAAAAATTAG
*
41834369 AAAACAAAAATTA-AACTA
1 AAAATAAAAATTATAAC-A
41834387 AAAATAAAAA-TATAACA
1 AAAATAAAAATTATAACA
41834404 AAAATAAAAAT
1 AAAATAAAAAT
41834415 GACTAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAATAAAAATTATAACA
Found at i:41836554 original size:20 final size:20
Alignment explanation
Indices: 41836531--41836572 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41836521 TAAATTTGAA
*
41836531 AATATAA-ATTATTTCTTTTT
1 AATATAATAATATTT-TTTTT
41836551 AATATAATAATATTTTTTTT
1 AATATAATAATATTTTTTTT
41836571 AA
1 AA
41836573 ATTATTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATAATAATATTTTTTTT
Found at i:41838770 original size:33 final size:34
Alignment explanation
Indices: 41838714--41838777 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
41838704 ACAATAAAAT
*
41838714 ATTTATTATATTTATCTGTGTTTT-TTAATAAAC
1 ATTTATTATATTTATCGGTGTTTTCTTAATAAAC
41838747 ATTTATTATATTTAT-GGTAGTTTTCTTAATA
1 ATTTATTATATTTATCGGT-GTTTTCTTAATA
41838778 TAAAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 2 0.07
33 20 0.71
34 6 0.21
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.58
Consensus pattern (34 bp):
ATTTATTATATTTATCGGTGTTTTCTTAATAAAC
Found at i:41848486 original size:25 final size:25
Alignment explanation
Indices: 41848444--41848514 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
41848434 AATTTCCTAA
*
41848444 AAAGTCTTTT-TGGTAAACTCTCTGT
1 AAAGT-TTTTGTGGCAAACTCTCTGT
41848469 AAAGTTTTTGTGGCAAACTCTCTGT
1 AAAGTTTTTGTGGCAAACTCTCTGT
***
41848494 AAAGCCCTTGTGGCAAACTCT
1 AAAGTTTTTGTGGCAAACTCT
41848515 TTGAAAATCC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.10
25 37 0.90
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (25 bp):
AAAGTTTTTGTGGCAAACTCTCTGT
Found at i:41848529 original size:25 final size:25
Alignment explanation
Indices: 41848443--41848531 Score: 88
Period size: 25 Copynumber: 3.6 Consensus size: 25
41848433 GAATTTCCTA
* * *
41848443 AAAAGTCTTTTTGGTAAACTCTCTG
1 AAAAGCCTTTGTGGCAAACTCTCTG
* **
41848468 TAAAGTTTTTGTGGCAAACTCTCTG
1 AAAAGCCTTTGTGGCAAACTCTCTG
* * *
41848493 TAAAGCCCTTGTGGCAAACTCTTTG
1 AAAAGCCTTTGTGGCAAACTCTCTG
*
41848518 AAAATCCTTTGTGG
1 AAAAGCCTTTGTGG
41848532 TGTATTATTC
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (25 bp):
AAAAGCCTTTGTGGCAAACTCTCTG
Found at i:41854760 original size:10 final size:10
Alignment explanation
Indices: 41854745--41854872 Score: 56
Period size: 10 Copynumber: 13.3 Consensus size: 10
41854735 TTAAAAAAAA
41854745 TTTATATATT
1 TTTATATATT
41854755 TTTATATA-T
1 TTTATATATT
41854764 TTTA-AT-TT
1 TTTATATATT
*
41854772 TTTATACATT
1 TTTATATATT
* * *
41854782 ATTATTTCTT
1 TTTATATATT
* * *
41854792 GTAATA-ATA
1 TTTATATATT
41854801 TTT-T-TATT
1 TTTATATATT
41854809 TTTATATATT
1 TTTATATATT
*
41854819 TTTAAGTTTATT
1 TTT-A-TATATT
*
41854831 ATTT-TA-CTT
1 -TTTATATATT
* * *
41854840 TTTAAAAATA
1 TTTATATATT
*
41854850 TTTATGTATT
1 TTTATATATT
41854860 TTTATATATT
1 TTTATATATT
41854870 TTT
1 TTT
41854873 TGACTTTTAG
Statistics
Matches: 83, Mismatches: 24, Indels: 22
0.64 0.19 0.17
Matches are distributed among these distances:
8 16 0.19
9 12 0.14
10 46 0.55
11 1 0.01
12 5 0.06
13 3 0.04
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTATATATT
Found at i:41854775 original size:17 final size:16
Alignment explanation
Indices: 41854753--41854820 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 16
41854743 AATTTATATA
41854753 TTTTTATATATTTTAAT
1 TTTTTATATATTTT-AT
*
41854770 TTTTTATACATTATTAT
1 TTTTTATATATT-TTAT
41854787 TTCTTGTAATAATATTTT-T
1 TT-TT-T-AT-ATATTTTAT
41854806 ATTTTTATATATTTT
1 -TTTTTATATATTTT
41854821 TAAGTTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
16 7 0.16
17 17 0.40
18 5 0.12
19 4 0.09
20 6 0.14
21 4 0.09
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (16 bp):
TTTTTATATATTTTAT
Found at i:41867150 original size:19 final size:19
Alignment explanation
Indices: 41867112--41867150 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41867102 AAATAGTGAT
*
41867112 AATTTATTTTCTAAGTATA
1 AATTTATTTTCTAAGAATA
41867131 AATTCTATTTTCT-AGAATA
1 AATT-TATTTTCTAAGAATA
41867150 A
1 A
41867151 CAATTCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:41870629 original size:20 final size:21
Alignment explanation
Indices: 41870597--41870635 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41870587 TATATTAACT
*
41870597 CCTAATATTATATTTTTATCC
1 CCTAATATTATATATTTATCC
41870618 CCTAAT-TTATATATTTAT
1 CCTAATATTATATATTTAT
41870636 TAAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (21 bp):
CCTAATATTATATATTTATCC
Found at i:41887132 original size:13 final size:13
Alignment explanation
Indices: 41887082--41887147 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
41887072 TAAACCAAAC
*
41887082 TTTTTAAAAGTAT
1 TTTTTAAAAGCAT
* *
41887095 TTCTCAAAAGCACT
1 TTTTTAAAAGCA-T
*
41887109 TTTTT-ACAGCAT
1 TTTTTAAAAGCAT
*
41887121 TTTTTAAAAGCAG
1 TTTTTAAAAGCAT
*
41887134 TTTTCAAAAGCAT
1 TTTTTAAAAGCAT
41887147 T
1 T
41887148 GTTAAACTAG
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
12 6 0.15
13 31 0.76
14 4 0.10
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (13 bp):
TTTTTAAAAGCAT
Found at i:41891786 original size:9 final size:9
Alignment explanation
Indices: 41891772--41891856 Score: 109
Period size: 9 Copynumber: 9.4 Consensus size: 9
41891762 TTTGGTTAAA
41891772 AATTAACCG
1 AATTAACCG
*
41891781 AATTAACTG
1 AATTAACCG
*
41891790 AATTACCCG
1 AATTAACCG
41891799 AATTAACCG
1 AATTAACCG
41891808 AATTAACCG
1 AATTAACCG
*
41891817 GATT-ACTCG
1 AATTAAC-CG
41891826 AATTAACCG
1 AATTAACCG
*
41891835 AATTACCCG
1 AATTAACCG
*
41891844 AATTAAACG
1 AATTAACCG
41891853 AATT
1 AATT
41891857 GAATCACTAC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
8 2 0.03
9 61 0.94
10 2 0.03
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:41897449 original size:2 final size:2
Alignment explanation
Indices: 41897442--41897480 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
41897432 GAAGAAAAAG
41897442 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
41897481 TACTGTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41906214 original size:22 final size:23
Alignment explanation
Indices: 41906189--41906231 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
41906179 CAACCGTTTT
*
41906189 CAAAAAAGAAAA-GAAGAAAGAA
1 CAAAAAAGAAAACAAAGAAAGAA
41906211 CAAAAAAGAAAACAAAGAAAG
1 CAAAAAAGAAAACAAAGAAAG
41906232 GGTAAGAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (23 bp):
CAAAAAAGAAAACAAAGAAAGAA
Found at i:41907000 original size:27 final size:25
Alignment explanation
Indices: 41906931--41907000 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 25
41906921 CCGTTTAAAA
41906931 AAATTATTTTGAAAATATTTTAAATT
1 AAATTATTTTGAAAAT-TTTTAAATT
41906957 -AA-TATGTTT-AAAA-TTTTAAATT
1 AAATTAT-TTTGAAAATTTTTAAATT
41906979 AAATTATTTTGAAGAATGTTTT
1 AAATTATTTTGAA-AAT-TTTT
41907001 GTACATTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
22 9 0.24
23 5 0.14
24 12 0.32
25 7 0.19
27 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (25 bp):
AAATTATTTTGAAAATTTTTAAATT
Found at i:41913271 original size:22 final size:22
Alignment explanation
Indices: 41913229--41913276 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
41913219 TAGATTGCCT
* *
41913229 CAAATCCACCTCACTAGGCATA
1 CAAATCCACCTCACAAAGCATA
41913251 CAAATCCGACCTCA-AAAGCATA
1 CAAATCC-ACCTCACAAAGCATA
41913273 -AAAT
1 CAAAT
41913277 ACCATCACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.17
22 13 0.57
23 6 0.26
ACGTcount: A:0.44, C:0.31, G:0.08, T:0.17
Consensus pattern (22 bp):
CAAATCCACCTCACAAAGCATA
Found at i:41917424 original size:25 final size:24
Alignment explanation
Indices: 41917396--41917472 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 24
41917386 ATTCCAAAAA
41917396 TAAAATTATTTTAATATTTTAATAT
1 TAAAATTATTTTAATA-TTTAATAT
* *
41917421 T-AAATGTAATTTAATATTT-ATCT
1 TAAAAT-TATTTTAATATTTAATAT
*
41917444 TAATAA-TATTTTATTAATTTAATAT
1 TAA-AATTATTTTAAT-ATTTAATAT
41917469 TAAA
