Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 143 of 170
Found at i:43041151 original size:126 final size:126
Alignment explanation
Indices: 43040864--43041398 Score: 731
Period size: 125 Copynumber: 4.3 Consensus size: 126
43040854 GCCAAACATG
*
43040864 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCAAAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
43040929 TAT-AAGC-TATTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTCTTTCAGGAC
66 T-TGAAGCGTATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
* ** * *
43040989 CAACTGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTCAGAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * * *
43041054 TTGAAGCGTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTT-TTTCAAGAC
66 TTGAAGCG-TATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
*
43041115 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCATAA-AGTATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCA-AATAGCATCCTG
* * * * *
43041179 GTAGAAGCG-ATTTTATACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCGGGAT
65 CTTGAAGCGTATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
* * * * * * *
43041240 CAACTATAGCAAAAGCGCGTCCAGGAGGGCGCGATTTCACAAATTCTTCACATATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
43041305 TTGAAGCGTTTTTTATACTATCTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGAC
66 TTGAAGCGTATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
* * *
43041365 CTACTGTAGCAAAAACGCGTACACGTGGGTGTGA
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGA
43041399 CTGCAAAAAT
Statistics
Matches: 355, Mismatches: 48, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
124 41 0.12
125 163 0.46
126 109 0.31
127 42 0.12
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TTGAAGCGTATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
Found at i:43041307 original size:251 final size:250
Alignment explanation
Indices: 43040864--43041398 Score: 854
Period size: 251 Copynumber: 2.1 Consensus size: 250
43040854 GCCAAACATG
43040864 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCAAAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCAAAAAGCATCCTGC
* * * * *
43040929 TATAAGCTATTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTCTTTCAGGACCAACT
66 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACT
* * *
43040994 GTAGCAAAAGCGCGTCCACAAGGGCGCGATTTCAGAAATTCTTCTCAAATAGCATCCTGCTTGAA
131 ATAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATTCTTCACAAATAGCATCCTGCTTGAA
* *
43041059 GCGTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTTCAAGAC
196 GCG-TTTTTTATACTATCTGCTCAGAAACGTCAACTCGAAATAATTTTTCCAAGAC
* * *
43041115 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCATAAAGTATCCTGG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCAAAAAGCATCCTGC
* *
43041180 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCGGGATCAACT
66 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACT
** *
43041245 ATAGCAAAAGCGCGTCCAGGAGGGCGCGATTTCACAAATTCTTCACATATAGCATCCTGCTTGAA
131 ATAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATTCTTCACAAATAGCATCCTGCTTGAA
* *
43041310 GCGTTTTTTATACTATCTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
196 GCGTTTTTTATACTATCTGCTCAGAAACGTCAACTCGAAATAATTTTTCCAAGAC
* * *
43041365 CTACTGTAGCAAAAACGCGTACACGTGGGTGTGA
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGA
43041399 CTGCAAAAAT
Statistics
Matches: 261, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
250 79 0.30
251 182 0.70
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (250 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCAAAAAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACT
ATAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATTCTTCACAAATAGCATCCTGCTTGAA
GCGTTTTTTATACTATCTGCTCAGAAACGTCAACTCGAAATAATTTTTCCAAGAC
Found at i:43044941 original size:12 final size:11
Alignment explanation
Indices: 43044896--43044950 Score: 65
Period size: 11 Copynumber: 4.7 Consensus size: 11
43044886 AATTTTTATT
43044896 TTTTAAAAAAA
1 TTTTAAAAAAA
*
43044907 TTCTTAACAATAA
1 TT-TTAA-AAAAA
*
43044920 TTCTAAAAAAA
1 TTTTAAAAAAA
43044931 TTTTAAAAAAA
1 TTTTAAAAAAA
43044942 TCTTTAAAA
1 T-TTTAAAA
43044951 TAAAAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 17 0.46
12 14 0.38
13 6 0.16
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (11 bp):
TTTTAAAAAAA
Found at i:43050549 original size:19 final size:19
Alignment explanation
Indices: 43050513--43050550 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
43050503 TTATGCTTGT
*
43050513 TTTTATTCTTTTATAATTA
1 TTTTATTCTATTATAATTA
43050532 TTTTATT-TATTATCAATTA
1 TTTTATTCTATTAT-AATTA
43050551 AAAAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTATTCTATTATAATTA
Found at i:43053610 original size:18 final size:18
Alignment explanation
Indices: 43053583--43053622 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
43053573 CAGATTTGTT
* *
43053583 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
43053601 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
43053619 TCCT
1 TCCT
43053623 TTTCCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:43053890 original size:21 final size:21
Alignment explanation
Indices: 43053864--43053910 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
43053854 CAACTCCGAC
43053864 AACCAG-ATGCCCTACCGGAAG
1 AACCAGAAT-CCCTACCGGAAG
* *
43053885 AACCAGAATCCCTGCCGGAGG
1 AACCAGAATCCCTACCGGAAG
43053906 AACCA
1 AACCA
43053911 CAACCGCCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.34, C:0.34, G:0.23, T:0.09
Consensus pattern (21 bp):
AACCAGAATCCCTACCGGAAG
Found at i:43054203 original size:49 final size:47
Alignment explanation
Indices: 43054163--43054754 Score: 557
Period size: 49 Copynumber: 12.4 Consensus size: 47
43054153 AATTTAATTG
* * *
43054163 AAAAACCCTAACTCCTTAACCTTAAAACTCTAAACCC--A---TAACCT
1 AAAAACCCTAACACCTTAACCTAAAAAC-CT-AACCCTAACCTTAACTT
43054207 AAAAACCCTAACACCTTAACCTAAAAACCCTAACCCTAACCCTAACCCTTAACTT
1 AAAAACCCTAACACCTTAACCT--AAA----AA-CCTAACCCTAA-CCTTAACTT
* * *
43054262 AAAAACCCTAACCCCTTAACCTAAAAACCTAAAACCTTAAACTCTAAACTT
1 AAAAACCCTAACACCTTAACCTAAAAACCT--AACCCT-AAC-CTTAACTT
* *
43054313 AAAAACCCTAACACTTTAACCTAAAAACTCCAACCCTAACCCTTAACTT
1 AAAAACCCTAACACCTTAACCTAAAAAC-CTAACCCTAA-CCTTAACTT
*
43054362 AAAAACCCTAACACCTTAACCTAAAAACCCCAACCCTAACCGTTAACTT
1 AAAAACCCTAACACCTTAACCTAAAAA-CCTAACCCTAACC-TTAACTT
* *
43054411 AAAAACCCTAACACCTTCACCTAAAAACCCCAACCCTAACCGTTAACTT
1 AAAAACCCTAACACCTTAACCTAAAAA-CCTAACCCTAACC-TTAACTT
* * *
43054460 AAAAACCTTAACCCCTTAACCTAAAAACCCTAACTCTAACCCTTAACTT
1 AAAAACCCTAACACCTTAACCTAAAAA-CCTAACCCTAA-CCTTAACTT
43054509 AAAAACCCTAAC-CCTTAACCTAAAAACCCTAACCCTAACCCTTAACTT
1 AAAAACCCTAACACCTTAACCTAAAAA-CCTAACCCTAA-CCTTAACTT
*
43054557 AAAAACCCTAACACCTTAACCTAAAAACCCTAACCCTAACTGTTAACTT
1 AAAAACCCTAACACCTTAACCTAAAAA-CCTAACCCTAAC-CTTAACTT
*
43054606 AAAAACCCTAATC-CCTTAACCT-AAAACCTTAA----ACCCTTAACTT
1 AAAAACCCTAA-CACCTTAACCTAAAAACC-TAACCCTAACCTTAACTT
*
43054649 AAAAACCCTAATC-CCTTAACCTAAAAACCCTAACCCT----TTAACCT
1 AAAAACCCTAA-CACCTTAACCTAAAAA-CCTAACCCTAACCTTAACTT
* * *
43054693 GAAAACCCTAAC-CCTTAACTTAAAAACCCTAA-CC---CCTTAACCT
1 AAAAACCCTAACACCTTAACCTAAAAA-CCTAACCCTAACCTTAACTT
43054736 AAAAACCCTAAC-CC-TAACC
1 AAAAACCCTAACACCTTAACC
43054755 CTTAACTTAA
Statistics
Matches: 486, Mismatches: 28, Indels: 70
0.83 0.05 0.12
Matches are distributed among these distances:
42 6 0.01
43 69 0.14
44 46 0.09
45 2 0.00
46 2 0.00
47 2 0.00
48 60 0.12
49 212 0.44
50 20 0.04
51 37 0.08
52 1 0.00
53 3 0.01
55 26 0.05
ACGTcount: A:0.42, C:0.36, G:0.01, T:0.21
Consensus pattern (47 bp):
AAAAACCCTAACACCTTAACCTAAAAACCTAACCCTAACCTTAACTT
Found at i:43054250 original size:21 final size:21
Alignment explanation
Indices: 43054163--43054792 Score: 368
Period size: 22 Copynumber: 27.4 Consensus size: 21
43054153 AATTTAATTG
43054163 AAAAACCCTAACTCCTTAACCT
1 AAAAACCCTAAC-CCTTAACCT
* * *
43054185 TAAAACTCTAAACCCATAACCT
1 AAAAACCCT-AACCCTTAACCT
43054207 AAAAACCCTAACACCTTAACCT
1 AAAAACCCTAAC-CCTTAACCT
43054229 AAAAACCCTAACCC-TAACCCT
1 AAAAACCCTAACCCTTAA-CCT
43054250 ---AACCCTTAA--C-T----T
1 AAAAACCC-TAACCCTTAACCT
43054262 AAAAACCCTAACCCCTTAACCT
1 AAAAACCCTAA-CCCTTAACCT
*
43054284 AAAAA-CCTAAAACCTTAAACTCTAAACTT
1 AAAAACCCT--AACC-----CT-TAA-CCT
*
43054313 AAAAACCCTAACACTTTAACCT
1 AAAAACCCTAAC-CCTTAACCT
*
43054335 AAAAACTCCAACCCTAACCCTTAACTT
1 --AAA----AACCCTAACCCTTAACCT
43054362 AAAAACCCTAACACCTTAACCT
1 AAAAACCCTAAC-CCTTAACCT
* *
43054384 AAAAACCCCAACCCTAACCGTTAACTT
1 --AAA----AACCCTAACCCTTAACCT
*
43054411 AAAAACCCTAACACCTTCACCT
1 AAAAACCCTAAC-CCTTAACCT
* *
43054433 AAAAACCCCAACCCTAACCGTTAACTT
1 --AAA----AACCCTAACCCTTAACCT
*
43054460 AAAAACCTTAACCCCTTAACCT
1 AAAAACCCTAAC-CCTTAACCT
*
43054482 AAAAACCCTAACTCTAACCCTTAACTT
1 AAAAA--C---C-CTAACCCTTAACCT
43054509 AAAAACCCTAACCCTTAACCT
1 AAAAACCCTAACCCTTAACCT
*
43054530 AAAAACCCTAACCCTAACCCTTAACTT
1 --AAA----AACCCTAACCCTTAACCT
43054557 AAAAACCCTAACACCTTAACCT
1 AAAAACCCTAAC-CCTTAACCT
*
43054579 AAAAACCCTAACCCTAACTGTTAACTT
1 AAAAACCCTAA-CC---C--TTAACCT
43054606 AAAAACCCTAATCCCTTAACCT
1 AAAAACCCTAA-CCCTTAACCT
* *
43054628 -AAAACCTTAAACCCTTAACTT
1 AAAAACCCT-AACCCTTAACCT
43054649 AAAAACCCTAATCCCTTAACCT
1 AAAAACCCTAA-CCCTTAACCT
43054671 AAAAACCCTAACCCTTTAACCT
1 AAAAACCCTAACCC-TTAACCT
* *
43054693 GAAAACCCTAACCCTTAACTT
1 AAAAACCCTAACCCTTAACCT
43054714 AAAAACCCTAACCCCTTAACCT
1 AAAAACCCTAA-CCCTTAACCT
*
43054736 AAAAACCCTAACCCTAACCCTTAACTT
1 --AAA----AACCCTAACCCTTAACCT
*
43054763 AAAAACCCTAACCCTTAACTT
1 AAAAACCCTAACCCTTAACCT
*
43054784 TAAAACCCT
1 AAAAACCCT
43054793 CACTGGTTGA
Statistics
Matches: 490, Mismatches: 41, Indels: 155
0.71 0.06 0.23
Matches are distributed among these distances:
12 1 0.00
14 3 0.01
15 5 0.01
17 3 0.01
18 6 0.01
19 3 0.01
20 3 0.01
21 122 0.25
22 163 0.33
23 12 0.02
24 15 0.03
25 17 0.03
27 81 0.17
28 45 0.09
29 8 0.02
30 3 0.01
ACGTcount: A:0.42, C:0.35, G:0.01, T:0.22
Consensus pattern (21 bp):
AAAAACCCTAACCCTTAACCT
Found at i:43054265 original size:33 final size:34
Alignment explanation
Indices: 43054210--43054355 Score: 120
Period size: 34 Copynumber: 4.2 Consensus size: 34
43054200 ATAACCTAAA
43054210 AACCCTAACACCTTAACCTAAAAACCCTAACCCT
1 AACCCTAACACCTTAACCTAAAAACCCTAACCCT
*
43054244 AACCCTAAC-CCTTAACTTAAAAACCCTAACCCCTT
1 AACCCTAACACCTTAACCTAAAAACCCTAA-CCC-T
* * * * * *
43054279 AA-CCTAAAAACCTAAAACCT-TAAACTCTAAACTT
1 AACCCT-AACACCT-TAACCTAAAAACCCTAACCCT
*
43054313 AAAAACCCTAACACTTTAACCTAAAAACTCC-AACCCT
1 ---AACCCTAACACCTTAACCTAAAAAC-CCTAACCCT
43054350 AACCCT
1 AACCCT
43054356 TAACTTAAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
33 19 0.22
34 22 0.26
35 6 0.07
36 16 0.19
37 19 0.22
38 4 0.05
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (34 bp):
AACCCTAACACCTTAACCTAAAAACCCTAACCCT
Found at i:43054457 original size:98 final size:98
Alignment explanation
Indices: 43054201--43054777 Score: 640
Period size: 98 Copynumber: 5.9 Consensus size: 98
43054191 TCTAAACCCA
*
43054201 TAACCTAAAAACCCTAACACCTTAACCTAAAAACCCTAACCCTAACCCTAACCCTTAACTTAAAA
