Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 128 of 373
Found at i:42285181 original size:46 final size:47
Alignment explanation
Indices: 42285081--42285494 Score: 249
Period size: 47 Copynumber: 8.7 Consensus size: 47
42285071 ACTGTTACAA
* ** * * *
42285081 CCAGTATAAGACCATGTCCAGGACATGGCATTGGCATTGAGATGAGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAGATG-TAG
*
42285129 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTTGAGATGTAAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAGATGT-AG
* * *
42285175 CCAGTGTAAGA-CATGTCTAGGACAT-GCATCTG-CTACGAGATGT-G
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-TGAGATGTAG
** * * *
42285219 TTAGTGTAAGACCATGTCTGGGGCATGGCATTGGCACGTAT-AGAGGT-G
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-C-T-TGAGATGTAG
* * ** * *
42285267 TCAGTGTAAGACCATGTCTAGGACATGGCATCGGTATGGATATGTGAGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAGATGT---AG
* * * * ** ** ** *
42285317 CTAGTGTAAGACCATGTTTGAGACATGGCGTTAGCCTCAATTTCAATAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAGAT--GTAG
* * * * *
42285366 TCAATGTAAGACCATGTTTGGGACATGGCAT-TGACTTGATAGATG-AG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTG--AGATGTAG
*
42285413 CCAGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGATGGATG-AG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGA--GATGTAG
* *
42285460 CCAGTGTAAGACTATCTCTGGGACATGGCATCGGC
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
42285495 ATCATACCCT
Statistics
Matches: 286, Mismatches: 60, Indels: 40
0.74 0.16 0.10
Matches are distributed among these distances:
44 10 0.03
45 15 0.05
46 63 0.22
47 84 0.29
48 50 0.17
49 30 0.10
50 33 0.12
52 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (47 bp):
CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAGATGTAG
Found at i:42289242 original size:42 final size:42
Alignment explanation
Indices: 42289196--42289316 Score: 163
Period size: 42 Copynumber: 2.9 Consensus size: 42
42289186 TATCATACTA
* *
42289196 ATGCCATATCCAAGATATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACATGGAATCTCATATCG
* * *
42289238 ATGCCAATAGCCCAGCTATGGTCTTACA-CGAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACATGGAATCTCATATCG
* *
42289280 ATGTCATATCCCAGATATGGTCTTACATGCAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACATGGAATCTCA
42289317 ACTAACCCTA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 20 0.30
42 28 0.42
43 19 0.28
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACATGGAATCTCATATCG
Found at i:42291338 original size:44 final size:44
Alignment explanation
Indices: 42291275--42291366 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
42291265 AATAAAAGAA
* *
42291275 ATTTCTATAACTTTGGAAATAATTTAATTGAGTCAATTTATTCG
1 ATTTCTATAACTTCGGAAATAATTTAATTCAGTCAATTTATTCG
*
42291319 ATTTCTATGACTTCGGAAATAATTTAATTCAGTCAATTTATTCG
1 ATTTCTATAACTTCGGAAATAATTTAATTCAGTCAATTTATTCG
42291363 ATTT
1 ATTT
42291367 TGAATTAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (44 bp):
ATTTCTATAACTTCGGAAATAATTTAATTCAGTCAATTTATTCG
Found at i:42292014 original size:32 final size:31
Alignment explanation
Indices: 42291978--42292078 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 31
42291968 TATTAAATTC
42291978 AATTTAATATTTATCTAGATAATATTTTTTTT
1 AATTTAATATTTATCT-GATAATATTTTTTTT
* * * * ***
42292010 AATTTAATAGTAATATGA-GATATTAAATTT
1 AATTTAATATTTATCTGATAATATTTTTTTT
* *
42292040 AATTTAACATTTATCTTGATAATA-TTTTATT
1 AATTTAATATTTATC-TGATAATATTTTTTTT
42292071 AATTTAAT
1 AATTTAAT
42292079 GTTAATGTGA
Statistics
Matches: 50, Mismatches: 17, Indels: 5
0.69 0.24 0.07
Matches are distributed among these distances:
30 19 0.38
31 15 0.30
32 16 0.32
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (31 bp):
AATTTAATATTTATCTGATAATATTTTTTTT
Found at i:42294396 original size:28 final size:29
Alignment explanation
Indices: 42294355--42294411 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
42294345 GCTGTAAATT
* *
42294355 ACGCTTTGGCAAATA-A-ATAAATTGAATA
1 ACGCTTTCGAAAATATATATAAA-TGAATA
42294383 ACGCTTTCGAAAATATATATAAATGAATA
1 ACGCTTTCGAAAATATATATAAATGAATA
42294412 TGAGTAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.52
29 7 0.28
30 5 0.20
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (29 bp):
ACGCTTTCGAAAATATATATAAATGAATA
Found at i:42297415 original size:22 final size:22
Alignment explanation
Indices: 42297390--42297432 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
42297380 TAAAATGATT
* *
42297390 TAAATGAAGTGTTAAGTGATAG
1 TAAATAAAGTGTGAAGTGATAG
42297412 TAAATAAAGTGTGAAGTGATA
1 TAAATAAAGTGTGAAGTGATA
42297433 TGATAGTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (22 bp):
TAAATAAAGTGTGAAGTGATAG
Found at i:42299731 original size:27 final size:27
Alignment explanation
Indices: 42299701--42299798 Score: 117
Period size: 27 Copynumber: 3.6 Consensus size: 27
42299691 TTAGTTTACC
* *
42299701 AAATTACCAAAATA-CCTCTGGTTTGTA
1 AAATCACCAAAATACCCT-TGGTTTATA
* *
42299728 AAATTACTAAAATACCCTTGGTTTATA
1 AAATCACCAAAATACCCTTGGTTTATA
* *
42299755 AAATCGCCAAAATACCCTTGGCTTATA
1 AAATCACCAAAATACCCTTGGTTTATA
*
42299782 AAATCAACAAAATACCC
1 AAATCACCAAAATACCC
42299799 CTAGTTTGTA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 59 0.95
28 3 0.05
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (27 bp):
AAATCACCAAAATACCCTTGGTTTATA
Found at i:42299836 original size:27 final size:27
Alignment explanation
Indices: 42299819--42300274 Score: 585
Period size: 27 Copynumber: 16.9 Consensus size: 27
42299809 GTTTTTTCGC
42299819 AATACCCCTGTAGGGTAGAATTACCGGA
1 AATACCCCTGTAGGGTAGAATTACC-GA
*
42299847 AA-ACCCCTGTAGGGTAGAATTAAC-A
1 AATACCCCTGTAGGGTAGAATTACCGA
*
42299872 GAATACCCCTGTAGGATAGAATTACCGA
1 -AATACCCCTGTAGGGTAGAATTACCGA
* *
42299900 AATACCCCTGTAGGGTAGAATTACTGG
1 AATACCCCTGTAGGGTAGAATTACCGA
*
42299927 AATACCTCTGTAGGGTAGAATTACCGA
1 AATACCCCTGTAGGGTAGAATTACCGA
* * *
42299954 AATACCCCTGTATGGTAGAATTGCAGA
1 AATACCCCTGTAGGGTAGAATTACCGA
*
42299981 AATACCCCTGTAGGGTAGAATTACAGA
1 AATACCCCTGTAGGGTAGAATTACCGA
*
42300008 AATACCCCTATAGGGTAGAATTACCGA
1 AATACCCCTGTAGGGTAGAATTACCGA
* *
42300035 AATACCCCTATAGGGTAGAATTACCGG
1 AATACCCCTGTAGGGTAGAATTACCGA
* *
42300062 AATACCCCTGTAGGGTAGAATTATCGG
1 AATACCCCTGTAGGGTAGAATTACCGA
* * *
42300089 AATACACCTATAGGGTAGAATTACTGA
1 AATACCCCTGTAGGGTAGAATTACCGA
** * *
42300116 AATACCCCTGTAACGTAGAATTATCGC
1 AATACCCCTGTAGGGTAGAATTACCGA
* *
42300143 AATACCCCTGTAGGGTAGAATTATCGC
1 AATACCCCTGTAGGGTAGAATTACCGA
*
42300170 AATACCCCTGTATGGTAGAATTACCGA
1 AATACCCCTGTAGGGTAGAATTACCGA
* **
42300197 AACACCCCTGTAGGGTAGAATTACTAA
1 AATACCCCTGTAGGGTAGAATTACCGA
*
42300224 AATACCCCTGTAGGGTGGAATTACCGA
1 AATACCCCTGTAGGGTAGAATTACCGA
* * * *
42300251 GATA-CCTTGTGGGGTAAAATTACC
1 AATACCCCTGTAGGGTAGAATTACC
42300275 ATTTTGGCCG
Statistics
Matches: 375, Mismatches: 50, Indels: 8
0.87 0.12 0.02
Matches are distributed among these distances:
25 1 0.00
26 18 0.05
27 353 0.94
28 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAGAATTACCGA
Found at i:42300753 original size:22 final size:22
Alignment explanation
Indices: 42300701--42300765 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
42300691 TTAAAGCCTT
* *
42300701 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
42300723 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
42300745 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
42300766 ACGTATTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:42301461 original size:34 final size:34
Alignment explanation
Indices: 42301418--42301485 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
42301408 TTGCCTTTAA
*
42301418 ATAAAGAGAACCTTGAGGAGAGTAAAGGTACCTT
1 ATAAAGAGAACCATGAGGAGAGTAAAGGTACCTT
42301452 ATAAAGAGAACCATGAGGAGAGTAAAGGTACCTT
1 ATAAAGAGAACCATGAGGAGAGTAAAGGTACCTT
42301486 TCTTGGCTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.43, C:0.12, G:0.26, T:0.19
Consensus pattern (34 bp):
ATAAAGAGAACCATGAGGAGAGTAAAGGTACCTT
Found at i:42301878 original size:27 final size:27
Alignment explanation
Indices: 42301848--42301961 Score: 156
Period size: 27 Copynumber: 4.2 Consensus size: 27
42301838 TTAGTTTACC
*
42301848 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
** *
42301875 AAATTATTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTATA
42301902 AAATTACCAAAATACCCCTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTATA
* * **
42301929 AAATCAACAAAATACCCCTGGTTTGGA
1 AAATTACCAAAATACCCCTGGTTTATA
42301956 AAATTA
1 AAATTA
42301962 TCGCAATACC
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTATA
Found at i:42301987 original size:27 final size:27
Alignment explanation
Indices: 42301957--42302555 Score: 688
Period size: 27 Copynumber: 22.3 Consensus size: 27
42301947 TGGTTTGGAA
* * * *
42301957 AATTATCGCAATACCCCAGTAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42301984 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
42302011 AATTACC-AGAATACCCCTGTAGGGTAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
* *
42302038 AATTACTGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42302065 AAATACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42302092 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42302119 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42302146 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42302173 AATTACCGGAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* **
42302200 AATTACCGGAATACCCCTGTAAAGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42302227 AATTATC-ACAATACCCTTGTAGGGTAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
*
42302254 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * **
42302281 AATTACTGAAACACTACTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
42302308 AATTATTGAAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42302335 AATTACCGAAATACCCTTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42302362 AATTACTGAAATA-CCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * * *
42302388 AATTGCTGAAATACCCTTATAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42302415 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42302442 AATTATCAC-AAA-ACCCCAGTAGGGTAG
1 AATTA-C-CGAAATACCCCTGTAGGGTAG
** * *
42302469 AATTACTAAAATACCCCTGTATGGTAT
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
42302496 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
