Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009580.1 Hibiscus syriacus cultivar Beakdansim tig00116954_pilon, whole genome shotgun sequence
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: 1633873
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 6 of 6
Found at i:1290307 original size:4 final size:4
Alignment explanation
Indices: 1290298--1290342 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
1290288 AATTCATGAA
* *
1290298 ATAC ATAC ATAC AT-- ATAT ATAC ATAC ATAC ACAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1290343 TATATTAGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
2 2 0.06
4 34 0.94
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:1304036 original size:23 final size:23
Alignment explanation
Indices: 1304006--1304049 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1303996 TTTCCACCAA
*
1304006 GTTGAGGAAGTCGACAATGATCG
1 GTTGAGGAAGACGACAATGATCG
1304029 GTTGAGGAAGACGACAATGAT
1 GTTGAGGAAGACGACAATGAT
1304050 GTTTTGTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.34, T:0.20
Consensus pattern (23 bp):
GTTGAGGAAGACGACAATGATCG
Found at i:1306879 original size:14 final size:13
Alignment explanation
Indices: 1306862--1306911 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
1306852 ATTTTTTTGT
1306862 TTATATGTTTAAGC
1 TTATAT-TTTAAGC
** *
1306876 TTATATTTTTTGT
1 TTATATTTTAAGC
1306889 TTATATATTTAAGC
1 TTATAT-TTTAAGC
1306903 TTATATTTT
1 TTATATTTT
1306912 TCTTAATGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
13 13 0.45
14 16 0.55
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.62
Consensus pattern (13 bp):
TTATATTTTAAGC
Found at i:1306889 original size:27 final size:27
Alignment explanation
Indices: 1306854--1306912 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
1306844 TTAGAAATAT
*
1306854 TTTTTTGTTTATATGTTTAAGCTTATA
1 TTTTTTGTTTATATATTTAAGCTTATA
1306881 TTTTTTGTTTATATATTTAAGCTTATA
1 TTTTTTGTTTATATATTTAAGCTTATA
1306908 TTTTT
1 TTTTT
1306913 CTTAATGCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.22, C:0.03, G:0.08, T:0.66
Consensus pattern (27 bp):
TTTTTTGTTTATATATTTAAGCTTATA
Found at i:1307348 original size:21 final size:21
Alignment explanation
Indices: 1307324--1307363 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1307314 CGACACCAAT
1307324 CGTTTGGAAG-AAAACATTAAA
1 CGTTT-GAAGAAAAACATTAAA
*
1307345 CGTTTTAAGAAAAACATTA
1 CGTTTGAAGAAAAACATTA
1307364 TTAGAACTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (21 bp):
CGTTTGAAGAAAAACATTAAA
Found at i:1317610 original size:13 final size:13
Alignment explanation
Indices: 1317592--1317617 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1317582 CATAGTTGAA
1317592 CAAACTTCATATG
1 CAAACTTCATATG
1317605 CAAACTTCATATG
1 CAAACTTCATATG
1317618 AGCATCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
CAAACTTCATATG
Found at i:1323008 original size:21 final size:21
Alignment explanation
Indices: 1322979--1323026 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1322969 TTTAAAAAAG
*
1322979 AATA-ATATACAATATATATA
1 AATATATATACAATACATATA
* *
1322999 ATTATATATATAATACATATA
1 AATATATATACAATACATATA
1323020 AATATAT
1 AATATAT
1323027 TTTGGTCGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATATATACAATACATATA
Found at i:1323658 original size:65 final size:65
Alignment explanation
Indices: 1323566--1323948 Score: 635
Period size: 65 Copynumber: 5.9 Consensus size: 65
1323556 TCTGAAATTG
* * ** * *
1323566 GGGAAGTTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCCGTCTTAAAC
1 GGGAAATT-TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACAC
1323631 T
65 T
* *
1323632 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGCGAAGTTGAACTTGTGTTGTCTGATACT
1 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACACT
* *
1323697 GGGAAATTTTTGTCGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTTTGACACT
1 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACACT
1323762 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACACT
1 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACACT
* *
1323827 GGGAAA-TTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTAAACTTGTGTTGTCTGACACT
1 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACACT
1323891 GGGAAA-TTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1323949 TGAGTGGCAC
Statistics
Matches: 300, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
64 112 0.37
65 181 0.60
66 7 0.02
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (65 bp):
GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACACT
Found at i:1331922 original size:30 final size:30
Alignment explanation
Indices: 1331866--1331994 Score: 215
Period size: 30 Copynumber: 4.3 Consensus size: 30
1331856 GAAGGACCTA
* * *
1331866 TCCAGAGGTCACACAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1331895 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1331925 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1331955 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
1331985 TCCATAGGTC
1 TCCAGAGGTC
1331995 CCGAAGAACC
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 15 0.16
30 80 0.84
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1332011 original size:30 final size:30
Alignment explanation
Indices: 1331887--1332084 Score: 139
Period size: 30 Copynumber: 6.5 Consensus size: 30
1331877 CACAGACCCC
* * * *
1331887 GGTAACTGTCCAGAGGTCATAAAGATCCTC
1 GGTAACTGTCCATAGGTCACAAAGAACCTA
* * * *
1331917 GGTAACTGTCCAGAGGTCATAAAGATCCTC
1 GGTAACTGTCCATAGGTCACAAAGAACCTA
* * * *
1331947 GGTAACTGTCCAGAGGTCATAAAGATCCTC
1 GGTAACTGTCCATAGGTCACAAAGAACCTA
* *
1331977 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATAGGTCACAAAGAACCTA
* ** *
1332007 GGTAAACTGTCCATATGTTC-CTTAGAACATA
1 GGT-AACTGTCCATA-GGTCACAAAGAACCTA
* * *
1332038 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATAGGTCAC-AAAGAACCTA
1332069 GGTAAAACTGTCCATA
1 GGT--AACTGTCCATA
1332085 TGTTCCGTAG
Statistics
Matches: 147, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
30 90 0.61
31 41 0.28
32 15 0.10
33 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (30 bp):
GGTAACTGTCCATAGGTCACAAAGAACCTA
Found at i:1332011 original size:60 final size:60
Alignment explanation
Indices: 1331866--1332019 Score: 211
Period size: 60 Copynumber: 2.6 Consensus size: 60
1331856 GAAGGACCTA
* **
1331866 TCCAGAGGTCACACAG-ACCCCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
* * *
1331925 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
* * *
1331985 TCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCA
1 TCCAGAGGTCACAAAGAACCTAGGT-AACTGTCCA
1332020 TATGTTCCTT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 14 0.17
60 60 0.72
61 9 0.11
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.21
Consensus pattern (60 bp):
TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1332090 original size:63 final size:61
Alignment explanation
Indices: 1331977--1332105 Score: 188
Period size: 63 Copynumber: 2.1 Consensus size: 61
1331967 AAAGATCCTC
* *
1331977 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
* *
1332038 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATA
1332101 GGTAA
1 GGTAA
1332106 ACCCTCGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.41
63 31 0.51
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:1332100 original size:32 final size:31
Alignment explanation
Indices: 1331980--1332107 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
1331970 GATCCTCGGT
* * * *
1331980 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
1332011 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
1332042 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
1332074 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
1332105 AAC
1 AAC
1332108 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:1332845 original size:22 final size:22
Alignment explanation
