Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008656.1 Hibiscus syriacus cultivar Beakdansim tig00111650_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: 2456495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1817750 original size:12 final size:12
Alignment explanation
Indices: 1817733--1817758 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1817723 AGAGAACATT
1817733 TTTTTATTATTA
1 TTTTTATTATTA
1817745 TTTTTATTATTA
1 TTTTTATTATTA
1817757 TT
1 TT
1817759 ATAGGATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:1817754 original size:15 final size:14
Alignment explanation
Indices: 1817730--1817760 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1817720 AGTAGAGAAC
1817730 ATTTTTTTATTATT
1 ATTTTTTTATTATT
1817744 ATTTTTATTATTATT
1 ATTTTT-TTATTATT
1817759 AT
1 AT
1817761 AGGATAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTTTTTATTATT
Found at i:1820989 original size:2 final size:2
Alignment explanation
Indices: 1820982--1821014 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1820972 CTATAATTTA
1820982 AT AT AT AT AT AT AT AT AT -T AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1821015 ATTTTCAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1821005 original size:7 final size:7
Alignment explanation
Indices: 1820982--1821013 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1820972 CTATAATTTA
1820982 ATATA-T
1 ATATATT
1820988 ATATA-T
1 ATATATT
1820994 ATATATT
1 ATATATT
1821001 ATATATT
1 ATATATT
1821008 ATATAT
1 ATATAT
1821014 AATTTTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 11 0.44
7 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
ATATATT
Found at i:1823005 original size:109 final size:109
Alignment explanation
Indices: 1822811--1823299 Score: 741
Period size: 109 Copynumber: 4.5 Consensus size: 109
1822801 TGATTACCAA
* * * *
1822811 ATGGCACTATGCGTACAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGTCACTTT
1 ATGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTT
*
1822876 GTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGT
66 GTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGT
*
1822920 ATAGGCACTTTGTGTGCAAAACTAAGAAATT-ATAATAAGTTTATGAATTTTCGTATGGGCACTT
1 AT-GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTT
* *
1822984 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTACAT
65 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGT
* * *** *
1823029 ATGGGCAATTTGTGTGCAAAACTAAAAAATTCATAATAAGTTTATGAATTTTTTTATAGGCACTT
1 AT-GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTT
1823094 TGTGTGCAAAACTAAGAAATTCATAATAAG-TTATGAATTTCCGT
65 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGT
*
1823138 ATGTGCACTTTGTGTG-AAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCACT
1 ATG-GCACTTTGTGTGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACT
* *
1823202 TTTTGTGCAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGT
64 TTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGT
* *
1823248 ATGGACACTTTGTGTGCAAAACTAAGAAATTCATTATAAATTTATGAATTTC
1 ATGG-CACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTC
1823300 TATATTGTTA
Statistics
Matches: 346, Mismatches: 27, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
108 5 0.01
109 195 0.56
110 142 0.41
111 4 0.01