1 TAAA
41917473 GTGATTATCT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
23 11 0.26
24 13 0.31
25 18 0.43
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (24 bp):
TAAAATTATTTTAATATTTAATAT
Found at i:41917468 original size:48 final size:51
Alignment explanation
Indices: 41917402--41917498 Score: 130
Period size: 48 Copynumber: 2.0 Consensus size: 51
41917392 AAAATAAAAT
*
41917402 TATTTTAATATTTTAATATTAAA-TG-TAAT-TTAATATT-TATCTTAATAA
1 TATTTTAATAATTTAATATTAAAGTGATAATCTTAATATTATAT-TTAATAA
* *
41917450 TATTTTATTAATTTAATATTAAAGTGATTATCTTAATATTATATTTAAT
1 TATTTTAATAATTTAATATTAAAGTGATAATCTTAATATTATATTTAAT
41917499 TTAACATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
48 21 0.50
49 2 0.05
50 3 0.07
51 13 0.31
52 3 0.07
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (51 bp):
TATTTTAATAATTTAATATTAAAGTGATAATCTTAATATTATATTTAATAA
Found at i:41920620 original size:21 final size:21
Alignment explanation
Indices: 41920596--41920637 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
41920586 AATATGGAGT
41920596 TAAATTTAGTTTAAAGTGGAA
1 TAAATTTAGTTTAAAGTGGAA
41920617 TAAATTTAGTTTAAAGTGGAA
1 TAAATTTAGTTTAAAGTGGAA
41920638 ATTGTATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (21 bp):
TAAATTTAGTTTAAAGTGGAA
Found at i:41920678 original size:20 final size:20
Alignment explanation
Indices: 41920642--41920679 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41920632 GTGGAAATTG
*
41920642 TATGAAAATATAGAATTAAA
1 TATGAAAATATAAAATTAAA
41920662 TATGAAGAATA-AAAATTA
1 TATGAA-AATATAAAATTA
41920680 GTCTCGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (20 bp):
TATGAAAATATAAAATTAAA
Found at i:41923069 original size:21 final size:21
Alignment explanation
Indices: 41923045--41923084 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41923035 CAGCTTATTA
41923045 GCATGGTTAAAT-TGTCTTAAT
1 GCAT-GTTAAATATGTCTTAAT
*
41923066 GCATGTTTAATATGTCTTA
1 GCATGTTAAATATGTCTTA
41923085 GGGATGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (21 bp):
GCATGTTAAATATGTCTTAAT
Found at i:41924067 original size:29 final size:29
Alignment explanation
Indices: 41924029--41924084 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
41924019 AAAAAAAAAT
*
41924029 CGTAGCAAAAAGAGAAGTGCGAAAGAATC
1 CGTAGAAAAAAGAGAAGTGCGAAAGAATC
*
41924058 CGTAGAAAAAAGAGAAGTGCGGAAGAA
1 CGTAGAAAAAAGAGAAGTGCGAAAGAA
41924085 AAAAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.50, C:0.11, G:0.30, T:0.09
Consensus pattern (29 bp):
CGTAGAAAAAAGAGAAGTGCGAAAGAATC
Found at i:41928637 original size:14 final size:14
Alignment explanation
Indices: 41928620--41928650 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41928610 AATAAAATAT
41928620 TTTCCGGAAAATGA
1 TTTCCGGAAAATGA
*
41928634 TTTCTGGAAAATGA
1 TTTCCGGAAAATGA
41928648 TTT
1 TTT
41928651 ACTTTTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (14 bp):
TTTCCGGAAAATGA
Found at i:41930997 original size:25 final size:25
Alignment explanation
Indices: 41930965--41931015 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
41930955 GGCGTGAAAG
41930965 TGCAGAGGAGAGCTTAGAAAATGTC
1 TGCAGAGGAGAGCTTAGAAAATGTC
*
41930990 TGCAGAGGAGAGCTTGGAAAATGTC
1 TGCAGAGGAGAGCTTAGAAAATGTC
41931015 T
1 T
41931016 TACGGAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.22
Consensus pattern (25 bp):
TGCAGAGGAGAGCTTAGAAAATGTC
Found at i:41937838 original size:18 final size:17
Alignment explanation
Indices: 41937805--41937843 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
41937795 TTGTATAAAT
41937805 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
41937823 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
41937840 TGTG
1 TGTG
41937844 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:41938096 original size:23 final size:23
Alignment explanation
Indices: 41938069--41938166 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
41938059 AGTGTTATTG
41938069 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
41938092 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
41938115 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
41938137 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
41938160 ATCAGTG
1 ATCAGTG
41938167 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:41938135 original size:45 final size:45
Alignment explanation
Indices: 41938071--41938159 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
41938061 TGTTATTGAT
* *
41938071 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
41938116 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
41938160 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:41942897 original size:26 final size:27
Alignment explanation
Indices: 41942850--41942902 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
41942840 ATTTGTGAGA
41942850 AAGGAACCACAAGCTCTAGTGGTCAGT
1 AAGGAACCACAAGCTCTAGTGGTCAGT
41942877 AAGGAACCAC-AGCTCTAGTGGTCAGT
1 AAGGAACCACAAGCTCTAGTGGTCAGT
41942903 TTTGATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (27 bp):
AAGGAACCACAAGCTCTAGTGGTCAGT
Found at i:41944776 original size:30 final size:30
Alignment explanation
Indices: 41944742--41944838 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
41944732 TAAACTAAAA
*
41944742 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
41944772 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
*
41944802 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCGTGAGCT-AAAGT
41944832 TGAGCTA
1 TGAGCTA
41944839 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:41951080 original size:20 final size:19
Alignment explanation
Indices: 41951055--41951092 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
41951045 TAAATTCAAG
41951055 TTAATTACATCCTTTTTTTT
1 TTAATTACAT-CTTTTTTTT
41951075 TTAATTACATCTTTTTTT
1 TTAATTACATCTTTTTTT
41951093 CAAAATGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (19 bp):
TTAATTACATCTTTTTTTT
Found at i:41951250 original size:30 final size:29
Alignment explanation
Indices: 41951195--41951252 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
41951185 TTAAAAATAC
*
41951195 AAGTACAGGGACTAAGTCCTAATTTTCATA
1 AAGTACAGGGACTAAGACC-AATTTTCATA
41951225 AAGTACAGGGACTATAGA-CACATTTTCA
1 AAGTACAGGGACTA-AGACCA-ATTTTCA
41951253 CAAAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 1 0.04
30 22 0.88
31 2 0.08
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (29 bp):
AAGTACAGGGACTAAGACCAATTTTCATA
Found at i:41964631 original size:24 final size:24
Alignment explanation
Indices: 41964603--41964659 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
41964593 ATTCTATTAA
*
41964603 CCTTTGTAGCGTATTCTGATTTGG
1 CCTTTGTAGCGTATTCTGATTAGG
* * * *
41964627 CCTTTATGGCGTGTTTTGATTAGG
1 CCTTTGTAGCGTATTCTGATTAGG
41964651 CCTTTGTAG
1 CCTTTGTAG
41964660 TATTTTGTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.46
Consensus pattern (24 bp):
CCTTTGTAGCGTATTCTGATTAGG
Found at i:41964675 original size:20 final size:20
Alignment explanation
Indices: 41964640--41964702 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
41964630 TTATGGCGTG
*
41964640 TTTTGATTAGGCCTTTGTAGTA
1 TTTTG-TTA-GCCTTTGTAGCA
* *
41964662 TTTTGTTAGCCTTTATGGCA
1 TTTTGTTAGCCTTTGTAGCA
* *
41964682 TTCTGTTAGCCTTTGTGGCA
1 TTTTGTTAGCCTTTGTAGCA
41964702 T
1 T
41964703 ATTTTGTATG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 28 0.78
21 3 0.08
22 5 0.14
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.49
Consensus pattern (20 bp):
TTTTGTTAGCCTTTGTAGCA
Found at i:41975448 original size:14 final size:14
Alignment explanation
Indices: 41975431--41975460 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41975421 TTTCATTTTT
*
41975431 ATATATTTTTTAAA
1 ATATAATTTTTAAA
41975445 ATATAATTTTTAAA
1 ATATAATTTTTAAA
41975459 AT
1 AT
41975461 TTTATGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATAATTTTTAAA
Found at i:41981595 original size:117 final size:117
Alignment explanation
Indices: 41981389--41981622 Score: 398
Period size: 117 Copynumber: 2.0 Consensus size: 117