Indices: 1332801--1332842 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1332791 TAAATCAATT
*
1332801 TCATATAACTCCTATAATCTTC
1 TCATATAACTCCTATAACCTTC
*
1332823 TCATATAACTTC-ATAACCTT
1 TCATATAACTCCTATAACCTT
1332843 TCTTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
TCATATAACTCCTATAACCTTC
Found at i:1333317 original size:21 final size:21
Alignment explanation
Indices: 1333293--1333333 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1333283 CCATGTTCGT
* *
1333293 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
1333314 TTGAATGGGTATCGATTCCC
1 TTGAAGGGGTATCGATTCCC
1333334 TTGCCCAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.22, G:0.32, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:1336502 original size:30 final size:30
Alignment explanation
Indices: 1336446--1336574 Score: 224
Period size: 30 Copynumber: 4.3 Consensus size: 30
1336436 GAAGGACCTA
* *
1336446 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1336475 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1336505 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1336535 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
1336565 TCCATAGGTC
1 TCCAGAGGTC
1336575 CCGAAGAACC
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 16 0.17
30 80 0.83
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1336591 original size:30 final size:30
Alignment explanation
Indices: 1336446--1336664 Score: 138
Period size: 30 Copynumber: 7.2 Consensus size: 30
1336436 GAAGGACCTA
* **
1336446 TCCAGAGGTCACAAAG-ACCCCGGTAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* * * *
1336475 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* * * *
1336505 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* * * *
1336535 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* *
1336565 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGT-AACTG
* * ** *
1336596 TCTATATGTTC-CTTAGAACATAGGTATACTG
1 TCCATA-GGTCACAAAGAACCTAGGTA-ACTG
* * *
1336627 TCCATATGTCTCGAAAG-ACATAGGTAAAACTG
1 TCCATAGGTCAC-AAAGAACCTAGGT--AACTG
1336659 TCCATA
1 TCCATA
1336665 TGTTCCGTAG
Statistics
Matches: 163, Mismatches: 19, Indels: 13
0.84 0.10 0.07
Matches are distributed among these distances:
29 15 0.09
30 93 0.57
31 39 0.24
32 15 0.09
33 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (30 bp):
TCCATAGGTCACAAAGAACCTAGGTAACTG
Found at i:1336591 original size:60 final size:60
Alignment explanation
Indices: 1336446--1336597 Score: 216
Period size: 60 Copynumber: 2.5 Consensus size: 60
1336436 GAAGGACCTA
**
1336446 TCCAGAGGTCACAAAG-ACCCCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
* * *
1336505 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
* * *
1336565 TCCATAGGTCCCGAAGAACCTAGGTAAACTGTC
1 TCCAGAGGTCACAAAGAACCTAGGT-AACTGTC
1336598 TATATGTTCC
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 15 0.18
60 60 0.73
61 7 0.09
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (60 bp):
TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1336614 original size:31 final size:31
Alignment explanation
Indices: 1336560--1336687 Score: 134
Period size: 31 Copynumber: 4.1 Consensus size: 31
1336550 GATCCTCGGT
* * *
1336560 AACTGTCCATAGGTCCCGA-AGAACCTAGGTA
1 AACTGTCCATATGTTCC-ATAGAACATAGGTA
* *
1336591 AACTGTCTATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* * *
1336622 TACTGTCCATATGTCTCGAAAG-ACATAGGTAA
1 AACTGTCCATATGT-TCCATAGAACATAGGT-A
*
1336654 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
1336685 AAC
1 AAC
1336688 CCTCGACTCT
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
31 53 0.67
32 26 0.33
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCATAGAACATAGGTA
Found at i:1336676 original size:63 final size:61
Alignment explanation
Indices: 1336557--1336685 Score: 179
Period size: 63 Copynumber: 2.1 Consensus size: 61
1336547 AAAGATCCTC
* * *
1336557 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCTATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
* *
1336618 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATA
1336681 GGTAA
1 GGTAA
1336686 ACCCTCGACT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.42
63 30 0.50
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:1337427 original size:22 final size:22
Alignment explanation
Indices: 1337383--1337424 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1337373 TAAATCAATT
*
1337383 TCATATAACTCCTATAATCTTC
1 TCATATAACTCCTATAACCTTC
*
1337405 TCATATAACTTC-ATAACCTT
1 TCATATAACTCCTATAACCTT
1337425 TCTTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
TCATATAACTCCTATAACCTTC
Found at i:1337898 original size:21 final size:21
Alignment explanation
Indices: 1337874--1337918 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1337864 CCATGTTCGT
* * *
1337874 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1337895 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1337916 TTG
1 TTG
1337919 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1343369 original size:2 final size:2
Alignment explanation
Indices: 1343364--1343406 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1343354 ATATAAAACG
1343364 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1343405 AT
1 AT
1343407 TTTAATAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1344488 original size:21 final size:21
Alignment explanation
Indices: 1344445--1344488 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1344435 AAAAAGAATA
* **
1344445 ATATACAATATATATAATTAT
1 ATATACAATACATATAAACAT
*
1344466 ATATATAATACATATAAACAT
1 ATATACAATACATATAAACAT
1344487 AT
1 AT
1344489 TTTGGTCGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATACAATACATATAAACAT
Found at i:1353439 original size:37 final size:37
Alignment explanation
Indices: 1353366--1353437 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
1353356 TGGAAAATAC
* *
1353366 TTATATATTTTCTTTAAAAAATTTAAATTCATAAAAT
1 TTATATATTTTCTTTAAAAAATTAAAAATCATAAAAT
*
1353403 TTATATAATTTT-TTTACAAAATTAAAAAT-ATAAAA
1 TTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAAA
1353438 ATGTTTAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 6 0.19
37 20 0.65
38 5 0.16
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (37 bp):
TTATATATTTTCTTTAAAAAATTAAAAATCATAAAAT
Found at i:1354573 original size:29 final size:28
Alignment explanation
Indices: 1354529--1354590 Score: 97
Period size: 29 Copynumber: 2.2 Consensus size: 28
1354519 TTCTAGATTA
* *
1354529 CTTAATGGTTGGTTGGTAAAGAATTTTT
1 CTTAATGGTTGGTTGGTAAAGAAGTGTT
1354557 CTTAATGGCTTGGTTGGTAAAGAAGTGTT
1 CTTAATGG-TTGGTTGGTAAAGAAGTGTT
1354586 CTTAA
1 CTTAA
1354591 ATGAAGGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.42
Consensus pattern (28 bp):
CTTAATGGTTGGTTGGTAAAGAAGTGTT
Found at i:1355879 original size:18 final size:18
Alignment explanation
Indices: 1355826--1355895 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
1355816 GTTAATGATC
*
1355826 AAGAGGA-GAACATGGAAG
1 AAGAGGAGGAAGA-GGAAG
* *
1355844 AAGAGGTGG-AGTATGAAG
1 AAGAGGAGGAAG-AGGAAG
* *
1355862 AAGTGGAGGTAGAGGAAG
1 AAGAGGAGGAAGAGGAAG
1355880 AAGAGGAGGAAGAGGA
1 AAGAGGAGGAAGAGGA
1355896 GGAAATAGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
18 37 0.90
19 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.46, T:0.09
Consensus pattern (18 bp):
AAGAGGAGGAAGAGGAAG
Found at i:1355896 original size:9 final size:9
Alignment explanation
Indices: 1355861--1355899 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1355851 GGAGTATGAA
*
1355861 GAAGTGGAG
1 GAAGAGGAG
* *
1355870 GTAGAGGAA
1 GAAGAGGAG
1355879 GAAGAGGAG
1 GAAGAGGAG
1355888 GAAGAGGAG
1 GAAGAGGAG
1355897 GAA
1 GAA
1355900 ATAGAAGAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.51, T:0.05
Consensus pattern (9 bp):
GAAGAGGAG
Found at i:1385288 original size:4 final size:4
Alignment explanation
Indices: 1385279--1385381 Score: 206