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (109 bp):
ATGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTT
GTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGT
Found at i:1823097 original size:164 final size:165
Alignment explanation
Indices: 1822826--1823299 Score: 767
Period size: 164 Copynumber: 2.9 Consensus size: 165
1822816 ACTATGCGTA
*
1822826 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGTCACTTTGTGTGCAAAACTAAG
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAG
1822891 AAATTCATAATAAGTTTATGAATTTCTGTATAGGCACTTTGTGTGCAAAACTAAGAAATT-ATAA
66 AAATTCATAATAAGTTTATGAATTTCTGTATAGGCACTTTGTGTGCAAAACTAAGAAATTCATAA
*
1822955 TAAGTTTATGAATTTTCGTATGGGCACTTTGTGTG
131 TAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
* * * *
1822990 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTACATATGGGCAATTTGTGTGCAAAACTAAA
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAG
* *
1823055 AAATTCATAATAAGTTTATGAATTTTTTTATAGGCACTTTGTGTGCAAAACTAAGAAATTCATAA
66 AAATTCATAATAAGTTTATGAATTTCTGTATAGGCACTTTGTGTGCAAAACTAAGAAATTCATAA
*
1823120 TAAG-TTATGAATTTCCGTATGTGCACTTTGTGTG
131 TAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
* * *
1823154 -AAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCACTTTTTGTGCAAAGCTAA
1 CAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAA
*
1823218 GAAATTCATAATAAGTTTATGAATTTCCGTAT-GGACACTTTGTGTGCAAAACTAAGAAATTCAT
65 GAAATTCATAATAAGTTTATGAATTTCTGTATAGG-CACTTTGTGTGCAAAACTAAGAAATTCAT
* *
1823282 TATAAATTTATGAATTTC
129 AATAAGTTTATGAATTTC
1823300 TATATTGTTA
Statistics
Matches: 285, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
163 6 0.02
164 260 0.91
165 19 0.07
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (165 bp):
CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAG
AAATTCATAATAAGTTTATGAATTTCTGTATAGGCACTTTGTGTGCAAAACTAAGAAATTCATAA
TAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
Found at i:1823321 original size:55 final size:55
Alignment explanation
Indices: 1822826--1823299 Score: 747
Period size: 55 Copynumber: 8.7 Consensus size: 55
1822816 ACTATGCGTA
*
1822826 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGTCACTTTGTGTG
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
* *
1822881 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATAGGCACTTTGTGTG
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
*
1822936 CAAAACTAAGAAATT-ATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTG
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
* * *
1822990 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTACATATGGGCAATTTGTGTG
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
* *** *
1823045 CAAAACTAAAAAATTCATAATAAGTTTATGAATTTTTTTATAGGCACTTTGTGTG
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
*
1823100 CAAAACTAAGAAATTCATAATAAG-TTATGAATTTCCGTATGTGCACTTTGTGTG
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
* *
1823154 -AAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCACTTTTTGTG
1 CAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
* *
1823209 CAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTTTGTGTG
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
* *
1823264 CAAAACTAAGAAATTCATTATAAATTTATGAATTTC
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTC
1823300 TATATTGTTA