42302523 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
42302549 AATTACC
1 AATTACC
42302556 ATTTTGGCCC
Statistics
Matches: 494, Mismatches: 69, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
26 43 0.09
27 445 0.90
28 5 0.01
29 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:42303034 original size:22 final size:22
Alignment explanation
Indices: 42302982--42303046 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
42302972 TTAAAGCCTT
*
42302982 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTTTGTGCCAAC
*
42303004 CT-ACATATGGCTTTGTGCCAAC
1 CTGA-TTATGGCTTTGTGCCAAC
*
42303026 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTTTGTGCCAA
42303047 ACGTATTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 35 0.95
23 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTTTGTGCCAAC
Found at i:42303235 original size:27 final size:27
Alignment explanation
Indices: 42303205--42303306 Score: 134
Period size: 27 Copynumber: 3.8 Consensus size: 27
42303195 ATTCTGTTAA
* *
42303205 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
*
42303232 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTCTG
*
42303259 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
* *
42303286 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
42303307 ATAATTGAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 8 0.12
27 52 0.78
28 7 0.10
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTCTG
Found at i:42303481 original size:6 final size:6
Alignment explanation
Indices: 42303443--42303553 Score: 59
Period size: 6 Copynumber: 17.8 Consensus size: 6
42303433 TTGCATTCAC
* * *
42303443 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
42303493 -TTACCTG ATAT-TG ATTTTG ATTCTG ATTATG -TCACCTG ATTCTG ATTCAG
1 ATT--CTG AT-TCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
42303543 ATTCTG ATTCT
1 ATTCTG ATTCT
42303554 AGTTTTGATA
Statistics
Matches: 80, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
5 6 0.08
6 57 0.71
7 13 0.16
8 3 0.04
9 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:42303489 original size:31 final size:31
Alignment explanation
Indices: 42303443--42303553 Score: 141
Period size: 31 Copynumber: 3.5 Consensus size: 31
42303433 TTGCATTCAC
*
42303443 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTCTGATTCTGTTACCTGATACTG
* *
42303475 ATTCTGATTTTGATTCTGTTACCTGATATTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
* * * *
42303506 ATTTTGATTCTGATTATGTCACCTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
*
42303537 ATTCAGATTCTGATTCT
1 ATTCTGATTCTGATTCT
42303554 AGTTTTGATA
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
31 62 0.90
32 7 0.10
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTG
Found at i:42303506 original size:19 final size:19
Alignment explanation
Indices: 42303453--42303508 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
42303443 ATTCTGATTT
42303453 TTGATTCTGTTACCTGATA
1 TTGATTCTGTTACCTGATA
*
42303472 CTGATTCTG--A--T--T-
1 TTGATTCTGTTACCTGATA
42303484 TTGATTCTGTTACCTGATA
1 TTGATTCTGTTACCTGATA
42303503 TTGATT
1 TTGATT
42303509 TTGATTCTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
12 8 0.29
13 1 0.04
14 1 0.04
15 1 0.04
16 1 0.04
17 1 0.04
18 1 0.04
19 14 0.50
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (19 bp):
TTGATTCTGTTACCTGATA
Found at i:42305380 original size:40 final size:41
Alignment explanation
Indices: 42305321--42305552 Score: 303
Period size: 40 Copynumber: 5.8 Consensus size: 41
42305311 CATTTGAATG
* * *
42305321 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
* *
42305361 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
* * * *
42305401 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
*
42305441 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
*
42305481 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
* * *
42305521 ATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
42305553 TTGTGGTTAT
Statistics
Matches: 168, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 2 0.01
40 161 0.96
41 5 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
Found at i:42305535 original size:120 final size:120
Alignment explanation
Indices: 42305321--42305572 Score: 418
Period size: 120 Copynumber: 2.1 Consensus size: 120
42305311 CATTTGAATG
* * *
42305321 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCA
42305386 TTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
66 TTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
* *
42305441 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGATTATATCCGGGCTAAGACCCGAAGGC
* *
42305505 ATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
65 ATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
42305561 ATATCC-GGCTAA
1 ATATCCGGGCTAA
42305573 ATTCCGAAGA
Statistics
Matches: 123, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
119 6 0.05
120 114 0.93
121 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (120 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:42305568 original size:80 final size:80
Alignment explanation
Indices: 42305321--42305552 Score: 340
Period size: 80 Copynumber: 2.9 Consensus size: 80
42305311 CATTTGAATG
* *
42305321 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
*
42305386 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGAT
* * *
42305401 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
42305466 TTTGTGCGAGTTGAT
66 TTTGTGCGAGTTGAT
* * * * *
42305481 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTTTATCCGGGCTAAGACCCGAAGGC
*
42305545 AATTGTGC
65 ATTTGTGC
42305553 TTGTGGTTAT
Statistics
Matches: 136, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
80 134 0.99
81 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGAT
Found at i:42313369 original size:40 final size:40
Alignment explanation
Indices: 42313310--42313501 Score: 287
Period size: 40 Copynumber: 4.8 Consensus size: 40
42313300 CATTTGAATG
* * *
42313310 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
* *
42313350 TTATCCGAGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
42313390 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
*
42313430 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* * *
42313470 ATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
42313502 TTGTGGTTAT
Statistics
Matches: 140, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 137 0.98
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
Found at i:42322204 original size:40 final size:40
Alignment explanation
Indices: 42322149--42322359 Score: 223
Period size: 40 Copynumber: 5.3 Consensus size: 40
42322139 ATTTGAATGA
*
42322149 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
42322189 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
42322229 TATCCGAGCTAAGACCCGAAGGCATTTGTG-TGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCT-AG-TGATTT
* * * *
42322269 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * * * *
42322309 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
42322349 TATCC-GGCTAA
1 TATCCGGGCTAA
42322360 ATTTCGAAGA
Statistics
Matches: 152, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
39 8 0.05
40 141 0.93
41 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:42327503 original size:27 final size:26
Alignment explanation
Indices: 42327472--42327649 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
42327462 TAAATTGTAC
*
42327472 AGCACTAAGGGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
42327499 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
42327525 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
42327553 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
42327581 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
42327608 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
42327635 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42327650 GGCTCAATAT
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.01
27 102 0.80
28 25 0.20
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:42327587 original size:82 final size:81
Alignment explanation
Indices: 42327473--42327628 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
42327463 AAATTGTACA
* *
42327473 GCACTAAGGGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGGGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42327537 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* * ** *
42327554 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGGGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42327619 TGCGAGTTGA
65 TGCGAATTGA
42327629 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 14 0.22
82 50 0.77
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGGGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42327640 original size:82 final size:81
Alignment explanation
Indices: 42327469--42327649 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
42327459 GATTAAATTG
* * *
42327469 TACAGCACTAAGGGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42327534 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
42327550 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42327614 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42327632 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42327650 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 17 0.21
82 65 0.79
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42327660 original size:27 final size:27
Alignment explanation
Indices: 42327554--42327660 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
42327544 TGACCATGCG
* * * *
42327554 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
42327582 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
42327609 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
42327636 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
42327661 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:42330074 original size:20 final size:20
Alignment explanation
Indices: 42330049--42330094 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
42330039 ATTGGGCCTT
42330049 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
42330069 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
42330088 GCCCATA
1 GCCCATA
42330095 ACAAAACAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:42330103 original size:19 final size:20