41981379 TGAGCGGTAT
* *
41981389 CGAGCTTTGAGTAAAATTTCAGATCATCCAACTCAAATGCTCATTTTTTTTAGTTTATCTTATGC
1 CGAGCTTTGAGTAAAATTTCAGATCATCCAACTCAAATGCTCATTTTCTTTAGTTTACCTTATGC
*
41981454 TGCGCGAATGGAATGAGTCAGAAGATTTTTTTCTGACCATTAAAAATCAATG
66 TGCGCGAATGGAATGAGTCAGAAGATTTCTTTCTGACCATTAAAAATCAATG
*
41981506 CGAGCTTTGAGTAAAATTTCAGATCATCCAACTCAAATGCT-AGTTTTCTTTAGTTTACCTTCTG
1 CGAGCTTTGAGTAAAATTTCAGATCATCCAACTCAAATGCTCA-TTTTCTTTAGTTTACCTTATG
* *
41981570 CTGCGCGATTGGAATGGGTCAGAAGATTTCTTTCTGACCATTAAAAATCAATG
65 CTGCGCGAATGGAATGAGTCAGAAGATTTCTTTCTGACCATTAAAAATCAATG
41981623 TTCAAACTTT
Statistics
Matches: 110, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
116 1 0.01
117 109 0.99
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (117 bp):
CGAGCTTTGAGTAAAATTTCAGATCATCCAACTCAAATGCTCATTTTCTTTAGTTTACCTTATGC
TGCGCGAATGGAATGAGTCAGAAGATTTCTTTCTGACCATTAAAAATCAATG
Found at i:41981800 original size:46 final size:45
Alignment explanation
Indices: 41981749--41982163 Score: 156
Period size: 44 Copynumber: 9.1 Consensus size: 45
41981739 TCAAGTTATA
41981749 TTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAAAATT
1 TTATGATTTTA-TAAATTCATATAAGAATATTTATTATTAAAAATT
* * * * **
41981795 TTATGA-ATTATATA-TCATTATTAAATAATATTTAATATTAATTATT
1 TTATGATTTTATAAATTCA-TA-T-AAGAATATTTATTATTAAAAATT
* * * * *
41981841 TTA-AATTATATAAATTCATATAAGAAAATTTATTATCAAGAATT
1 TTATGATTTTATAAATTCATATAAGAATATTTATTATTAAAAATT
** * * **
41981885 TTATGAAATTATATA-TCATTATTAA-ATTATATTTAATATTAATTATT
1 TTATGATTTTATAAATTCA-TA-TAAGA--ATATTTATTATTAAAAATT
* * * * *
41981932 TTA-AATTATATAAATTCATATAACAA-AGTTTATTATCAAGAATT
1 TTATGATTTTATAAATTCATATAAGAATA-TTTATTATTAAAAATT
** * * **
41981976 TTATGAAATTATATA-TCATTATTAA-ATTATATTTAATATTAATTATT
1 TTATGATTTTATAAATTCA-TA-TAAGA--ATATTTATTATTAAAAATT
* * * * *
41982023 TTA-AATTATATAAATTCATATAACAA-AGTTTATTATCAAGAATT
1 TTATGATTTTATAAATTCATATAAGAATA-TTTATTATTAAAAATT
** * * **
41982067 TTATGAAATTATATA-TCATTATTAA-ATTATATTTAATATTAATTATT
1 TTATGATTTTATAAATTCA-TA-TAAGA--ATATTTATTATTAAAAATT
* * * * * *
41982114 TTA-AATTATATAAATTCATATAACAAAATTTATTATCAAGAATT
1 TTATGATTTTATAAATTCATATAAGAATATTTATTATTAAAAATT
*
41982158 TGATGA
1 TTATGA
41982164 AGTTATATAT
Statistics
Matches: 264, Mismatches: 74, Indels: 63
0.66 0.18 0.16
Matches are distributed among these distances:
43 5 0.02
44 82 0.31
45 43 0.16
46 71 0.27
47 61 0.23
48 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (45 bp):
TTATGATTTTATAAATTCATATAAGAATATTTATTATTAAAAATT
Found at i:41981927 original size:91 final size:91
Alignment explanation
Indices: 41981761--41982227 Score: 801
Period size: 91 Copynumber: 5.1 Consensus size: 91
41981751 ATGATTTTAG
* * * * *
41981761 TAAATTCATATAAGAATATTTATTATTAAAAATTTTATG-AATTATATATCATTATTAAATAATA
1 TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
41981825 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
41981851 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
41981916 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
41981942 TAAATTCATATAACAAAGTTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
41982007 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
41982033 TAAATTCATATAACAAAGTTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
41982098 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
* * *
41982124 TAAATTCATATAACAAAATTTATTATCAAGAATTTGATGAAGTTATATATTATTATTAAATTATA
1 TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
* *
41982189 TTTAATAATAATTATATTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
41982215 CAAATTCATATAA
1 TAAATTCATATAA
41982228 TTAAATTATA
Statistics
Matches: 363, Mismatches: 13, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
90 36 0.10
91 327 0.90
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATA
Found at i:41982190 original size:10 final size:10
Alignment explanation
Indices: 41982172--41982322 Score: 56
Period size: 10 Copynumber: 15.8 Consensus size: 10
41982162 GAAGTTATAT
41982172 ATTATTATTAA
1 ATTA-TATTAA
*
41982183 ATTATATTTA
1 ATTATATTAA
41982193 A-TA-A-T-A
1 ATTATATTAA
41982199 ATTATATTAA
1 ATTATATTAA
*
41982209 ATTATA-CAA
1 ATTATATTAA
41982218 ATTCATATAATTAA
1 A-T--TAT-ATTAA
*
41982232 ATTATATTTA
1 ATTATATTAA
* *
41982242 ATAATAAT-A
1 ATTATATTAA
*
41982251 ATTATTTTAA
1 ATTATATTAA
*
41982261 ATTTTATTAA
1 ATTATATTAA
* *
41982271 ATCATA-TAT
1 ATTATATTAA
*
41982280 TTTA-ATTAA
1 ATTATATTAA
* *
41982289 AATATATTTA
1 ATTATATTAA
41982299 A-TA-A-T-A
1 ATTATATTAA
*
41982305 ATTATTTTAA
1 ATTATATTAA
41982315 ATTATATT
1 ATTATATT
41982323 TTATACTATC
Statistics
Matches: 102, Mismatches: 22, Indels: 33
0.65 0.14 0.21
Matches are distributed among these distances:
6 4 0.04
7 6 0.06
8 4 0.04
9 23 0.23
10 50 0.49
11 7 0.07
12 3 0.03
13 2 0.02
14 3 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTATATTAA
Found at i:41982283 original size:17 final size:16
Alignment explanation
Indices: 41982261--41982314 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
41982251 ATTATTTTAA
41982261 ATTTT-ATTAAATCATAT
1 ATTTTAATTAAA--ATAT
41982278 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
41982294 A-TTTAA-TAATAAT-T
1 ATTTTAATTAA-AATAT
41982308 ATTTTAA
1 ATTTTAA
41982315 ATTATATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.15
15 13 0.38
16 5 0.15
17 5 0.15
18 6 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:41982287 original size:52 final size:55
Alignment explanation
Indices: 41982178--41982569 Score: 196
Period size: 54 Copynumber: 6.8 Consensus size: 55
41982168 ATATATTATT
* * * *
41982178 ATTAAATTATATTTAATAATAATTATATTAAATTATA-CAAATTCATATAATTAA
1 ATTAAAATATATATAATAATAATTATTTTAAATTATATTAAATTCATATAATTAA
* * * * *
41982232 ATT-ATATTTA-ATAATAATAATTATTTTAAATTTTATTAAA-TCATATATTTTA
1 ATTAAAATATATATAATAATAATTATTTTAAATTATATTAAATTCATATAATTAA
* *
41982284 ATTAAAATATATTTAATAATAATTATTTTAAATTATATTTTATACTATCATAT-ATTATGA
1 ATTAAAATATATATAATAATAATTATTTTAAATTATA--TTA-AAT-TCATATAATTA--A
* * * *
41982344 TTTTAGGAAAT-TCATATAATAAT-ATTGAGATTATTAAGAATTTTATTAAA-TCATATATTTTA
1 -ATTA--AAATAT-ATATAATAATAATT---ATT-TT-A-AATTATATTAAATTCATATAATTAA
* * * *
41982406 ATTAAAATATATTTAATAATAATTATCTTAAATTATATTTTATAGT-ATCATAATTATGA
1 ATTAAAATATATATAATAATAATTATTTTAAATTATA--TTAAATTCAT-ATAATTA--A
* * * *
41982465 ATTGAGTAAAT-TCATATAACAAT-ATTGATTATTTATAATTGTATTAAATT-ATATATTTTA
1 ATT-A--AAATAT-ATATAATAATAATT-A-T-TTTA-AATTATATTAAATTCATATAATTAA
* * *
41982525 ATTAAAATATATTTAATAATAATTATGTTAAAATATGATTAAATT
1 ATTAAAATATATATAATAATAATTATTTTAAATTAT-ATTAAATT
41982570 ATTTATTATT
Statistics
Matches: 256, Mismatches: 42, Indels: 79
0.68 0.11 0.21
Matches are distributed among these distances:
52 35 0.14
53 12 0.05
54 36 0.14
55 12 0.05
56 12 0.05
57 22 0.09
58 6 0.02
59 24 0.09
60 10 0.04
61 10 0.04
62 23 0.09
63 27 0.11
64 5 0.02
65 10 0.04
66 5 0.02
67 1 0.00
68 6 0.02
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (55 bp):
ATTAAAATATATATAATAATAATTATTTTAAATTATATTAAATTCATATAATTAA
Found at i:41982289 original size:28 final size:29
Alignment explanation
Indices: 41982257--41982339 Score: 71
Period size: 28 Copynumber: 2.8 Consensus size: 29
41982247 AATAATTATT
41982257 TTAAATTTTATTAAATCATATATTTT-AA
1 TTAAATTTTATTAAATCATATATTTTAAA
* * * *
41982285 TTAAAATATATTTAATAATAATTATTTTAAA
1 TTAAATTTTATTAAATCAT-A-TATTTTAAA
* *
41982316 TTATATTTTA-TACTATCATATATT
1 TTAAATTTTATTA-AATCATATATT
41982340 ATGATTTTAG
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
28 15 0.37
29 5 0.12
30 8 0.20
31 13 0.32
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (29 bp):
TTAAATTTTATTAAATCATATATTTTAAA
Found at i:41982540 original size:119 final size:121
Alignment explanation
Indices: 41982251--41982556 Score: 474
Period size: 122 Copynumber: 2.5 Consensus size: 121
41982241 AATAATAATA
*
41982251 ATTATTT-TAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTTAA
1 ATTATTTAT-AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAA
* * *
41982315 ATTATATTTTATACTATCATATATTATGATTTTAGGAAATTCATATAATAATATTGAG