1 TAACTTAAAAACCCTAACACCTTAACCTAAAAA--C---CCC-AACCCTAACCCTTAACTTAAAA
* *
43054266 ACCCTAACCCCTTAACCTAAAAA-CCTAAAACCTTAAACTC-T
60 ACCCTAACACCTTAACCTAAAAACCCT--AACCCT-AAC-CGT
* * *
43054307 AAACTTAAAAACCCTAACACTTTAACCTAAAAACTCCAACCCTAACCCTTAACTTAAAAACCCTA
1 TAACTTAAAAACCCTAACACCTTAACCTAAAAACCCCAACCCTAACCCTTAACTTAAAAACCCTA
*
43054372 ACACCTTAACCTAAAAACCCCAACCCTAACCGT
66 ACACCTTAACCTAAAAACCCTAACCCTAACCGT
* * *
43054405 TAACTTAAAAACCCTAACACCTTCACCTAAAAACCCCAACCCTAACCGTTAACTTAAAAACCTTA
1 TAACTTAAAAACCCTAACACCTTAACCTAAAAACCCCAACCCTAACCCTTAACTTAAAAACCCTA
* * *
43054470 ACCCCTTAACCTAAAAACCCTAACTCTAACCCT
66 ACACCTTAACCTAAAAACCCTAACCCTAACCGT
*
43054503 TAACTTAAAAACCCTAAC-CCTTAACCTAAAAACCCTAACCCTAACCCTTAACTTAAAAACCCTA
1 TAACTTAAAAACCCTAACACCTTAACCTAAAAACCCCAACCCTAACCCTTAACTTAAAAACCCTA
*
43054567 ACACCTTAACCTAAAAACCCTAACCCTAACTGT
66 ACACCTTAACCTAAAAACCCTAACCCTAACCGT
**
43054600 TAACTTAAAAACCCTAATC-CCTTAACCT-AAAA-CCTTA----AACCCTTAACTTAAAAACCCT
1 TAACTTAAAAACCCTAA-CACCTTAACCTAAAAACCCCAACCCTAACCCTTAACTTAAAAACCCT
43054658 AATC-CCTTAACCTAAAAACCCTAACCCT-----T
65 AA-CACCTTAACCTAAAAACCCTAACCCTAACCGT
* * * * *
43054687 TAACCTGAAAACCCTAAC-CCTTAACTTAAAAACCCTAA--C---CCCTTAACCTAAAAACCCTA
1 TAACTTAAAAACCCTAACACCTTAACCTAAAAACCCCAACCCTAACCCTTAACTTAAAAACCCTA
*
43054746 ACCCTAACCCTTAACTTAAAAACCCTAACCCT
66 A--C--A-CCTTAACCTAAAAACCCTAACCCT
43054778 TAACTTTAAA
Statistics
Matches: 426, Mismatches: 33, Indels: 38
0.86 0.07 0.08
Matches are distributed among these distances:
86 9 0.02
87 40 0.09
88 5 0.01
92 70 0.16
93 1 0.00
96 4 0.01
97 93 0.22
98 120 0.28
99 5 0.01
100 44 0.10
101 4 0.01
104 1 0.00
106 30 0.07
ACGTcount: A:0.42, C:0.36, G:0.01, T:0.21
Consensus pattern (98 bp):
TAACTTAAAAACCCTAACACCTTAACCTAAAAACCCCAACCCTAACCCTTAACTTAAAAACCCTA
ACACCTTAACCTAAAAACCCTAACCCTAACCGT
Found at i:43054536 original size:15 final size:15
Alignment explanation
Indices: 43054518--43054565 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
43054508 TAAAAACCCT
43054518 AACCCTTAACCTAAA
1 AACCCTTAACCTAAA
43054533 AACCC-TAACCCT---
1 AACCCTTAA-CCTAAA
*
43054545 AACCCTTAACTTAAA
1 AACCCTTAACCTAAA
43054560 AACCCT
1 AACCCT
43054566 AACACCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
12 7 0.26
13 3 0.11
14 3 0.11
15 14 0.52
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCTTAACCTAAA
Found at i:43054786 original size:27 final size:27
Alignment explanation
Indices: 43054316--43054777 Score: 292
Period size: 27 Copynumber: 18.2 Consensus size: 27
43054306 TAAACTTAAA
*
43054316 AACCCTAACACTTTAACCTAAAAACTCC-
1 AACCCTAAC-CCTTAACCTAAAAAC-CCT
*
43054344 AACCCTAACCCTTAACTTAAAAACCCT
1 AACCCTAACCCTTAACCTAAAAACCCT
*
43054371 AA--C--A-CCTTAACCTAAAAACCCC
1 AACCCTAACCCTTAACCTAAAAACCCT
* *
43054393 AACCCTAACCGTTAACTTAAAAACCCT
1 AACCCTAACCCTTAACCTAAAAACCCT
* *
43054420 AA--C--A-CCTTCACCTAAAAACCCC
1 AACCCTAACCCTTAACCTAAAAACCCT
* * *
43054442 AACCCTAACCGTTAACTTAAAAACCTT
1 AACCCTAACCCTTAACCTAAAAACCCT
43054469 AA--C---CCCTTAACCTAAAAACCCT
1 AACCCTAACCCTTAACCTAAAAACCCT
* *
43054491 AACTCTAACCCTTAA-CT-TAAA----
1 AACCCTAACCCTTAACCTAAAAACCCT
43054512 AACCCTAACCCTTAACCTAAAAACCCT
1 AACCCTAACCCTTAACCTAAAAACCCT
*
43054539 AACCCTAACCCTTAACTTAAAAACCCT
1 AACCCTAACCCTTAACCTAAAAACCCT
43054566 AA--C--A-CCTTAACCTAAAAACCCT
1 AACCCTAACCCTTAACCTAAAAACCCT
** *
43054588 AACCCTAACTGTTAACTTAAAAACCCT
1 AACCCTAACCCTTAACCTAAAAACCCT
* * *
43054615 AATCCCTTAA-CCTAAAACCTTAAACCCTTAACTT
1 AA-CCC-TAACCCT-TAACCTAAAAACC----C-T
43054649 AAAAACCCTAATCCCTTAACCTAAAAACCCT
1 ---AACCCTAA-CCCTTAACCTAAAAACCCT
*
43054680 AACCCT-----TTAACCTGAAAACCCT
1 AACCCTAACCCTTAACCTAAAAACCCT
*
43054702 -A-----ACCCTTAACTTAAAAACCCT
1 AACCCTAACCCTTAACCTAAAAACCCT
43054723 AA--C---CCCTTAACCTAAAAACCCT
1 AACCCTAACCCTTAACCTAAAAACCCT
*
43054745 AACCCTAACCCTTAACTTAAAAACCCT
1 AACCCTAACCCTTAACCTAAAAACCCT
43054772 AACCCT
1 AACCCT
43054778 TAACTTTAAA
Statistics
Matches: 342, Mismatches: 41, Indels: 103
0.70 0.08 0.21
Matches are distributed among these distances:
21 29 0.08
22 109 0.32
23 6 0.02
24 5 0.01
25 7 0.02
26 7 0.02
27 123 0.36
28 19 0.06
29 12 0.04
31 1 0.00
32 1 0.00
33 1 0.00
34 1 0.00
35 3 0.01
36 13 0.04
37 5 0.01
ACGTcount: A:0.41, C:0.36, G:0.01, T:0.22
Consensus pattern (27 bp):
AACCCTAACCCTTAACCTAAAAACCCT
Found at i:43055798 original size:127 final size:125
Alignment explanation
Indices: 43055518--43055910 Score: 538
Period size: 126 Copynumber: 3.1 Consensus size: 125
43055508 CCCAAACATG
* * * *
43055518 CTACTGTAGAAAAAGCGCATCCACGTGGGTGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * * * *
43055583 TAGAAGCG-ATTTTATACTGTTTGCTTAGAAACGCCAAGTCAAAATTATTTTTCCAAGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
* * * *
43055642 CTATTATAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATTCTTCTTA-AATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* * *
43055706 CTTGCAGCGTTGTTTTATATTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
65 CTTGAAGCGTT-TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAAGAC
* * * *
43055769 CAACTGTAGCAAAAGCGCGTCCATGAGGGCGCGATTTCAAAAATTCTTCTCATAAAGCATCCTTC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
*
43055834 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
43055894 CTACTGTAGCAAAAGCG
1 CTACTGTAGCAAAAGCG
43055911 AGTACATGTG
Statistics
Matches: 233, Mismatches: 31, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
123 2 0.01
124 60 0.26
125 24 0.10
126 74 0.32
127 71 0.30
128 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
Found at i:43056096 original size:8 final size:9
Alignment explanation
Indices: 43056075--43056112 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
43056065 TTTTTTCTCC
*
43056075 AAAAACCCT
1 AAAAATCCT
43056084 AAAAATCCT
1 AAAAATCCT
*
43056093 AAAAACCCT
1 AAAAATCCT
43056102 AAAAATCCT
1 AAAAATCCT
43056111 AA
1 AA
43056113 CTGGGAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.58, C:0.26, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAATCCT
Found at i:43056098 original size:18 final size:18
Alignment explanation
Indices: 43056075--43056112 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
43056065 TTTTTTCTCC
43056075 AAAAACCCTAAAAATCCT
1 AAAAACCCTAAAAATCCT
43056093 AAAAACCCTAAAAATCCT
1 AAAAACCCTAAAAATCCT
43056111 AA
1 AA
43056113 CTGGGAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.26, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAACCCTAAAAATCCT
Found at i:43056948 original size:13 final size:13
Alignment explanation
Indices: 43056924--43056948 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43056914 GGAATTTTGG
43056924 AATTTAATTTTTC
1 AATTTAATTTTTC
43056937 AATTTAATTTTT
1 AATTTAATTTTT
43056949 AAAAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTTAATTTTTC
Found at i:43078493 original size:17 final size:18
Alignment explanation
Indices: 43078461--43078494 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43078451 TGAAATCATG
43078461 ATAATTACACATTTAAAA
1 ATAATTACACATTTAAAA
*
43078479 ATAATTAGA-ATTTAAA
1 ATAATTACACATTTAAA
43078495 CAATTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAATTACACATTTAAAA
Found at i:43085471 original size:14 final size:14
Alignment explanation
Indices: 43085452--43085492 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
43085442 TGATTAAAGA
* *
43085452 TTAATTAATTTAGT
1 TTAATTAATTAAGC
43085466 TTAATTAACTTAAGC
1 TTAATTAA-TTAAGC
43085481 TTAATTAATTAA
1 TTAATTAATTAA
43085493 CCATTAAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (14 bp):
TTAATTAATTAAGC
Found at i:43088125 original size:30 final size:30
Alignment explanation
Indices: 43088067--43088125 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
43088057 TATTATATGT
**
43088067 TAATTAATTAAGGTAATTAAGGTAAAAACA
1 TAATTAATTAAGGTAATTAACCTAAAAACA
* * *
43088097 TAATTAATTATGTTAATTAACCTTAAAAC
1 TAATTAATTAAGGTAATTAACCTAAAAAC
43088126 TAAGTATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (30 bp):
TAATTAATTAAGGTAATTAACCTAAAAACA
Found at i:43089377 original size:20 final size:19
Alignment explanation
Indices: 43089344--43089386 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
43089334 TTAATAAGGT
43089344 TAAA-AACATATGAATTAA
1 TAAATAACATATGAATTAA
*
43089362 CTAAATAACATGTGAATTAA
1 -TAAATAACATATGAATTAA
43089382 TAAAT
1 TAAAT
43089387 GAAACAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (19 bp):
TAAATAACATATGAATTAA
Found at i:43092735 original size:21 final size:21
Alignment explanation
Indices: 43092690--43092729 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
43092680 AAAATGTTAC
*
43092690 TAAATTTATCATAAAAAATTA
1 TAAATTTATCATAAAAAATAA
43092711 TAAATTT-T-ATAAAAAATAA
1 TAAATTTATCATAAAAAATAA
43092730 ATTAAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTTATCATAAAAAATAA
Found at i:43095134 original size:13 final size:13
Alignment explanation
Indices: 43095074--43095134 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
43095064 TAAACCAAAA
* *
43095074 TTTTTAAAAATAC
1 TTTTCAAAAACAC
*
43095087 TTATCAAAATA-AC
1 TTTTCAAAA-ACAC
*
43095100 TTTTCTAAAACAC
1 TTTTCAAAAACAC
*
43095113 TTTTTAAAAACAC
1 TTTTCAAAAACAC
*
43095126 TTCTCAAAA
1 TTTTCAAAA
43095135 GTAATGTTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
12 1 0.03
13 36 0.95
14 1 0.03
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTTCAAAAACAC
Found at i:43096850 original size:21 final size:21
Alignment explanation
Indices: 43096799--43096850 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
43096789 AATTCATTAT
* *
43096799 AAAAATATTAAAATTAAATCA
1 AAAAATATTTAAATTAAATAA
*
43096820 AATAAT-TTTAAA-TAAACTAA
1 AAAAATATTTAAATTAAA-TAA
43096840 AAAAATATTTA
1 AAAAATATTTA
43096851 TTTTCTCACA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATATTTAAATTAAATAA
Found at i:43104455 original size:20 final size:21
Alignment explanation
Indices: 43104414--43104453 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43104404 ATAATATTAA
*
43104414 TTTCAATATTAACTGTAAAAT
1 TTTCAATATTAACTATAAAAT
43104435 TTTCAATATTAACTATAAA
1 TTTCAATATTAACTATAAA
43104454 TTATGGCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (21 bp):
TTTCAATATTAACTATAAAAT
Found at i:43110429 original size:43 final size:42
Alignment explanation
Indices: 43110363--43110519 Score: 183
Period size: 43 Copynumber: 3.7 Consensus size: 42
43110353 GGCTCGTACA
*
43110363 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAACG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAAT-ACG
* *
43110406 ATGCCACTGTCCCAGACAG-GGTCTTACATGTAATCATATACG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACATGTAATCAAATACG
** * *
43110448 ACACCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAAT-CG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGT-AA--TCAAATACG
*
43110492 ATGCCAATGTCCTAGACGTGGTCTTACA
1 ATGCCAATGTCCCAGACGTGGTCTTACA
43110520 CGATATCACA
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
42 28 0.29
43 36 0.38
44 27 0.28
45 5 0.05
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATACG
Found at i:43117736 original size:18 final size:18
Alignment explanation
Indices: 43117715--43117869 Score: 76