Alignment explanation
Indices: 42330061--42330103 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
42330051 CCATATTAAC
** *
42330061 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
42330081 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
42330100 ACAG
1 ACAG
42330104 CCTCATATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:42336220 original size:25 final size:25
Alignment explanation
Indices: 42336192--42336243 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
42336182 GAAAATAGAC
42336192 ATAATAATATTTCATTTCATAACTT
1 ATAATAATATTTCATTTCATAACTT
*
42336217 ATAATAATATTTGATTTCATAACTT
1 ATAATAATATTTCATTTCATAACTT
42336242 AT
1 AT
42336244 TCATCATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (25 bp):
ATAATAATATTTCATTTCATAACTT
Found at i:42337842 original size:40 final size:40
Alignment explanation
Indices: 42337742--42338046 Score: 436
Period size: 40 Copynumber: 7.7 Consensus size: 40
42337732 GCTCCTCGTT
* * ** *
42337742 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
*
42337782 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
42337821 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
*
42337861 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
42337901 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
*
42337941 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
* * * * * *
42337981 CGAATGCCTTCGGAACTTAATCCGGATATATTC-ACTTAGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCA
*
42338022 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
42338047 CAGCATTCAA
Statistics
Matches: 245, Mismatches: 17, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
39 35 0.14
40 202 0.82
41 8 0.03
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
Found at i:42368277 original size:28 final size:26
Alignment explanation
Indices: 42368209--42368278 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 26
42368199 TTTACTATAA
* *
42368209 AAATAAATAAAATTAATTTTTTTTAT
1 AAATATATAAAATTAATTTTTTTAAT
42368235 AAATATACTACAAATTAATTATTTTATAATT
1 AAATATA-TA-AAATTAATT-TTTT-TAA-T
42368266 AAA-ATATAAAATT
1 AAATATATAAAATT
42368279 CTAAAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 6 0.16
27 2 0.05
28 14 0.38
29 6 0.16
30 5 0.14
31 4 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATATATAAAATTAATTTTTTTAAT
Found at i:42378071 original size:22 final size:22
Alignment explanation
Indices: 42378004--42378073 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
42377994 TTTAGAAATA
*
42378004 TTTATTTTAT-TAT-TTTATGTT
1 TTTATTTTATATTTATTTAT-TT
** *
42378025 TTTAATTTT-TATTCTAACTACTT
1 TTT-ATTTTATATT-TATTTATTT
42378048 TTTATTTTATATTTATTTATTT
1 TTTATTTTATATTTATTTATTT
42378070 TTTA
1 TTTA
42378074 GCAGATTTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
21 4 0.11
22 21 0.57
23 10 0.27
24 2 0.05
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.71
Consensus pattern (22 bp):
TTTATTTTATATTTATTTATTT
Found at i:42379779 original size:46 final size:46
Alignment explanation
Indices: 42379707--42379882 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
42379697 TGTAACCCGC
* *
42379707 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* * * *
42379753 CCATAGGTGAACTCGGACTCATCTCAACGAGTTCAGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-G--GAC--GTTCGCAT
* * *
42379803 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
42379846 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42379883 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 2 0.02
46 60 0.57
47 26 0.25
48 1 0.01
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:42379873 original size:93 final size:93
Alignment explanation
Indices: 42379714--42379885 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
42379704 CGCCCATAAG
* * *
42379714 CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAGGTGAACTCGGACTCATCTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
42379779 ACGAGTTCAGATGCCTAGTTACATCTCA
66 ACGAGTTCAGATGCCTAGTTACATCTCA
*
42379807 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
42379872 ACGAGTTCGGATGC
66 ACGAGTTCAGATGC
42379886 TCAACCATTC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCAGATGCCTAGTTACATCTCA
Found at i:42379901 original size:46 final size:45
Alignment explanation
Indices: 42379715--42379901 Score: 134
Period size: 46 Copynumber: 4.0 Consensus size: 45
42379705 GCCCATAAGC
* * * *
42379715 GAACTCGGACTCAACTCAACGAGCTCGGACGTTC--GCATCCATAGGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-C-TA-GT
* * *
42379761 GAACTCGGACTCATCTCAACGAGTTCAGATGC-CTAGTTA-CATCTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT-AGT
* * * *
42379808 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCTAGT
42379854 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATTCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCA-TCTAGT
42379900 GA
1 GA
42379902 CATGTCACTT
Statistics
Matches: 111, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
44 8 0.07
45 3 0.03
46 60 0.54
47 29 0.26
48 1 0.01
49 6 0.05
50 4 0.04
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCTAGT
Found at i:42382315 original size:40 final size:40
Alignment explanation
Indices: 42382135--42382355 Score: 223
Period size: 40 Copynumber: 5.5 Consensus size: 40
42382125 CTCGTTCAAG
* * * * *
42382135 TGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AA
1 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
* * *
42382174 TGCCTTCGGGACATAACCCGGATTCAACAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
42382214 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
* * *
42382254 TGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
* ** * * * *
42382294 GGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-AA
1 TGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACGAA
* *
42382334 AGCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGACTTAACCCGGA
42382356 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 34 0.22
40 114 0.73
41 8 0.05
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
Found at i:42382364 original size:41 final size:41
Alignment explanation
Indices: 42382287--42382364 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42382277 TTAGTATCTC
* * *
42382287 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
42382328 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
42382365 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:42384559 original size:5 final size:5
Alignment explanation
Indices: 42384549--42384577 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
42384539 TTGTTCTTAA
42384549 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
42384578 AACTATGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:42387084 original size:17 final size:18
Alignment explanation
Indices: 42387064--42387103 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
42387054 TAGGGTTCGT
*
42387064 ATACATAT-AGGGTTTAC
1 ATACATATAAAGGTTTAC
*
42387081 ATACATATAAAGGTTTGC
1 ATACATATAAAGGTTTAC
42387099 ATACA
1 ATACA
42387104 AAGGTAAGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (18 bp):
ATACATATAAAGGTTTAC
Found at i:42387787 original size:17 final size:17
Alignment explanation
Indices: 42387765--42387797 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42387755 AAAAGAAAAA
*
42387765 AAAAACATAATATTTTG
1 AAAAACACAATATTTTG
42387782 AAAAACACAATATTTT
1 AAAAACACAATATTTT
42387798 ACACATGTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAAACACAATATTTTG
Found at i:42389639 original size:40 final size:40
Alignment explanation
Indices: 42389567--42389748 Score: 201
Period size: 40 Copynumber: 4.6 Consensus size: 40
42389557 GCTACTCGTT
* * *
42389567 CAAATGCTTTCGGGACATAGCCCAG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
42389607 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
42389647 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
42389686 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
42389727 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
42389749 AGACATCATT
Statistics
Matches: 120, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.27
40 73 0.61
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:42389684 original size:39 final size:40
Alignment explanation
Indices: 42389595--42389698 Score: 165
Period size: 39 Copynumber: 2.6 Consensus size: 40
42389585 AGCCCAGTTA
*
42389595 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
* *
42389635 TAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
*
42389674 TAGTATCTCGCACAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGG
42389699 ATCTTAGTCC
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
39 34 0.58
40 25 0.42
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
Found at i:42389711 original size:79 final size:80
Alignment explanation
Indices: 42389595--42389748 Score: 197
Period size: 79 Copynumber: 1.9 Consensus size: 80
42389585 AGCCCAGTTA
* * *
42389595 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCACCAATGCCTTCG
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTTAGCA-CAAAGCCTTCG
42389659 GG-CTTAGCCCGGAAT
65 GGACTTAGCCCGGAAT
* ** * *
42389674 TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCG
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAACTTAGCACAAAGCCTTCG
42389738 GGACTTAGCCC
65 GGACTTAGCCC
42389749 AGACATCATT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
78 3 0.05
79 49 0.77
80 12 0.19
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGG
GACTTAGCCCGGAAT
Found at i:42398240 original size:90 final size:91
Alignment explanation
Indices: 42398086--42398262 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 91
42398076 TTCTTTGACT
*
42398086 GGTGTTTTTTAGAAAAAAAGGAAATTTAAACCCCACCTACATTTCTGGCTACACAGATCCTTATC
1 GGTGTTTTCTAGAAAAAAAGGAAATTTAAACCCCACCTACATTTCTGGCTACACAGATCCTTATC
42398151 ATTCCTGATTTTCAATCGAACGAACC
66 ATTCCTGATTTTCAATCGAACGAACC
* * * *
42398177 GGTGTTTTCTAG-AAAAAAGGAAATTTAAACCGCACCTACGTTTTTGGCTACACGGATCCTTATC
1 GGTGTTTTCTAGAAAAAAAGGAAATTTAAACCCCACCTACATTTCTGGCTACACAGATCCTTATC
*
42398241 GTTCCTGATTTTCAATCGAACG
66 ATTCCTGATTTTCAATCGAACG
42398263 GCCGTCTCCT
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 69 0.86
91 11 0.14
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.32
Consensus pattern (91 bp):
GGTGTTTTCTAGAAAAAAAGGAAATTTAAACCCCACCTACATTTCTGGCTACACAGATCCTTATC
ATTCCTGATTTTCAATCGAACGAACC