65 ATTATATTTTATACTATCATATATTATGAATTGAGGAAATTCATATAACAATATT-AG
* *
41982373 ATTATTAAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAA
1 ATTATTTATAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAA
* *
41982438 TTATATTTTATAGTATCATA-ATTATGAATTGAGTAAATTCATATAACAATATT-G
66 TTATATTTTATACTATCATATATTATGAATTGAGGAAATTCATATAACAATATTAG
* * *
41982492 ATTATTTATAATTGTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 ATTATTTATAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAA
41982557 ATATGATTAA
Statistics
Matches: 170, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
119 61 0.36
121 29 0.17
122 80 0.47
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (121 bp):
ATTATTTATAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAA
TTATATTTTATACTATCATATATTATGAATTGAGGAAATTCATATAACAATATTAG
Found at i:41991201 original size:21 final size:22
Alignment explanation
Indices: 41991160--41991202 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
41991150 TTCTTGAAAG
*
41991160 TGCCTATTGGGATCATGGACTT
1 TGCCTATTGGGATCATCGACTT
41991182 TGCC-ATTGGGATTC-TCGACTT
1 TGCCTATTGGGA-TCATCGACTT
41991203 CCTTGTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (22 bp):
TGCCTATTGGGATCATCGACTT
Found at i:41998643 original size:41 final size:41
Alignment explanation
Indices: 41998598--41998744 Score: 204
Period size: 41 Copynumber: 3.6 Consensus size: 41
41998588 TCTACCTAGT
*
41998598 AGGCTTAATGCCAGTGTACCATATTAGGCTTTACGCTTAGC
1 AGGCTTAATGCCAGTGTACCATATCAGGCTTTACGCTTAGC
* * * *
41998639 AGGCTTAATGTCGGTGTACCATATCAGGCTTTACGCCTAGT
1 AGGCTTAATGCCAGTGTACCATATCAGGCTTTACGCTTAGC
* *
41998680 AGGCTTAATGCCGGTGTACCATATCAGGCTTTACACTTAGC
1 AGGCTTAATGCCAGTGTACCATATCAGGCTTTACGCTTAGC
** *
41998721 AGGCTTCGTGCCAGTGTATCATAT
1 AGGCTTAATGCCAGTGTACCATAT
41998745 TAAGATTTGT
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (41 bp):
AGGCTTAATGCCAGTGTACCATATCAGGCTTTACGCTTAGC
Found at i:41998738 original size:82 final size:82
Alignment explanation
Indices: 41998592--41998744 Score: 234
Period size: 82 Copynumber: 1.9 Consensus size: 82
41998582 GGGCTATCTA
* * * *
41998592 CCTAGTAGGCTTAATGCCAGTGTACCATATTAGGCTTTACGCTTAGCAGGCTTAATGTCGGTGTA
1 CCTAGTAGGCTTAATGCCAGTGTACCATATCAGGCTTTACACTTAGCAGGCTTAATGCCAGTGTA
41998657 CCATATCAGGCTTTACG
66 CCATATCAGGCTTTACG
* **
41998674 CCTAGTAGGCTTAATGCCGGTGTACCATATCAGGCTTTACACTTAGCAGGCTTCGTGCCAGTGTA
1 CCTAGTAGGCTTAATGCCAGTGTACCATATCAGGCTTTACACTTAGCAGGCTTAATGCCAGTGTA
*
41998739 TCATAT
66 CCATAT
41998745 TAAGATTTGT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (82 bp):
CCTAGTAGGCTTAATGCCAGTGTACCATATCAGGCTTTACACTTAGCAGGCTTAATGCCAGTGTA
CCATATCAGGCTTTACG
Found at i:42000905 original size:20 final size:20
Alignment explanation
Indices: 42000876--42000915 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42000866 TGGACTTATT
*
42000876 TAAAACAAAACATAAAAATA
1 TAAAAAAAAACATAAAAATA
*
42000896 TAAAAAAAAACTTAAAAATA
1 TAAAAAAAAACATAAAAATA
42000916 GGGGTCACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (20 bp):
TAAAAAAAAACATAAAAATA
Found at i:42002108 original size:45 final size:45
Alignment explanation
Indices: 42002057--42002166 Score: 148
Period size: 45 Copynumber: 2.4 Consensus size: 45
42002047 GGTGTCTTTT
* *
42002057 AGCTATGGTATTAATCGTTTGAATCATGATGCCATAACGTATTTC
1 AGCTATGGTCTTACTCGTTTGAATCATGATGCCATAACGTATTTC
* * * * *
42002102 AGCTATGGTCTTACTCATTTGATTCATGGTGCCATAGCGTCTTTC
1 AGCTATGGTCTTACTCGTTTGAATCATGATGCCATAACGTATTTC
*
42002147 AACTATGGTCTTACTCGTTT
1 AGCTATGGTCTTACTCGTTT
42002167 TTTTTCAACC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (45 bp):
AGCTATGGTCTTACTCGTTTGAATCATGATGCCATAACGTATTTC
Found at i:42004217 original size:18 final size:17
Alignment explanation
Indices: 42004184--42004222 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
42004174 TTTTATAAAT
42004184 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
42004202 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
42004219 TGTG
1 TGTG
42004223 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:42010758 original size:6 final size:6
Alignment explanation
Indices: 42010747--42010773 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
42010737 ATTAGGCTTC
42010747 TTTCAA TTTCAA TTTCAA TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTTCAA TTT
42010774 TGTTTGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTCAA
Found at i:42011802 original size:18 final size:18
Alignment explanation
Indices: 42011768--42011805 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
42011758 TTTAATAAAG
*
42011768 TATTTAATATTATAATTT
1 TATTTAATAATATAATTT
42011786 TATTATAATAATA-AATTT
1 TATT-TAATAATATAATTT
42011804 TA
1 TA
42011806 AATAATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTAATAATATAATTT
Found at i:42014294 original size:21 final size:21
Alignment explanation
Indices: 42014269--42014314 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
42014259 CCAAATACTT
42014269 GCAGCAAACTCTAGACATAGA
1 GCAGCAAACTCTAGACATAGA
* *
42014290 GCAGCAAACTTTAGACATAGT
1 GCAGCAAACTCTAGACATAGA
42014311 GCAG
1 GCAG
42014315 TGTTTCTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (21 bp):
GCAGCAAACTCTAGACATAGA
Found at i:42021080 original size:9 final size:9
Alignment explanation
Indices: 42021066--42021090 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42021056 ATTATAATTG
42021066 AACTCTCTA
1 AACTCTCTA
42021075 AACTCTCTA
1 AACTCTCTA
42021084 AACTCTC
1 AACTCTC
42021091 CTTATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (9 bp):
AACTCTCTA
Found at i:42023256 original size:22 final size:23
Alignment explanation
Indices: 42023222--42023265 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
42023212 TAATGATGTG
*
42023222 CAAACTATGAAATAATTAAAAACA
1 CAAACTA-GAAATAACTAAAAACA
42023246 CAAACTA-AAATAACTAAAAA
1 CAAACTAGAAATAACTAAAAA
42023266 TTAATGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.66, C:0.14, G:0.02, T:0.18
Consensus pattern (23 bp):
CAAACTAGAAATAACTAAAAACA
Found at i:42029184 original size:12 final size:12
Alignment explanation
Indices: 42029167--42029211 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
42029157 ACTAATCCTT
42029167 TCTCAAATTTCC
1 TCTCAAATTTCC
*
42029179 TCTC-AATTTGC
1 TCTCAAATTTCC
42029190 TCTCAAA-TTCC
1 TCTCAAATTTCC
42029201 T-TCCAAATTTC
1 TCT-CAAATTTC
42029212 TCTGAAATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 1 0.04
11 18 0.64
12 9 0.32
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.42
Consensus pattern (12 bp):
TCTCAAATTTCC
Found at i:42029209 original size:23 final size:21
Alignment explanation
Indices: 42029167--42029219 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
42029157 ACTAATCCTT
42029167 TCTCAAATTTCCTCTCAATTTGC
1 TCTCAAA-TTCCTCTCAATTT-C
42029190 TCTCAAATTCCT-TCCAAATTTC
1 TCTCAAATTCCTCT-C-AATTTC
*
42029212 TCTGAAAT
1 TCTCAAAT
42029220 CCATATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.04
22 14 0.52
23 12 0.44
ACGTcount: A:0.26, C:0.28, G:0.04, T:0.42
Consensus pattern (21 bp):
TCTCAAATTCCTCTCAATTTC
Found at i:42031122 original size:12 final size:12
Alignment explanation
Indices: 42031105--42031149 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
42031095 ACTAATCCTT
42031105 TCTCAAATTTCC
1 TCTCAAATTTCC
*
42031117 TCTC-AATTTGC
1 TCTCAAATTTCC
42031128 TCTCAAA-TTCC
1 TCTCAAATTTCC
42031139 T-TCCAAATTTC
1 TCT-CAAATTTC
42031150 TCTGAAATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 1 0.04
11 18 0.64
12 9 0.32
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.42
Consensus pattern (12 bp):
TCTCAAATTTCC
Found at i:42031147 original size:23 final size:21
Alignment explanation
Indices: 42031105--42031157 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
42031095 ACTAATCCTT
42031105 TCTCAAATTTCCTCTCAATTTGC
1 TCTCAAA-TTCCTCTCAATTT-C
42031128 TCTCAAATTCCT-TCCAAATTTC
1 TCTCAAATTCCTCT-C-AATTTC
*
42031150 TCTGAAAT
1 TCTCAAAT
42031158 CCATATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.04
22 14 0.52
23 12 0.44
ACGTcount: A:0.26, C:0.28, G:0.04, T:0.42