Period size: 18 Copynumber: 8.9 Consensus size: 18
43117705 ATATTAAGAA
43117715 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
43117733 TTTTATTAAA-T-TATA-
1 TTTTATTAAATTATATAT
* *
43117748 -TTTAAT-AATTATTTAT
1 TTTTATTAAATTATATAT
* * * *
43117764 TTTAAATTATATTTTATAG
1 TTT-TATTAAATTATATAT
* * *
43117783 TATTA-TATATTAT-GA-
1 TTTTATTAAATTATATAT
* *
43117798 TTTTAGTAAATTCATATAG
1 TTTTATTAAATT-ATATAT
** * *
43117817 TAATATTTAATATTA-AGAA
1 TTTTA-TTAA-ATTATATAT
43117836 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
43117854 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
43117870 TTAATAATAA
Statistics
Matches: 100, Mismatches: 24, Indels: 26
0.67 0.16 0.17
Matches are distributed among these distances:
13 2 0.02
14 6 0.06
15 7 0.07
16 10 0.10
17 16 0.16
18 36 0.36
19 16 0.16
20 4 0.04
21 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:43117904 original size:20 final size:21
Alignment explanation
Indices: 43117879--43117920 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
43117869 TTTAATAATA
*
43117879 ATTATTTTAAATTAT-ATTTT
1 ATTATTATAAATTATGATTTT
*
43117899 ATTATTATATATTATGATTTT
1 ATTATTATAAATTATGATTTT
43117920 A
1 A
43117921 GTAAATTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTATTATAAATTATGATTTT
Found at i:43118062 original size:119 final size:120
Alignment explanation
Indices: 43117649--43118125 Score: 849
Period size: 121 Copynumber: 4.0 Consensus size: 120
43117639 TAGATTATAT
* *
43117649 ATTAT-TTTTATAGTATTATATATTATGATTTTAGGAAATTCATATAATAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
*
43117713 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATTATTTATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAA-TAATTATTTTAA
43117769 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATAT-AGTAATATTTAATATTAA
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAG-AATATTTAATATTAA
43117833 GAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
65 GAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
43117889 ATTATATTTTAT--TATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
43117952 AATTTTA-TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
*
43118006 ATTAAATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
*
43118071 AATTTTATTAAATTATATA-TTTTATTAAATTATATTTAATAATAATTATGTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
43118125 A
1 A
43118126 ATATGATTAA
Statistics
Matches: 346, Mismatches: 5, Indels: 13
0.95 0.01 0.04
Matches are distributed among these distances:
117 58 0.17
118 55 0.16
119 95 0.27
120 40 0.12
121 98 0.28
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (120 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
Found at i:43118079 original size:237 final size:238
Alignment explanation
Indices: 43117649--43118125 Score: 845
Period size: 237 Copynumber: 2.0 Consensus size: 238
43117639 TAGATTATAT
*
43117649 ATTATTTTTATAGTATTATATATTATGATTTTAGGAAATTCATATAATAATATTTAATATTAAGA
1 ATTATTTTTATA-TATTATATATTATGATTTTAGGAAATTCATATAAGAATATTTAATATTAAGA
* *
43117714 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATTATTTATTTTAAATTATATTTT
65 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATTAATTATTTTAAATTAAATTTT
43117779 ATAGTATTATATATTATGATTTTAGTAAATTCATATAGTAATATTTAATATTAAGAATTTTATTA
130 ATAGTATTATATATTATGATTTTAGTAAATTCATATAGTAATATTTAATATTAAGAATTTTATTA
*
43117844 AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
195 AATTATATA-TTTTATTAAATTATATTTAATAATAATTATGTTAA
*
43117889 ATTATATTTTAT-TATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGA
1 ATTAT-TTTTATATATTATATATTATGATTTTAGGAAATTCATATAAGAATATTTAATATTAAGA
43117953 ATTTTA-TAAATTATATATTTTTATTAAATTATATTTAATAA-TAATTATTTTAAATTAAATTTT
65 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATTAATTATTTTAAATTAAATTTT
43118016 ATAGTATTATATATTATGATTTTAGTAAATTCATATAAG-AATATTTAATATTAAGAATTTTATT
130 ATAGTATTATATATTATGATTTTAGTAAATTCATAT-AGTAATATTTAATATTAAGAATTTTATT
43118080 AAATTATATATTTTATTAAATTATATTTAATAATAATTATGTTAA
194 AAATTATATATTTTATTAAATTATATTTAATAATAATTATGTTAA
43118125 A
1 A
43118126 ATATGATTAA
Statistics
Matches: 230, Mismatches: 5, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
236 35 0.15
237 91 0.40
238 37 0.16
239 56 0.24
240 5 0.02
241 6 0.03
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (238 bp):
ATTATTTTTATATATTATATATTATGATTTTAGGAAATTCATATAAGAATATTTAATATTAAGAA
TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATTAATTATTTTAAATTAAATTTTA
TAGTATTATATATTATGATTTTAGTAAATTCATATAGTAATATTTAATATTAAGAATTTTATTAA
ATTATATATTTTATTAAATTATATTTAATAATAATTATGTTAA
Found at i:43118088 original size:22 final size:18
Alignment explanation
Indices: 43118072--43118106 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
43118062 AATATTAAGA
43118072 ATTTTATTAAATTATA-T
1 ATTTTATTAAATTATATT
43118089 ATTTTATTAAATTATATT
1 ATTTTATTAAATTATATT
43118107 TAATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTATTAAATTATATT
Found at i:43118325 original size:44 final size:45
Alignment explanation
Indices: 43118262--43118358 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
43118252 CTATTACACC
*
43118262 TCCATTCCATTCAACCAAACACA-AGA-ATACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGATATACTATTACGCCTCTAT
* * *
43118306 TCCATTACATTCAACCAAACAATTGATTTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
43118351 TCCATTAC
1 TCCATTAC
43118359 GCTTCTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.47
45 24 0.51
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
Found at i:43118359 original size:16 final size:16
Alignment explanation
Indices: 43118338--43118386 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
43118328 TTGATTTGCT
43118338 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
43118354 ATTACGCTTCTATTCC
1 ATTACGCCTCTATTCC
43118370 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
43118386 A
1 A
43118387 ATACAGCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.20, C:0.35, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:43119764 original size:3 final size:3
Alignment explanation
Indices: 43119756--43119804 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
43119746 ATGTTATGTC
* * *
43119756 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAG CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43119804 T
1 T
43119805 GTAAATATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:43119940 original size:23 final size:22
Alignment explanation
Indices: 43119889--43119964 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 22
43119879 TAGCAATAGT
*
43119889 AATAAT-GTAATAATAAAGTAAA
1 AATAATAGTAATAATTAA-TAAA
* *
43119911 AAAAATAGTAATACATTAATAAG
1 AATAATAGTAATA-ATTAATAAA
* * *
43119934 AATAATAATAGTATATTAATAAC
1 AATAATAGTAATA-ATTAATAAA
43119957 AATAATAG
1 AATAATAG
43119965 AAAATAATGA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
22 5 0.12
23 34 0.79
24 4 0.09
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (22 bp):
AATAATAGTAATAATTAATAAA
Found at i:43120149 original size:3 final size:3
Alignment explanation
Indices: 43119883--43120119 Score: 53
Period size: 3 Copynumber: 79.7 Consensus size: 3
43119873 TGATGATAGC
* * * * * *
43119883 AAT AGT AAT AAT -GT AAT AAT AA- AGT AAA AAA AAT AGT AAT ACATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T
* * * * *
43119928 AAT AAG AAT AAT AAT AGT -AT ATT AAT AAC AAT AAT AGAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* * * * * * *
43119973 GAC GA- AAT AAT AAT AAT AAT AA- ACT AA- AGAGT ACT AAT AGT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT
* * * * *
43120017 AAC AAT AAT -AT AAAT AAT AAT GAA- AAC AAA AAG AGA- AAT AAT AAC
1 AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT
* * * * ** *
43120062 AAT AA- CAG AAT AAA AAT AAT GAT AAT AAT AAT AAT AGC AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
43120109 AAA AAT AAT AA
1 AAT AAT AAT AA
43120120 ATAAATATAA
Statistics
Matches: 166, Mismatches: 50, Indels: 36
0.66 0.20 0.14
Matches are distributed among these distances:
2 12 0.07
3 142 0.86
4 9 0.05
5 3 0.02
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:43121099 original size:8 final size:8
Alignment explanation
Indices: 43121086--43121110 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
43121076 GGTGTTCGGC
43121086 GCAAGTGG
1 GCAAGTGG
43121094 GCAAGTGG
1 GCAAGTGG
43121102 GCAAGTGG
1 GCAAGTGG
43121110 G
1 G
43121111 GGGTAGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.52, T:0.12
Consensus pattern (8 bp):
GCAAGTGG
Found at i:43121524 original size:40 final size:40
Alignment explanation
Indices: 43121480--43121629 Score: 282
Period size: 40 Copynumber: 3.8 Consensus size: 40
43121470 GTGTTTTTAG
*
43121480 TCTGCTCCACTACTATTTAGGGAGATAAGATTGGGTGTGA
1 TCTGCTCCACTACTACTTAGGGAGATAAGATTGGGTGTGA
43121520 TCTGCTCCACTACTACTTAGGGAGATAAGATTGGGTGTGA
1 TCTGCTCCACTACTACTTAGGGAGATAAGATTGGGTGTGA
*
43121560 TCTGCTCCACTGCTACTTAGGGAGATAAGATTGGGTGTGA
1 TCTGCTCCACTACTACTTAGGGAGATAAGATTGGGTGTGA
43121600 TCTGCTCCACTACTACTTAGGGAGATAAGA
1 TCTGCTCCACTACTACTTAGGGAGATAAGA
43121630 CCTGAAATCT
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 107 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (40 bp):
TCTGCTCCACTACTACTTAGGGAGATAAGATTGGGTGTGA
Found at i:43121787 original size:134 final size:134
Alignment explanation
Indices: 43121626--43121938 Score: 581
Period size: 134 Copynumber: 2.3 Consensus size: 134
43121616 TTAGGGAGAT
* * *
43121626 AAGACCTGAAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGCTTCCATG
1 AAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGCTTCAATG
*
43121691 TACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGA
66 TACTCCACTGTAGTCAAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGA
43121756 AGGC
131 AGGC
43121760 AAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGCTTCAATG
1 AAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGCTTCAATG
43121825 TACTCCACTGTAGTCAAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGA
66 TACTCCACTGTAGTCAAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGA
43121890 AGGC
131 AGGC
*
43121894 AAGATCTGCAATCTTCAATCTATTCCACTGCCCGATACAGGGAGA
1 AAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGA
43121939 CAAGATCTGC
Statistics
Matches: 174, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
134 174 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.26
Consensus pattern (134 bp):
AAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGCTTCAATG
TACTCCACTGTAGTCAAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGA
AGGC
Found at i:43121948 original size:46 final size:45
Alignment explanation
Indices: 43121636--43121953 Score: 170
Period size: 46 Copynumber: 7.1 Consensus size: 45
43121626 AAGACCTGAA
** * *
43121636 ATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTAT-C
1 ATCTTCAATCTATTCCACTGCCAGATACAGGGAGGCA-AGATCTGC
** * * * * * *
43121681 GGCTTCCATGTACTCCACTG-TAG-T-CAGGGAGGTAAAATCTGCC
1 ATCTTCAATCTATTCCACTGCCAGATACAGGGAGGCAAGATCTG-C
* * * * *
43121724 ATCTTCGATCTGCTT-CGCTGCCAAATACAGGAAGGCAAGATCTGC