Period size: 4 Copynumber: 25.8 Consensus size: 4
1385269 GATATACTTT
1385279 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1385327 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1385375 ATAC ATA
1 ATAC ATA
1385382 TATTGTAATC
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 99 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:1387370 original size:60 final size:60
Alignment explanation
Indices: 1387274--1387394 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
1387264 TGACTTAATA
1387274 CCTGCTAAAGGAATGATTCTGAATAATTCCCAGTTTTTAGTTATTTTAAGAACTTTTAAC
1 CCTGCTAAAGGAATGATTCTGAATAATTCCCAGTTTTTAGTTATTTTAAGAACTTTTAAC
*
1387334 CCTGCTAAAGGAATGATTCTGAATAATTCCCGGTTTTTAGTTATTTTAAGAACTTTTAAC
1 CCTGCTAAAGGAATGATTCTGAATAATTCCCAGTTTTTAGTTATTTTAAGAACTTTTAAC
1387394 C
1 C
1387395 GTGTTGGTTG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (60 bp):
CCTGCTAAAGGAATGATTCTGAATAATTCCCAGTTTTTAGTTATTTTAAGAACTTTTAAC
Found at i:1391802 original size:62 final size:59
Alignment explanation
Indices: 1391681--1391821 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 59
1391671 TTAAATGTTA
* * * * * *
1391681 CAATTTTATCCCTAAATTATGACTATCATTTTAAATTAGTCCTTAAATTTTTGAACATTT
1 CAATTTCATCCC-AAACTATGGCTTTCATTCTAAATTAGTCCATAAATTTTTGAACATTT
* * *
1391741 CATTTTCATCCTCAAACTATGGCTTTCATTCTAAATTGGTCCCATAAACTTTTTGATCATTT
1 CAATTTCATCC-CAAACTATGGCTTTCATTCTAAATTAGT-CCATAAA-TTTTTGAACATTT
1391803 CAATTTCATCCCAAACTAT
1 CAATTTCATCCCAAACTAT
1391822 ATATATATAC
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
60 31 0.46
61 15 0.22
62 22 0.32
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (59 bp):
CAATTTCATCCCAAACTATGGCTTTCATTCTAAATTAGTCCATAAATTTTTGAACATTT
Found at i:1392072 original size:60 final size:60
Alignment explanation
Indices: 1391940--1392105 Score: 192
Period size: 60 Copynumber: 2.8 Consensus size: 60
1391930 GATGATTTGG
* * * * *
1391940 GGATGAAATTGAAAGATTCAACAGTTTGAGGATGAATTTAAAATGAAGTTCATAGTTTGA
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGATGAATTTAAAATGAAGTTCATAGTTTAA
* * * * *
1392000 GGGTGAAGTTGGAATTTTCAAAAGTTTAAGGACT-AATTTAGAATGAAAGTT-ATCGTTTAA
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGA-TGAATTTAAAATG-AAGTTCATAGTTTAA
* *
1392060 GGATGAAATTGGAATATTCAAAAGTTTAAGAATCAATTTAAAATGA
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGATGAATTTAAAATGA
1392106 GGATCATATG
Statistics
Matches: 88, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
59 2 0.02
60 80 0.91
61 6 0.07
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.33
Consensus pattern (60 bp):
GGATGAAATTGGAATATTCAAAAGTTTAAGGATGAATTTAAAATGAAGTTCATAGTTTAA
Found at i:1393240 original size:30 final size:32
Alignment explanation
Indices: 1393204--1393264 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
1393194 GATTTGAAAA
*
1393204 AAAAATAA-AGTTT-GGATATTAAA-ATATAAT
1 AAAAATAATAATTTAGG-TATTAAACATATAAT
1393234 AAAAATAATAATTTAGGTATTAAACATATAA
1 AAAAATAATAATTTAGGTATTAAACATATAA
1393265 CCTATCCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 8 0.30
31 11 0.41
32 8 0.30
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (32 bp):
AAAAATAATAATTTAGGTATTAAACATATAAT
Found at i:1395129 original size:27 final size:27
Alignment explanation
Indices: 1395098--1395152 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1395088 ATAAAAGTAT
*
1395098 AAATAAATATCATTATCAATAATAAAA
1 AAATAAATATCATTAACAATAATAAAA
* * *
1395125 AAATAAGTATTATTAACACTAATAAAA
1 AAATAAATATCATTAACAATAATAAAA
1395152 A
1 A
1395153 TAAATAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (27 bp):
AAATAAATATCATTAACAATAATAAAA
Found at i:1395716 original size:26 final size:26
Alignment explanation
Indices: 1395678--1395737 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
1395668 CCGCCCCAAT
*
1395678 TTTTTAT-TCTT-AATTAGGGCCTCTAA
1 TTTTTATATCTTAAATTA-AGCC-CTAA
1395704 TTTTTATAT-TTAAAATTAAGCCCTAA
1 TTTTTATATCTT-AAATTAAGCCCTAA
1395730 TTTTTATA
1 TTTTTATA
1395738 ATTCCATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 21 0.70
27 4 0.13
28 5 0.17
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.52
Consensus pattern (26 bp):
TTTTTATATCTTAAATTAAGCCCTAA
Found at i:1402344 original size:267 final size:268
Alignment explanation
Indices: 1401864--1402400 Score: 1058
Period size: 267 Copynumber: 2.0 Consensus size: 268
1401854 GCATAAACAT
1401864 AAAATGTGTCTCCATCCGCATAAACAACTTATTGATCGAATAAACTGGGTGCAGTTTAGGTGATA
1 AAAATGTGTCTCCATCCGCATAAACAACTTATTGATCGAATAAACTGGGTGCAGTTTAGGTGATA
1401929 GGCTGCATGAGTATCACCATAAAGATCAAGACTCGAGTTCAGTATATTTTCACATACAGGAAAGG
66 GGCTGCATGAGTATCACCATAAAGATCAAGACTCGAGTTCAGTATATTTTCACATACAGGAAAGG
1401994 TATACCTGGAAACCCGAAGTAAAAATTACACAGGCAATGACTGACATGGTTGTAACTCTTTGAAA
131 TATACCTGGAAACCCGAAGTAAAAATTACACAGGCAATGACTGACATGGTTGTAACTCTTTGAAA
*
1402059 TATTGTAACACTTTTGTAGTCTTTACTAAAAATTGAGTGACGTGTACCGTAATTTACCC-TTTCT
196 TATTGTAACACATTTGTAGTCTTTACTAAAAATTGAGTGACGTGTACCGTAATTTACCCTTTTCT
1402123 TTTCTAAA
261 TTTCTAAA
1402131 AAAATGTGTCTCCATCCGCATAAACAACTTATTGATCGAATAAACTGGGTGCAGTTTAGGTGATA
1 AAAATGTGTCTCCATCCGCATAAACAACTTATTGATCGAATAAACTGGGTGCAGTTTAGGTGATA
1402196 GGCTGCATGAGTATCACCATAAAGATCAAGACTCGAGTTCAGTATATTTTCACATACAGGAAAGG
66 GGCTGCATGAGTATCACCATAAAGATCAAGACTCGAGTTCAGTATATTTTCACATACAGGAAAGG
1402261 TATACCTGGAAACCCGAAGTAAAAATTACACAGGCAATGACTGACATGGTTGTAACTCTTTGAAA
131 TATACCTGGAAACCCGAAGTAAAAATTACACAGGCAATGACTGACATGGTTGTAACTCTTTGAAA
1402326 TATTGTAACACATTTGTAGTCTTTACTAAAAATTGAGTGACGTGTACCGTAATTTACCCTTTTCT
196 TATTGTAACACATTTGTAGTCTTTACTAAAAATTGAGTGACGTGTACCGTAATTTACCCTTTTCT
1402391 TTTCTAAA
261 TTTCTAAA
1402399 AA
1 AA
1402401 TAGAAAAGAA
Statistics
Matches: 268, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
267 253 0.94
268 15 0.06
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (268 bp):
AAAATGTGTCTCCATCCGCATAAACAACTTATTGATCGAATAAACTGGGTGCAGTTTAGGTGATA
GGCTGCATGAGTATCACCATAAAGATCAAGACTCGAGTTCAGTATATTTTCACATACAGGAAAGG
TATACCTGGAAACCCGAAGTAAAAATTACACAGGCAATGACTGACATGGTTGTAACTCTTTGAAA
TATTGTAACACATTTGTAGTCTTTACTAAAAATTGAGTGACGTGTACCGTAATTTACCCTTTTCT
TTTCTAAA
Found at i:1403381 original size:54 final size:54
Alignment explanation
Indices: 1403267--1403389 Score: 210
Period size: 54 Copynumber: 2.3 Consensus size: 54
1403257 GGTTCTCGCA
* *
1403267 TAAGGCATGGGCACAGCTTATTCATCCTGAGCTATCACAGAAGAAGTATTCAGT
1 TAAGGCGTGGGCACGGCTTATTCATCCTGAGCTATCACAGAAGAAGTATTCAGT
*
1403321 TAAGGCGTGGGCACGGCTTATTCATCCTGAGCTATCACAGAAGAAGTCTTCAGT
1 TAAGGCGTGGGCACGGCTTATTCATCCTGAGCTATCACAGAAGAAGTATTCAGT
*
1403375 TAAGGCGGGGGCACG
1 TAAGGCGTGGGCACG
1403390 CCGACTATCG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (54 bp):
TAAGGCGTGGGCACGGCTTATTCATCCTGAGCTATCACAGAAGAAGTATTCAGT
Found at i:1418836 original size:10 final size:10
Alignment explanation
Indices: 1418829--1418866 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1418819 GAACGTTCAG
1418829 TTATGTTCGT
1 TTATGTTCGT
* *
1418839 TTTTGTTCGG
1 TTATGTTCGT
1418849 TTATGTTCGT
1 TTATGTTCGT
1418859 TTATGTTC
1 TTATGTTC
1418867 ATTCATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.08, C:0.11, G:0.21, T:0.61
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:1418846 original size:20 final size:20
Alignment explanation
Indices: 1418823--1418867 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1418813 GTTCGTGAAC
*
1418823 GTTCAGTTATGTTCGTTTTT
1 GTTCAGTTATGTTCGTTTAT
*
1418843 GTTCGGTTATGTTCGTTTAT
1 GTTCAGTTATGTTCGTTTAT
1418863 GTTCA
1 GTTCA
1418868 TTCATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.11, G:0.22, T:0.56
Consensus pattern (20 bp):
GTTCAGTTATGTTCGTTTAT
Found at i:1419497 original size:16 final size:16
Alignment explanation
Indices: 1419476--1419542 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
1419466 GTCTCCAATG
1419476 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
1419492 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
* *
1419508 TTTATGTTTGTGTTCG