Statistics
Matches: 385, Mismatches: 30, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
53 4 0.01
54 95 0.25
55 283 0.74
56 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (55 bp):
CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
Found at i:1823321 original size:219 final size:219
Alignment explanation
Indices: 1822826--1823304 Score: 748
Period size: 219 Copynumber: 2.2 Consensus size: 219
1822816 ACTATGCGTA
** *
1822826 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGTCACTTTGTGTGCAAAACTAAG
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTATATAGTCACTTTGTGTGCAAAACTAAG
*
1822891 AAATTCATAATAAGTTTATGAATTTCTGTATAGGCACTTTGTGTGCAAAACTAAGAAATTATAAT
66 AAATTCATAATAAGTTTATGAATTTCCGTATAGGCACTTTGTGTGCAAAACTAAGAAATTATAAT
* *
1822956 AAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGA
131 AAGTTTATGAATTTCCGTATGAGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGA
*
1823021 ATTTACATATGGGCAATTTGTGTG
196 ATTTACATATGGACAATTTGTGTG
* * * *
1823045 CAAAACTAAAAAATTCATAATAAGTTTATGAATTTTTTTATAGGCACTTTGTGTGCAAAACTAAG
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTATATAGTCACTTTGTGTGCAAAACTAAG
1823110 AAATTCATAATAAG-TTATGAATTTCCGTAT-GTGCACTTTGTGTG-AAAAGCTAAGAAATTCAT
66 AAATTCATAATAAGTTTATGAATTTCCGTATAG-GCACTTTGTGTGCAAAA-CTAAGAAATT-AT
* *
1823172 AATAAGTTTATGAATTTCCGTATGAGCACTTTTTGTGCAAAGCTAAGAAATTCATAATAAGTTTA
128 AATAAGTTTATGAATTTCCGTATGAGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTA
* * *
1823237 TGAATTTCCGTATGGACACTTTGTGTG
193 TGAATTTACATATGGACAATTTGTGTG
* *
1823264 CAAAACTAAGAAATTCATTATAAATTTATGAATTTCTATAT
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTATAT
1823305 TGTTAGTGGA
Statistics
Matches: 237, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
217 5 0.02
218 37 0.16
219 195 0.82
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (219 bp):
CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTATATAGTCACTTTGTGTGCAAAACTAAG
AAATTCATAATAAGTTTATGAATTTCCGTATAGGCACTTTGTGTGCAAAACTAAGAAATTATAAT
AAGTTTATGAATTTCCGTATGAGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGA
ATTTACATATGGACAATTTGTGTG
Found at i:1823654 original size:46 final size:46
Alignment explanation
Indices: 1823597--1823684 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
1823587 TTAGATGAAG
* *
1823597 AACAGTGCATAATTGGCATGAAAGGATG-TCATAAATGAAAATGTAT
1 AACAATGCATAATTGGCATGAAAGGATGCT-ACAAATGAAAATGTAT
1823643 AACAATGCATAATTGGCATGAAAGGATGCTACAAATGAAAAT
1 AACAATGCATAATTGGCATGAAAGGATGCTACAAATGAAAAT
1823685 ACGTAGCGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
46 38 0.97
47 1 0.03
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.24
Consensus pattern (46 bp):
AACAATGCATAATTGGCATGAAAGGATGCTACAAATGAAAATGTAT
Found at i:1828572 original size:17 final size:16
Alignment explanation
Indices: 1828552--1828611 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 16
1828542 CATAATTAAA
*
1828552 AAAATTAAATAACAAAT
1 AAAATAAAATAA-AAAT
1828569 AAAATAAAATAAAAATAGT
1 AAAATAAAAT-AAAA-A-T
*
1828588 AAAAAAAGAATAAAAAT
1 AAAATAA-AATAAAAAT
1828605 AAAATAA
1 AAAATAA
1828612 TGACCTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 18 0.50
18 4 0.11
19 11 0.31
20 3 0.08
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAATAAAATAAAAAT
Found at i:1828583 original size:11 final size:11