Consensus pattern (21 bp):
TCTCAAATTCCTCTCAATTTC
Found at i:42033605 original size:21 final size:22
Alignment explanation
Indices: 42033601--42034777 Score: 1459
Period size: 22 Copynumber: 55.0 Consensus size: 22
42033591 AAAAACCATA
*
42033601 ACCCT-AACCCTTAACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
**
42033622 ACCCTAAACTTTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42033644 ACCTTAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
* * * *
42033666 ACTCT-AATCCTTGACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42033687 ACCCTAAACCCATAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42033709 ACCATAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42033731 ATCCTAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42033753 ACCCT-AACCCTTAACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
* *
42033774 ACCCTAAACTCGTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42033796 ACCCT-AACCCTTAACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
* *
42033817 ACCTTAAACTCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42033839 ACTCTAAACCCTTAACTT-AAA
1 ACCCTAAACCCTTAACTTAAAA
* *
42033860 ACACT-AACCATTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42033881 ACACT-AACCCTT-ACTT-AAA
1 ACCCTAAACCCTTAACTTAAAA
*
42033900 ACCC-ATAACCCTTAACTTTAAA
1 ACCCTA-AACCCTTAACTTAAAA
42033922 ACCCTAAA-CCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
42033943 ACCCTAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
42033965 ACCCTAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
* *
42033987 ACCCT-AACCCTTGACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034008 ACCTTAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034030 ACCCT-AACCCTTAACAT-AAA
1 ACCCTAAACCCTTAACTTAAAA
42034050 ACCCT-AACCCTTAACTT-AAA
1 ACCCTAAACCCTTAACTTAAAA
42034070 ACCCT-AACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
* * *
42034091 A-ACTTAACCCTTAACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034112 ACCCTAAACTCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034134 ACCATAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034156 ACCCT-AACCCTTAACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
* *
42034177 ACCTTAAACTCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034199 ACCATAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
** *
42034221 ACCCT-AACTTTTAACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034242 ACCCTAAACCCTTAA-TTTAAA
1 ACCCTAAACCCTTAACTTAAAA
42034263 ACCCTAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
* *
42034285 A-CCTTAACCCTTAACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
42034306 ACCCTAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
* *
42034328 A-CCTTAACCCTTAACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034349 ACCCTAAACTCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
* *
42034371 ACCATAAACCCTTAACCTAAAA
1 ACCCTAAACCCTTAACTTAAAA
* *
42034393 ACCATAAACCCTTAACCTAAAA
1 ACCCTAAACCCTTAACTTAAAA
* * *
42034415 ACACT-AACCCTTGACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
42034436 ACCCTAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034458 ACCCT-AACCCTTAACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034479 ACCCTAAACCCTTAATTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
42034501 ACCCTAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
* *
42034523 ACACT-AACCCTTAACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034544 ATCCTAAA-CCTTAACTGT-AAA
1 ACCCTAAACCCTTAACT-TAAAA
* * * *
42034565 ACTCTAAACTCTCAAATTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034587 ACCTTAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034609 ACCCT-AACCTTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
* * *
42034630 ACCAT-AACCCTTAAATTTAAA
1 ACCCTAAACCCTTAACTTAAAA
* *
42034651 ACCTTAAACCCTTAACCTAAAA
1 ACCCTAAACCCTTAACTTAAAA
42034673 ACCCTAAACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
* *
42034695 A-CCTTAACCCTTAACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034716 ACCCT-AACCCTTAACTTTAAA
1 ACCCTAAACCCTTAACTTAAAA
42034737 ACCCT-AACCCTTAACTTAAAA
1 ACCCTAAACCCTTAACTTAAAA
*
42034758 ATCCT-AACCCTTAACTTAAA
1 ACCCTAAACCCTTAACTTAAA
42034778 TATAATTTGA
Statistics
Matches: 1005, Mismatches: 123, Indels: 56
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.01
20 63 0.06
21 432 0.43
22 503 0.50
23 1 0.00
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (22 bp):
ACCCTAAACCCTTAACTTAAAA
Found at i:42033609 original size:27 final size:28
Alignment explanation
Indices: 42033572--42033624 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
42033562 TTAATTGACA
42033572 AACCCTAAACCCTTAACTTAAAAACCAT
1 AACCCTAAACCCTTAACTTAAAAACCAT
*
42033600 AACCCT-AACCCTTAACTTTAAAACC
1 AACCCTAAACCCTTAACTTAAAAACC
42033625 CTAAACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (28 bp):
AACCCTAAACCCTTAACTTAAAAACCAT
Found at i:42033684 original size:65 final size:65
Alignment explanation
Indices: 42033571--42034777 Score: 1445
Period size: 65 Copynumber: 18.7 Consensus size: 65
42033561 TTTAATTGAC
* **
42033571 AAACCCTAAACCCTTAACTTAAAAACCATAACCCTAACCCTTAACTTTAAAACCCTAAACTTTTA
1 AAACCCTAAACCCTTAACTT---AA--A-AACCCTAACCCTTAACTTAAAAACCCTAAACCCTTA
42033636 ACTTAA
60 ACTTAA
* * * * * *
42033642 AAACCTTAAACCCTTAACTTAAAAACTCTAATCCTTGACTTTAAAACCCTAAACCCATAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
42033707 AAACCATAAACCCTTAACTTAAAAATCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTT
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
42033771 A
65 A
* * * * *
42033772 AAACCCTAAACTCGTAACTTAAAAACCCTAACCCTTAACTTTAAAACCTTAAACTCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * *
42033837 AAACTCTAAACCCTTAACTT-AAAACACTAACCATTAACTTAAAAACACT-AACCCTT-ACTT-A
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
42033898 AAACCC-ATAACCCTTAACTTTAAAACCCTAAACCTTAACTTAAAAACCCTAAACCCTTAACTTA
1 AAACCCTA-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
42033962 A
65 A
* * *
42033963 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTGACTTTAAAACCTTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
42034028 AAACCCT-AACCCTTAACAT-AAAACCCTAACCCTTAACTT-AAAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * * *
42034089 AAA-ACTTAACCCTTAACTTTAAAACCCTAAACTCTTAACTTAAAAACCATAAACCCTTAACTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
42034153 A
65 A
* * * *
42034154 AAACCCT-AACCCTTAACTTTAAAACCTTAAACTCTTAACTTAAAAACCATAAACCCTTAACTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
42034218 A
65 A
** * *
42034219 AAACCCT-AACTTTTAACTTTAAAACCCTAAACCCTTAA-TTTAAAACCCTAAACCCTTAACTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
42034282 A
65 A
* * * *
42034283 AAA-CCTTAACCCTTAACTTTAAAACCCTAAACCCTTAACTTAAAAA-CCTTAACCCTTAACTTT
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
42034346 A
65 A
* * * * *
42034347 AAACCCTAAACTCTTAACTTAAAAACCATAAACCCTTAACCTAAAAACCATAAACCCTTAACCTA
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
42034412 A
65 A
* * * *
42034413 AAACACT-AACCCTTGACTTTAAAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTT
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
42034476 A
65 A
* * *
42034477 AAACCCTAAACCCTTAATTTAAAAACCCTAAACCCTTAACTTAAAAACACT-AACCCTTAACTTT
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
42034541 A
65 A
* * * * * *
42034542 AAATCCTAAA-CCTTAACTGT-AAAACTCTAAACTCTCAAATTAAAAACCTTAAACCCTTAACTT
1 AAACCCTAAACCCTTAACT-TAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTT
42034605 AA
64 AA
* * * * * *
42034607 AAACCCT-AACCTTTAACTTAAAAACCATAACCCTTAAATTTAAAACCTTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
42034671 AAACCCTAAACCCTTAACTTAAAAACCTTAACCCTTAACTTTAAAACCCT-AACCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
42034735 AAACCCT-AACCCTTAACTTAAAAATCCTAACCCTTAACTTAAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
42034778 TATAATTTGA
Statistics
Matches: 1001, Mismatches: 111, Indels: 56
0.86 0.10 0.05