Found at i:42398935 original size:12 final size:12
Alignment explanation
Indices: 42398918--42398942 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42398908 GAAAATCACT
42398918 TTCATTTCCAAA
1 TTCATTTCCAAA
42398930 TTCATTTCCAAA
1 TTCATTTCCAAA
42398942 T
1 T
42398943 AATTCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (12 bp):
TTCATTTCCAAA
Found at i:42403792 original size:117 final size:117
Alignment explanation
Indices: 42403586--42403834 Score: 444
Period size: 117 Copynumber: 2.1 Consensus size: 117
42403576 ACATTGAATT
* * *
42403586 TTATTGCATCGACAATCACCTACACTTTTATACCCAGTGAGCATTTAGTATTCTGCTGAAGATTT
1 TTATTGCATCGACAATCACCTACACTTTTATACCCAGTAAACATTTAGTATTCTGCTGAAGATTC
*
42403651 ATGTTGGGGATCCCAGTTTATCACTATCATATTTTATTTTATTGTTTTCAAG
66 ATGTTGAGGATCCCAGTTTATCACTATCATATTTTATTTTATTGTTTTCAAG
*
42403703 TTATTGCATCGACAATCACCTACACTTTTATACCTAGTAAACATTTAGTATTCTGCTGAAGATTC
1 TTATTGCATCGACAATCACCTACACTTTTATACCCAGTAAACATTTAGTATTCTGCTGAAGATTC
42403768 ATGTTGAGGATCCCAGTTTATCACTATCATATTTTATTTTATTGTTTTCAAG
66 ATGTTGAGGATCCCAGTTTATCACTATCATATTTTATTTTATTGTTTTCAAG
*
42403820 TTTTTGCATCGACAA
1 TTATTGCATCGACAA
42403835 CTATCCTCAC
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
117 126 1.00
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (117 bp):
TTATTGCATCGACAATCACCTACACTTTTATACCCAGTAAACATTTAGTATTCTGCTGAAGATTC
ATGTTGAGGATCCCAGTTTATCACTATCATATTTTATTTTATTGTTTTCAAG
Found at i:42404452 original size:11 final size:10
Alignment explanation
Indices: 42404432--42404470 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
42404422 AATGATGATG
42404432 AAAA-AAAGA
1 AAAAGAAAGA
42404441 AAAGAGAAAGA
1 AAA-AGAAAGA
*
42404452 AAAAGAAAAA
1 AAAAGAAAGA
42404462 AAAAGAAAG
1 AAAAGAAAG
42404471 GCTCTCATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 3 0.12
10 15 0.58
11 8 0.31
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:42405783 original size:40 final size:40
Alignment explanation
Indices: 42405728--42405945 Score: 271
Period size: 40 Copynumber: 5.5 Consensus size: 40
42405718 TGGATGATAA
* * *
42405728 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
42405768 CCGGGCGAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
42405808 CCGGGATAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
42405848 CCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
42405888 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
42405928 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
42405946 TACTTGGCTT
Statistics
Matches: 158, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
39 16 0.10
40 142 0.90
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:42412472 original size:19 final size:19
Alignment explanation
Indices: 42412448--42412486 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42412438 AAATGATGAT
*
42412448 GAAAAA-AAGAAAAGAGAAA
1 GAAAAAGAA-AAAAAAGAAA
42412467 GAAAAAGAAAAAAAAGAAA
1 GAAAAAGAAAAAAAAGAAA
42412486 G
1 G
42412487 GCTCTCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
GAAAAAGAAAAAAAAGAAA
Found at i:42413799 original size:40 final size:40
Alignment explanation
Indices: 42413744--42413961 Score: 309
Period size: 40 Copynumber: 5.5 Consensus size: 40
42413734 TGGATGATAA
* *
42413744 CCGGGCTAAGTCCCGAAGGCATTTGCT-CTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTA-TAT
42413784 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
42413824 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
42413864 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
42413904 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
42413944 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
42413962 TACTTGGCTT
Statistics
Matches: 166, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
39 17 0.10
40 149 0.90
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:42422899 original size:14 final size:15
Alignment explanation
Indices: 42422880--42422909 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
42422870 AAAATGAAAG
42422880 AAGGAGGAG-AAGAA
1 AAGGAGGAGAAAGAA
42422894 AAGGAGGAGAAAGAA
1 AAGGAGGAGAAAGAA
42422909 A
1 A
42422910 CATCATCCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (15 bp):
AAGGAGGAGAAAGAA
Found at i:42423042 original size:17 final size:17
Alignment explanation
Indices: 42423020--42423053 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42423010 GATAAATATA
*
42423020 TATTGTCATTGCATTTT
1 TATTGTCATTACATTTT
42423037 TATTGTCATTACATTTT
1 TATTGTCATTACATTTT
42423054 CATGTTTGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (17 bp):
TATTGTCATTACATTTT
Found at i:42435308 original size:17 final size:18
Alignment explanation
Indices: 42435273--42435311 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
42435263 CTAGCATGAC
42435273 ATTT-TATATTTTATCTT
1 ATTTCTATATTTTATCTT
*
42435290 ATTTCTATATTTT-TTTT
1 ATTTCTATATTTTATCTT
42435307 ATTTC
1 ATTTC
42435312 CTAATATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTCTATATTTTATCTT
Found at i:42439366 original size:40 final size:40
Alignment explanation
Indices: 42439307--42439447 Score: 221
Period size: 40 Copynumber: 3.5 Consensus size: 40
42439297 CTACTCGCTT
*
42439307 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
*
42439347 AATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
* * *
42439387 AATGCCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACA
42439427 AATGCCTTCGGGACTTAGCCC
1 AATGCCTTCGGGACTTAGCCC
42439448 AGTTATCATC
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
39 1 0.01
40 93 0.99
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
Found at i:42442110 original size:13 final size:13
Alignment explanation
Indices: 42442092--42442122 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
42442082 CTTGGTATTC
42442092 GTTTCGGTGTCGT
1 GTTTCGGTGTCGT
42442105 GTTTCGGTGTCGT
1 GTTTCGGTGTCGT
42442118 GTTTC
1 GTTTC
42442123 AGTTATTCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.35, T:0.48
Consensus pattern (13 bp):
GTTTCGGTGTCGT
Found at i:42451493 original size:27 final size:27
Alignment explanation
Indices: 42451455--42451600 Score: 184
Period size: 27 Copynumber: 5.4 Consensus size: 27
42451445 TGGATAAGTT
* *
42451455 GTAGAATTACCGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
*
42451482 GTAGAATTACCGAAATACCCTTATAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
*
42451509 ATAGAATTACCGAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
* * *
42451536 GTAGAAATACTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
* * * *
42451563 GTAAAATTACTGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCTTGTAGG
*
42451590 GTAAAATTACC
1 GTAGAATTACC
42451601 ATTTTGCCCC
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 106 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCTTGTAGG
Found at i:42456605 original size:38 final size:38
Alignment explanation
Indices: 42456540--42456652 Score: 136
Period size: 38 Copynumber: 2.9 Consensus size: 38
42456530 ATTTGATGTG
**
42456540 TATCCGGGCTTAAAGACCAGCAGGCTTCGTGCTGGTAAAA
1 TATCCGGG-TTAAATCCCA-CAGGCTTCGTGCTGGTAAAA
**
42456580 TATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTAAAA
* * * *
42456618 TATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTA
1 TATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTA
42456653 TTATATTCGG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
38 49 0.75
39 8 0.12
40 8 0.12
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.26
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTAAAA
Found at i:42456653 original size:38 final size:38
Alignment explanation
Indices: 42456559--42456663 Score: 147
Period size: 38 Copynumber: 2.8 Consensus size: 38
42456549 TTAAAGACCA
** *
42456559 GCAGGCTTCGTGCTGGTAAAATATCCGGGTTAAATCCC
1 GCAGGCTTCGTGCTGGTATTATATCCGGGATAAATCCC
*
42456597 ACAGGCTTCGTGCTGGTATTATATCCGGGATAAATCCC
1 GCAGGCTTCGTGCTGGTATTATATCCGGGATAAATCCC
* * *
42456635 GCAGGCCTAGTGCTGGTATTATATTCGGG
1 GCAGGCTTCGTGCTGGTATTATATCCGGG
42456664 CCTTCGTGCC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 59 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (38 bp):
GCAGGCTTCGTGCTGGTATTATATCCGGGATAAATCCC
Found at i:42456736 original size:43 final size:43
Alignment explanation
Indices: 42456656--42456737 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
42456646 GCTGGTATTA
* * ** *
42456656 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTATCGGTGATGTG
1 TATTCGGGCCTTCATGCCTAGCAGGCGTAATACCGGTGATGTG
*
42456699 TATTCGGGCCTTCATGCCTAGCAGGCGTAATGCCGGTGA
1 TATTCGGGCCTTCATGCCTAGCAGGCGTAATACCGGTGA
42456738 AATGATATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (43 bp):
TATTCGGGCCTTCATGCCTAGCAGGCGTAATACCGGTGATGTG
Found at i:42462798 original size:40 final size:40
Alignment explanation
Indices: 42462695--42462801 Score: 196
Period size: 40 Copynumber: 2.7 Consensus size: 40
42462685 CAACTCGCAC
* *
42462695 AAATGCCTTCGGGTCTTAGCCCGAATAAAATCACTAGCAT
1 AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
42462735 AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
1 AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
42462775 AAATGCCTTCGGGACTTAGCCCGGATA
1 AAATGCCTTCGGGACTTAGCCCGGATA
42462802 TCATTCAAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
Found at i:42466204 original size:27 final size:27
Alignment explanation
Indices: 42466164--42466308 Score: 177
Period size: 27 Copynumber: 5.4 Consensus size: 27
42466154 TGGATAAGTT
*
42466164 GTAGAATTACCGAAATACCCATGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
* *
42466191 GTAGAATTATCGAAATACCC--CTAGAG
1 GTAGAATTACCGAAATACCCTTGTAG-G
*
42466217 ATAGAATTACCGAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
** *
42466244 GTAGAAACACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
* *
42466271 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCTTGTAGG
*
42466298 GTAAAATTACC
1 GTAGAATTACC
42466309 ATTTTGCCCC
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
25 3 0.03
26 19 0.19
27 75 0.75
28 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCTTGTAGG
Found at i:42466245 original size:53 final size:54
Alignment explanation
Indices: 42466165--42466308 Score: 193
Period size: 53 Copynumber: 2.7 Consensus size: 54
42466155 GGATAAGTTG
* *
42466165 TAGAATTACCGAAATACCCATGTAGGGTAGAATTATCGAAATACCCC--TAGAGA
1 TAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAG-GA