Alignment explanation
Indices: 1828551--1828611 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 11
1828541 ACATAATTAA
*
1828551 AAAAATTAAAT
1 AAAAATAAAAT
1828562 AACAAATAAAAT
1 AA-AAATAAAAT
1828574 -AAAATAAAAAT
1 AAAAAT-AAAAT
*
1828585 AGTAAAAAAAGAAT
1 A--AAAATAA-AAT
1828599 AAAAATAAAAT
1 AAAAATAAAAT
1828610 AA
1 AA
1828612 TGACCTAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
10 4 0.10
11 13 0.32
12 14 0.34
13 2 0.05
14 8 0.20
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:1831783 original size:20 final size:20
Alignment explanation
Indices: 1831760--1831810 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1831750 GTTTCCAAAT
*
1831760 TCGCAATGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
* *
1831780 TCGCTACGCGAATTTGTAAA
1 TCGCAACGCGAATCTGTAAA
1831800 TCGCAACGCGA
1 TCGCAACGCGA
1831811 TAGTCAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:1832903 original size:18 final size:18
Alignment explanation
Indices: 1832880--1832915 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1832870 AAGCAAAAGG
*
1832880 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1832898 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1832916 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1833718 original size:18 final size:18
Alignment explanation
Indices: 1833697--1833733 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1833687 GTAATTGGAG
1833697 TTTGAATTTCAATTTCAA
1 TTTGAATTTCAATTTCAA
* *
1833715 TTTGAGTTTGAATTTCAA
1 TTTGAATTTCAATTTCAA
1833733 T
1 T
1833734 ATAAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTCAATTTCAA
Found at i:1833740 original size:24 final size:24
Alignment explanation
Indices: 1833689--1833741 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1833679 TTTCATATGT
* * *
1833689 AATTGGAGTTTGAATTTCAATTTC
1 AATTTGAGTTTGAATTTCAATATA
1833713 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTCAATATA
1833737 AATTT
1 AATTT
1833742 TGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTCAATATA
Found at i:1834084 original size:38 final size:39
Alignment explanation
Indices: 1834042--1834127 Score: 147
Period size: 38 Copynumber: 2.2 Consensus size: 39
1834032 TCCGATGCTC
*
1834042 ATCAAAATCCAAAGCTCATATGGTGCCAA-CAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAAGAA
*
1834080 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAAGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAAGAA
1834119 ATCAAAATC
1 ATCAAAATC
1834128 TACAACTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 28 0.62
39 17 0.38
ACGTcount: A:0.49, C:0.21, G:0.13, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAAGAA
Found at i:1834360 original size:20 final size:20
Alignment explanation
Indices: 1834335--1834420 Score: 78
Period size: 20 Copynumber: 4.7 Consensus size: 20
1834325 CCAAAAATTA
1834335 CGTTGCGAATTTGACTTTCG
1 CGTTGCGAATTTGACTTTCG
*
1834355 CGTTGCGAATTTGACTATCG
1 CGTTGCGAATTTGACTTTCG
***
1834375 CAAAGC----TT-A-TTTCG
1 CGTTGCGAATTTGACTTTCG
*
1834389 CGTTGTGAATTTGACTTT-G
1 CGTTGCGAATTTGACTTTCG
1834408 CGTTGCGAATTTG
1 CGTTGCGAATTTG
1834421 TACCTTCAAC
Statistics
Matches: 50, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
14 6 0.12
15 1 0.02
16 2 0.04
18 2 0.04
19 14 0.28
20 25 0.50