1 TTTATGTTCGTGTTCA
1419524 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
1419538 TTTAT
1 TTTAT
1419543 TAAATGAACG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 40 0.85
ACGTcount: A:0.10, C:0.09, G:0.19, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1419629 original size:16 final size:16
Alignment explanation
Indices: 1419604--1419634 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1419594 AAAAACATTT
1419604 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
1419620 TGTTCCTTTATGTTC
1 TGTTCATTTATGTTC
1419635 ATTTATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:1422456 original size:28 final size:27
Alignment explanation
Indices: 1422395--1422457 Score: 85
Period size: 25 Copynumber: 2.4 Consensus size: 27
1422385 GACACTACAT
*
1422395 AATTTGATTAGTTATAATAAGCAATTT
1 AATTTGATTAGTTATAATAAGCAATTA
*
1422422 AA--TGATTAGTTATAATAAGCAGTTA
1 AATTTGATTAGTTATAATAAGCAATTA
1422447 AATTTTGATTA
1 AA-TTTGATTA
1422458 AGAAAATTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 23 0.74
27 2 0.06
28 6 0.19
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.43
Consensus pattern (27 bp):
AATTTGATTAGTTATAATAAGCAATTA
Found at i:1424976 original size:48 final size:48
Alignment explanation
Indices: 1424921--1425016 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
1424911 GAAGCTTCCT
1424921 CTCTTTTGCCTTCTGACTCCAAGAAAGTTAGTGATTTATGGAGTGAGA
1 CTCTTTTGCCTTCTGACTCCAAGAAAGTTAGTGATTTATGGAGTGAGA
1424969 CTCTTTTGCCTTCTGACTCCAAGAAAGTTAGTGATTTATGGAGTGAGA
1 CTCTTTTGCCTTCTGACTCCAAGAAAGTTAGTGATTTATGGAGTGAGA
1425017 TTAGGGTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (48 bp):
CTCTTTTGCCTTCTGACTCCAAGAAAGTTAGTGATTTATGGAGTGAGA
Found at i:1427553 original size:22 final size:22
Alignment explanation
Indices: 1427528--1427571 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1427518 CTCTCAATTC
1427528 AATTTG-TTCTGTCAAAATTAGA
1 AATTTGTTTC-GTCAAAATTAGA
1427550 AATTTGTTTCGTCAAAATTAGA
1 AATTTGTTTCGTCAAAATTAGA
1427572 TGTTGCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (22 bp):
AATTTGTTTCGTCAAAATTAGA
Found at i:1427705 original size:32 final size:32
Alignment explanation
Indices: 1427669--1427731 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
1427659 ATACAATAAC
* *
1427669 TTTAATAGTCATTCTATAATAGTATAATAAAA
1 TTTAATAATCATTCTATAATAATATAATAAAA
* * *
1427701 TTTAATAATTATTTTATAATAATTTAATAAA
1 TTTAATAATCATTCTATAATAATATAATAAA
1427732 TAATGATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (32 bp):
TTTAATAATCATTCTATAATAATATAATAAAA
Found at i:1427714 original size:11 final size:11
Alignment explanation
Indices: 1427693--1427735 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1427683 TATAATAGTA
1427693 TAATAA-AATT
1 TAATAATAATT
*
1427703 TAATAATTATT
1 TAATAATAATT
*
1427714 TTATAATAATT
1 TAATAATAATT
1427725 TAATAAATAAT
1 TAAT-AATAAT
1427736 GATTATTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 6 0.22
11 15 0.56
12 6 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAATAATAATT
Found at i:1435831 original size:19 final size:19
Alignment explanation
Indices: 1435784--1435865 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 19
1435774 TAAAAATAAT
* *
1435784 AATTATATATATATATATATA
1 AATTA-ATATATTTA-ATTTA
*
1435805 ATATTAATAAATTTAATTTA
1 A-ATTAATATATTTAATTTA
* *
1435825 AATTAATATATAT-ATATA
1 AATTAATATATTTAATTTA
*
1435843 ATATTTATATATTTAATTTA
1 A-ATTAATATATTTAATTTA
1435863 AAT
1 AAT
1435866 ATATATACCC
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
18 5 0.10
19 22 0.45
20 10 0.20
21 8 0.16
22 4 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTAATATATTTAATTTA
Found at i:1435842 original size:38 final size:36
Alignment explanation
Indices: 1435769--1435872 Score: 131
Period size: 38 Copynumber: 2.9 Consensus size: 36
1435759 CGGCCCGATA
* *
1435769 AATATTAA-AAATAATAA-TTATATATATATATATAT
1 AATATTAATAAAT-TTAATTTAAATATATATATATAT
1435804 AATATTAATAAATTTAATTTAAATTAATATATATATAT
1 AATATTAATAAATTTAATTTAAA-T-ATATATATATAT
* *
1435842 AATATTTATATATTTAATTTAAATATATATA
1 AATATTAATAAATTTAATTTAAATATATATA
1435873 CCCGGCCTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
35 11 0.18
36 15 0.25
37 2 0.03
38 33 0.54
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (36 bp):
AATATTAATAAATTTAATTTAAATATATATATATAT
Found at i:1436044 original size:11 final size:11
Alignment explanation
Indices: 1436024--1436054 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1436014 GGGGACCAAT
*
1436024 ACCCGGCCCGA
1 ACCCGACCCGA
1436035 ACCCGACCCGA
1 ACCCGACCCGA
1436046 ACCCGACCC
1 ACCCGACCC
1436055 ATTGTCATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (11 bp):
ACCCGACCCGA
Found at i:1437428 original size:29 final size:30
Alignment explanation
Indices: 1437395--1437454 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
1437385 TTCGTTTTTC
1437395 CAGTTTAGTGCCTAACATTT-ATTTCATTA
1 CAGTTTAGTGCCTAACATTTCATTTCATTA
* * *
1437424 CAGTTTGGTGCCTAACGTTTCATTTCGTTA
1 CAGTTTAGTGCCTAACATTTCATTTCATTA
1437454 C
1 C
1437455 TCAAAATGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (30 bp):
CAGTTTAGTGCCTAACATTTCATTTCATTA
Found at i:1437988 original size:2 final size:2
Alignment explanation
Indices: 1437953--1437980 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1437943 TCTTTTTTTA
1437953 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1437981 TTTATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1444173 original size:20 final size:20
Alignment explanation
Indices: 1444150--1444191 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1444140 GAGTGTCCAA
1444150 CATATCTGGTGTTCAGGTCT
1 CATATCTGGTGTTCAGGTCT
1444170 CATATCTGGTGTTCAGGTCT
1 CATATCTGGTGTTCAGGTCT
1444190 CA
1 CA
1444192 GGATGCCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (20 bp):
CATATCTGGTGTTCAGGTCT
Found at i:1446219 original size:160 final size:159
Alignment explanation
Indices: 1445877--1446392 Score: 687
Period size: 160 Copynumber: 3.2 Consensus size: 159
1445867 AACAATGCAA
* * * * *
1445877 ATTGTAAAAACAAAAGACATTGATAACCGATTTAAATCGTCGAAAAATCGTATCCGACACTCA-T
1 ATTGTCAAAACAAAAGACATTCATAACCAATTTAAATCGTCGAAAACTCGTATCTGACACTCACT
* * * *
1445941 AATCGAATCTAAATAACATAGCTTCGATGATCGAATTCATGTGTATCATTATGAAAACTCAAATT
66 -CTCGAGTCTAAATAACATAGCTTCGATGATCGAATT--TGCGTATCATAATGAAAACTCAAATT
* * * *
1446006 TACCTTGAAAGCAAGAGAAGGATCTGCAACAC
128 TACCTTGAAAGCAAGAGCATGATCTACCACAC
* ** * *
1446038 ATTGTCAAAACAAAAGACATTCATAACCGATTTAAATCGTCGAAAACTCACATTTGACGCTCACT
1 ATTGTCAAAACAAAAGACATTCATAACCAATTTAAATCGTCGAAAACTCGTATCTGACACTCACT
* *
1446103 CTCGGGTCTAAATAACATAACTTCGATG-TCCGAATTTGACGTATCATAATGAAAACTCAAATTT
66 CTCGAGTCTAAATAACATAGCTTCGATGAT-CGAATTTG-CGTATCATAATGAAAACTCAAATTT
1446167 ACCTTGAAAGCAAGAGCATGATCTACCACAC
129 ACCTTGAAAGCAAGAGCATGATCTACCACAC
* * * * *
1446198 GTTGTCAAAATAAAAGACATTCATAACCAATTTAAATCGTTGAAAACTCGTATCTAACACTCACA
1 ATTGTCAAAACAAAAGACATTCATAACCAATTTAAATCGTCGAAAACTCGTATCTGACACTCACT
* * * *
1446263 CTCGAGTCTAAATAACATAGTTTCGATGATTGAATTTGCGTCTCA-AATGAAAACTCAGATTTAC
66 CTCGAGTCTAAATAACATAGCTTCGATGATCGAATTTGCGTATCATAATGAAAACTCAAATTTAC
* *
1446327 CTTAAAAGCAAGAGCATGGTCTACCACAC
131 CTTGAAAGCAAGAGCATGATCTACCACAC
1446356 ATTGTCAAAACAAAAGACATTCATAACCAATTTAAAT
1 ATTGTCAAAACAAAAGACATTCATAACCAATTTAAAT
1446393 AATCAAAAAA
Statistics
Matches: 313, Mismatches: 38, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
158 80 0.26
159 8 0.03
160 138 0.44
161 86 0.27
162 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (159 bp):
ATTGTCAAAACAAAAGACATTCATAACCAATTTAAATCGTCGAAAACTCGTATCTGACACTCACT
CTCGAGTCTAAATAACATAGCTTCGATGATCGAATTTGCGTATCATAATGAAAACTCAAATTTAC
CTTGAAAGCAAGAGCATGATCTACCACAC
Found at i:1449768 original size:36 final size:38
Alignment explanation
Indices: 1449695--1449770 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 38
1449685 TATTCAGCAC
*
1449695 AGCAGGAAGACGAAGCTTGAAGTTAACCTATAAAAGGCA
1 AGCAGGAAGAAGAAGCTTGAAGTT-ACCTATAAAAGGCA