** *
42466218 TAGAATTACCGAAATACCCTTGTAGGGTAGAAACACCGAAATACCCCTGTAGGG
1 TAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGA
* * *
42466272 TAGAATTACCGAGATACCCTTGTGGGGTAAAATTACC
1 TAGAATTACCGAAATACCCTTGTAGGGTAGAATTACC
42466309 ATTTTGCCCC
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
53 43 0.54
54 33 0.42
55 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (54 bp):
TAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGA
Found at i:42467046 original size:67 final size:68
Alignment explanation
Indices: 42466938--42467079 Score: 189
Period size: 71 Copynumber: 2.1 Consensus size: 68
42466928 GAGGAAGCGT
* * * *
42466938 TCTGGCAGTCTCGCTGCAATCTGGTGGCCTTGCCAC-ATATATCTGTTCTGGTGACTTCGTCACA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTTGCCACAATATATCTGTTCTGGTGACCTAGCCACA
42467002 ATA
66 ATA
*
42467005 TCTGGCAGCCTCGCTGCAATCTGGTGG-TTTCGCCACATATATATATCTGTTCTGGTGACCTAGC
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTT-GCCAC--A-ATATATCTGTTCTGGTGACCTAGC
42467069 CACAATA
62 CACAATA
42467076 TCTG
1 TCTG
42467080 TATCTGGTGA
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
66 2 0.03
67 31 0.48
71 32 0.49
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32
Consensus pattern (68 bp):
TCTGGCAGCCTCGCTGCAATCTGGTGGCCTTGCCACAATATATCTGTTCTGGTGACCTAGCCACA
ATA
Found at i:42467102 original size:28 final size:26
Alignment explanation
Indices: 42467047--42467107 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
42467037 CCACATATAT
*
42467047 ATATCTGTTCTGGTGACCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCAACA
* *
42467073 ATATCTGTATCTGGTGACTTCGTCAACA
1 ATATCTGT-TCTGGTGACCTAG-CAACA
42467101 ATATCTG
1 ATATCTG
42467108 GCAGCCCCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 8 0.27
27 11 0.37
28 11 0.37
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCAACA
Found at i:42471049 original size:12 final size:12
Alignment explanation
Indices: 42471032--42471056 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42471022 TGGACAAAAA
42471032 TTGGCTTTTAAT
1 TTGGCTTTTAAT
42471044 TTGGCTTTTAAT
1 TTGGCTTTTAAT
42471056 T
1 T
42471057 CATTTAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TTGGCTTTTAAT
Found at i:42476399 original size:28 final size:28
Alignment explanation
Indices: 42476356--42476454 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 28
42476346 TCTTTGATGT
*
42476356 CTCGCACACTATGTGCCATACTCGATAC
1 CTCGCACACTAAGTGCCATACTCGATAC
* * * * **
42476384 CTCGCACGCTAAGTGCTATTCTGGATGT
1 CTCGCACACTAAGTGCCATACTCGATAC
* *
42476412 TTCGCACACTAAGTGCCATCCTCGATAC
1 CTCGCACACTAAGTGCCATACTCGATAC
* **
42476440 TTTTCACACTAAGTG
1 CTCGCACACTAAGTG
42476455 TCATTTATAT
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.29
Consensus pattern (28 bp):
CTCGCACACTAAGTGCCATACTCGATAC
Found at i:42476538 original size:40 final size:39
Alignment explanation
Indices: 42476472--42476557 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 39
42476462 TATATATATA
*
42476472 TAGCCGAAGCTATCTCAAATTGCACACCAAGTGGCACTTT
1 TAGCCGAAGCTATCTCAAATTGCACACCAAGTGCCA-TTT
* * *
42476512 TAGCCGAAGCTATTTCGAATCT-CACACTAAGTGCCATTT
1 TAGCCGAAGCTATCTCAAAT-TGCACACCAAGTGCCATTT
42476551 TAGCCGA
1 TAGCCGA
42476558 TAAGTCGTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
39 10 0.24
40 30 0.73
41 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (39 bp):
TAGCCGAAGCTATCTCAAATTGCACACCAAGTGCCATTT
Found at i:42480937 original size:12 final size:12
Alignment explanation
Indices: 42480920--42480944 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42480910 CGAAAAAAAC
42480920 TTGGCTTTTAAT
1 TTGGCTTTTAAT
42480932 TTGGCTTTTAAT
1 TTGGCTTTTAAT
42480944 T
1 T
42480945 CATTTAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TTGGCTTTTAAT
Found at i:42482536 original size:21 final size:21
Alignment explanation
Indices: 42482507--42482554 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
42482497 AGTGTAATTC
*
42482507 AGAATAATCTTCAGGAGCTAAA
1 AGAA-AATCTTCAAGAGCTAAA
42482529 AGAAAATCTTCAAGAGCTAAA
1 AGAAAATCTTCAAGAGCTAAA
42482550 AGAAA
1 AGAAA
42482555 TATGGGATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (21 bp):
AGAAAATCTTCAAGAGCTAAA
Found at i:42491981 original size:13 final size:13
Alignment explanation
Indices: 42491965--42491989 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42491955 TCGCCACATG
42491965 GCCTAAGCACACT
1 GCCTAAGCACACT
42491978 GCCTAAGCACAC
1 GCCTAAGCACAC
42491990 GGACTTGGCC
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:0.40, G:0.16, T:0.12
Consensus pattern (13 bp):
GCCTAAGCACACT
Found at i:42494775 original size:94 final size:94
Alignment explanation
Indices: 42494512--42494782 Score: 339
Period size: 94 Copynumber: 2.9 Consensus size: 94
42494502 CAAAGTTAAA
* * * * * *
42494512 ATAGCAAATCTTATCTCTATAAAGTTGCAGTGGAGTAAGATGAAACTACAAATCTTATACCTAC-
1 ATAGCGAATCTTATCTCCATAAAGTTGCAGTGGAGCAAGATGAAGCTACAATTCCTATACCT-CT
* * * *
42494576 GAAGTTGTAGTAAATTAGATTGAATTTACC
65 GAAGTTGCAGTGAGTTGGATTGAATTTACC
* * * *
42494606 ATAGCGAATCTAATCTCCTTAAATTTGCAGTGGAGCAGGATGAAGCTACAATTCCTATACC-CTT
1 ATAGCGAATCTTATCTCCATAAAGTTGCAGTGGAGCAAGATGAAGCTACAATTCCTATACCTC-T
* **
42494670 GAAGTTGCAGTGGGTTGGATTGAATTTATT
65 GAAGTTGCAGTGAGTTGGATTGAATTTACC
* *
42494700 ATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAATTCCTATACCTCTG
1 ATAGCGAATCTTATCTCCATAAAGTTGCAGTGGAGCAAGATGAAGCTACAATTCCTATACCTCTG
42494765 AAGTTGCAGTGAGTTGGA
66 AAGTTGCAGTGAGTTGGA
42494783 ATAAAGCTAC
Statistics
Matches: 151, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
92 1 0.01
94 149 0.99
95 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (94 bp):
ATAGCGAATCTTATCTCCATAAAGTTGCAGTGGAGCAAGATGAAGCTACAATTCCTATACCTCTG
AAGTTGCAGTGAGTTGGATTGAATTTACC
Found at i:42494819 original size:94 final size:94
Alignment explanation
Indices: 42494511--42494826 Score: 273
Period size: 94 Copynumber: 3.4 Consensus size: 94
42494501 TCAAAGTTAA
* ** * * * *
42494511 AATAGCAAATCTTATCTCTATAAAGTTGCAGTGGAGTAAGATGAAACTACAAATCTTATA-CCTA
1 AATAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTACAATTCCTATACCCT-
* * * * * * * **
42494575 CGAAGTTGTAGTAAATTAGATTGAATTTAC
65 TGAAGTTGCAGTGAGTTGGAATAAAGCTAC
* * * * *
42494605 CATAGCGAAT-CTAATCTCCTTAAATTTGCAGTGGAGCAGGATGAAGCTACAATTCCTATACCCT
1 AATAGCAAATCCT-ATCTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTACAATTCCTATACCCT
* * * ** *
42494669 TGAAGTTGCAGTGGGTTGGATTGAATTTAT
65 TGAAGTTGCAGTGAGTTGGAATAAAGCTAC
* * * *
42494699 TATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAATTCCTATA-CCTC
1 AATAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTACAATTCCTATACCCT-
42494763 TGAAGTTGCAGTGAGTTGGAATAAAGCTAC
65 TGAAGTTGCAGTGAGTTGGAATAAAGCTAC
42494793 AACTA-CAAATCCTATAC-CCCTAAAGTTGCAGTGG
1 AA-TAGCAAATCCTAT-CTCCCTAAAGTTGCAGTGG
42494827 GTCAGATTGA
Statistics
Matches: 182, Mismatches: 34, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
93 4 0.02
94 171 0.94
95 7 0.04
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (94 bp):
AATAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTACAATTCCTATACCCTT
GAAGTTGCAGTGAGTTGGAATAAAGCTAC
Found at i:42494819 original size:144 final size:144
Alignment explanation
Indices: 42494651--42494919 Score: 405
Period size: 144 Copynumber: 1.9 Consensus size: 144
42494641 CAGGATGAAG
* * * **
42494651 CTACAATTCCTATACCCTTGAAGTTGCAGTGGGTTGGATTGAATTTATTATAGCGAATCTTATCT
1 CTACAAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTGAATTTATTATAGCGAATCTTATCT
* * *
42494716 CCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAATTCCTATA-CCTCTGAAGTTGCAGTGAGTT
66 CCCTGAAATTACAGTGGAGCAAGATGAAGCTACAACTCCTATATCCT-TGAAGTTGCAGTGAGTT
42494780 GGAATAAAGCTACAA
130 GGAATAAAGCTACAA
*
42494795 CTACAAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTGAATTTATTATAGCTAATCTTATCT
1 CTACAAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTGAATTTATTATAGCGAATCTTATCT
* * * *
42494860 CCTTGAAATTATAGTGGAGCAAGATGAAGCTACAACTCTTATATCCTTGAAGTTGTAGTG
66 CCCTGAAATTACAGTGGAGCAAGATGAAGCTACAACTCCTATATCCTTGAAGTTGCAGTG
42494920 GATCGGATTG
Statistics
Matches: 111, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
144 108 0.97
145 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (144 bp):
CTACAAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTGAATTTATTATAGCGAATCTTATCT
CCCTGAAATTACAGTGGAGCAAGATGAAGCTACAACTCCTATATCCTTGAAGTTGCAGTGAGTTG
GAATAAAGCTACAA
Found at i:42494988 original size:95 final size:94
Alignment explanation
Indices: 42494795--42495026 Score: 320
Period size: 95 Copynumber: 2.5 Consensus size: 94
42494785 AAAGCTACAA
* * * * * * * *
42494795 CTACAAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTGAATTTATTATAGCTAATCTTATCT
1 CTACAACTCCTATATCCTTGAAGTTGTAGTGGATCGGATTGAATTTATTATAGCGAATCTTATCT
* * * *
42494860 CCTTGAAATTATAGTGGAGCAAGATGAAG
66 CCCTGAAATTACAGTGAAGCAAGATAAAG
*
42494889 CTACAACTCTTATATCCTTGAAGTTGTAGTGGATCGGATTGAATTTATTATAGGCGAATCTTATC
1 CTACAACTCCTATATCCTTGAAGTTGTAGTGGATCGGATTGAATTTATTATA-GCGAATCTTATC
* *
42494954 TCCCTGAAGTTGCAGTGAAGCAAGATAAAG
65 TCCCTGAAATTACAGTGAAGCAAGATAAAG
42494984 CTACAACTCCTATATCCTTGAAGTTGTAGTGGATCGGATTGAA
1 CTACAACTCCTATATCCTTGAAGTTGTAGTGGATCGGATTGAA
42495027 ACTACAATTT
Statistics
Matches: 121, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
94 44 0.36
95 77 0.64
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (94 bp):
CTACAACTCCTATATCCTTGAAGTTGTAGTGGATCGGATTGAATTTATTATAGCGAATCTTATCT
CCCTGAAATTACAGTGAAGCAAGATAAAG
Found at i:42501920 original size:6 final size:6
Alignment explanation
Indices: 42501906--42501945 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
42501896 TGATGACATA
*
42501906 ATAAAC ATAACC ATAAAC ATAAAC ATAAAC ATAAAC ATAA
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAA
42501946 GTTTATTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.65, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAC
Found at i:42512666 original size:23 final size:23
Alignment explanation
Indices: 42512636--42512681 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
42512626 ACACGGTAGG
42512636 GGCATTTGTTAATCCAAATGACA
1 GGCATTTGTTAATCCAAATGACA
42512659 GGCATTTGTTAATCCAAATGACA
1 GGCATTTGTTAATCCAAATGACA
42512682 TAACAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (23 bp):
GGCATTTGTTAATCCAAATGACA
Found at i:42514557 original size:94 final size:95
Alignment explanation