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGAATTTGACTTTCG
Found at i:1834562 original size:66 final size:60
Alignment explanation
Indices: 1834480--1834619 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 60
1834470 TTTTAGAAAT
*
1834480 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATT----AAGC-AAAAAATAAATCTTATTTACACATC-AATT
1834545 A
60 A
* * *
1834546 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACACATCAATTA
1834606 AACAAATCAACTTT
1 AACAAATCAACTTT
1834620 CAATGTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
60 19 0.27
61 22 0.31
62 3 0.04
66 26 0.37
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.31
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACACATCAATTA
Found at i:1837980 original size:19 final size:20
Alignment explanation
Indices: 1837910--1837973 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
1837900 AAACTTAAAT
1837910 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1837930 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
1837950 TCGCAACACGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
1837969 TCGCA
1 TCGCA
1837974 TTGCGAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
19 9 0.21
20 33 0.79
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1839426 original size:20 final size:20
Alignment explanation
Indices: 1839401--1839456 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1839391 TATTTAAAAC
1839401 AATAAAAAAATAAAACTTT-A
1 AATAAAAAAATAAAA-TTTAA
*
1839421 AATAAATTAAA-AAAATTTAA
1 AATAAA-AAAATAAAATTTAA
1839441 AATAATAAAAATAAAA
1 AATAA-AAAAATAAAA
1839457 ATAATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 3 0.10
20 19 0.63
21 8 0.27
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
AATAAAAAAATAAAATTTAA
Found at i:1844411 original size:17 final size:17
Alignment explanation
Indices: 1844389--1844427 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1844379 TATTTTATTC
*
1844389 ATGTAAAGTT-AGATTAA
1 ATGTAAA-TTAAGATGAA
1844406 ATGTAAATTAAGATGAA
1 ATGTAAATTAAGATGAA
1844423 ATGTA
1 ATGTA
1844428 CCTAACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (17 bp):
ATGTAAATTAAGATGAA
Found at i:1845983 original size:45 final size:45
Alignment explanation
Indices: 1845894--1846062 Score: 252
Period size: 45 Copynumber: 3.8 Consensus size: 45
1845884 GTAAACATGT
* * *
1845894 AAATAAGCTTAAGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1845938 AAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* **
1845983 AAATAAACTTACGAGCTTATGAAATAAATGGTAAGTATATTAATA
1 AAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
1846028 AAATAAGCTTACGAGCTTAT-GAGATAAATGGTAAG
1 AAATAAACTTACGAGCTTATGGA-ATAAATGGTAAG
1846063 AAATTTTATA
Statistics
Matches: 115, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
44 24 0.21
45 91 0.79
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.30
Consensus pattern (45 bp):
AAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:1850225 original size:20 final size:20
Alignment explanation
Indices: 1850200--1850250 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1850190 GCCTGACCAA
1850200 TATCGATACTATGCTCATGG
1 TATCGATACTATGCTCATGG
1850220 TATCGATACTATGCTCATGG
1 TATCGATACTATGCTCATGG
1850240 TATCGATACTA
1 TATCGATACTA
1850251 CTTTGTGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (20 bp):