1 ATCTTCAATCT-ATTCCACTGCCAGATACAGGGAGGCAAGATCTGC
** * *
43121769 AATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTAT-C
1 -ATCTTCAATCTATTCCACTGCCAGATACAGGGAGGCA-AGATCTGC
** * * * * * *
43121815 GGCTTCAATGTACTCCACTG-TAG-T-CAAGGAGGTAAAATCTGCC
1 ATCTTCAATCTATTCCACTGCCAGATACAGGGAGGCAAGATCTG-C
* * * * *
43121858 ATCTTCGATCTGCTT-CGCTGCCAAATACAGGAAGGCAAGATCTGC
1 ATCTTCAATCT-ATTCCACTGCCAGATACAGGGAGGCAAGATCTGC
* *
43121903 AATCTTCAATCTATTCCACTGCCCGATACAGGGAGACAAGATCTGC
1 -ATCTTCAATCTATTCCACTGCCAGATACAGGGAGGCAAGATCTGC
43121949 ATCTT
1 ATCTT
43121954 GGATCCACTT
Statistics
Matches: 195, Mismatches: 61, Indels: 34
0.67 0.21 0.12
Matches are distributed among these distances:
41 6 0.03
42 17 0.09
43 26 0.13
44 8 0.04
45 44 0.23
46 90 0.46
47 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.26
Consensus pattern (45 bp):
ATCTTCAATCTATTCCACTGCCAGATACAGGGAGGCAAGATCTGC
Found at i:43122098 original size:132 final size:132
Alignment explanation
Indices: 43121936--43122694 Score: 1337
Period size: 132 Copynumber: 5.8 Consensus size: 132
43121926 CGATACAGGG
43121936 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
1 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
* *
43122001 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGTGATCTATTTCGCCACCAATATGG
66 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
43122066 GA
131 GA
*
43122068 AGACAAGATCTGCATATTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
1 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
43122133 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
66 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
43122198 GA
131 GA
* * * *
43122200 AGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGA--TGCTACCTTCGA
1 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
* *
43122263 TCTACTTCATGCCAATACATGAAGACAATATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
66 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
43122328 GA
131 GA
43122330 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
1 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
43122395 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
66 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
43122460 GA
131 GA
* * * * *
43122462 AGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGATCTGCTACCTTCGA
1 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
*
43122527 TCTACTTCATGCCAATACATGAAGAC-A-ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
66 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
43122590 GA
131 GA
43122592 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
1 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
* *
43122657 TCTGCTTCACGCCAATACATGAAGACAAGATCTACTTT
66 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
43122695 AATGACTTCA
Statistics
Matches: 593, Mismatches: 30, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
130 246 0.41
131 2 0.00
132 345 0.58
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (132 bp):
AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
GA
Found at i:43122403 original size:262 final size:262
Alignment explanation
Indices: 43121936--43122694 Score: 1378
Period size: 262 Copynumber: 2.9 Consensus size: 262
43121926 CGATACAGGG
* * * *
43121936 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
1 AGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGA-CTGCTACCTTCGA
* * *
43122001 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGTGATCTATTTCGCCACCAATATGG
65 TCTACTTCATGCCAATACATGAAGACAA-ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
*
43122066 GAAGACAAGATCTGCATATTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTC
129 GAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTC
43122131 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
194 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
43122196 GGGA
259 GGGA
43122200 AGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGA-TGCTACCTTCGAT
1 AGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGACTGCTACCTTCGAT
43122264 CTACTTCATGCCAATACATGAAGACAATATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGG
66 CTACTTCATGCCAATACATGAAGACAA-ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGG
43122329 AAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCG
130 AAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCG
43122394 ATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATG
195 ATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATG
43122459 GGA
260 GGA
43122462 AGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGATCTGCTACCTTCGA
1 AGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGA-CTGCTACCTTCGA
43122527 TCTACTTCATGCCAATACATGAAGAC-AATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGG
65 TCTACTTCATGCCAATACATGAAGACAAATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGG
43122591 AAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCG
130 AAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCG
* *
43122656 ATCTGCTTCACGCCAATACATGAAGACAAGATCTACTTT
195 ATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
43122695 AATGACTTCA
Statistics
Matches: 482, Mismatches: 11, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
262 395 0.82
263 1 0.00
264 86 0.18
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (262 bp):
AGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGACTGCTACCTTCGAT
CTACTTCATGCCAATACATGAAGACAAATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGA
AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
GA
Found at i:43122673 original size:394 final size:394
Alignment explanation
Indices: 43121936--43122694 Score: 1333
Period size: 394 Copynumber: 1.9 Consensus size: 394
43121926 CGATACAGGG
43121936 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
1 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
* *
43122001 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGTGATCTATTTCGCCACCAATATGG
66 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
* * * *
43122066 GAAGACAAGATCTGCATATTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTC
131 GAAGACAAGATCTGCATATTCGATCCACTTCCTACCAATATAGAAAGATAGGACCTGCTACCTTC
43122131 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
196 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
43122196 GGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGATGCTACCTTC
261 GGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGATGCTACCTTC
* * *
43122261 GATCTACTTCATGCCAATACATGAAGACAATATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
326 GATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTGCGATCTACTTCGCCACCAATAT
43122326 GGGA
391 GGGA
43122330 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
1 AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
43122395 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
66 TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
* *
43122460 GAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGATCTGCTACCTTC
131 GAAGACAAGATCTGCATATTCGATCCACTTCCTACCAATATAGAAAGATAGGACCTGCTACCTTC
*
43122525 GATCTACTTCATGCCAATACATGAAGAC-A-ATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
196 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
* * * *
43122588 GGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCT
261 GGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGA--TGCTACCT
*
43122653 TCGATCTGCTTCACGCCAATACATGAAGACAAGATCTACTTT
324 TCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTT
43122695 AATGACTTCA
Statistics
Matches: 346, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
392 86 0.25
393 1 0.00
394 259 0.75
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (394 bp):
AGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
TCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGG
GAAGACAAGATCTGCATATTCGATCCACTTCCTACCAATATAGAAAGATAGGACCTGCTACCTTC
GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
GGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGATGCTACCTTC
GATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTGCGATCTACTTCGCCACCAATAT
GGGA
Found at i:43161107 original size:3 final size:3
Alignment explanation
Indices: 43161099--43161162 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
43161089 TGTGTTCAAA
*
43161099 AAT AAT AAT AAT AAT AAT AAT AAT AAT -GT AGAT AGAT ACAT AA- AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT A-AT AAT AAT
*
43161144 AAT GAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
43161163 ACTAAGGAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 7 0.13
3 37 0.70
4 9 0.17
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:43162418 original size:23 final size:21
Alignment explanation
Indices: 43162366--43162423 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 21
43162356 GGGTTTGTAA
* *
43162366 ATTGGGCTCAGGTAGTTTTAGG
1 ATTGGGCT-AGGTTGGTTTAGG
43162388 ATTGGGCTAGGTTGGTTTAGGG
1 ATTGGGCTAGGTTGGTTTA-GG
43162410 TATTGGGCTAGGTT
1 -ATTGGGCTAGGTT
43162424 AGTTGGGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 9 0.28
22 10 0.31
23 13 0.41
ACGTcount: A:0.16, C:0.07, G:0.40, T:0.38
Consensus pattern (21 bp):
ATTGGGCTAGGTTGGTTTAGG
Found at i:43162627 original size:41 final size:41
Alignment explanation
Indices: 43162581--43162728 Score: 260
Period size: 41 Copynumber: 3.6 Consensus size: 41
43162571 CAGGCTTAGC
43162581 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
* * *
43162622 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATTAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
*
43162663 GCCTAGCAGGCTAAGTGCCGGTGAACTGACTCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
43162704 GCCTAGCAGGCTAAGTGCCGGTGAA
1 GCCTAGCAGGCTAAGTGCCGGTGAA
43162729 TCTGTTTAAA
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 100 1.00
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (41 bp):
GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
Found at i:43162709 original size:82 final size:83
Alignment explanation
Indices: 43162581--43162732 Score: 288
Period size: 82 Copynumber: 1.8 Consensus size: 83
43162571 CAGGCTTAGC
43162581 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAGCCTAGCAGGCTAAGTGCCGGTG-
1 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAGCCTAGCAGGCTAAGTGCCGGTGA
43162645 ATCTGAATTAGGCTATAA
66 ATCTGAATTAGGCTATAA
*
43162663 GCCTAGCAGGCTAAGTGCCGGTGAACTGACTCAGGTTATAAGCCTAGCAGGCTAAGTGCCGGTGA
1 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAGCCTAGCAGGCTAAGTGCCGGTGA
43162728 ATCTG
66 ATCTG
43162733 TTTAAATTAA
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
82 63 0.93
83 5 0.07
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (83 bp):
GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAGCCTAGCAGGCTAAGTGCCGGTGA
ATCTGAATTAGGCTATAA
Found at i:43162950 original size:36 final size:35
Alignment explanation
Indices: 43162909--43163009 Score: 91
Period size: 36 Copynumber: 2.9 Consensus size: 35
43162899 TATATTTAGA
*
43162909 TATATATGTATGCATTCGGCATATGTGGATT-ATAAG
1 TATATATGTATGCATT-GGCATATGTAG-TTGATAAG
* *