1449734 AGCAGGAAGAAGAAGCTTGAAG-T-CCTATAAAAGGCA
1 AGCAGGAAGAAGAAGCTTGAAGTTACCTATAAAAGGCA
1449770 A
1 A
1449771 TGACATGGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
36 14 0.39
38 1 0.03
39 21 0.58
ACGTcount: A:0.45, C:0.14, G:0.26, T:0.14
Consensus pattern (38 bp):
AGCAGGAAGAAGAAGCTTGAAGTTACCTATAAAAGGCA
Found at i:1474923 original size:4 final size:4
Alignment explanation
Indices: 1474914--1474940 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1474904 AGTCACTGTT
1474914 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1474941 TCACATCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1477479 original size:201 final size:202
Alignment explanation
Indices: 1477134--1477536 Score: 799
Period size: 201 Copynumber: 2.0 Consensus size: 202
1477124 TCTTCACTGA
1477134 CTGCTCAAGACATCGAGACACGTCGAGGAACGAATGTAATATGTATTGTCTCGATTGCATGAAAC
1 CTGCTCAAGACATCGAGACACGTCGAGGAACGAATGTAATATGTATTGTCTCGATTGCATGAAAC
1477199 ATGCATTTTGCTTCTACTGCCGATCCTCCGCACACAAAGATCATCTCGTGATTCAGGTGCACGTC
66 ATGCATTTTGCTTCTACTGCCGATCCTCCGCACACAAAGATCATCTCGTGATTCAGGTGCACGTC
1477264 ACATTTCTTTTTCTATTTTTCATTTGCCATAAGAGATAAATCCGGGTGAGCTAACCAAGTT-AAC
131 ACATTTCTTTTTCTATTTTTCATTTGCCATAAGAGATAAATCCGGGTGAGCTAACCAAGTTAAAC
1477328 TCTAGGT
196 TCTAGGT
1477335 CTGCTCAAGACATCGAGACACGTCGAGGAACGAATGTAATATGTATTGTCTCGATTGCATGAAAC
1 CTGCTCAAGACATCGAGACACGTCGAGGAACGAATGTAATATGTATTGTCTCGATTGCATGAAAC
1477400 ATGCATTTTGCTTCTACTGCCGATCCTCCGCACACAAAGATCATCTCGTGATTCAGGTGCACGTC
66 ATGCATTTTGCTTCTACTGCCGATCCTCCGCACACAAAGATCATCTCGTGATTCAGGTGCACGTC
1477465 ACATTTCTTTTTCTATTTTTCATTTGCCATAAGAGATAAATCCGGGTGAGCTAACCAAGTTAAAC
131 ACATTTCTTTTTCTATTTTTCATTTGCCATAAGAGATAAATCCGGGTGAGCTAACCAAGTTAAAC
1477530 TCTAGGT
196 TCTAGGT
1477537 TTCCTCGAAT
Statistics
Matches: 201, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
201 191 0.95
202 10 0.05
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (202 bp):
CTGCTCAAGACATCGAGACACGTCGAGGAACGAATGTAATATGTATTGTCTCGATTGCATGAAAC
ATGCATTTTGCTTCTACTGCCGATCCTCCGCACACAAAGATCATCTCGTGATTCAGGTGCACGTC
ACATTTCTTTTTCTATTTTTCATTTGCCATAAGAGATAAATCCGGGTGAGCTAACCAAGTTAAAC
TCTAGGT
Found at i:1480055 original size:2 final size:2
Alignment explanation
Indices: 1480048--1480098 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1480038 TAAACAAATG
1480048 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1480090 TA TA TA TA T
1 TA TA TA TA T
1480099 TTATCCATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1484776 original size:125 final size:124
Alignment explanation
Indices: 1484479--1484813 Score: 387
Period size: 125 Copynumber: 2.7 Consensus size: 124
1484469 AGTTAACGGA
* * * * **
1484479 TAACAGAGTCCGAACCATAATAATGTAGATCATACTCCGAATCGGGTCACCACAAGGTCGAATCA
1 TAACAGAGTTCGAACCATAATAATATGGATCATACTCCGGATCTAGTCACCACAAGGTCGAATCA
*
1484544 AATATTAGAAACAA-AAATAAATAAACAATGGTTAAATATAATAAAAAAAGTCAATAGT
66 AATATTAGAAACAATAAATAAACAAACAATGGTTAAATATAATAAAAAAAGTCAATAGT
* * *
1484602 TAACAGAG-TCTGAACCATAATAATACGGATCATA-TCCCGA-GTAGGGTCACCACAAGGTCGAA
1 TAACAGAGTTC-GAACCATAATAATATGGATCATACTCCGGATCTA--GTCACCACAAGGTCGAA
* * *
1484664 TCTAATATTAGAAATAATAAATAAACAAA-AATGGTTAAAGT-TAAATAAATAAAAGTTAATAGT
63 TCAAATATTAGAAACAATAAATAAACAAACAATGGTTAAA-TAT-AATAAA-AAAAGTCAATAGT
* * * * *
1484727 TAGCAGAGTTCGAACCATAATGATATGGATCATACTCTGGATCTAGTCACCAAAAGGTCGAATCC
1 TAACAGAGTTCGAACCATAATAATATGGATCATACTCCGGATCTAGTCACCACAAGGTCGAATCA
*
1484792 AATAATA-ACAACAATAAATAAA
66 AATATTAGA-AACAATAAATAAA
1484814 TAAATAAACA
Statistics
Matches: 178, Mismatches: 23, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
122 5 0.03
123 71 0.40
124 18 0.10
125 76 0.43
126 6 0.03
127 2 0.01
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (124 bp):
TAACAGAGTTCGAACCATAATAATATGGATCATACTCCGGATCTAGTCACCACAAGGTCGAATCA
AATATTAGAAACAATAAATAAACAAACAATGGTTAAATATAATAAAAAAAGTCAATAGT
Found at i:1484846 original size:30 final size:30
Alignment explanation
Indices: 1484811--1484878 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
1484801 AACAATAAAT
* *
1484811 AAATAAATAAA-CAATGGTTAGA-ATGTAATA
1 AAATAAA-AAATCAATAGTTA-ATATGCAATA
1484841 AAATAAAAAATCAATAGTTAATATGCAATA
1 AAATAAAAAATCAATAGTTAATATGCAATA
1484871 AAATAAAA
1 AAATAAAA
1484879 TTAGTAGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.62, C:0.04, G:0.09, T:0.25
Consensus pattern (30 bp):
AAATAAAAAATCAATAGTTAATATGCAATA
Found at i:1492376 original size:18 final size:17
Alignment explanation
Indices: 1492354--1492386 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1492344 GATTCTAATT
1492354 TTTTTTTGAGTTCAAGC
1 TTTTTTTGAGTTCAAGC
1492371 TTTTTTTGAGTTCAAG
1 TTTTTTTGAGTTCAAG
1492387 TTTCAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (17 bp):
TTTTTTTGAGTTCAAGC
Found at i:1492792 original size:24 final size:24
Alignment explanation
Indices: 1492760--1492816 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
1492750 ACAGAGGTCC
*
1492760 CGAAGGACCGCGTAGAATTTGTCA
1 CGAAAGACCGCGTAGAATTTGTCA
*
1492784 CGAATGACCGCGTAGAATTTGTCA
1 CGAAAGACCGCGTAGAATTTGTCA
1492808 CGAAAGACC
1 CGAAAGACC
1492817 ACATATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (24 bp):
CGAAAGACCGCGTAGAATTTGTCA
Found at i:1493045 original size:29 final size:30
Alignment explanation
Indices: 1493003--1493072 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
1492993 ACATAATTTA
* *
1493003 TATCACATAGACATAACA-TTCTATACCTT
1 TATCACATAAACATAACATTTCCATACCTT
**
1493032 TATCACATAAACATTTCATTTTCCATACCTT
1 TATCACATAAACATAACA-TTTCCATACCTT
*
1493063 TATCCCATAA
1 TATCACATAA
1493073 TTCATATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 15 0.44
31 19 0.56
ACGTcount: A:0.36, C:0.26, G:0.01, T:0.37
Consensus pattern (30 bp):
TATCACATAAACATAACATTTCCATACCTT
Found at i:1500841 original size:23 final size:23
Alignment explanation
Indices: 1500810--1500878 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
1500800 CACCACAGCT
*
1500810 CGTATAATTGCACCTAAGTGCCA
1 CGTAGAATTGCACCTAAGTGCCA
* *
1500833 CTTAGAATTGCACC-AGAGTGCCG
1 CGTAGAATTGCACCTA-AGTGCCA
1500856 CGTAGAATTGCACCGT-AGTGCCA
1 CGTAGAATTGCACC-TAAGTGCCA
1500879 TATAATAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 1 0.03
23 37 0.97
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCTAAGTGCCA
Found at i:1501025 original size:103 final size:103
Alignment explanation
Indices: 1500894--1501111 Score: 427
Period size: 103 Copynumber: 2.1 Consensus size: 103
1500884 TAATGTCCAT
1500894 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1500959 GACCTCACACATGTTCCAAAGAATACATATATGCCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGCCCCG
1500997 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
1501062 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGCCCCG
1501100 AAGGACCACATA
1 AAGGACCACATA
1501112 GACCCTCTAC
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 114 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.24
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGCCCCG
Found at i:1501681 original size:21 final size:21
Alignment explanation
Indices: 1501657--1501699 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1501647 TCATATTCGT
*
1501657 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
1501678 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
1501699 T
1 T
1501700 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:1507987 original size:103 final size:103
Alignment explanation
Indices: 1507816--1508033 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
1507806 TAATGTCCAT
* * *
1507816 AAGGACCACATATCATTCTTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATACGCCAAGGATCAAGTATGTGTCTCACCA
1507881 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
1507919 AAGGACCACATATCATTCCTTAAGAATCATATACATACGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATACGCCAAGGATCAAGTATGTGTCTCACCA
1507984 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