TATCGATACTATGCTCATGG
Found at i:1853672 original size:11 final size:11
Alignment explanation
Indices: 1853652--1853683 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1853642 ATACTTTGTA
*
1853652 AAATTATTTTG
1 AAATTGTTTTG
1853663 AAATTGTTTTG
1 AAATTGTTTTG
1853674 AAATTGTTTT
1 AAATTGTTTT
1853684 TAAGATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (11 bp):
AAATTGTTTTG
Found at i:1854419 original size:21 final size:21
Alignment explanation
Indices: 1854395--1854434 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1854385 ATAATGAATA
*
1854395 GTCAAATTGAAATATTAAAAG
1 GTCAAATTAAAATATTAAAAG
**
1854416 GTCATTTTAAAATATTAAA
1 GTCAAATTAAAATATTAAA
1854435 TGACCAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (21 bp):
GTCAAATTAAAATATTAAAAG
Found at i:1858256 original size:23 final size:23
Alignment explanation
Indices: 1858226--1858270 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1858216 GGTGGCCTTG
*
1858226 ATGGAAGATGGTGTTGATGTTGA
1 ATGGAAGATGGTGGTGATGTTGA
1858249 ATGGAAGATGGTGGTGATGTTG
1 ATGGAAGATGGTGGTGATGTTG
1858271 TATCTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.33
Consensus pattern (23 bp):
ATGGAAGATGGTGGTGATGTTGA
Found at i:1883111 original size:30 final size:30
Alignment explanation
Indices: 1883075--1883133 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
1883065 ACTTTGGCTT
* *
1883075 TTCTTTTAGGATAATGATTATTTAGGTAAG
1 TTCTTTTAGAATAATGATTATTTACGTAAG
*
1883105 TTCTTTTAGAATAGTGATTATTTACGTAA
1 TTCTTTTAGAATAATGATTATTTACGTAA
1883134 ATAACACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (30 bp):
TTCTTTTAGAATAATGATTATTTACGTAAG
Found at i:1885778 original size:210 final size:211
Alignment explanation
Indices: 1885378--1885811 Score: 536
Period size: 210 Copynumber: 2.1 Consensus size: 211
1885368 GATACACATG
* * * * * *
1885378 TTGTATCGTATTGGTATCATATCACTCAAAATATAATTTCTTAAGGTTAGGGCTTGATAAAAGTT
1 TTGTACCGTATTGGTACCATATCACCCAAAATAGAATTTCTTAAGGTTAGGACCTGATAAAAGTT
** * * *
1885443 GGAGGAAAATAGATAAGAGACATACCTATAGAACCAAACTATGTGTTTACCGGTACGCTTATTAA
66 GGAGGAAAATAGATAAGAGACATACCTATAGAACCAAACTATGTGCGTACCAGTACGATCATTAA
* * ** ** **
1885508 TGAGTATCAGTACGTTTAACAGAAAGGGACCGGTACGTATCGTGTATCGATATGATTGAAACACA
131 TGAGTACCAGTACGCTTAACAGAAAGGGACCAATACCCATCGTGTATCGATACAATTGAAACACA
1885573 CTGAAATTTCCCATAA
196 CTGAAATTTCCCATAA
*
1885589 TTGTACCGTATTGGTACCGTATCACCCAAAATAGAATTTCTTAAGGTTAGGACCTGATAAAA-TT
1 TTGTACCGTATTGGTACCATATCACCCAAAATAGAATTTCTTAAGGTTAGGACCTGATAAAAGTT
* *
1885653 GG-GGAAAACGT-G-TAAGAGACATACTTATAGCACCTAAACTATGTGCGTACCAGTACGATCAT
66 GGAGGAAAA--TAGATAAGAGACATACCTATAGAACC-AAACTATGTGCGTACCAGTACGATCAT
* * *
1885715 TAATTAGTACCAGTACGCTTAATAGAAAGGGATCAATACCCATCGTGTATC-AGTACAATTGAAA
128 TAATGAGTACCAGTACGCTTAACAGAAAGGGACCAATACCCATCGTGTATCGA-TACAATTGAAA
* * **
1885779 CACAGTGGAATTTTGCATAA
192 CACACTGAAATTTCCCATAA
1885799 TTGTACCGTATTG
1 TTGTACCGTATTG
1885812 ATACACATGT
Statistics
Matches: 190, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
209 27 0.14
210 107 0.56
211 56 0.29
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (211 bp):
TTGTACCGTATTGGTACCATATCACCCAAAATAGAATTTCTTAAGGTTAGGACCTGATAAAAGTT
GGAGGAAAATAGATAAGAGACATACCTATAGAACCAAACTATGTGCGTACCAGTACGATCATTAA
TGAGTACCAGTACGCTTAACAGAAAGGGACCAATACCCATCGTGTATCGATACAATTGAAACACA