43162945 TATATATG--TGCATTGACACATGTAGTTGATAAG
1 TATATATGTATGCATTGGCATATGTAGTTGATAAG
* * * *
43162978 TATAAATATATGCTTTTGGCATATGTATTTGA
1 TATATATGTATGC-ATTGGCATATGTAGTTGA
43163010 AAAATCATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
32 2 0.04
33 19 0.37
34 6 0.12
35 3 0.06
36 22 0.42
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.41
Consensus pattern (35 bp):
TATATATGTATGCATTGGCATATGTAGTTGATAAG
Found at i:43169248 original size:43 final size:43
Alignment explanation
Indices: 43169187--43169365 Score: 152
Period size: 43 Copynumber: 4.2 Consensus size: 43
43169177 ATTAAAACGT
*
43169187 CGCTAAAGACCATGACCTTTAGCGACGCTTTTCTCACAAAAGC
1 CGCTAAAAACCATGACCTTTAGCGACGCTTTTCTCACAAAAGC
* * * *
43169230 CGCTAAAAACCAGGACCTTTAGTGGCACTTTTC-CTA-AAAATGC
1 CGCTAAAAACCATGACCTTTAGCGACGCTTTTCTC-ACAAAA-GC
* * * *
43169273 CGCTAAAGACCAAGACCTTTAGC-AGCGCTTTTTCCCACAAACGC
1 CGCTAAAAACCATGACCTTTAGCGA-CGC-TTTTCTCACAAAAGC
* * * * * *
43169317 TGCTAAAAA-CATGATCTTTTGCAACGC-TTTATCACAAACGC
1 CGCTAAAAACCATGACCTTTAGCGACGCTTTTCTCACAAAAGC
43169358 CGCTAAAA
1 CGCTAAAA
43169366 GTACAATTCT
Statistics
Matches: 110, Mismatches: 19, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
41 19 0.17
42 5 0.05
43 66 0.60
44 16 0.15
45 4 0.04
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.24
Consensus pattern (43 bp):
CGCTAAAAACCATGACCTTTAGCGACGCTTTTCTCACAAAAGC
Found at i:43171445 original size:40 final size:40
Alignment explanation
Indices: 43171382--43171466 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
43171372 TAGCTTGAAC
* * *
43171382 ATCAACACTTCAATATTTAATATGTAAGGAATTATCAAAA
1 ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
* *
43171422 ATCAACATTTCAATAATTT-ATATGCAAGAAATTAACACAA
1 ATCAACACTTCAAT-ATTTAATATGCAAGAAATTAACAAAA
43171462 ATCAA
1 ATCAA
43171467 TCTTACAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (40 bp):
ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
Found at i:43171640 original size:86 final size:85
Alignment explanation
Indices: 43171542--43171729 Score: 252
Period size: 86 Copynumber: 2.2 Consensus size: 85
43171532 GGCATTAGGG
* * * * **
43171542 CTAAATCTTCAATTTCTATAACGATTTATATGCAACAAATTAACAAAAATCAATGGTTCAAGTTC
1 CTAAATTTTCAATTT-TATAACAACTTATATGCAACAAATTAACAAAAATAAATGGACCAAGTTC
* *
43171607 ATGTATTTACCAAAAATCAGA
65 ATGCATTTACCAAAAAGCAGA
*
43171628 CT-AATTTGTCAATATTTATAACAACTTATATGCAACAAATTAGCAAAAATAAATGGACCAAGTT
1 CTAAATTT-TCAAT-TTTATAACAACTTATATGCAACAAATTAACAAAAATAAATGGACCAAGTT
*
43171692 CATGCATTTACCAACAAGCAGA
64 CATGCATTTACCAAAAAGCAGA
43171714 CTAAATTTTCAATTTT
1 CTAAATTTTCAATTTT
43171730 CAATTTTTAA
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
85 7 0.08
86 75 0.84
87 7 0.08
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (85 bp):
CTAAATTTTCAATTTTATAACAACTTATATGCAACAAATTAACAAAAATAAATGGACCAAGTTCA
TGCATTTACCAAAAAGCAGA
Found at i:43171992 original size:86 final size:87
Alignment explanation
Indices: 43171825--43171994 Score: 200
Period size: 86 Copynumber: 2.0 Consensus size: 87
43171815 ATTTCAGCAA
* * * * * * * *
43171825 TTTACATGCAAAAAATTAGCAAAAATTAACAGTTCATGTATAATGTATTTACCAAAAACCGGACC
1 TTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTCACCAAAAACCAGACC
*
43171890 AACTTGTCAATTTTTATAACAT
66 AAATTGTCAATTTTTATAACAT
* * *
43171912 TTTAAATGCAACAAATTAACACAAATTAACAATACAAGT-TCATATATTCACCAAAAACCAG-CC
1 TTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTCACCAAAAACCAGACC
*
43171975 TAAATTTTCAATTTTTATAA
66 -AAATTGTCAATTTTTATAA
43171995 AATAAGAGGA
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
85 2 0.03
86 35 0.51
87 32 0.46
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (87 bp):
TTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTCACCAAAAACCAGACC
AAATTGTCAATTTTTATAACAT
Found at i:43175254 original size:10 final size:10
Alignment explanation
Indices: 43175206--43175266 Score: 61
Period size: 10 Copynumber: 5.8 Consensus size: 10
43175196 AAAATAAAAG
43175206 TTTAAAATCTT
1 TTTAAAATC-T
* *
43175217 TTTTAAATTT
1 TTTAAAATCT
43175227 TTTAAAAAT-T
1 TTT-AAAATCT
43175237 TTTAAAATCT
1 TTTAAAATCT
43175247 TTTAAAATTCAT
1 TTTAAAA-TC-T
43175259 TTTAAAAT
1 TTTAAAAT
43175267 TTTAAATCAC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
9 5 0.12
10 16 0.37
11 14 0.33
12 8 0.19
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTAAAATCT
Found at i:43176185 original size:7 final size:7
Alignment explanation
Indices: 43176165--43176269 Score: 61
Period size: 7 Copynumber: 14.6 Consensus size: 7
43176155 ACTCTAACCC
43176165 AACCCTTA
1 AACCC-TA
*
43176173 ACCCCTA
1 AACCCTA
43176180 AACCCTA
1 AACCCTA
*
43176187 AACCTTA
1 AACCCTA
* *
43176194 AACCGTT
1 AACCCTA
*
43176201 AACCATA
1 AACCCTA
*
43176208 AACCTTAA
1 AACCCT-A
43176216 AACCCTA
1 AACCCTA
*
43176223 AACTC-A
1 AACCCTA
43176229 TAACCCTCA
1 -AACCCT-A
*
43176238 ACCCCT-
1 AACCCTA
43176244 AACCTCTA
1 AACC-CTA
*
43176252 ACCCCTA
1 AACCCTA
*
43176259 ACCCCTA
1 AACCCTA
43176266 AACC
1 AACC
43176270 TTATTTAATA
Statistics
Matches: 76, Mismatches: 15, Indels: 13
0.73 0.14 0.12
Matches are distributed among these distances:
6 4 0.05
7 53 0.70
8 18 0.24
9 1 0.01
ACGTcount: A:0.38, C:0.42, G:0.01, T:0.19
Consensus pattern (7 bp):
AACCCTA
Found at i:43176193 original size:21 final size:21
Alignment explanation
Indices: 43176160--43176269 Score: 89
Period size: 21 Copynumber: 5.2 Consensus size: 21
43176150 ACCATACTCT
43176160 AACCC-AACCCTTAACCCCTA
1 AACCCTAACCCTTAACCCCTA
* * * *
43176180 AACCCTAAACCTTAAACCGTT
1 AACCCTAACCCTTAACCCCTA
* * *
43176201 AACCATAAACCTTAAAACCCTA
1 AACCCTAACCCTT-AACCCCTA
* *
43176223 AACTCATAACCCTCAACCCCT-
1 AAC-CCTAACCCTTAACCCCTA
*
43176244 AACCTCTAACCCCTAACCCCTA
1 AACC-CTAACCCTTAACCCCTA
43176266 AACC
1 AACC
43176270 TTATTTAATA
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
20 6 0.08
21 39 0.54
22 19 0.26
23 8 0.11
ACGTcount: A:0.38, C:0.43, G:0.01, T:0.18
Consensus pattern (21 bp):
AACCCTAACCCTTAACCCCTA
Found at i:43176986 original size:41 final size:41
Alignment explanation
Indices: 43176916--43177056 Score: 122
Period size: 41 Copynumber: 3.4 Consensus size: 41
43176906 ATTAGCTTCA
* ** **
43176916 TGAAAAACGCCGTTAAAGGTTTGCACATTAACGGCGATTCC
1 TGAAAAACGCCGCTAAAGGTCAGTGCATTAACGGCGATTCC
* * ** *
43176957 TTACAAACGCCGCTAAAGGTCAGTGCATTAGTGGCGCTTCC
1 TGAAAAACGCCGCTAAAGGTCAGTGCATTAACGGCGATTCC
* * ** * *
43176998 TGAAAAACGCCGCTAAAGGTCCA-CGCATTAGCGATGCTTCT
1 TGAAAAACGCCGCTAAAGGT-CAGTGCATTAACGGCGATTCC
43177039 TGAAAAACGCCGCTAAAG
1 TGAAAAACGCCGCTAAAG
43177057 ACCCACAAGG
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
41 80 0.98
42 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (41 bp):
TGAAAAACGCCGCTAAAGGTCAGTGCATTAACGGCGATTCC
Found at i:43177144 original size:40 final size:41
Alignment explanation
Indices: 43177094--43177227 Score: 116
Period size: 40 Copynumber: 3.3 Consensus size: 41
43177084 TGGGCTTAGG
* *
43177094 TTTTTTGCGGCGTTCTTTAGAAAAACGCCGCTAATGATC-A
1 TTTTTAGCGGCGTTCTTTAGAAAAGCGCCGCTAATGATCAA
** *
43177134 TTTTTAGCGGCG--CTTTCCTAAAAGCGCCGCTAAT-ACTCGA
1 TTTTTAGCGGCGTTCTTT-AGAAAAGCGCCGCTAATGA-TCAA
* * ** * *
43177174 TCTTTAGCGGCGTT-TTTTGTGAAGCGCCGCTACTGCTCAA
1 TTTTTAGCGGCGTTCTTTAGAAAAGCGCCGCTAATGATCAA
43177214 TTTTTAGCGGCGTT
1 TTTTTAGCGGCGTT
43177228 TTTTGTACAA
Statistics
Matches: 75, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
38 5 0.07
39 16 0.21
40 51 0.68
41 3 0.04
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35
Consensus pattern (41 bp):
TTTTTAGCGGCGTTCTTTAGAAAAGCGCCGCTAATGATCAA
Found at i:43177228 original size:40 final size:40
Alignment explanation
Indices: 43177155--43177233 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
43177145 GCTTTCCTAA
*
43177155 AAGCGCCGCTAATACTCGATCTTTAGCGGCGTTTTTTGTG
1 AAGCGCCGCTAATACTCAATCTTTAGCGGCGTTTTTTGTG
* * *
43177195 AAGCGCCGCTACTGCTCAATTTTTAGCGGCGTTTTTTGT
1 AAGCGCCGCTAATACTCAATCTTTAGCGGCGTTTTTTGT
43177234 ACAAACGCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (40 bp):
AAGCGCCGCTAATACTCAATCTTTAGCGGCGTTTTTTGTG
Found at i:43178298 original size:76 final size:76
Alignment explanation
Indices: 43178203--43178402 Score: 194
Period size: 78 Copynumber: 2.6 Consensus size: 76
43178193 GAAATTAGGG
* * *
43178203 ATGTATAT-ATTAGATTCGAATATGTATGAGTATACAAGTATAAGTTCATGTTTTGATTATAAG-
1 ATGTATATGA-TAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGA-AATAAGA
43178266 TATGTAA-TTATAT
64 TATG-AATTTATAT
* * * * * * *
43178279 ATGTATATGATAGACTCGAATATATAAATAAATATACATGTATAAATTCTTGTATTGAAATTAGA
1 ATGTATATGATAGATTCGAATATGT--ATGAGTATACATGTATAAGTTCATGTATTGAAATAAGA
43178344 TATGAATTTATAT
64 TATGAATTTATAT
* *
43178357 ATGTATATG-TGAGGTTCGAATGTGTATG-GTTATACATGTATAAGTT
1 ATGTATATGAT-AGATTCGAATATGTATGAG-TATACATGTATAAGTT
43178403 TTATATTGAA
Statistics
Matches: 100, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
76 38 0.38
77 8 0.08
78 54 0.54
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.41
Consensus pattern (76 bp):
ATGTATATGATAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGAAATAAGATA
TGAATTTATAT
Found at i:43178840 original size:41 final size:41
Alignment explanation
Indices: 43178794--43178986 Score: 314
Period size: 41 Copynumber: 4.7 Consensus size: 41
43178784 CAGGCTTAGC
* *
43178794 GCCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
43178835 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
43178876 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
* * * *
43178917 GCATAGCAGGCTAAGTGCTGGTGAACTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
*
43178958 GCCTAGCAGGCTAAGTGCCAGTGAATCTG
1 GCCTAGCAGGCTAAGTGCCGGTG-ATCTG
43178987 TTTAAATTAA
Statistics
Matches: 141, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
41 137 0.97
42 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (41 bp):
GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
Found at i:43182996 original size:3 final size:3
Alignment explanation
Indices: 43182988--43183024 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
43182978 TAAAAAGCAC
43182988 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
43183025 GTTGTTCTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:43187921 original size:16 final size:16
Alignment explanation
Indices: 43187885--43187927 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
43187875 GATTATAGCT
* *
43187885 CTATTCTATTACAACT
1 CTATTCCATTACAACC
* *
43187901 TTATTTCATTACAACC
1 CTATTCCATTACAACC
43187917 CTATTCCATTA
1 CTATTCCATTA
43187928 TAGTGAAGTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (16 bp):
CTATTCCATTACAACC
Found at i:43195008 original size:6 final size:6
Alignment explanation
Indices: 43194992--43195029 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
43194982 TGGTTTTCTC
*
43194992 AAAATG GAAATG AAAATG AAAATG AAAATG AGAAATG A
1 AAAATG AAAATG AAAATG AAAATG AAAATG A-AAATG A
43195030 TTCATTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:43202386 original size:12 final size:12
Alignment explanation
Indices: 43202369--43202394 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43202359 AATAAAACGA
43202369 AGCCAATAGTTT