1508022 AAGGACCACATA
1 AAGGACCACATA
1508034 GACCCTCTAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATACGCCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1511686 original size:63 final size:63
Alignment explanation
Indices: 1511571--1511696 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
1511561 TATTAACCAT
* * * * ** *
1511571 CTCGACTTCATTATGGATTTCTGCATTACCAACTTCTTCATGCACGGTGGTGGTATTTGGTAA
1 CTCGACTTCATAATGGACTTCTGCATCACCAACTTCTTCATACACGACGGTGGTATTTAGTAA
* * *
1511634 CTCGACTTCATAATGTACTTCTGCATCACCATCTTCTTCATATACGACGGTGGTATTTAGTAA
1 CTCGACTTCATAATGGACTTCTGCATCACCAACTTCTTCATACACGACGGTGGTATTTAGTAA
1511697 GTGATTGGTA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37
Consensus pattern (63 bp):
CTCGACTTCATAATGGACTTCTGCATCACCAACTTCTTCATACACGACGGTGGTATTTAGTAA
Found at i:1514300 original size:19 final size:19
Alignment explanation
Indices: 1514278--1514321 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1514268 CTAACTGATT
* *
1514278 CTTATCAAACTAACAGTTC
1 CTTAACAAACAAACAGTTC
1514297 CTTAACAAACAAACAGTTC
1 CTTAACAAACAAACAGTTC
1514316 CTTAAC
1 CTTAAC
1514322 TACCATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.41, C:0.27, G:0.05, T:0.27
Consensus pattern (19 bp):
CTTAACAAACAAACAGTTC
Found at i:1514339 original size:22 final size:22
Alignment explanation
Indices: 1514308--1514358 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1514298 TTAACAAACA
*
1514308 AACAGTTCCTTAACTACCATTT
1 AACAGCTCCTTAACTACCATTT
1514330 AACAGCTCCTTAACTACCATTT
1 AACAGCTCCTTAACTACCATTT
1514352 AACAGCT
1 AACAGCT
1514359 TATGCCAACG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.31
Consensus pattern (22 bp):
AACAGCTCCTTAACTACCATTT
Found at i:1535256 original size:8 final size:8
Alignment explanation
Indices: 1535243--1535269 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1535233 ATAAAAGTAG
1535243 AATAGTTT
1 AATAGTTT
1535251 AATAGTTT
1 AATAGTTT
1535259 AATAGTTT
1 AATAGTTT
1535267 AAT
1 AAT
1535270 GACTTATTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (8 bp):
AATAGTTT
Found at i:1536583 original size:2 final size:2
Alignment explanation
Indices: 1536578--1536617 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1536568 TATATATATA
1536578 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1536618 AACATAAGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1540311 original size:40 final size:40
Alignment explanation
Indices: 1540253--1540414 Score: 288
Period size: 40 Copynumber: 4.0 Consensus size: 40
1540243 ACTGTAGTGC
* *
1540253 TACACATAAGGTCATGCCCACCATATACACCGAAGTATAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1540293 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1540333 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
1540373 TACACATAAGGTTGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1540413 TA
1 TA
1540415 TAAACCTGCA
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 118 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1545030 original size:16 final size:16
Alignment explanation
Indices: 1545006--1545040 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1544996 AATTGTAACC
*
1545006 ATTGTTGATATCACTT
1 ATTGATGATATCACTT
*
1545022 ATTGATGATTTCACTT
1 ATTGATGATATCACTT
1545038 ATT
1 ATT
1545041 CATCAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.51
Consensus pattern (16 bp):
ATTGATGATATCACTT
Found at i:1546629 original size:30 final size:30
Alignment explanation
Indices: 1546593--1546653 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1546583 ATTAATATTA
*
1546593 TGCATCGATACGCTACAGTAACCGCTACAG
1 TGCATCGATACGCTACAATAACCGCTACAG
1546623 TGCATCGATACGCTACAATAACCGCTACAG
1 TGCATCGATACGCTACAATAACCGCTACAG
1546653 T
1 T
1546654 AATTTCAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (30 bp):
TGCATCGATACGCTACAATAACCGCTACAG
Found at i:1547225 original size:40 final size:40
Alignment explanation
Indices: 1547181--1547258 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
1547171 ACCGTAGTGC
1547181 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTTT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTTT
*
1547221 TACACATAAGGTCGTGCTCACCATATACACCGAAGTGT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGT
1547259 ATTATAAACC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTTT
Found at i:1552825 original size:2 final size:2
Alignment explanation
Indices: 1552818--1552843 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1552808 ATCATTGATA
1552818 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
1552844 AACATAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1554111 original size:23 final size:23
Alignment explanation
Indices: 1554083--1554166 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
1554073 CTCGTATAAA
*
1554083 TGCACCTAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
1554106 TACACCGAAGTGCCGCGTATAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
1554129 TGCACCGAAGTGCCGCTTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1554152 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
1554167 TATAAAATGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1554142 original size:46 final size:46
Alignment explanation
Indices: 1554075--1554165 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
1554065 CACCACAGCT
*
1554075 CGTATAAATGCACCTAAGTGCCACGTAGAATTACACCGAAGTGCCG
1 CGTATAAATGCACCGAAGTGCCACGTAGAATTACACCGAAGTGCCG
* * * *
1554121 CGTATAATTGCACCGAAGTGCCGCTTAGAATTGCACCGAAGTGCC
1 CGTATAAATGCACCGAAGTGCCACGTAGAATTACACCGAAGTGCC
1554166 ATATAAAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (46 bp):
CGTATAAATGCACCGAAGTGCCACGTAGAATTACACCGAAGTGCCG
Found at i:1555670 original size:24 final size:20
Alignment explanation
Indices: 1555617--1555674 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1555607 TTCCCTTTGA
*
1555617 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
1555637 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1555660 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1555675 CTACCCATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1555752 original size:63 final size:63
Alignment explanation
Indices: 1555662--1555820 Score: 187
Period size: 63 Copynumber: 2.5 Consensus size: 63
1555652 TCTTTAACAT
* * * * * *
1555662 GTGCATCGATGCACTACCCATGTATCGATACACAAATTACCTTCGATGTTTTC-A-TTTAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATTACATTCAATGTTTCCAATTTTAAGAG
* *
1555724 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTACATTCAATGTTTCCAATTTTAAGAG
1 G-TGCATCGATGCACTCC-TATGCATCGATACACAAATTACATTCAATGTTTCCAATTTTAAGAG
*
1555789 GTGCATCGATGCACTTCCTGTGCATCGATACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACA
1555821 TACTGAACAA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
62 3 0.04
63 42 0.51
64 26 0.32
65 11 0.13
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATTACATTCAATGTTTCCAATTTTAAGAG
Found at i:1558774 original size:12 final size:12
Alignment explanation
Indices: 1558757--1558788 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1558747 TTGCTCTTCT
1558757 TCGCTTCTATTC
1 TCGCTTCTATTC
1558769 TCGCTTCTATTC
1 TCGCTTCTATTC
1558781 TCGCTTCT
1 TCGCTTCT
1558789 GTAACCTACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.34, G:0.09, T:0.50
Consensus pattern (12 bp):
TCGCTTCTATTC
Found at i:1559303 original size:23 final size:23
Alignment explanation
Indices: 1559277--1559330 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
1559267 AAATGCACAT
*
1559277 AAGTGCCACATAGAATTGCACTG
1 AAGTGCCACATAGAATTGCACCG
* *
1559300 AAGTGCCGCGTAGAATTGCACCG
1 AAGTGCCACATAGAATTGCACCG
1559323 AAGTGCCA
1 AAGTGCCA
1559331 TATAAAATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (23 bp):
AAGTGCCACATAGAATTGCACCG
Found at i:1560898 original size:64 final size:63
Alignment explanation
Indices: 1560820--1560981 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 63