CTGAAATTTCCCATAA
Found at i:1886260 original size:234 final size:232
Alignment explanation
Indices: 1885593--1886390 Score: 874
Period size: 233 Copynumber: 3.4 Consensus size: 232
1885583 CCATAATTGT
*
1885593 ACCGTATTGGTACCGTATCACCCAAAATAGAATTTCTTAAGGTTA-GGACCTGAT-AAAATTGGG
1 ACCGTATTGGTACCGTATCACCCAAAATAGAATTTCTTAAGGTTAGGGA-TTGATAAAAATTGGG
** * *
1885656 GAAAACGTGTAAGAGACATACTTATAGCACCTAAACTATGTGCGTACC-AGTACGA-TCATTAAT
65 GAAAACGAATAAGAGACATACATATAGCACCCAAACTATGTGCGTACCGA-TAC-ACTCATTAAT
* * * * ** * *
1885719 TAGTACCAGTACGCTTAATAGAAAGGGATCAATACCCATCGTGTATCAGTACAATTGAAACACAG
128 AAGTATCAGTACGATTAATAGAAA-AGATCGGTACCCATCGTGTATCGGTACAATTGAAACACAC
** * *
1885784 TGGAATTTTGCATAATTGTACCGTATTGATACACATGTTAT-
192 TGGAATTTCACATAATTGTACCGTATCGATACTCATGTT-TC
* * * *
1885825 ACTGTATTGGTACCGTATCACCCAAAATAGAATTTCTTAAGGTTATGGCTTGATAAAACTTGGGG
1 ACCGTATTGGTACCGTATCACCCAAAATAGAATTTCTTAAGGTTAGGGATTGATAAAAATTGGGG
* * * * *
1885890 AAAAC-ATATAAGAGACACACCTATAGCACCCAAACTATAG-GCGTAGCGATACACTTATTAATG
66 AAAACGA-ATAAGAGACATACATATAGCACCCAAACTAT-GTGCGTACCGATACACTCATTAATA
* * * * * * * *
1885953 AGTATCAGTACAATTAACAGAATGAGATAGGTATCCATTGTGTATCGGTATAATTAAAACACACT
129 AGTATCAGTACGATTAATAGAA-AAGATCGGTACCCATCGTGTATCGGTACAATTGAAACACACT
1886018 GGAATTTCACATAATTGTACCGTATCGATACTCATGTTTC
193 GGAATTTCACATAATTGTACCGTATCGATACTCATGTTTC
* * * * *
1886058 ACCGTATTCGTACTGCATCACCCAAAATATAATTTCTTAAGATTAGGGATTGATAAAAATTGAGG
1 ACCGTATTGGTACCGTATCACCCAAAATAGAATTTCTTAAGGTTAGGGATTGATAAAAATTG-GG
* * * * *
1886123 GAAAACGAATAAGAGACATACATCTCGAACCCAAATTATGTGTGTACCGATACACTCATTAATAA
65 GAAAACGAATAAGAGACATACATATAGCACCCAAACTATGTGCGTACCGATACACTCATTAATAA
** * * * *
1886188 GTATTGGTATGATTAATAGAACAAGATCGGTACCCATCGTGGATTGGTACAGTTGAAACACACTG
130 GTATCAGTACGATTAATAGAA-AAGATCGGTACCCATCGTGTATCGGTACAATTGAAACACACTG
* * ** * *
1886253 AAATTTCATATAATTGTACTTTATCGATACTCGTGTTGC
194 GAATTTCACATAATTGTACCGTATCGATACTCATGTTTC
* * * *
1886292 ATCGTATTGGTACTGTATCACCCAAAATAAAATTTCTTAAGGTTAGGGCTTGA-ACAAAATTGGG
1 ACCGTATTGGTACCGTATCACCCAAAATAGAATTTCTTAAGGTTAGGGATTGATA-AAAATTGGG
* * *
1886356 GAAAACGGATAAGAGACATACCTTTAGCACCCAAA
65 GAAAACGAATAAGAGACATACATATAGCACCCAAA
1886391 TACGCTCGTA
Statistics
Matches: 472, Mismatches: 82, Indels: 23
0.82 0.14 0.04
Matches are distributed among these distances:
232 50 0.11
233 229 0.49
234 192 0.41
235 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (232 bp):
ACCGTATTGGTACCGTATCACCCAAAATAGAATTTCTTAAGGTTAGGGATTGATAAAAATTGGGG
AAAACGAATAAGAGACATACATATAGCACCCAAACTATGTGCGTACCGATACACTCATTAATAAG
TATCAGTACGATTAATAGAAAAGATCGGTACCCATCGTGTATCGGTACAATTGAAACACACTGGA
ATTTCACATAATTGTACCGTATCGATACTCATGTTTC
Found at i:1886619 original size:22 final size:21
Alignment explanation
Indices: 1886571--1886623 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1886561 TAATTGCATT
*
1886571 GTATCAATACACATGGTTTTC
1 GTATCGATACACATGGTTTTC
1886592 GTATCGATACACAT-GTTTTACC
1 GTATCGATACACATGGTTTT--C
1886614 GTATCGATAC
1 GTATCGATAC
1886624 GTGATGTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 5 0.17
21 13 0.45
22 11 0.38
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (21 bp):
GTATCGATACACATGGTTTTC
Found at i:1890321 original size:20 final size:20
Alignment explanation
Indices: 1890296--1890351 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1890286 CTAATGTAAA