Indices: 42514268--42514585 Score: 271
Period size: 94 Copynumber: 3.4 Consensus size: 95
42514258 TGGGTAAGGC
* * * * *
42514268 GCCGATGCCATGTTCCAGACATGGTCTCACACTGGCTA-TCATCTTCGA-GGCCGATGCCATGTC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGC-ACTCATC-TC-ATAGCCAATGCCATGTC
* * *
42514331 CTAAACATGGTCTTACACTAGCTCTCGCATAACTGT-
61 CCAGACATGGTCTTACACTAGCTCT-ACATAA-TGTG
* * * *
42514367 GCCGATGCCATGTCCTAGA-ATGGTCTTACACT-G-ACTCATCTCGTAGCCGATG-TATGTCCCA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCATCTCATAGCCAATGCCATGTCCCA
* * *** *
42514428 GACAT-GTCTTACACTGGCT-TACGTCCCGAG
64 GACATGGTCTTACACTAGCTCTACATAATGTG
* * * *
42514458 ACCGATGCATGTCCCAGACATGTTTTACACTAGCACTCGTCTCA-ATGCTAATGCCATGTCCCAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCATA-GCCAATGCCATGTCCCAG
42514522 ACATGGTCTTACACTAGCTCT-CATAATGTG
65 ACATGGTCTTACACTAGCTCTACATAATGTG
42514552 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
42514586 TCACACAAAT
Statistics
Matches: 178, Mismatches: 31, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
90 20 0.11
91 12 0.07
92 14 0.08
93 26 0.15
94 60 0.34
95 11 0.06
96 5 0.03
97 1 0.01
98 12 0.07
99 17 0.10
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (95 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCATAGCCAATGCCATGTCCCAGA
CATGGTCTTACACTAGCTCTACATAATGTG
Found at i:42514587 original size:46 final size:48
Alignment explanation
Indices: 42514268--42514587 Score: 222
Period size: 46 Copynumber: 6.8 Consensus size: 48
42514258 TGGGTAAGGC
* * * * ** *
42514268 GCCGATGCCATGTTCCAGACATGGTCTCACACTGGCTATCATCTTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAT-GTG
* *
42514317 GCCGATGCCATGTCCTAAACATGGTCTTACACTAGCTCTCGCATAACTGT-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT--CATAA-TGTG
* * * *
42514367 GCCGATGCCATGTCCTAGA-ATGGTCTTACACT-G-ACTCAT-CTCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAT-GTG
* * * *** *
42514412 GCCGATG-TATGTCCCAGACAT-GTCTTACACTGGCT-TACGTCCCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATAATGTG
* *
42514458 ACCGATG-CATGTCCCAGACAT-GTTTTACACTAGCACTCGTC-TCAA--T-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG--CTC-TCAT-AATGTG
**
42514504 GCTAATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTG
42514552 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC
42514588 ACACAAATGA
Statistics
Matches: 218, Mismatches: 32, Indels: 45
0.74 0.11 0.15
Matches are distributed among these distances:
43 1 0.00
44 21 0.10
45 18 0.08
46 55 0.25
47 32 0.15
48 20 0.09
49 47 0.22
50 19 0.09
51 4 0.02
52 1 0.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTG
Found at i:42521453 original size:27 final size:27
Alignment explanation
Indices: 42521395--42521823 Score: 436
Period size: 27 Copynumber: 15.9 Consensus size: 27
42521385 CCTAAATCGA
* * *
42521395 TAAAATGACTATTTTGCCCTTTATGTGG
1 TAAAATGATTGTTTTGCCC-TTATGAGG
*
42521423 TAAAATGATTGTGTTGCCCTTATGAGG
1 TAAAATGATTGTTTTGCCCTTATGAGG
* *
42521450 TAAAATAATTGTTTTTCCCTTAT-AGGG
1 TAAAATGATTGTTTTGCCCTTATGA-GG
* * * *
42521477 TTAGATGACTGTTTTGCCCTTATAAGG
1 TAAAATGATTGTTTTGCCCTTATGAGG
* *
42521504 TAAAATGACTATTTTGCCCTTATGAGG
1 TAAAATGATTGTTTTGCCCTTATGAGG
* * *
42521531 TAAAATGACTATTTTGACCTTAT-ATGG
1 TAAAATGATTGTTTTGCCCTTATGA-GG
* *
42521558 TAAAATGACTATTTTGCCCTTATGAGG
1 TAAAATGATTGTTTTGCCCTTATGAGG
*
42521585 TAAAATGATTGTTTTGCCCTTATGTGG
1 TAAAATGATTGTTTTGCCCTTATGAGG
* * *
42521612 TAAAATGACTATTTTG-CCTTATGGGG
1 TAAAATGATTGTTTTGCCCTTATGAGG
* * * * *
42521638 AAAAATGACTATTTTTCCCTTATGGGG
1 TAAAATGATTGTTTTGCCCTTATGAGG
42521665 TAAAATGATTGTTTTGCCCTTAT-AGGG
1 TAAAATGATTGTTTTGCCCTTATGA-GG
* **
42521692 TAAAATGGTTGTTTTGCTTTTATGAGG
1 TAAAATGATTGTTTTGCCCTTATGAGG
*
42521719 TAAAATGATTGTTTTGCTCTTATGAGG
1 TAAAATGATTGTTTTGCCCTTATGAGG
* * * *
42521746 TAAAATAATTGTTATGCCCTCATGTGG
1 TAAAATGATTGTTTTGCCCTTATGAGG
*
42521773 TAAAATGATTGTTTTGCCCTT-TTATGG
1 TAAAATGATTGTTTTGCCCTTATGA-GG
* * *
42521800 TAAGATGATTGTTTTACCCCTATG
1 TAAAATGATTGTTTTGCCCTTATG
42521824 TGATCTATGT
Statistics
Matches: 342, Mismatches: 50, Indels: 18
0.83 0.12 0.04
Matches are distributed among these distances:
26 26 0.08
27 296 0.87
28 20 0.06
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (27 bp):
TAAAATGATTGTTTTGCCCTTATGAGG
Found at i:42522203 original size:18 final size:18
Alignment explanation
Indices: 42522136--42522207 Score: 85
Period size: 18 Copynumber: 4.1 Consensus size: 18
42522126 GGACTTGCAT
*
42522136 ACTATTTACTGTTACTGC
1 ACTATTTACTATTACTGC
* *
42522154 ATTGTTTACTATTACTGC
1 ACTATTTACTATTACTGC
*
42522172 ACTA-TTACTATTACTGT
1 ACTATTTACTATTACTGC
42522189 ACTATTTAC-AGTTACTGC
1 ACTATTTACTA-TTACTGC
42522207 A
1 A
42522208 ATGGGCCAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
17 17 0.38
18 28 0.62
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.44
Consensus pattern (18 bp):
ACTATTTACTATTACTGC
Found at i:42528086 original size:15 final size:15
Alignment explanation
Indices: 42528066--42528121 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
42528056 CGTATCTTGG
42528066 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
42528081 TTTCTTTATT-TCGGG
1 TTTCTTTATTCT-GGA
* *
42528096 TTTC-TCAATCTTGGA
1 TTTCTTTATTC-TGGA
42528111 TTTCTTTATTC
1 TTTCTTTATTC
42528122 AGTTTTCTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
14 4 0.13
15 22 0.71
16 5 0.16
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:42530320 original size:21 final size:21
Alignment explanation
Indices: 42530294--42530365 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
42530284 TTCGCATACG
42530294 AGGTAAGTTCATGTGTAAATA
1 AGGTAAGTTCATGTGTAAATA
** * * * **
42530315 AGGTAACATAATTTTTATTTTA
1 AGGTAAGTTCATGTGTA-AATA
42530337 AGTTGTAAGTTCATGTGTAAATA
1 AG--GTAAGTTCATGTGTAAATA
42530360 AGGTAA
1 AGGTAA
42530366 CATAATTTTT
Statistics
Matches: 34, Mismatches: 14, Indels: 6
0.63 0.26 0.11
Matches are distributed among these distances:
21 16 0.47
22 4 0.12
23 4 0.12
24 10 0.29
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
AGGTAAGTTCATGTGTAAATA
Found at i:42530345 original size:45 final size:45
Alignment explanation
Indices: 42530296--42530384 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
42530286 CGCATACGAG
42530296 GTAAGTTCATGTGTAAATAAGGTAACATAATTTTTATTTTAAGTT
1 GTAAGTTCATGTGTAAATAAGGTAACATAATTTTTATTTTAAGTT
42530341 GTAAGTTCATGTGTAAATAAGGTAACATAATTTTTATTTTAAGT
1 GTAAGTTCATGTGTAAATAAGGTAACATAATTTTTATTTTAAGT
42530385 GATTTAATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (45 bp):
GTAAGTTCATGTGTAAATAAGGTAACATAATTTTTATTTTAAGTT
Found at i:42532378 original size:49 final size:48
Alignment explanation
Indices: 42532306--42532479 Score: 188
Period size: 51 Copynumber: 3.5 Consensus size: 48
42532296 CTGATACGCA
* *
42532306 TAGTAGCCTGCACTTAGTACTACACATGCGATCAACAATCCGGTACACG
1 TAGTAGCCTACACTTAGTACTACACATGCGATCAACAAT-TGGTACACG
* * * * *
42532355 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTC-ATTGAGTACGCA
1 TAGTAGCCTACACTTAGTACTACACATGCGATC-AA--CAATTG-GTACACG
* * *
42532406 TAGTAGCCTACACTTAGTACTACACATGCGACTTAACAGTATGATACACG
1 TAGTAGCCTACACTTAGTACTACACATGCGA-TCAACAAT-TGGTACACG
42532456 TAGTAGCCTACACTTAGTACTACA
1 TAGTAGCCTACACTTAGTACTACA
42532480 TAGGTGTATT
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
49 32 0.30
50 32 0.30
51 39 0.37
52 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (48 bp):
TAGTAGCCTACACTTAGTACTACACATGCGATCAACAATTGGTACACG
Found at i:42543412 original size:16 final size:16
Alignment explanation
Indices: 42543391--42543423 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
42543381 CTAGCACACG
42543391 GGCATGTGACTTGGCC
1 GGCATGTGACTTGGCC
42543407 GGCATGTGACTTGGCC
1 GGCATGTGACTTGGCC
42543423 G
1 G
42543424 TGTGACCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.39, T:0.24
Consensus pattern (16 bp):
GGCATGTGACTTGGCC
Found at i:42559076 original size:40 final size:40
Alignment explanation
Indices: 42558993--42559295 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
42558983 TTGAATGCTG
* * * * * *
42558993 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
42559033 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
42559073 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
42559113 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
42559153 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
42559193 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
42559233 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
42559272 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
42559296 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.15
40 198 0.82
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:42565397 original size:14 final size:14
Alignment explanation
Indices: 42565378--42565407 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
42565368 TGAAGTTGAG
42565378 TTTGCTATTGAGCT
1 TTTGCTATTGAGCT
42565392 TTTGCTATTGAGCT
1 TTTGCTATTGAGCT
42565406 TT
1 TT
42565408 ATCCTGGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.20, T:0.53
Consensus pattern (14 bp):
TTTGCTATTGAGCT
Found at i:42566830 original size:23 final size:23
Alignment explanation
Indices: 42566804--42566848 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
42566794 GGAGATTTTG
42566804 ATGTTAATTGTGAAGGTATATTA
1 ATGTTAATTGTGAAGGTATATTA
42566827 ATGTTAATTGTGAAGGTATATT
1 ATGTTAATTGTGAAGGTATATT
42566849 GAACTTTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (23 bp):
ATGTTAATTGTGAAGGTATATTA
Found at i:42568388 original size:27 final size:27
Alignment explanation
Indices: 42568346--42568460 Score: 133
Period size: 27 Copynumber: 4.3 Consensus size: 27
42568336 TAGATAAGTT
42568346 GTAGAATTACCGAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
* *
42568373 ATAGAATTACCAAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
* * *
42568400 GT-GAAATACTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
* * * *
42568426 GCAGAATTACCGAGATCCCCTTGTGGG
1 GTAGAATTACCGAAATACCCTTGTAGG
*
42568453 GTAAAATT
1 GTAGAATT
42568461 GCCATTTTGC
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
26 21 0.30
27 50 0.70
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCTTGTAGG
Found at i:42568424 original size:53 final size:53
Alignment explanation
Indices: 42568357--42568459 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
42568347 TAGAATTACC
* * *
42568357 GAAATACCCTTGTAGGATAGAATTACCAAAATACCCTTGTAGGGTGAAATACT