1 AGCCAATAGTTT
43202381 AGCCAATAGTTT
1 AGCCAATAGTTT
43202393 AG
1 AG
43202395 TGACCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (12 bp):
AGCCAATAGTTT
Found at i:43202820 original size:85 final size:86
Alignment explanation
Indices: 43202702--43202860 Score: 241
Period size: 85 Copynumber: 1.9 Consensus size: 86
43202692 GCTAAAGTTA
* * * *
43202702 AGTTAAATATTTCCGTAGGATGTATTTTAGTTAGAGTCATTGT-TTTGCTTGAGGACAAGCAAAA
1 AGTTAAATATTTCCGTAAGATGCATTTTAGTTAGAGTCATTGTGTTT-CTTGAGGAAAAACAAAA
*
43202766 TTTTAAGTGTCGGAGTACGATG
65 GTTTAAGTGTCGGAGTACGATG
*
43202788 AGTTAAAT-TTTTCGTAAGATGCATTTTAGTTAGAGTCATTGTGTTTCTTGAGGAAAAACAAAAG
1 AGTTAAATATTTCCGTAAGATGCATTTTAGTTAGAGTCATTGTGTTTCTTGAGGAAAAACAAAAG
43202852 TTTAAGTGT
66 TTTAAGTGT
43202861 GGGGATATGA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
85 55 0.83
86 11 0.17
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (86 bp):
AGTTAAATATTTCCGTAAGATGCATTTTAGTTAGAGTCATTGTGTTTCTTGAGGAAAAACAAAAG
TTTAAGTGTCGGAGTACGATG
Found at i:43205801 original size:21 final size:21
Alignment explanation
Indices: 43205756--43205828 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
43205746 TGTTAAGTCA
* * * *
43205756 TATGAGTTTCTGTTTAACCTT
1 TATGGGTTTCCGTTCAACCCT
43205777 TATGGGTTTCCGTTCAACTCC-
1 TATGGGTTTCCGTTCAAC-CCT
* *
43205798 TATGAGCTTCCGTTCAACCCT
1 TATGGGTTTCCGTTCAACCCT
*
43205819 TACGGGTTTC
1 TATGGGTTTC
43205829 TGTTTAGCAC
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 2 0.05
21 38 0.93
22 1 0.02
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (21 bp):
TATGGGTTTCCGTTCAACCCT
Found at i:43220495 original size:13 final size:13
Alignment explanation
Indices: 43220477--43220501 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43220467 ACAAACGATA
43220477 AAATTTTCACACG
1 AAATTTTCACACG
43220490 AAATTTTCACAC
1 AAATTTTCACAC
43220502 ACATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:43224216 original size:26 final size:27
Alignment explanation
Indices: 43224187--43224242 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
43224177 TAGCAACCAC
*
43224187 CAATGAAT-AGGGGAATCAGCACTTAG
1 CAATCAATCAGGGGAATCAGCACTTAG
**
43224213 CAATCCCTCAGGGGAATCAGCACTTAG
1 CAATCAATCAGGGGAATCAGCACTTAG
43224240 CAA
1 CAA
43224243 CCCCCTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (27 bp):
CAATCAATCAGGGGAATCAGCACTTAG
Found at i:43224296 original size:103 final size:103
Alignment explanation
Indices: 43224059--43224427 Score: 605
Period size: 103 Copynumber: 3.6 Consensus size: 103
43224049 TAACCGTTAT
* * *
43224059 CGGTGGATTCCGCACTTAGCAACCACCAATGAATCGGGGAATCAACACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
* * *
43224124 GAATCAGCACTTAGCAACCCCC-TTCACATTTTAGATG
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* ** * **
43224161 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAATCCCTCAGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
43224226 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
43224264 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
43224329 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* *
43224367 CGGTGGAATCAGCACTTAGAAACCATCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
43224428 TATATGCAAT
Statistics
Matches: 246, Mismatches: 20, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
102 78 0.32
103 168 0.68
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.19
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
Found at i:43225519 original size:11 final size:12
Alignment explanation
Indices: 43225491--43225524 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
43225481 GCCCAAACGT
43225491 CGAAATTTTTGAA
1 CGAAATTTTT-AA
43225504 CGAAATTTTT-A
1 CGAAATTTTTAA
43225515 CGAAATTTTT
1 CGAAATTTTT
43225525 CCGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:43235467 original size:24 final size:20
Alignment explanation
Indices: 43235425--43235465 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
43235415 TTTCTGCTTA
43235425 TATGGTTGAATCATTTTGTT
1 TATGGTTGAATCATTTTGTT
43235445 TATGGTTGAATCATTTTGTT
1 TATGGTTGAATCATTTTGTT
43235465 T
1 T
43235466 GTGGCATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.56
Consensus pattern (20 bp):
TATGGTTGAATCATTTTGTT
Found at i:43244944 original size:13 final size:13
Alignment explanation
Indices: 43244926--43244951 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43244916 CTTGCAGGGG
43244926 TATGATATTATTT
1 TATGATATTATTT
43244939 TATGATATTATTT
1 TATGATATTATTT
43244952 GTCTTGTTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATGATATTATTT
Found at i:43249379 original size:43 final size:43
Alignment explanation
Indices: 43249331--43249596 Score: 331
Period size: 43 Copynumber: 6.2 Consensus size: 43
43249321 TTCTAAAAAT
** *
43249331 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTGTCACAAAC
1 GCCGCTAAAGACCACAACCTTTAGCGGCGCTTTTGTCGCAAAC
* * * *
43249374 GCCGCTAAAGACCACGACCTTTAGTGGCGCTTCTGCCGCAAAC
1 GCCGCTAAAGACCACAACCTTTAGCGGCGCTTTTGTCGCAAAC
** *
43249417 GCCGCTAAAGACCACAACCTTTAGCAACGCTTCTGTCGCAAAC
1 GCCGCTAAAGACCACAACCTTTAGCGGCGCTTTTGTCGCAAAC
* * *
43249460 GCCGCTAAAGACCACGACCTTTAGCGGCACTTTTGTCGCAAAT
1 GCCGCTAAAGACCACAACCTTTAGCGGCGCTTTTGTCGCAAAC
* * *
43249503 GCCGTTAAAGACCACAACCTTTAGTGACGCTTTTGTCGCAAAC
1 GCCGCTAAAGACCACAACCTTTAGCGGCGCTTTTGTCGCAAAC
* *
43249546 GCCGCTATAGAACA-AACCTTTAGCGGCGC-TTT-TCGCAAAAAC
1 GCCGCTAAAGACCACAACCTTTAGCGGCGCTTTTGTCGC--AAAC
43249588 GCCGCTAAA
1 GCCGCTAAA
43249597 AACATATGCA
Statistics
Matches: 193, Mismatches: 28, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
40 4 0.02
41 3 0.02
42 25 0.13
43 161 0.83
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.21
Consensus pattern (43 bp):
GCCGCTAAAGACCACAACCTTTAGCGGCGCTTTTGTCGCAAAC
Found at i:43250526 original size:43 final size:43
Alignment explanation
Indices: 43250478--43250639 Score: 211
Period size: 43 Copynumber: 3.8 Consensus size: 43
43250468 GCGTCGCTAA
*
43250478 CTTTAGCGGCGTTTTTCCCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* *
43250521 CTTTAGCGGCGCTTTACCCACAAATGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* ** *
43250564 CTTTAGTGGCGCTTTTGTCACAAACGCCGCTAAAGAACAAG-C
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
** *
43250606 CTTTAGCGGCG-TTTCTTGCAAAAACGCCGCTAAA
1 CTTTAGCGGCGCTTT-TCCCACAAACGCCGCTAAA
43250640 AATATAACCT
Statistics
Matches: 105, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
41 3 0.03
42 27 0.26
43 75 0.71
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:43250825 original size:35 final size:35
Alignment explanation
Indices: 43250790--43250857 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
43250780 CTATGAAAAT
43250790 TTTAACTTTA-AAAGTAAATATAA-AAATTAATAAA
1 TTTAACTTTAGAAAGTAAA-ATAATAAATTAATAAA
* **
43250824 TTTAATTTTAGAATTTAAAATAATAAATTAATAA
1 TTTAACTTTAGAAAGTAAAATAATAAATTAATAA
43250858 CACAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 13 0.45
35 16 0.55
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (35 bp):
TTTAACTTTAGAAAGTAAAATAATAAATTAATAAA
Found at i:43251389 original size:23 final size:23
Alignment explanation
Indices: 43251339--43251390 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
43251329 GTTAGGTGTC
* *
43251339 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
43251362 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
43251385 AGTATG
1 AGTATG
43251391 TTCAAAGTGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:43256037 original size:33 final size:33
Alignment explanation
Indices: 43255976--43256045 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
43255966 ACTAATTAAT
* *
43255976 CTAATCCCTAAACCCTAACCTGACCCTAAATCC
1 CTAATCCCTAAACCCTAACCTAACCCTAAACCC
*
43256009 CTAATCCCTAAACCCTAA-CTCAATCCTAAACCC
1 CTAATCCCTAAACCCTAACCT-AACCCTAAACCC
43256042 CTAA
1 CTAA
43256046 ACATTATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.36, C:0.41, G:0.01, T:0.21
Consensus pattern (33 bp):
CTAATCCCTAAACCCTAACCTAACCCTAAACCC
Found at i:43256911 original size:41 final size:39
Alignment explanation
Indices: 43256865--43256982 Score: 119
Period size: 41 Copynumber: 2.9 Consensus size: 39
43256855 TTTTATTATT
*
43256865 ATTAGCGGCGTTTTTGAAAAAGCGCCGCTAAAGGCCGAAGC
1 ATTAGCGGCGTTTTTCAAAAA-CGCCGCTAAAGGCCG-AGC
* * *
43256906 ATTAGCAGCACTTTCTCAAAAACGCCGCTAAAGGCTCGAGC
1 ATTAGCGGC-GTTTTTCAAAAACGCCGCTAAAGGC-CGAGC
* ** *
43256947 ATTAACGGCGCTTTCACAAAAACGCCACTAAAGGCC
1 ATTAGCGGCG-TTTTTCAAAAACGCCGCTAAAGGCC
43256983 CCAAAAACTT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
40 1 0.02
41 53 0.82
42 11 0.17
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (39 bp):
ATTAGCGGCGTTTTTCAAAAACGCCGCTAAAGGCCGAGC
Found at i:43260756 original size:7 final size:7
Alignment explanation
Indices: 43260740--43260828 Score: 51
Period size: 7 Copynumber: 12.7 Consensus size: 7
43260730 CCTTGAATCT
*
43260740 CTAAATC
1 CTAAACC
43260747 CTAAACC
1 CTAAACC
43260754 CTAAATCC
1 CTAAA-CC
43260762 CT-AACTC
1 CTAAAC-C
43260769 CT-AACC
1 CTAAACC
43260775 CTTAAACC
1 C-TAAACC
*
43260783 TTAAATCC
1 CTAAA-CC
43260791 C--AACC
1 CTAAACC
*
43260796 TTAAACC
1 CTAAACC
* *
43260803 ATAATCC
1 CTAAACC
*
43260810 CTAATCC
1 CTAAACC
*
43260817 CTAATCC
1 CTAAACC
43260824 CTAAA
1 CTAAA
43260829 TCCATATATA
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
5 2 0.03
6 5 0.07
7 50 0.75
8 10 0.15
ACGTcount: A:0.38, C:0.37, G:0.00, T:0.25
Consensus pattern (7 bp):
CTAAACC
Found at i:43260776 original size:21 final size:21
Alignment explanation
Indices: 43260735--43260831 Score: 76
Period size: 21 Copynumber: 4.6 Consensus size: 21
43260725 CCGACCCTTG
*
43260735 AATCTCTAAATCCTAAACCCTA
1 AATCCCTAAATCCT-AACCCTA
*
43260757 AATCCCTAACTCCTAACCCTTA
1 AATCCCTAAATCCTAACCC-TA
* * *
43260779 AA-CCTTAAATCCCAACCTTA
1 AATCCCTAAATCCTAACCCTA
*
43260799 AA-CCAT-AATCCCTAATCCCT-
1 AATCCCTAAAT-CCTAA-CCCTA
43260819 AATCCCTAAATCC
1 AATCCCTAAATCC
43260832 ATATATAATT
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
19 3 0.05
20 13 0.22
21 25 0.42
22 19 0.32
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (21 bp):
AATCCCTAAATCCTAACCCTA
Found at i:43261169 original size:14 final size:14
Alignment explanation
Indices: 43261152--43261198 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
43261142 CCCTAGCCTT
43261152 TAAACCATAAACCC
1 TAAACCATAAACCC
*
43261166 TAAACCATATACCC
1 TAAACCATAAACCC
* *
43261180 TAAACCAAAAACCA
1 TAAACCATAAACCC
43261194 TAAAC
1 TAAAC
43261199 TGTAGTGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:43261438 original size:22 final size:22
Alignment explanation
Indices: 43261410--43261453 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
43261400 TTAGAAAACG
*
43261410 CCGCTAAAAGCCCTGAGCATTA
1 CCGCTAAAAGCCATGAGCATTA
*
43261432 CCGCTAAAAGTCATGAGCATTA
1 CCGCTAAAAGCCATGAGCATTA
43261454 GCGGCGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.20
Consensus pattern (22 bp):
CCGCTAAAAGCCATGAGCATTA
Found at i:43261492 original size:41 final size:41
Alignment explanation
Indices: 43261445--43261604 Score: 234
Period size: 41 Copynumber: 3.9 Consensus size: 41