1560810 TCTTTAACAT
* * * *
1560820 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCA-TTTTAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGAG
* * * * *
1560883 GATGCATCGATGCACTCCTTATACATTGATGCACCAATTGCATTCGATGTTTCCATTTTTAAGAG
1 G-TGCATCGATGCACTCC-TATGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGAG
* * *
1560948 GTGTATTGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
1560982 CTGAACAATT
Statistics
Matches: 79, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
63 3 0.04
64 64 0.81
65 12 0.15
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGAG
Found at i:1561511 original size:24 final size:23
Alignment explanation
Indices: 1561450--1561507 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1561440 TATCATCTAA
1561450 TAATCAAAAACCAATCTTAAATT
1 TAATCAAAAACCAATCTTAAATT
*
1561473 TAACCAAAAACCAATCTTAAATT
1 TAATCAAAAACCAATCTTAAATT
*
1561496 TAATTAAAAACC
1 TAATCAAAAACC
1561508 CAATAATCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (23 bp):
TAATCAAAAACCAATCTTAAATT
Found at i:1561841 original size:3 final size:3
Alignment explanation
Indices: 1561827--1561901 Score: 132
Period size: 3 Copynumber: 24.7 Consensus size: 3
1561817 AGAGATATTC
*
1561827 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCT TCTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT
1561873 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1561902 ATGTACGAGA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
3 66 0.96
4 3 0.04
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:1562508 original size:64 final size:64
Alignment explanation
Indices: 1562439--1562597 Score: 196
Period size: 64 Copynumber: 2.5 Consensus size: 64
1562429 TTGAAGGTGT
** **
1562439 ATCGATGCATTGGTAGTGCATCGATGCACT-CTTTTAA-AATAAAAACATAGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCA-TACCATTAATAAT-AAAACATAGAATGCAATTCATG
1562502 C
64 C
* * * *
1562503 ATCGATGCATAAGTAGTGCATCGATGCATACCATTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATACCATTAATAATAAAACATAGAATGCAATTCATGC
* *
1562567 ACCGATGCATCAGTAGTGCATCGATGCATAC
1 ATCGATGCATAAGTAGTGCATCGATGCATAC
1562598 TTTCATTGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 1 0.01
64 79 0.95
65 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATACCATTAATAATAAAACATAGAATGCAATTCATGC
Found at i:1563290 original size:31 final size:31
Alignment explanation
Indices: 1563252--1563396 Score: 263
Period size: 31 Copynumber: 4.7 Consensus size: 31
1563242 AGGGTCGAGG
1563252 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1563283 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1563314 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1563345 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1563376 GTTTACCTAGGTTCTTCGGGA
1 GTTTACCTATGTTCTTCGGGA
1563397 TCTATAGACT
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 112 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1564306 original size:23 final size:23
Alignment explanation
Indices: 1564253--1564309 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
1564243 CTTATATAGC
* *
1564253 ACTTCGGTGCATTTCTACGCGGC
1 ACTTCGGTGCAATTCTACGCGGA
*
1564276 A-TTACGGTGCAATTCTACGTGGA
1 ACTT-CGGTGCAATTCTACGCGGA
1564299 ACTTCGGTGCA
1 ACTTCGGTGCA
1564310 TTTATTTGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 2 0.07
23 25 0.86
24 2 0.07
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
ACTTCGGTGCAATTCTACGCGGA
Found at i:1571806 original size:2 final size:2
Alignment explanation
Indices: 1571801--1571849 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
1571791 TTAAAATCTG
* * *
1571801 AT AT AT AT AT AT AT AT AT AT AT AC AT AT TT A- AT AT AT TT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1571841 AT AT -T AT AT
1 AT AT AT AT AT
1571850 TAAAATGGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1572223 original size:23 final size:23
Alignment explanation
Indices: 1572178--1572223 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1572168 AATATCATTT
*
1572178 TAATCAAAATATTAATTATTAAG
1 TAATCAAAATATTAATTAATAAG
*
1572201 TAATTAAAATATT-ATTAAATAAG
1 TAATCAAAATATTAATT-AATAAG
1572224 AATATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (23 bp):
TAATCAAAATATTAATTAATAAG
Found at i:1572276 original size:24 final size:23
Alignment explanation
Indices: 1572217--1572285 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
1572207 AAATATTATT
1572217 AAATAAGAATATAATAAATATAAA
1 AAATAA-AATATAATAAATATAAA
* ** *
1572241 TAATCATTATATTATAAATATATAA
1 AAAT-AAAATATAATAAATATA-AA
*
1572266 AAATAAAATATAAAAAATAT
1 AAATAAAATATAATAAATAT
1572286 TTAATAAAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
24 28 0.82
25 6 0.18
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (23 bp):
AAATAAAATATAATAAATATAAA
Found at i:1572385 original size:33 final size:32
Alignment explanation
Indices: 1572347--1572410 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
1572337 ATGATAATGT
*
1572347 ATATTT-AAATTTAATAATTTAATATATTTAAAG
1 ATATTTAAAATATAATAA-TTAATAT-TTTAAAG
*
1572380 ATATTTAAAATATACTAATTAATATTTTAAA
1 ATATTTAAAATATAATAATTAATATTTTAAA
1572411 AATAATAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 6 0.21
33 13 0.46
34 9 0.32
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (32 bp):
ATATTTAAAATATAATAATTAATATTTTAAAG
Found at i:1576979 original size:21 final size:23
Alignment explanation
Indices: 1576955--1577008 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1576945 ATTAACATAT
1576955 TAAATCATACA-TGA-AATAATA
1 TAAATCATACATTGAGAATAATA
*
1576976 TAAAT-ATATATTTGAGAATAATA
1 TAAATCATACA-TTGAGAATAATA
1576999 TAAATACATA
1 TAAAT-CATA
1577009 AATATGAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.15
21 5 0.19
22 3 0.11
23 12 0.44
25 3 0.11
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (23 bp):
TAAATCATACATTGAGAATAATA
Found at i:1580176 original size:348 final size:350
Alignment explanation
Indices: 1579529--1580178 Score: 1151
Period size: 350 Copynumber: 1.9 Consensus size: 350
1579519 AATATGGATT
*
1579529 AGGATTTCAAAGATAGTGTAAATTGAGTAAAAAATACCTAGAAATGTAATATTGATGATTCTTTC
1 AGGATTTCAAAGATAGTGTAAATTGAGTAAAAAATACCTA-AAATGTAATATTAATGATTCTTTC
1579594 TCAAAGCCTTGCTGATATAGTAATGATGTTGAAATTTCTAGTTCATAATTGGATTTGATAAATCC
65 TCAAAGCCTTGCTGATATAGTAATGATGTTGAAATTTCTAGTTCATAATTGGATTTGATAAATCC
1579659 AAATTTCTATACTTTTCATCTATATATTGTATTGAATCCCAACTATTTCCCTCTAGTGTATACAT
130 AAATTTCTATACTTTTCATCTATATATTGTATTGAATCCCAACTA-TTCCCTCTAGTGTATACAT
1579724 TTCATTCTTATCATTTACATGATAAAAGAAGTCCAAACTCAAATTTTGAAATCCAAGTTCCCAAA
194 TTCATTCTTATCATTTACATGATAAAAGAAGTCCAAACTCAAATTTTGAAATCCAAGTTCCCAAA
*
1579789 TGGAGCATTAAGATTTTAGAGAAATTCTCATGCAGAACTAATTTGAAGAACTAATTATTGCAAAC
259 CGGAGCATTAAGATTTTAGAGAAATTCTCATGCAGAACTAATTTGAAGAACTAATTATTGCAAAC
1579854 GCATACATACCTTTTAGATTTAAGAAA
324 GCATACATACCTTTTAGATTTAAGAAA
*
1579881 AGGATTTCAAAGATAGTGTAAATTGAGTAAACAATACCT-AAATGTAATATTAATGATTCTTTCT
1 AGGATTTCAAAGATAGTGTAAATTGAGTAAAAAATACCTAAAATGTAATATTAATGATTCTTTCT
* * * *
1579945 CAAAGCCTTGCTGATATAGTAATGATTTTGAAATTTTTAGTTTATATTTGGATTTGATAAATCCA
66 CAAAGCCTTGCTGATATAGTAATGATGTTGAAATTTCTAGTTCATAATTGGATTTGATAAATCCA
* * *
1580010 AGTTTCTATACTTTTCATCTATATATTGTATTGAATCCTAACTA-TCTCTCTAGTGTATACATTT
131 AATTTCTATACTTTTCATCTATATATTGTATTGAATCCCAACTATTCCCTCTAGTGTATACATTT
* * *
1580074 CATTCTTATCGTTTACATGATAAATGAAGTCCAAACTCAAATTTTGAAATCCAAGTTCCCGAACG
196 CATTCTTATCATTTACATGATAAAAGAAGTCCAAACTCAAATTTTGAAATCCAAGTTCCCAAACG
1580139 GAGCATTAAGATTTTAGAGAAATTCTCATGCAGAACTAAT
261 GAGCATTAAGATTTTAGAGAAATTCTCATGCAGAACTAAT
1580179 CATTGCAAAT
Statistics
Matches: 285, Mismatches: 13, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
348 120 0.42
350 127 0.45
352 38 0.13
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (350 bp):
AGGATTTCAAAGATAGTGTAAATTGAGTAAAAAATACCTAAAATGTAATATTAATGATTCTTTCT
CAAAGCCTTGCTGATATAGTAATGATGTTGAAATTTCTAGTTCATAATTGGATTTGATAAATCCA