1 GAAATACCCCTGTAGGACAGAATTACCAAAATACCCTTGTAGGGTAAAATACT
* * * * *
42568410 GAAATACCCCTGTAGGGCAGAATTACCGAGATCCCCTTGTGGGGTAAAAT
1 GAAATACCCCTGTAGGACAGAATTACCAAAATACCCTTGTAGGGTAAAAT
42568460 TGCCATTTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (53 bp):
GAAATACCCCTGTAGGACAGAATTACCAAAATACCCTTGTAGGGTAAAATACT
Found at i:42569218 original size:31 final size:32
Alignment explanation
Indices: 42569180--42569241 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
42569170 CTCGCTGCAA
*
42569180 TCTGGTGGCTTCGCCAC-ATATATATATCTGT
1 TCTGGTGGCCTCGCCACAATATATATATCTGT
*
42569211 TCTGGTGGCCTCGCCACAATATCTATATCTG
1 TCTGGTGGCCTCGCCACAATATATATATCTG
42569242 GTGACATCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.35
Consensus pattern (32 bp):
TCTGGTGGCCTCGCCACAATATATATATCTGT
Found at i:42569243 original size:27 final size:29
Alignment explanation
Indices: 42569179--42569262 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 29
42569169 CCTCGCTGCA
* *
42569179 ATCTGGTGGCTTCGCCACATATATATATCTG
1 ATCTGGTGGCATCGCCACA-ATATCTA-CTG
* *
42569210 TTCTGGTGGCCTCGCCACAATATCTA-T-
1 ATCTGGTGGCATCGCCACAATATCTACTG
* *
42569237 ATCTGGTGACATCGTCACAATATCTA
1 ATCTGGTGGCATCGCCACAATATCTA
42569263 GCAGCCTCGC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
27 22 0.48
28 1 0.02
30 6 0.13
31 17 0.37
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (29 bp):
ATCTGGTGGCATCGCCACAATATCTACTG
Found at i:42571267 original size:17 final size:18
Alignment explanation
Indices: 42571245--42571278 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42571235 TGAAGCATAC
42571245 AGAAAGA-CAGAATCGTG
1 AGAAAGATCAGAATCGTG
*
42571262 AGAAAGATCGGAATCGT
1 AGAAAGATCAGAATCGT
42571279 TTTAGGAGAG
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:0.44, C:0.12, G:0.29, T:0.15
Consensus pattern (18 bp):
AGAAAGATCAGAATCGTG
Found at i:42575994 original size:27 final size:27
Alignment explanation
Indices: 42575914--42576032 Score: 105
Period size: 27 Copynumber: 4.4 Consensus size: 27
42575904 TGGATAAGTT
* *
42575914 GTAGAATTAACGAAATACCCCTGTAGA
1 GTAGAATTACCGAAATACCCCTGTAGG
* * * *
42575941 ATAGAATTACCAAAATACCCTTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
42575968 GTAGAAATACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * * * *
42575995 GAAGAATCACC-AAGATGCCCTTGTGGG
1 GTAGAATTACCGAA-ATACCCCTGTAGG
*
42576022 GTAAAATTACC
1 GTAGAATTACC
42576033 ATTTTGCCCC
Statistics
Matches: 71, Mismatches: 20, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
26 2 0.03
27 69 0.97
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:42576024 original size:54 final size:54
Alignment explanation
Indices: 42575914--42576016 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
42575904 TGGATAAGTT
* *
42575914 GTAGAATTAACGAAATACCCCTGTAGAATAGAATTACCAAAATACCCTTATAGG
1 GTAGAAATAACGAAATACCCCTGTAGAATAGAATCACCAAAATACCCTTATAGG
* * * *
42575968 GTAGAAATACCGAAATACCCCTGTAGGGA-AGAATCACCAAGATGCCCTT
1 GTAGAAATAACGAAATACCCCTGTA-GAATAGAATCACCAAAATACCCTT
42576017 GTGGGGTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 40 0.95
55 2 0.05
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (54 bp):
GTAGAAATAACGAAATACCCCTGTAGAATAGAATCACCAAAATACCCTTATAGG
Found at i:42580267 original size:21 final size:20
Alignment explanation
Indices: 42580239--42580277 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
42580229 GCATGAGTTT
42580239 TGAAGTTTCTTGATAGATTA
1 TGAAGTTTCTTGATAGATTA
*
42580259 TGAATGTTTGTTGATAGAT
1 TGAA-GTTTCTTGATAGAT
42580278 ATACAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.46
Consensus pattern (20 bp):
TGAAGTTTCTTGATAGATTA
Found at i:42583359 original size:79 final size:78
Alignment explanation
Indices: 42583257--42583479 Score: 265
Period size: 79 Copynumber: 2.8 Consensus size: 78
42583247 GCTCCTCGTT
* *
42583257 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
42583322 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
42583337 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
42583400 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * *
42583415 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
42583478 GA
63 GA
42583480 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 47 0.38
79 57 0.46
80 20 0.16
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:42583374 original size:39 final size:40
Alignment explanation
Indices: 42583257--42583479 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
42583247 GCTCCTCGTT
* *
42583257 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
42583297 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
42583337 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
42583376 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
42583415 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
42583456 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42583480 CATCATTCAA
Statistics
Matches: 166, Mismatches: 9, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 64 0.39
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:42591350 original size:79 final size:78
Alignment explanation
Indices: 42591248--42591470 Score: 256
Period size: 79 Copynumber: 2.8 Consensus size: 78
42591238 GCTCCTCGTT
* *
42591248 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
42591313 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
42591328 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
42591391 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * * *
42591406 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTCAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
42591469 GA
63 GA
42591471 CATCATTCAA
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
78 47 0.38
79 56 0.45
80 20 0.16
81 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:42591365 original size:39 final size:40
Alignment explanation
Indices: 42591248--42591470 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
42591238 GCTCCTCGTT
* *
42591248 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
42591288 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
42591328 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
42591367 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
42591406 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
*
42591447 C-AA-GCCTTCGGGACTCAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42591471 CATCATTCAA
Statistics
Matches: 165, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 88 0.53
40 64 0.39
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:42595903 original size:12 final size:12
Alignment explanation
Indices: 42595886--42595917 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
42595876 AGTTTGGCAC
42595886 GGCCTAGCACAT
1 GGCCTAGCACAT
42595898 GGCCTAGCACAT
1 GGCCTAGCACAT
*
42595910 GGGCTAGC
1 GGCCTAGC
42595918 CACACTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.16
Consensus pattern (12 bp):
GGCCTAGCACAT
Found at i:42597701 original size:43 final size:43
Alignment explanation
Indices: 42597597--42597747 Score: 178
Period size: 43 Copynumber: 3.5 Consensus size: 43
42597587 CATCCCAAAT
* ** * *
42597597 ATGGTCTTACATGTTATCACATATTGATGCCACTGTCCAAGAC
1 ATGGTCTTACATGTAATCACATAACGATGCCAATGTCCCAGAC
* *** *
42597640 AGGGTCTTACACAAAATCATATAACGATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACATAACGATGCCAATGTCCCAGAC
*
42597683 ATGGTCTTACATGTAATCACA-ATACAATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACATA-ACGATGCCAATGTCCCAGAC
*
42597726 ATGGTCATACATGTAATCACAT
1 ATGGTCTTACATGTAATCACAT
42597748 CTTGGTAACC
Statistics
Matches: 89, Mismatches: 17, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
42 1 0.01
43 88 0.99
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATAACGATGCCAATGTCCCAGAC
Found at i:42598747 original size:76 final size:76
Alignment explanation
Indices: 42598667--42598818 Score: 261
Period size: 76 Copynumber: 2.0 Consensus size: 76
42598657 AAAATTAATA
* * *
42598667 TAAGGCCATTTAT-GACAAATTCCACTATCAATGGTCTAATATCAAACATAAGGACCTTTCATTT
1 TAAGGCCATTTATAAAAAAATTCCACTATCAATGGTCTAATATC-AACATAAGGACCTTCCATTT
42598731 AATAAACCATAG
65 AATAAACCATAG
42598743 TAAGGCCATTTATAAAAAAATTCCACTATCAATGGTCTAATATCAACATAAGGACCTTCCATTTA
1 TAAGGCCATTTATAAAAAAATTCCACTATCAATGGTCTAATATCAACATAAGGACCTTCCATTTA
42598808 ATAAACCATAG
66 ATAAACCATAG
42598819 AAAATAGAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
76 44 0.61
77 28 0.39
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.30
Consensus pattern (76 bp):
TAAGGCCATTTATAAAAAAATTCCACTATCAATGGTCTAATATCAACATAAGGACCTTCCATTTA
ATAAACCATAG
Found at i:42610582 original size:9 final size:9
Alignment explanation
Indices: 42610568--42610594 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
42610558 CCGAGATAAA
42610568 AATGAACAT
1 AATGAACAT
42610577 AATGAACAT
1 AATGAACAT
42610586 AATGAACAT
1 AATGAACAT
42610595 TTGAGAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (9 bp):
AATGAACAT
Found at i:42613087 original size:17 final size:18
Alignment explanation
Indices: 42613065--42613101 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42613055 TGGATTCTAG
42613065 TAGCT-AGAAGAATTAAA
1 TAGCTAAGAAGAATTAAA
*
42613082 TAGCTAATAAGAATTAAA
1 TAGCTAAGAAGAATTAAA
42613100 TA
1 TA
42613102 CATGCTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.27
Consensus pattern (18 bp):
TAGCTAAGAAGAATTAAA
Found at i:42613372 original size:57 final size:58
Alignment explanation
Indices: 42613247--42613380 Score: 143
Period size: 57 Copynumber: 2.4 Consensus size: 58
42613237 ACCTCATTAC
* *
42613247 AGAAA-AA-ATTTAGCCTGGACTGGTAATCTTGATATAAGCCCTATTGAGCATATGTT
1 AGAAACAAGATTTAGCCTGGAATGGTAATCTTGATATAAGCCCTATTGAGCATATATT
* * * *
42613303 ATAGATAGGATTTAGCCT-GAATGGGTAATCTTGA-ATAAGCTCCTA-TGAGCATATATT
1 AGAAACAAGATTTAGCCTGGAAT-GGTAATCTTGATATAAGC-CCTATTGAGCATATATT
* *
42613360 GGAAACAAGATTTAGCTTGGA
1 AGAAACAAGATTTAGCCTGGA
42613381 CAAGTAATCA
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
56 3 0.05
57 33 0.53
58 26 0.42
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (58 bp):
AGAAACAAGATTTAGCCTGGAATGGTAATCTTGATATAAGCCCTATTGAGCATATATT
Found at i:42615143 original size:41 final size:41
Alignment explanation
Indices: 42615089--42615171 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
42615079 ATATCATTAG
42615089 TTAGAAATTAGTTATGAGAGTATCTACACATATTTGACTCA