43261435 CTAAAAGTCA
* *
43261445 TGAGCATTAGCGGCGCTTTCTTAAAAACGCTGCTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
*
43261486 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
*
43261527 TTAGCATTAGCGGCGCTTT-TCCAAAAACGCCGCTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCT-CAAAAACGCCGCTAAAGCCC
* *
43261568 TTAGCATTAGCGGCGC-TTCGCCAAAAACGCCGCTAAA
1 TGAGCATTAGCGGCGCTTTC-TCAAAAACGCCGCTAAA
43261605 TCCCCAAAAA
Statistics
Matches: 110, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
40 2 0.02
41 108 0.98
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (41 bp):
TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
Found at i:43265030 original size:16 final size:17
Alignment explanation
Indices: 43265009--43265045 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
43264999 TTTGGTTCGC
43265009 TGTATT-GGATTAGAGG
1 TGTATTGGGATTAGAGG
43265025 TGTATTGGGATTAGAGG
1 TGTATTGGGATTAGAGG
43265042 TGTA
1 TGTA
43265046 ATAGCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (17 bp):
TGTATTGGGATTAGAGG
Found at i:43265302 original size:18 final size:17
Alignment explanation
Indices: 43265281--43265315 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43265271 TTATTATTAA
*
43265281 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
43265299 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
43265316 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:43265362 original size:61 final size:61
Alignment explanation
Indices: 43265296--43265483 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
43265286 TTTTAATTAA
43265296 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * *
43265357 AATATATGATACT-ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATCAT
*
43265416 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
43265477 AATATAT
1 AATATAT
43265484 GATACTATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 30 0.31
60 23 0.24
61 37 0.39
62 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:43265429 original size:14 final size:15
Alignment explanation
Indices: 43265380--43265431 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
43265370 ATAAAATATA
43265380 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
43265395 TATTAAATATATTAT
1 AATTAAATATATTAT
43265410 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
43265423 AATTTAATA
1 AATTAAATA
43265432 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:43265477 original size:120 final size:121
Alignment explanation
Indices: 43265264--43265556 Score: 518
Period size: 120 Copynumber: 2.4 Consensus size: 121
43265254 ATCATATTTA
43265264 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
43265329 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT-
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* *
43265384 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
43265449 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* *
43265505 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
43265557 TAAAATAATT
Statistics
Matches: 165, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
120 163 0.99
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
Found at i:43265603 original size:101 final size:93
Alignment explanation
Indices: 43265497--43265779 Score: 317
Period size: 91 Copynumber: 3.0 Consensus size: 93
43265487 ACTATAAAAG
* * * *
43265497 ATAATTTGAAATAATTAATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATTTAAA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTT---
* *
43265561 ATAATTATAACTAATAAATTATCTTATATGAATTTGT
62 -T--CT-TAA-TAATAAATTATCTTATATGAATTTAT
* *
43265598 ATAATTTAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
* *
43265661 GATAATAAATTTTCTTATATGAATTTAT
66 AATAATAAATTATCTTATATGAATTTAT
* *
43265689 ACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
43265752 AATAATAAAATGT-TCTTATATGAATTTA
66 AATAAT-AAAT-TATCTTATATGAATTTA
43265780 CTAAAATCAA
Statistics
Matches: 164, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
91 88 0.54
92 21 0.13
93 2 0.01
95 1 0.01
99 1 0.01
100 3 0.02
101 48 0.29
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (93 bp):
ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
AATAATAAATTATCTTATATGAATTTAT
Found at i:43265626 original size:26 final size:28
Alignment explanation
Indices: 43265597--43265657 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
43265587 TATGAATTTG
*
43265597 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
43265623 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
43265651 TAAAATT
1 TATAATT
43265658 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:43265655 original size:47 final size:46
Alignment explanation
Indices: 43265604--43265747 Score: 113
Period size: 47 Copynumber: 3.1 Consensus size: 46
43265594 TTGTATAATT
43265604 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
43265651 TAAAAT--TCT-TGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
43265695 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
43265742 TAAAAT
1 TAAAAT
43265748 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.19
46 12 0.17
47 15 0.21
48 9 0.12
49 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:43265667 original size:91 final size:90
Alignment explanation
Indices: 43265572--43265779 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 90
43265562 TAATTATAAC
* * * *
43265572 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
43265637 AATATATAATTTCATAAAATTCTTGA
65 AATATATAATTTCATAAAATTCTTAA
43265663 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAA-TTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
43265728 GATATATAATTTCATAAAATTCTTAA
65 AATATATAATTTCATAAAATTCTTAA
43265754 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAAT-TTCTTATATGAATTTA
43265780 CTAAAATCAA
Statistics
Matches: 108, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
91 87 0.81
92 21 0.19
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATA
ATATATAATTTCATAAAATTCTTAA
Found at i:43265739 original size:44 final size:43
Alignment explanation
Indices: 43265597--43265739 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
43265587 TATGAATTTG
* *
43265597 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
43265641 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
43265688 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
43265732 TATAATTT
1 TATAATTT
43265740 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:43265754 original size:47 final size:47
Alignment explanation
Indices: 43265622--43265760 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
43265612 TTATTATTAC
* *
43265622 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
43265669 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
43265713 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
43265760 A
1 A
43265761 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:43271715 original size:26 final size:26
Alignment explanation
Indices: 43271659--43271709 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
43271649 TTGGCATTTA
43271659 TTTTTGTCATTGATATTAGCTGCAGG
1 TTTTTGTCATTGATATTAGCTGCAGG
*
43271685 TTTTTGTCATTGGTATTAGCTGCAG
1 TTTTTGTCATTGATATTAGCTGCAG
43271710 TATTTTACGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.47
Consensus pattern (26 bp):
TTTTTGTCATTGATATTAGCTGCAGG
Found at i:43276223 original size:120 final size:120
Alignment explanation
Indices: 43276026--43277008 Score: 1885
Period size: 120 Copynumber: 8.2 Consensus size: 120
43276016 TTTTCAAGTT
43276026 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
43276091 TAATATAAGAACATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
43276146 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
43276211 TAATATAAGAACATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
43276266 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
43276331 TAATATAAGAACATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
43276386 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
43276451 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
43276506 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
43276571 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
*
43276626 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
43276691 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
43276746 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
43276811 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
* *
43276866 TTATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
43276931 TAATATAATAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
43276986 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
43277009 TAAATATGAT
Statistics
Matches: 852, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 852 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
Found at i:43276625 original size:18 final size:17
Alignment explanation
Indices: 43276597--43276631 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43276587 ATTATTAAGA
*
43276597 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43276614 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43276632 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43276865 original size:18 final size:17
Alignment explanation
Indices: 43276837--43276871 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
43276827 ATTATTAAGA
43276837 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
43276854 ATTTTAATTAAATTATAT
1 ATTTT-ATTAAATTATAT
43276872 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:43277252 original size:16 final size:16
Alignment explanation
Indices: 43277227--43277295 Score: 111
Period size: 16 Copynumber: 4.2 Consensus size: 16
43277217 GATTAGCTAT
*
43277227 TACACATCTAATCCAA
1 TACACCTCTAATCCAA
43277243 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
43277260 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
43277276 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
43277292 TACA
1 TACA
43277296 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
16 33 0.67
17 16 0.33
ACGTcount: A:0.38, C:0.36, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:43277270 original size:33 final size:32
Alignment explanation
Indices: 43277227--43277295 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
43277217 GATTAGCTAT
43277227 TACACATCTAATCCAATACACCTCTAATCCCAA
1 TACACATCTAATCCAATACACCTCTAAT-CCAA
* *
43277260 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACATCTAATCCAATACACCTCTAATCCAA
43277292 TACA
1 TACA
43277296 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 8 0.24
33 26 0.76
ACGTcount: A:0.38, C:0.36, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACATCTAATCCAATACACCTCTAATCCAA
Found at i:43283520 original size:26 final size:26
Alignment explanation
Indices: 43283484--43283537 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
43283474 TTTGTCATTC
43283484 TACATGTAATTTTTAAATTGATTGAA
1 TACATGTAATTTTTAAATTGATTGAA
43283510 TACATGTAATTTTTAAATTGATTGAA
1 TACATGTAATTTTTAAATTGATTGAA
43283536 TA
1 TA