AATTTCTATACTTTTCATCTATATATTGTATTGAATCCCAACTATTCCCTCTAGTGTATACATTT
CATTCTTATCATTTACATGATAAAAGAAGTCCAAACTCAAATTTTGAAATCCAAGTTCCCAAACG
GAGCATTAAGATTTTAGAGAAATTCTCATGCAGAACTAATTTGAAGAACTAATTATTGCAAACGC
ATACATACCTTTTAGATTTAAGAAA
Found at i:1582857 original size:24 final size:24
Alignment explanation
Indices: 1582830--1582936 Score: 160
Period size: 24 Copynumber: 4.5 Consensus size: 24
1582820 ACTGGCGAAC
* * *
1582830 GAGATCTACGATGTAAAGGTGATG
1 GAGATCTACGACGCATAGGTGATG
* *
1582854 GAGATCTATGACGTATAGGTGATG
1 GAGATCTACGACGCATAGGTGATG
*
1582878 GAGATCTACGACGCATAGGTGAAG
1 GAGATCTACGACGCATAGGTGATG
1582902 GAGATCTACGACGCATAGGTGATG
1 GAGATCTACGACGCATAGGTGATG
1582926 GAGATCTACGA
1 GAGATCTACGA
1582937 TATCGAACAG
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.32, C:0.13, G:0.33, T:0.22
Consensus pattern (24 bp):
GAGATCTACGACGCATAGGTGATG
Found at i:1582860 original size:72 final size:72
Alignment explanation
Indices: 1582784--1582937 Score: 168
Period size: 72 Copynumber: 2.1 Consensus size: 72
1582774 AGGCAGCAAG
** * *
1582784 GATCTACGATGTATAGGAGAAGGAGATCTGTGA-GAA-ACTGGCGAACGAGATCTACGATGTAAA
1 GATCTACGATGTATAGGAGAAGGAGATCTACGACGAATA--GGCGAACGAGATCTACGACGCAAA
1582847 GGTGATGGA
64 GGTGATGGA
* * * * * * * *
1582856 GATCTATGACGTATAGGTGATGGAGATCTACGACGCATAGGTGAAGGAGATCTACGACGCATAGG
1 GATCTACGATGTATAGGAGAAGGAGATCTACGACGAATAGGCGAACGAGATCTACGACGCAAAGG
1582921 TGATGGA
66 TGATGGA
1582928 GATCTACGAT
1 GATCTACGAT
1582938 ATCGAACAGG
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
72 63 0.95
73 2 0.03
74 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.22
Consensus pattern (72 bp):
GATCTACGATGTATAGGAGAAGGAGATCTACGACGAATAGGCGAACGAGATCTACGACGCAAAGG
TGATGGA
Found at i:1592052 original size:29 final size:31
Alignment explanation
Indices: 1592020--1592081 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1592010 CCTCGTATAT
* *
1592020 TTATACCTA-TTTA-AACTTTCGTACCTAAA
1 TTATACCAATTTTATAACTTTAGTACCTAAA
*
1592049 TTATACCAATTTTATAAGTTTAGTACCTAAA
1 TTATACCAATTTTATAACTTTAGTACCTAAA
1592080 TT
1 TT
1592082 GTTTACAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.29
30 4 0.14
31 16 0.57
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (31 bp):
TTATACCAATTTTATAACTTTAGTACCTAAA
Found at i:1601873 original size:38 final size:38
Alignment explanation
Indices: 1601817--1601892 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
1601807 TTTCACCCTG
*
1601817 AACCCGAACCTGACCGACCCAAATATCACACTTAAAAA
1 AACCCGAACCCGACCGACCCAAATATCACACTTAAAAA
*
1601855 AACCCG-ACCCGACTCGACCCGAATATCACACTTAAAAA
1 AACCCGAACCCGAC-CGACCCAAATATCACACTTAAAAA
1601893 CCCGACTCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 6 0.17
38 29 0.83
ACGTcount: A:0.42, C:0.36, G:0.09, T:0.13
Consensus pattern (38 bp):
AACCCGAACCCGACCGACCCAAATATCACACTTAAAAA
Found at i:1610257 original size:16 final size:16
Alignment explanation
Indices: 1610233--1610266 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1610223 TATCGCCGAC
*
1610233 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1610249 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1610265 CG
1 CG
1610267 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1613468 original size:30 final size:30
Alignment explanation
Indices: 1613434--1613500 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
1613424 CTATCTCTTG
1613434 TAAAAATATGGATTTTTATAGTATATGTAT
1 TAAAAATATGGATTTTTATAGTATATGTAT
1613464 TAAAAATATGGATTTTTATAGTATATGTAT
1 TAAAAATATGGATTTTTATAGTATATGTAT
1613494 TAAAAAT
1 TAAAAAT
1613501 CATGTTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (30 bp):
TAAAAATATGGATTTTTATAGTATATGTAT
Found at i:1619556 original size:18 final size:18
Alignment explanation
Indices: 1619533--1619592 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
1619523 ACCGGTCACA
1619533 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
1619551 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
1619569 ACCTGACCCTTGA-CCGTTG
1 ACCCGACCC--GACCCGTTG
1619588 ACCCG
1 ACCCG
1619593 TTGACTGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 25 0.69
19 9 0.25
20 2 0.06
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.17
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1619602 original size:15 final size:14
Alignment explanation
Indices: 1619572--1619605 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1619562 CCCGTTTACC
1619572 TGACCCTTGACCGT
1 TGACCCTTGACCGT
*
1619586 TGACCCGTTGACTGT
1 TGACCC-TTGACCGT
1619601 TGACC
1 TGACC
1619606 GGAGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.15, C:0.32, G:0.24, T:0.29
Consensus pattern (14 bp):
TGACCCTTGACCGT
Found at i:1620926 original size:18 final size:18
Alignment explanation
Indices: 1620900--1620935 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1620890 TCGAAAGGAC
*
1620900 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1620918 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1620936 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1622144 original size:24 final size:24
Alignment explanation
Indices: 1622074--1622163 Score: 121
Period size: 23 Copynumber: 3.8 Consensus size: 24
1622064 TCCGACTTGA
* *
1622074 ATTCTGTTATGAT-CCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
1622097 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
1622120 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
1622144 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
1622164 TTGAATTATG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
23 32 0.56
24 25 0.44
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:1624354 original size:13 final size:13
Alignment explanation
Indices: 1624354--1624397 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1624344 CCGTTGACCC
1624354 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1624367 TACCCGACCCGTT
1 GACCCGACCCGTT
*
1624380 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
1624395 GAC
1 GAC
1624398 TGTTGACCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
15 11 0.42
ACGTcount: A:0.16, C:0.41, G:0.23, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1624355 original size:18 final size:18
Alignment explanation
Indices: 1624332--1624377 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
1624322 ACCGGTCACA
1624332 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
1624350 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
1624368 ACCCGACCCG
1 ACCCGACCCG
1624378 TTGACCGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1624392 original size:15 final size:15
Alignment explanation
Indices: 1624372--1624405 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1624362 CCGTTTACCC
1624372 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
*
1624387 GACCCGTTGACTGTT
1 GACCCGTTGACCGTT
1624402 GACC
1 GACC
1624406 GGAGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.32, G:0.26, T:0.26
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:1625726 original size:18 final size:18
Alignment explanation
Indices: 1625700--1625735 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1625690 TCGAAAGGAC
*
1625700 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1625718 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1625736 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1626933 original size:24 final size:24
Alignment explanation
Indices: 1626863--1626952 Score: 121
Period size: 23 Copynumber: 3.8 Consensus size: 24
1626853 TCCGACTTGA
* *
1626863 ATTCTGTTATGAT-CCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
1626886 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
1626909 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
1626933 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
1626953 TTGAATTATG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
23 32 0.56
24 25 0.44
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Done.