1 TTAGAAATTAGTTATGAGAGTATCTACACATATTTGACTCA
42615130 TTAGAAATTAGTTATGAGAGTATCTACACATATTTGACTCA
1 TTAGAAATTAGTTATGAGAGTATCTACACATATTTGACTCA
42615171 T
1 T
42615172 ACTTTATTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.37
Consensus pattern (41 bp):
TTAGAAATTAGTTATGAGAGTATCTACACATATTTGACTCA
Found at i:42616885 original size:57 final size:60
Alignment explanation
Indices: 42616824--42616938 Score: 139
Period size: 61 Copynumber: 1.9 Consensus size: 60
42616814 AATCTAGATC
* *
42616824 AAGCTC-ATTAGAGCATATGT-CA-T-AAAAAGGATTTAGCTTGGACTGGTAATCCTGACT
1 AAGCTCTATT-GAGCATATATACATTGAAAAAGGATTTAGCCTGGACTGGTAATCCTGACT
* * *
42616881 AAGCTCTATTGAGTATATATACATTGGAGACAGGATTTAGCCTGGACTGGTAATCCTG
1 AAGCTCTATTGAGCATATATACATT-GAAAAAGGATTTAGCCTGGACTGGTAATCCTG
42616939 TTGTATACAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
57 14 0.29
58 5 0.10
59 1 0.02
61 28 0.58
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (60 bp):
AAGCTCTATTGAGCATATATACATTGAAAAAGGATTTAGCCTGGACTGGTAATCCTGACT
Found at i:42618795 original size:80 final size:79
Alignment explanation
Indices: 42618711--42618882 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
42618701 GGACTAAGAT
*
42618711 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
42618775 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
42618791 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
42618856 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
42618870 CCGAAGGCATTTG
1 CCGAAGGCATTTG
42618883 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:42618862 original size:39 final size:39
Alignment explanation
Indices: 42618658--42618880 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
42618648 TTGAATGCTG
* * * * *
42618658 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-ATTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
42618698 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
42618737 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
42618778 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
42618818 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
42618857 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
42618881 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:42618900 original size:79 final size:80
Alignment explanation
Indices: 42618738--42618915 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
42618728 AGATACAAAT
* * * *
42618738 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
42618803 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
42618818 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
42618882 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
42618897 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
42618916 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:42633755 original size:39 final size:39
Alignment explanation
Indices: 42633600--42633818 Score: 221
Period size: 39 Copynumber: 5.6 Consensus size: 39
42633590 TTGAATGCTG
* * * * * *
42633600 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTATTAAA
** * * *
42633640 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATA-CAAA
1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTATTAAA
42633679 TCCGGGTTAAG-CCCGAAGGCATTGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTATTAAA
42633717 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTATTAAA
* * *
42633756 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTATTAAA
* * *
42633795 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
42633819 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
37 12 0.08
38 29 0.19
39 77 0.49
40 29 0.19
41 9 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTATTAAA
Found at i:42633842 original size:78 final size:78
Alignment explanation
Indices: 42633676--42633853 Score: 198
Period size: 78 Copynumber: 2.3 Consensus size: 78
42633666 TGCGAGATAC
* * * *
42633676 AAATCCGGGTT-AAGCCCGAAGGCATTGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAT
1 AAATCCGGGTTAAATCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** ***
42633740 TCGTGCGAGTTTT
66 TCGAACGAGAGCT
** * *
42633753 AAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCAT
1 AAATCCGGGTTAAATCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
*
42633818 TTGAACGAGGAGCT
66 TCGAACGA-GAGCT
*
42633832 ATATCC-GGTTAAATCCCGAAGG
1 AAATCCGGGTTAAATCCCGAAGG
42633854 TACGTGATTT
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
77 11 0.13
78 64 0.78
79 7 0.09
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (78 bp):
AAATCCGGGTTAAATCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
TCGAACGAGAGCT
Found at i:42641697 original size:38 final size:39
Alignment explanation
Indices: 42641547--42641715 Score: 180
Period size: 40 Copynumber: 4.3 Consensus size: 39
42641537 GGACTAAGAT
* * * *
42641547 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCA-TTGTGTGAGTTACTAAA-TCCGGGTTATGTC
* * * *
42641587 CCGAAGGCCTTTGTGTTAGATACTAAATCCGGGTTAAGTC
1 CCGAAGG-CATTGTGTGAGTTACTAAATCCGGGTTATGTC
* *
42641627 CCGAAGGCATTCGTGAGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATT-GTGTGAGTTACTAAATCCGGGTTATGTC
* *
42641667 CCGAA-GCATTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTGTGTGAGTTACTAAATCCGGGTTATGTC
42641705 CCGAAGGCATT
1 CCGAAGGCATT
42641716 TGAACGAGGA
Statistics
Matches: 111, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
38 29 0.26
39 13 0.12
40 65 0.59
41 4 0.04
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
CCGAAGGCATTGTGTGAGTTACTAAATCCGGGTTATGTC
Found at i:42641710 original size:78 final size:80
Alignment explanation
Indices: 42641547--42641715 Score: 200
Period size: 78 Copynumber: 2.1 Consensus size: 80
42641537 GGACTAAGAT
* * * *
42641547 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGTTAGATACTA
1 CCGAAGGCATTCGTGAGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCATTGTGTGAGATACTA
* *
42641612 AATCCGGGTTAAGTC
66 AAACCGGGCTAAGTC
* * * * *
42641627 CCGAAGGCATTCGTGAGAGTTATTAAA-TCCGGGTTATGTCCCGAA-G-CATTGTGTGAGTTACT
1 CCGAAGGCATTCGTGAGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCATTGTGTGAGATACT
*
42641689 AAAACCGGGCTATGTC
65 AAAACCGGGCTAAGTC
42641705 CCGAAGGCATT
1 CCGAAGGCATT
42641716 TGAACGAGGA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
78 37 0.49
79 1 0.01
80 35 0.46
81 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (80 bp):
CCGAAGGCATTCGTGAGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCATTGTGTGAGATACTA
AAACCGGGCTAAGTC
Found at i:42643692 original size:79 final size:81
Alignment explanation
Indices: 42643550--42643732 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
42643540 TACTCGTTCA
* * * *
42643550 AATGCCTTCGGGACATAGCCCTG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGAACTTAACCCGGA
* *
42643614 TTTAGTAAC-TCGCACC
66 TATAGTAACTTAGCA-C
**
42643630 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GAATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGAA-CTTAACCCGG
* *
42643692 ATATGGTCACTTAGCAC
65 ATATAGTAACTTAGCAC
*
42643709 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
42643733 CATCATTCGA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 2 0.02
79 58 0.66
80 28 0.32
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGAACTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:42643732 original size:40 final size:40
Alignment explanation
Indices: 42643529--42643732 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
42643519 CGGAATTTAA
** *
42643529 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
42643569 CCTGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42643609 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42643648 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GAATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42643688 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42643728 CCGGA
1 CCGGA
42643733 CATCATTCGA
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 1 0.01
39 33 0.24
40 92 0.67
41 11 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42651776 original size:39 final size:40
Alignment explanation
Indices: 42651651--42651781 Score: 167
Period size: 40 Copynumber: 3.3 Consensus size: 40
42651641 GCTACTCGTT
* * * *
42651651 CAAATTCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAAT-TAGTAACTCGCA
*
42651691 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
* * *
42651731 CCAATGCCTTCGGG-CTTAGCTCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
42651770 CAAATGCCTTCG
1 CAAATGCCTTCG
42651782 ATCTTAGTCC
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 33 0.40
40 47 0.57
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
Found at i:42651788 original size:39 final size:38
Alignment explanation
Indices: 42651679--42651834 Score: 145
Period size: 39 Copynumber: 3.9 Consensus size: 38
42651669 AGCCCGGTTA
* *
42651679 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTC--GACTTAGCCCGGAAT
* * *
42651719 TAGTAACTCGCACCAATGCCTTCGGGCTTAGCTCGGAAT
1 TAGTAACTCGCACAAATGCCTTC-GACTTAGCCCGGAAT
*
42651758 TAGTAACTCGCACAAATGCCTTCGATCTTAGTCCGG-AT
1 TAGTAACTCGCACAAATGCCTTCGA-CTTAGCCCGGAAT
* * *
42651796 ATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 -TAGTAAC-TCGCACAAATGCCTTC--GACTTAGCCCGGA
42651835 CATCATTCGA
Statistics
Matches: 97, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
38 3 0.03
39 53 0.55
40 39 0.40
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (38 bp):
TAGTAACTCGCACAAATGCCTTCGACTTAGCCCGGAAT
Found at i:42651828 original size:79 final size:80
Alignment explanation
Indices: 42651657--42651834 Score: 204
Period size: 79 Copynumber: 2.2 Consensus size: 80
42651647 CGTTCAAATT
* * *
42651657 CCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTA
1 CCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGACTTAACCCGGATATA
* *
42651721 GTAACTCGCACCAATG
65 GTAACTAGCACCAAAG
* ** *
42651737 CCTTCGGG-CTTAGCTCGGAAT-TAGTAACTCGCACAAATGCCTTC-GATCTTAGTCCGGATATG
1 CCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGA-CTTAACCCGGATATA
*
42651799 GTCACTTAGCA-CAAAG
65 GTAAC-TAGCACCAAAG
42651815 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAGCCCGGA
42651835 CATCATTCGA
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
77 2 0.02
78 27 0.33
79 45 0.54
80 9 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGATATAG
TAACTAGCACCAAAG
Done.