43283538 AATAAAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (26 bp):
TACATGTAATTTTTAAATTGATTGAA
Found at i:43283546 original size:26 final size:26
Alignment explanation
Indices: 43283491--43283546 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
43283481 TTCTACATGT
* **
43283491 AATTTTTAAATTGATTGAATACATGT
1 AATTTTTAAATTGATTGAATAAATAA
43283517 AATTTTTAAATTGATTGAATAAATAA
1 AATTTTTAAATTGATTGAATAAATAA
43283543 AATT
1 AATT
43283547 CCATAATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (26 bp):
AATTTTTAAATTGATTGAATAAATAA
Found at i:43295016 original size:21 final size:23
Alignment explanation
Indices: 43294961--43295017 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
43294951 GTACTTCAAA
43294961 TTTGTGAGATTATAATTGAATAATC
1 TTTGTGAGATTATAATT--ATAATC
* *
43294986 ATTG-GCGATTATAATT-TAAT-
1 TTTGTGAGATTATAATTATAATC
43295006 TTTGTGAGATTA
1 TTTGTGAGATTA
43295018 AGCTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
20 3 0.11
21 10 0.37
24 11 0.41
25 3 0.11
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.46
Consensus pattern (23 bp):
TTTGTGAGATTATAATTATAATC
Found at i:43301381 original size:22 final size:22
Alignment explanation
Indices: 43301331--43301383 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
43301321 GTCCACGTAT
* *
43301331 AATTTATAAAAATTAGTAAAAA
1 AATTTAAAAAAATTAATAAAAA
*
43301353 AAATTAAAAAAATTAATAAAAA
1 AATTTAAAAAAATTAATAAAAA
**
43301375 CTTTTAAAA
1 AATTTAAAA
43301384 TATTTATTCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
AATTTAAAAAAATTAATAAAAA
Found at i:43302358 original size:21 final size:21
Alignment explanation
Indices: 43302328--43302368 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
43302318 TTCGGGCTTC
43302328 TACTCAGCCTGATTGATGGAA
1 TACTCAGCCTGATTGATGGAA
*
43302349 TACTCGGCCTGATTGATGGA
1 TACTCAGCCTGATTGATGGA
43302369 CAAGTCTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (21 bp):
TACTCAGCCTGATTGATGGAA
Found at i:43303879 original size:11 final size:11
Alignment explanation
Indices: 43303859--43303949 Score: 79
Period size: 11 Copynumber: 8.6 Consensus size: 11
43303849 TTAAAAATTA
43303859 AAAAAGTATTTT
1 AAAAA-TATTTT
43303871 AAAAATATTTT
1 AAAAATATTTT
43303882 --AAA-A--TT
1 AAAAATATTTT
*
43303888 AAAAAAATTTT
1 AAAAATATTTT
*
43303899 AAAAGTATTTT
1 AAAAATATTTT
43303910 AAAAATATTTT
1 AAAAATATTTT
*
43303921 -AAAAT-TTTAA
1 AAAAATATTT-T
43303931 AAAAAGTATTTT
1 AAAAA-TATTTT
43303943 AAAAATA
1 AAAAATA
43303950 AAAAAATAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
6 2 0.03
8 4 0.06
9 7 0.11
10 5 0.08
11 33 0.51
12 11 0.17
13 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:43303896 original size:39 final size:40
Alignment explanation
Indices: 43303851--43303935 Score: 136
Period size: 39 Copynumber: 2.1 Consensus size: 40
43303841 AATTTATTTT
43303851 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA-TTAA
1 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTTAA
**
43303890 AAAAATTTTAAAAGTATTTTAAAAATATTTTAAAATTTTAA
1 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA-TTTAA
43303931 AAAAA
1 AAAAA
43303936 GTATTTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 33 0.79
41 9 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (40 bp):
AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTTAA
Found at i:43303954 original size:22 final size:21
Alignment explanation
Indices: 43303910--43303955 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
43303900 AAAGTATTTT
* *
43303910 AAAAATATTTTAAAATTTTAAA
1 AAAAATATTTTAAAA-ATAAAA
*
43303932 AAAAGTATTTTAAAAATAAAA
1 AAAAATATTTTAAAAATAAAA
43303953 AAA
1 AAA
43303956 TAAAAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAAATATTTTAAAAATAAAA
Found at i:43304412 original size:20 final size:19
Alignment explanation
Indices: 43304384--43304422 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
43304374 TTAAAAGTCC
43304384 AAAAAATATATATTTAATA
1 AAAAAATATATATTTAATA
43304403 AAAAATATATATATTTAATA
1 AAAAA-ATATATATTTAATA
43304423 TATAATTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAATATATATTTAATA
Found at i:43313146 original size:24 final size:25
Alignment explanation
Indices: 43313114--43313160 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
43313104 AAATCAAACT
43313114 TAATCACTTTAA-TATTAAATTAATA
1 TAATCAC-TTAATTATTAAATTAATA
*
43313139 TAAT-ACTTAATTATTAGATTAA
1 TAATCACTTAATTATTAAATTAA
43313161 ATTTAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (25 bp):
TAATCACTTAATTATTAAATTAATA
Found at i:43315250 original size:19 final size:21
Alignment explanation
Indices: 43315228--43315273 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
43315218 TAATTAAAAC
43315228 AACTAAATA-A-GATTAATTA
1 AACTAAATACATGATTAATTA
*
43315247 AACTATATACATGATTAATTA
1 AACTAAATACATGATTAATTA
*
43315268 AGCTAA
1 AACTAA
43315274 TCATTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 8 0.36
20 1 0.05
21 13 0.59
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (21 bp):
AACTAAATACATGATTAATTA
Found at i:43317680 original size:33 final size:32
Alignment explanation
Indices: 43317636--43317778 Score: 88
Period size: 33 Copynumber: 4.3 Consensus size: 32
43317626 TGATGATTAT
*
43317636 ATGTAAAACCATAGCTGGGCTATGACATTCTG
1 ATGTAAGACCATAGCTGGGCTATGACATTCTG
* * * * *
43317668 ATGATAAGACCATAACTGGGTTATGGCACTATG
1 ATG-TAAGACCATAGCTGGGCTATGACATTCTG
* * * * * * * *
43317701 AACGTAAGACCATGGTTAGACCATGACAGTGTTTAT
1 -ATGTAAGACCATAGCTGGGCTATGACA-T-TCT-G
* *
43317737 ATGTAAGACCATAGCTGGGCTATGGCATTCTA
1 ATGTAAGACCATAGCTGGGCTATGACATTCTG
43317769 ATGATAAGAC
1 ATG-TAAGAC
43317779 TATAATTGAG
Statistics
Matches: 78, Mismatches: 27, Indels: 11
0.67 0.23 0.09
Matches are distributed among these distances:
32 6 0.08
33 47 0.60
34 3 0.04
35 22 0.28
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGCTATGACATTCTG
Found at i:43335338 original size:5 final size:5
Alignment explanation
Indices: 43335324--43335390 Score: 127
Period size: 5 Copynumber: 13.6 Consensus size: 5
43335314 AAATCTTAAG
43335324 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
43335373 TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TAT
43335391 TAATGTATAA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.06
5 58 0.94
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:43335439 original size:32 final size:32
Alignment explanation
Indices: 43335403--43335469 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
43335393 ATGTATAATA
* *
43335403 AAACAAAAT-AAAAGAAATAGAAATAGAAAAAG
1 AAACAAAATGAAAAGAAACAGAAAGA-AAAAAG
* *
43335435 AAACAAAGTGAAACGAAACAGAAAGAAAAAAG
1 AAACAAAATGAAAAGAAACAGAAAGAAAAAAG
43335467 AAA
1 AAA
43335470 GAAGGAGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.73, C:0.06, G:0.15, T:0.06
Consensus pattern (32 bp):
AAACAAAATGAAAAGAAACAGAAAGAAAAAAG
Found at i:43336170 original size:24 final size:24
Alignment explanation
Indices: 43336143--43336189 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
43336133 ATTGAAATAG
43336143 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
43336167 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
43336190 GATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:43336454 original size:40 final size:40
Alignment explanation
Indices: 43336409--43336485 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
43336399 AGGTACCAAT
** *
43336409 TTACTTCGGTTTAACCAATGAGACACTGGGTGTCAAATTA
1 TTACTTCGAATTAACCAATGAGACACTGGGTGCCAAATTA
* * *
43336449 TTACTTTGAATTATCCAATGAGGCACTGGGTGCCAAA
1 TTACTTCGAATTAACCAATGAGACACTGGGTGCCAAA
43336486 CTAGTGTGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (40 bp):
TTACTTCGAATTAACCAATGAGACACTGGGTGCCAAATTA
Found at i:43340093 original size:14 final size:14
Alignment explanation
Indices: 43340074--43340104 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43340064 AGGAGGACTC
*
43340074 AAAATATCAAAATT
1 AAAATATAAAAATT
43340088 AAAATATAAAAATT
1 AAAATATAAAAATT
43340102 AAA
1 AAA
43340105 TTTGAAATTT
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:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:43341006 original size:180 final size:180
Alignment explanation
Indices: 43340704--43341047 Score: 670
Period size: 180 Copynumber: 1.9 Consensus size: 180
43340694 AAAAAATCAA
* *
43340704 TATATGCATAATTCGAGCCGAATGTGATTTTGGATGGGATGATAACATGAAAACGATCACATGTG
1 TATATGCACAATTCGAGCCAAATGTGATTTTGGATGGGATGATAACATGAAAACGATCACATGTG
43340769 ATAAATCGGCATATGATACGACAGTGATGATAATATATTTATATATATGTTAAATATATCTCAGC
66 ATAAATCGGCATATGATACGACAGTGATGATAATATATTTATATATATGTTAAATATATCTCAGC
43340834 ATTATATTCTTTACTTGTTATCCTAATTTTGTATGTGATAAATAGCAAAT
131 ATTATATTCTTTACTTGTTATCCTAATTTTGTATGTGATAAATAGCAAAT
43340884 TATATGCACAATTCGAGCCAAATGTGATTTTGGATGGGATGATAACATGAAAACGATCACATGTG
1 TATATGCACAATTCGAGCCAAATGTGATTTTGGATGGGATGATAACATGAAAACGATCACATGTG
43340949 ATAAATCGGCATATGATACGACAGTGATGATAATATATTTATATATATGTTAAATATATCTCAGC
66 ATAAATCGGCATATGATACGACAGTGATGATAATATATTTATATATATGTTAAATATATCTCAGC
43341014 ATTATATTCTTTACTTGTTATCCTAATTTTGTAT
131 ATTATATTCTTTACTTGTTATCCTAATTTTGTAT
43341048 AATATCCAAT
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 162 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (180 bp):
TATATGCACAATTCGAGCCAAATGTGATTTTGGATGGGATGATAACATGAAAACGATCACATGTG
ATAAATCGGCATATGATACGACAGTGATGATAATATATTTATATATATGTTAAATATATCTCAGC
ATTATATTCTTTACTTGTTATCCTAATTTTGTATGTGATAAATAGCAAAT
Found at i:43341635 original size:46 final size:46
Alignment explanation
Indices: 43341585--43341689 Score: 165
Period size: 46 Copynumber: 2.3 Consensus size: 46
43341575 ACCAATTATA
* **
43341585 TGGTGTAATACTAGTTATGCACTTGGACGATATTGTAGTTAACATG
1 TGGTGTACTACTAGTTATGCACTTGGAAAATATTGTAGTTAACATG
*
43341631 TGGTGTACTACTAGTTATGCACTTGGAAAATATTGTAGTTATCATG
1 TGGTGTACTACTAGTTATGCACTTGGAAAATATTGTAGTTAACATG
*
43341677 CGGTGTACTACTA
1 TGGTGTACTACTA
43341690 ATTTGTAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (46 bp):
TGGTGTACTACTAGTTATGCACTTGGAAAATATTGTAGTTAACATG
Found at i:43343919 original size:98 final size:98
Alignment explanation
Indices: 43343750--43343944 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
43343740 ATACAATAAA
*
43343750 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
43343815 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* *
43343848 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
43343913 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
43343945 CATGATTTTT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:43345041 original size:19 final size:19
Alignment explanation
Indices: 43345017--43345108 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
43345007 AATCATATAT
43345017 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
43345036 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
43345055 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
43345074 TCTAGGATTACATATCATA
1 TCTAAGATTGCATATCATA
43345093 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
43345109 CTCAAAAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 65 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Done.