Matches are distributed among these distances:
60 3 0.00
61 46 0.05
62 44 0.04
63 79 0.08
64 250 0.25
65 516 0.52
66 42 0.04
68 2 0.00
71 19 0.02
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (65 bp):
AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
Found at i:42033688 original size:43 final size:43
Alignment explanation
Indices: 42033571--42034777 Score: 1403
Period size: 43 Copynumber: 28.0 Consensus size: 43
42033561 TTTAATTGAC
* *
42033571 AAACCCTAAACCCTTAACTTAAAAACCATAACCCTAACCCTTAACTTTA
1 AAACCCT-AACCCTTAACTTAAAAACCCT-A----AACCCTTAACTTAA
** *
42033620 AAACCCTAAACTTTTAACTTAAAAACCTTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * * *
42033664 AAACTCTAATCCTTGACTTTAAAACCCTAAACCCATAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
42033707 AAACCATAAACCCTTAACTTAAAAATCCTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
42033751 AAACCCTAACCCTTAACTTTAAAACCCTAAACTCGTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
42033794 AAACCCTAACCCTTAACTTTAAAACCTTAAACTCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
42033837 AAACTCTAAACCCTTAACTT-AAAACACT-AACCATTAACTTAA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
42033879 AAACACTAACCCTT-ACTT-AAAACCC-ATAACCCTTAACTTTA
1 AAACCCTAACCCTTAACTTAAAAACCCTA-AACCCTTAACTTAA
*
42033920 AAACCCTAAACCTTAACTTAAAAACCCTAAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
42033963 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTGACTTTA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
42034006 AAACCTTAAACCCTTAACTTAAAAACCCT-AACCCTTAACAT-A
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
42034048 AAACCCTAACCCTTAACTT-AAAACCCT-AACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * *
42034089 AAAACTTAACCCTTAACTTTAAAACCCTAAACTCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
42034132 AAACCATAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTTA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
42034175 AAACCTTAAACTCTTAACTTAAAAACCATAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
** * *
42034219 AAACCCTAACTTTTAACTTTAAAACCCTAAACCCTTAA-TTTA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
42034261 AAACCCTAAACCCTTAACTTAAAAA-CCTTAACCCTTAACTTTA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
42034304 AAACCCTAAACCCTTAACTTAAAAA-CCTTAACCCTTAACTTTA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
42034347 AAACCCTAAACTCTTAACTTAAAAACCATAAACCCTTAACCTAA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * * *
42034391 AAACCATAAACCCTTAACCTAAAAACACT-AACCCTTGACTTTA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
42034434 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTTA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
42034477 AAACCCTAAACCCTTAATTTAAAAACCCTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
42034521 AAACACTAACCCTTAACTTTAAAATCCTAAA-CCTTAACTGT-A
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACT-TAA
* * * * *
42034563 AAACTCTAAACTCTCAAATTAAAAACCTTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * *
42034607 AAACCCTAACCTTTAACTTAAAAACCAT-AACCCTTAAATTTA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
42034649 AAACCTTAAACCCTTAACCTAAAAACCCTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
42034693 AAACCTTAACCCTTAACTTTAAAACCCT-AACCCTTAACTTTA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
42034735 AAACCCTAACCCTTAACTTAAAAATCCT-AACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
42034777 A
1 A
42034778 TATAATTTGA
Statistics
Matches: 1017, Mismatches: 118, Indels: 53
0.86 0.10 0.04
Matches are distributed among these distances:
40 29 0.03
41 61 0.06
42 144 0.14
43 537 0.53
44 219 0.22
48 1 0.00
49 26 0.03
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (43 bp):
AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
Found at i:42034977 original size:114 final size:114
Alignment explanation
Indices: 42034777--42035055 Score: 513
Period size: 114 Copynumber: 2.4 Consensus size: 114
42034767 CTTAACTTAA
*
42034777 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATTTTACATTCACATAA
1 ATATAATTTGATAATTTTACTAACAATTAATACAATTATCAATTAATAATTTTACATTCACATAA
* *
42034842 TGTTAGATTTGAAAAATTGTTTTGACTGGTATTAACAATTAATAATTTG
66 TGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
* *
42034891 ATATAATTTGATAATTTTACTAACTATTAATACAATTATCGATTAATAATTTTACATTCACATAA
1 ATATAATTTGATAATTTTACTAACAATTAATACAATTATCAATTAATAATTTTACATTCACATAA
42034956 TGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
66 TGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
42035005 ATATAATTTGATAATTTTACTAACAATTAATACAATTATCAATTAATAATT
1 ATATAATTTGATAATTTTACTAACAATTAATACAATTATCAATTAATAATT
42035056 GAAAAAAATA
Statistics
Matches: 159, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 159 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.43
Consensus pattern (114 bp):
ATATAATTTGATAATTTTACTAACAATTAATACAATTATCAATTAATAATTTTACATTCACATAA
TGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
Found at i:42038406 original size:126 final size:126
Alignment explanation
Indices: 42038174--42038579 Score: 554
Period size: 126 Copynumber: 3.2 Consensus size: 126
42038164 AACATGCTAT
* *
42038174 TGTAGCAAAAGCGCATCCTCGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGA
* * * *
42038239 AGCATTTTTTTTAAACTATTTGCTTAAAAACGTCAA-GCGAAATTATTTCTTCCAGGACCTAC
66 AGC--TTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAAGACCTAC
* * * *
42038301 T-TAGTAAAAGCGCGTCCACGAGAGCGCGATTTCACAAATTCTTCTCAAATAGTATCCTGCTTAA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGA
* *
42038365 AGCGTTTTTTTAAACTATTTCCTCAGAAACGTCAACTCGAAATTATTTCTTCCAAGACCTAT
66 AGC-TTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAAGACCTAC
* *
42038427 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCATAATTTCTTCTCATAA-AGCATCCTGCTTG
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTGCTTG
* * *
42038491 AAGC-ATTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TT-CATGACCTAC
65 AAGCTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAAGACCTAC
* * *
42038550 TGTAGCAAAAGCACGTACACGTGGGCGCGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGA
42038580 CTTTAGAAAT
Statistics
Matches: 249, Mismatches: 27, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
123 35 0.14
124 2 0.01
125 68 0.27
126 84 0.34
127 58 0.23
128 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (126 bp):
TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGA
AGCTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAAGACCTAC
Found at i:42041093 original size:10 final size:10
Alignment explanation
Indices: 42041078--42041103 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
42041068 TTTTTCGGGA
42041078 CTTATTCGAG
1 CTTATTCGAG
42041088 CTTATTCGAG
1 CTTATTCGAG
42041098 CTTATT
1 CTTATT
42041104 TACTAACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.46
Consensus pattern (10 bp):
CTTATTCGAG
Found at i:42044068 original size:42 final size:42
Alignment explanation
Indices: 42044014--42044129 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
42044004 AAATGCTAAA
42044014 AAAAACCCATAAGGGTTGAACGGAAGCTCATAAGAGCTGAAC
1 AAAAACCCATAAGGGTTGAACGGAAGCTCATAAGAGCTGAAC
* *
42044056 AAAAACCTATAAGGGTT-AA-GTTGAAGCAT-AAAAGAGCTGAAC
1 AAAAACCCATAAGGGTTGAACG--GAAGC-TCATAAGAGCTGAAC
** * * *
42044098 GGAAACCCATTAGGGTTGAACAGAAACTCATA
1 AAAAACCCATAAGGGTTGAACGGAAGCTCATA
42044130 TGAGTAAACA
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
40 1 0.02
41 3 0.05
42 52 0.88
43 3 0.05
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.17
Consensus pattern (42 bp):
AAAAACCCATAAGGGTTGAACGGAAGCTCATAAGAGCTGAAC
Found at i:42044153 original size:20 final size:21
Alignment explanation
Indices: 42044116--42044163 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
42044106 ATTAGGGTTG
42044116 AACAGAAACTCATATGAG-TA
1 AACAGAAACTCATATGAGCTA
* *
42044136 AACAGAAACTCGTGTGAGCTA
1 AACAGAAACTCATATGAGCTA
42044157 AAC-GAAA
1 AACAGAAA
42044164 AGTAAACACG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.17
Consensus pattern (21 bp):
AACAGAAACTCATATGAGCTA
Found at i:42051592 original size:22 final size:22
Alignment explanation
Indices: 42051567--42051615 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
42051557 CGCATCAATA
* *
42051567 TATGTGAGCCCTT-TATGGGACG
1 TATGAGAG-CCTTATATGAGACG
42051589 TATGAGAGCCTTATATGAGACG
1 TATGAGAGCCTTATATGAGACG
42051611 TATGA
1 TATGA
42051616 AAGTCCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (22 bp):
TATGAGAGCCTTATATGAGACG
Found at i:42056445 original size:93 final size:93
Alignment explanation
Indices: 42056337--42056522 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
42056327 ATTAGCTGCA
*
42056337 ACACCCTTATCTTTCAGATTTAACCCAGAGCTGGCCTCCCCCGATTCTCTCCTTTATTGTTGTCT
1 ACACCCTTATATTTCAGATTTAACCCAGAGCTGGCCTCCCCCGATTCTCTCCTTTATTGTTGTCT
42056402 GTCCCTAAATTAGTGGGATTTTCATCGT
66 GTCCCTAAATTAGTGGGATTTTCATCGT
42056430 ACACCCTTATATTTCAGATTTAACCCAGAGCTGGCCTCCCCCGATTCTCTCCTTTATTGTTGTCT
1 ACACCCTTATATTTCAGATTTAACCCAGAGCTGGCCTCCCCCGATTCTCTCCTTTATTGTTGTCT
42056495 GTCCCTAAATTAGTGGGATTTTCATCGT
66 GTCCCTAAATTAGTGGGATTTTCATCGT
42056523 CCAAATTTGT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.38
Consensus pattern (93 bp):
ACACCCTTATATTTCAGATTTAACCCAGAGCTGGCCTCCCCCGATTCTCTCCTTTATTGTTGTCT
GTCCCTAAATTAGTGGGATTTTCATCGT
Found at i:42056999 original size:27 final size:26
Alignment explanation
Indices: 42056954--42057013 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
42056944 AAACTTTCAT
42056954 AATTTTTAAAAAAAATTTAAATTTTGA
1 AATTTTTAAAAAAAATTT-AATTTTGA
* * * *
42056981 AATTTTTATAAATATTTTAATTTTTA
1 AATTTTTAAAAAAAATTTAATTTTGA
*
42057007 ATTTTTT
1 AATTTTT
42057014 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
AATTTTTAAAAAAAATTTAATTTTGA
Found at i:42057012 original size:26 final size:26
Alignment explanation
Indices: 42056953--42057013 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
42056943 GAAACTTTCA
*
42056953 TAATTTTTAAAAAAAATTTAAATTTT
1 TAATTTTTTAAAAAAATTTAAATTTT
* * * * *
42056979 GAAATTTTTATAAATATTTTAATTTT
1 TAATTTTTTAAAAAAATTTAAATTTT
42057005 TAATTTTTT
1 TAATTTTTT
42057014 TTTAATTTTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TAATTTTTTAAAAAAATTTAAATTTT
Found at i:42057880 original size:24 final size:24
Alignment explanation
Indices: 42057848--42057899 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
42057838 CCGCAAGTAG
42057848 CTAATCGCCCATCCAACCACCCGT
1 CTAATCGCCCATCCAACCACCCGT
42057872 CTAATCGCCCATCCAACCACCCGT
1 CTAATCGCCCATCCAACCACCCGT
42057896 -TAAT
1 CTAAT
42057900 AGAGGATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.27, C:0.46, G:0.08, T:0.19
Consensus pattern (24 bp):
CTAATCGCCCATCCAACCACCCGT
Found at i:42058288 original size:15 final size:15
Alignment explanation
Indices: 42058268--42058300 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
42058258 TATAAGTTCC
42058268 CTTCTTTATCTTCTT
1 CTTCTTTATCTTCTT
42058283 CTTCTTTATCTTCTT
1 CTTCTTTATCTTCTT
42058298 CTT
1 CTT
42058301 ATTGTTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTCTTTATCTTCTT
Found at i:42058686 original size:132 final size:132
Alignment explanation
Indices: 42058493--42058742 Score: 349
Period size: 137 Copynumber: 1.9 Consensus size: 132
42058483 TTAAACTACG
* *
42058493 GTCTTCGCTTTTGTGCTCTTTCAATTCAATTAAAATGGGTTTGTTTGTTTTTACTT-TTTTTTTG
1 GTCTTCGCTTTTGTGCTCTTTCAATTAAATTAAAATGGGTTTGTCTGTTTTTACTTCTTTTTTTG
* **
42058557 TACTATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTGTTGTTCTTGGCTCTTTGCAAATTA
66 TACTATTTGATTCTTATTGATTGCCCCTTTTGTTAATTTTACTGTTCTTGGCTCTTTGCAAATTA
42058622 CA
131 CA
* * * *
42058624 GTCTTTGCTTTTGTGCTCTTTCAGTTAAAATTTAATTGGGTTTGTCTGTTTTTACTTCTTTTTTT
1 GTCTTCGCTTTTGTGCTCTTTCAATT-AAATTAAAATGGGTTTGTCTGTTTTTACTTC----TTT
* *
42058689 TTTTGTACTGTTTGATTCTTATTGATTGCTCCTTTTGTTAATTTTACTGTTCTT
61 TTTTGTACTATTTGATTCTTATTGATTGCCCCTTTTGTTAATTTTACTGTTCTT
42058743 AGCTATTGGC
Statistics
Matches: 102, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
131 24 0.24
132 26 0.25
137 52 0.51
ACGTcount: A:0.14, C:0.14, G:0.15, T:0.58
Consensus pattern (132 bp):
GTCTTCGCTTTTGTGCTCTTTCAATTAAATTAAAATGGGTTTGTCTGTTTTTACTTCTTTTTTTG
TACTATTTGATTCTTATTGATTGCCCCTTTTGTTAATTTTACTGTTCTTGGCTCTTTGCAAATTA
CA
Found at i:42060343 original size:65 final size:65
Alignment explanation
Indices: 42060239--42060369 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
42060229 GATGGAGTAG
*
42060239 AGGAAAGCATTCACTATTGTAGTTTTCCTCAATAAGAAGGAAAGGTATTCTTCATCTTTGTTGTA
1 AGGAAAGCATCCACTATTGTAGTTTTCCTCAATAAGAAGGAAAGGTATTCTTCATCTTTGTTGTA
42060304 AGGAAAGCATCCACTATTGTAGTTTTCCTCAATAAGAAGGAAAGGTATTCTTCATCTTTGTTGTA
1 AGGAAAGCATCCACTATTGTAGTTTTCCTCAATAAGAAGGAAAGGTATTCTTCATCTTTGTTGTA
42060369 A
1 A
42060370 TTATTCATCA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (65 bp):
AGGAAAGCATCCACTATTGTAGTTTTCCTCAATAAGAAGGAAAGGTATTCTTCATCTTTGTTGTA
Found at i:42063346 original size:2 final size:2
Alignment explanation
Indices: 42063339--42063400 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
42063329 TTAAGAAAAT
*
42063339 CA CA CA CA CA CA CA CA CA CA CA CG CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
42063381 CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA
42063401 TATATATCCT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.48, C:0.50, G:0.02, T:0.00
Consensus pattern (2 bp):
CA
Found at i:42064224 original size:5 final size:5
Alignment explanation
Indices: 42064214--42064242 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
42064204 AAACATGCCA
42064214 ATATT ATATT ATATT ATATT ATATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
42064243 AAAAGGCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:42064514 original size:30 final size:30
Alignment explanation
Indices: 42064478--42064542 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
42064468 AGGCAAGAAC
42064478 TCTTTATCCCATACAATTAGTACTCTTGCA
1 TCTTTATCCCATACAATTAGTACTCTTGCA
42064508 TCTTTATCCCATACAATTAGTACTCTTGCA
1 TCTTTATCCCATACAATTAGTACTCTTGCA
42064538 TCTTT
1 TCTTT
42064543 CCTCTTATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.25, C:0.26, G:0.06, T:0.43
Consensus pattern (30 bp):
TCTTTATCCCATACAATTAGTACTCTTGCA
Found at i:42073506 original size:26 final size:26
Alignment explanation
Indices: 42073477--42073527 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
42073467 ACAAAGAGAA
*
42073477 GGGATTGCATGAAACTGTGATTCCAG
1 GGGATTGCATGAAACTCTGATTCCAG
*
42073503 GGGATTGTATGAAACTCTGATTCCA
1 GGGATTGCATGAAACTCTGATTCCA
42073528 TTTCATCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (26 bp):
GGGATTGCATGAAACTCTGATTCCAG
Found at i:42073760 original size:15 final size:14
Alignment explanation
Indices: 42073736--42073766 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
42073726 AAAAAATTAC
42073736 TTTAGTTCAGACCT
1 TTTAGTTCAGACCT
42073750 TTTATGTTCAGACCT
1 TTTA-GTTCAGACCT
42073765 TT
1 TT
42073767 GCTTACTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.48
Consensus pattern (14 bp):
TTTAGTTCAGACCT
Found at i:42077922 original size:20 final size:20
Alignment explanation
Indices: 42077888--42077929 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
42077878 AGCTATTTAA
** *
42077888 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
42077908 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
42077928 AT
1 AT
42077930 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:42078703 original size:5 final size:5
Alignment explanation
Indices: 42078693--42078718 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42078683 TGAGCATTCG
42078693 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
42078719 AATTTTCGAG
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:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:42079735 original size:9 final size:9
Alignment explanation
Indices: 42079718--42079748 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42079708 TCGAGTTGAT
42079718 TCGAATAAC
1 TCGAATAAC
*
42079727 TCGATTAAC
1 TCGAATAAC
42079736 TCGAATAAC
1 TCGAATAAC
42079745 TCGA
1 TCGA
42079749 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:42084167 original size:20 final size:20
Alignment explanation
Indices: 42084133--42084174 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
42084123 AGCTATTTAA
** *
42084133 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
42084153 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
42084173 AT
1 AT
42084175 GTGCTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:42086919 original size:102 final size:105
Alignment explanation
Indices: 42086800--42087052 Score: 332
Period size: 110 Copynumber: 2.4 Consensus size: 105
42086790 TGTTTTAAAA
* *
42086800 TTATTTAAAAGTTATTTTGTTAGTAATTATTATAAATAGTTTGTTTAGTTTAATGTTTATTGTGA
1 TTATTTTAAAGTTATTTTGTTAGTAATTATTATAAATAGTTTGTTTAGTTTAATATTTATTGTGA
*
42086865 TTTGTTAGGTTATGAATGTAAT-TTTT-TTA-TTTTTAAT
66 TTTGCTAGGTTATGAATGTAATCTTTTATTATTTTTTAAT
* *
42086902 TTATTTTAAAGTTATTTTGTTAGTAATTTTTGTGATTAGGTTAATTGTTTGTTTAGTTTAATATT
1 TTATTTTAAAGTTATTTTGTTAGTAA----T-T-ATTA--TAAATAGTTTGTTTAGTTTAATATT
42086967 TATTGTGATTTGCTAGGTTATGAATGTAATCTTTTATTATTTTTTTAAT
58 TATTGTGATTTGCTAGGTTATGAATGTAATCTTTTATTA-TTTTTTAAT
* * *
42087016 TTATTTTAAAGTTATTTTGTCAATAACTATTATAAAT
1 TTATTTTAAAGTTATTTTGTTAGTAATTATTATAAAT
42087053 TCGAAAAAAA
Statistics
Matches: 130, Mismatches: 9, Indels: 20
0.82 0.06 0.13
Matches are distributed among these distances:
102 25 0.19
106 5 0.04
107 1 0.01
108 8 0.06
109 1 0.01
110 51 0.39
111 4 0.03
112 3 0.02
114 32 0.25
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (105 bp):
TTATTTTAAAGTTATTTTGTTAGTAATTATTATAAATAGTTTGTTTAGTTTAATATTTATTGTGA
TTTGCTAGGTTATGAATGTAATCTTTTATTATTTTTTAAT
Found at i:42092498 original size:24 final size:24
Alignment explanation
Indices: 42092451--42092545 Score: 79
Period size: 24 Copynumber: 4.0 Consensus size: 24
42092441 TTTAAAAAAA
* *
42092451 TAAAATAATAATGCATAACAAATT
1 TAAAATAATAATACATAATAAATT
* * *
42092475 TGAAATGATAATACATAATGAATT
1 TAAAATAATAATACATAATAAATT
*
42092499 TAAAA-ACA-AATACATAATAAATC
1 TAAAATA-ATAATACATAATAAATT
** *
42092522 TAAGCTAATAATACATGA-AAATT
1 TAAAATAATAATACATAATAAATT
42092545 T
1 T
42092546 TATGATGCTA
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
23 22 0.40
24 33 0.60
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.29
Consensus pattern (24 bp):
TAAAATAATAATACATAATAAATT
Found at i:42094588 original size:42 final size:44
Alignment explanation
Indices: 42094494--42094602 Score: 141
Period size: 42 Copynumber: 2.5 Consensus size: 44
42094484 GATCCACCCT
* *
42094494 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGTTCC
1 ACTGCAACTTCAGGGAGATAAGATCTATTACTTTAATCCGCTCC
* * * *
42094538 ACTACAACTTCAGGGAGATAGGAT-TA-TGCTTTAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATCTATTACTTTAATCCGCTCC
*
42094580 ATTGCAACTTCAGGGAGATAAGA
1 ACTGCAACTTCAGGGAGATAAGA
42094603 GTTGCCATCT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 33 0.59
43 2 0.04
44 21 0.38
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGATCTATTACTTTAATCCGCTCC
Found at i:42094886 original size:88 final size:88
Alignment explanation
Indices: 42094737--42095264 Score: 849
Period size: 88 Copynumber: 6.0 Consensus size: 88
42094727 AAGATTCACC
* * *
42094737 GTCTTTGATCTGCTTCACTGTCGATGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTA
1 GTCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
42094802 CAACCGAGGGAGGCAAGGTTTGT
66 CAACCGAGGGAGGCAAGGTTTGT
* * *
42094825 GTCTTCGATCTGCTTCGCTGTCGATACAGGAAGGTAAGATCTGCTATCTTCAACCAGCTCCACTA
1 GTCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
42094890 CAACCGAGGGAGGCAAGGTTTGT
66 CAACCGAGGGAGGCAAGGTTTGT
* * * * * * *
42094913 GTCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTACTATCTTCCACCAGATTCACTA
1 GTCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
42094978 CAACCGAGGGAGGCAAGGTTTGT
66 CAACCGAGGGAGGCAAGGTTTGT
* *
42095001 GTCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCAGTA
1 GTCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
*
42095066 CAACTGAGGGAGGCAAGGTTTGT
66 CAACCGAGGGAGGCAAGGTTTGT
* * *
42095089 GTCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCCACTAGCTCTACTA
1 GTCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
42095154 CAACCGAGGGAGGCAAGGTTTGT
66 CAACCGAGGGAGGCAAGGTTTGT
* * *
42095177 ATCTTCGATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCCACCAGCTCCACTA
1 GTCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
*
42095242 CAATCGAGGGAGGCAAGGTTTGT
66 CAACCGAGGGAGGCAAGGTTTGT
42095265 TCGATCTTCA
Statistics
Matches: 409, Mismatches: 31, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 409 1.00
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.27
Consensus pattern (88 bp):
GTCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
CAACCGAGGGAGGCAAGGTTTGT
Found at i:42097983 original size:17 final size:17
Alignment explanation
Indices: 42097950--42097991 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
42097940 TTTTTTATTC
*
42097950 ATAAAAAAATGAAAGAA
1 ATAAAAGAATGAAAGAA
42097967 ATAAAAGAA-GAAGAGAA
1 ATAAAAGAATGAA-AGAA
42097984 A-AAAAGAA
1 ATAAAAGAA
42097992 AACGAAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (17 bp):
ATAAAAGAATGAAAGAA
Found at i:42103172 original size:52 final size:53
Alignment explanation
Indices: 42103106--42103285 Score: 240
Period size: 56 Copynumber: 3.4 Consensus size: 53
42103096 TACTCTTCTA
42103106 TTTTTTTT-CTTCTCCTTCTCCTCTCGTACCTATTCTGCTTCTC-TTTTTTTC
1 TTTTTTTTCCTTCTCCTTCTCCTCTCGTACCTATTCTGCTTCTCTTTTTTTTC
* *
42103157 TTTTTTTTCCTTCTCCTTTTCCTCTCGTACCTATTCTTCTTCTCTCTTTTTTTTTC
1 TTTTTTTTCCTTCTCCTTCTCCTCTCGTACCTATTCTGC-T-TCTC-TTTTTTTTC
* * *
42103213 TTTTTTTCCCTTCTCCTTCTCCTCTCATACCTATTATGCTTCTCTTTTTTTTC
1 TTTTTTTTCCTTCTCCTTCTCCTCTCGTACCTATTCTGCTTCTCTTTTTTTTC
*
42103266 TTCCTTTTTTCCCT-TCCTTC
1 TT--TTTTTTCCTTCTCCTTC
42103286 CCTTCCCTTC
Statistics
Matches: 113, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
51 8 0.07
52 28 0.25
53 12 0.11
54 14 0.12
55 9 0.08
56 42 0.37
ACGTcount: A:0.04, C:0.32, G:0.02, T:0.61
Consensus pattern (53 bp):
TTTTTTTTCCTTCTCCTTCTCCTCTCGTACCTATTCTGCTTCTCTTTTTTTTC
Found at i:42103205 original size:46 final size:46
Alignment explanation
Indices: 42103106--42103210 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 46
42103096 TACTCTTCTA
42103106 TTTTTTTTCTTCTCCTTCTCCTCTCGTACCTATTCTGCTTCTCTTTTTTTC
1 TTTTTTTTCTTCTCCTTCTCCTCTCGTACCTATTCTGCTTCTC-----TTC
* *
42103157 TTTTTTTTCCTTCTCCTTTTCCTCTCGTACCTATTCTTCTTCTC-TC
1 TTTTTTTT-CTTCTCCTTCTCCTCTCGTACCTATTCTGCTTCTCTTC
42103203 TTTTTTTT
1 TTTTTTTT
42103211 TCTTTTTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
46 10 0.20
51 8 0.16
52 33 0.65
ACGTcount: A:0.04, C:0.30, G:0.03, T:0.63
Consensus pattern (46 bp):
TTTTTTTTCTTCTCCTTCTCCTCTCGTACCTATTCTGCTTCTCTTC
Found at i:42103322 original size:5 final size:5
Alignment explanation
Indices: 42103274--42103312 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
42103264 TCTTCCTTTT
42103274 TTCCC TT-CC TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC
1 TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC
42103313 GTTCTCTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
TTCCC
Found at i:42104796 original size:43 final size:43
Alignment explanation
Indices: 42104673--42104825 Score: 123
Period size: 43 Copynumber: 3.5 Consensus size: 43
42104663 CATTAGAATT
* * *
42104673 TCGTATATGATTTACGTATAAGATCATAT-TCGGGACGTTGGCA
1 TCGTATATGATTTACGTGTAAGATCCTATCT-GGGACATTGGCA
* * ** * * * *
42104716 TCAATTTAAAATTTACGCGTAATA-CCTTGTCTAGGACATTGGCA
1 TC-GTATATGATTTACGTGTAAGATCC-TATCTGGGACATTGGCA
*
42104760 TCGTATATGATTTACGTGTAAGATCCTATCTGGGACAGTGGCA
1 TCGTATATGATTTACGTGTAAGATCCTATCTGGGACATTGGCA
* *
42104803 TCGATATTTGA-TTACATGTAAGA
1 TCG-TATATGATTTACGTGTAAGA
42104826 CCACATCTCG
Statistics
Matches: 83, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
43 46 0.55
44 36 0.43
45 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (43 bp):
TCGTATATGATTTACGTGTAAGATCCTATCTGGGACATTGGCA
Done.