1890296 AATTAGGGTTCAATTATTCT
1 AATTAGGGTTCAATTATTCT
*
1890316 AATTAGGGTTCAATTGTTCT
1 AATTAGGGTTCAATTATTCT
1890336 AATTAGGGTTCTAATT
1 AATTAGGGTTC-AATT
1890352 TAGGAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 30 0.88
21 4 0.12
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.45
Consensus pattern (20 bp):
AATTAGGGTTCAATTATTCT
Found at i:1890348 original size:12 final size:12
Alignment explanation
Indices: 1890296--1890351 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
1890286 CTAATGTAAA
1890296 AATTAGGGTTC-
1 AATTAGGGTTCT
1890307 AATTA---TTCT
1 AATTAGGGTTCT
1890316 AATTAGGGTTC-
1 AATTAGGGTTCT
1890327 AATT---GTTCT
1 AATTAGGGTTCT
1890336 AATTAGGGTTCT
1 AATTAGGGTTCT
1890348 AATT
1 AATT
1890352 TAGGAAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
8 7 0.19
9 9 0.24
11 9 0.24
12 12 0.32
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.45
Consensus pattern (12 bp):
AATTAGGGTTCT
Found at i:1895306 original size:24 final size:24
Alignment explanation
Indices: 1895267--1895312 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1895257 AGTCAGGGTT
*
1895267 CTATGTGGTCCGTCGGGACAAAAC
1 CTATGTGGTCCGTCGGAACAAAAC
**
1895291 CTATGTGGTCTTTCGGAACAAA
1 CTATGTGGTCCGTCGGAACAAA
1895313 TATATGGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (24 bp):
CTATGTGGTCCGTCGGAACAAAAC
Found at i:1901626 original size:17 final size:17
Alignment explanation
Indices: 1901606--1901644 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1901596 ATTATTTTGA
1901606 TTTATTTCAAATTTTAT
1 TTTATTTCAAATTTTAT
***
1901623 TTTATTTTTTATTTTAT
1 TTTATTTCAAATTTTAT
1901640 TTTAT
1 TTTAT
1901645 ATCCTTGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTCAAATTTTAT
Found at i:1901632 original size:12 final size:12
Alignment explanation
Indices: 1901617--1901642 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1901607 TTATTTCAAA
1901617 TTTTATTTTATT
1 TTTTATTTTATT
1901629 TTTTATTTTATT
1 TTTTATTTTATT
1901641 TT
1 TT
1901643 ATATCCTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:1903131 original size:28 final size:28
Alignment explanation
Indices: 1903100--1903162 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
1903090 TCATTTACAT
*
1903100 TTTGCAT-TCCCATTTTTGTATCTTTGCA
1 TTTGCATGT-CCATTTTTGCATCTTTGCA
*
1903128 TTTGCATGTGCATTTTTGCATCTTTGCA
1 TTTGCATGTCCATTTTTGCATCTTTGCA
*
1903156 TTAGCAT
1 TTTGCAT
1903163 CTATACATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.16, C:0.19, G:0.14, T:0.51
Consensus pattern (28 bp):
TTTGCATGTCCATTTTTGCATCTTTGCA
Found at i:1904510 original size:16 final size:15
Alignment explanation
Indices: 1904489--1904688 Score: 168
Period size: 13 Copynumber: 13.1 Consensus size: 15
1904479 AAAGACATAG
*
1904489 AAAAGAAAGAAAGGAA
1 AAAAGAAA-AAAAGAA
1904505 AAAAGAGAAAAAGAGAA
1 AAAAGA-AAAAA-AGAA
1904522 AAAGAGAAAAAAAGAGAA
1 AAA-AG-AAAAAA-AGAA
*
1904540 AAAAGAAAAAAAAAAA
1 AAAAG-AAAAAAAGAA
1904556 AAAAGAAAAAAA-AA
1 AAAAGAAAAAAAGAA
1904570 AAAA-AAAAAAA-AA
1 AAAAGAAAAAAAGAA
1904583 AAAA-AAAAAAA-AA
1 AAAAGAAAAAAAGAA
1904596 AAAA-AAAAAAA-AA
1 AAAAGAAAAAAAGAA
1904609 AAAA-AAAAGAAA-AA
1 AAAAGAAAA-AAAGAA
*
1904623 AAAAAAAAAAAAGAA
1 AAAAGAAAAAAAGAA
*
1904638 AAATAAAAAAAAGAGAA
1 AAA-AGAAAAAA-AGAA
1904655 AAAGAGAAAAAAAGAGA
1 AAA-AGAAAAAAAGA-A
*
1904672 AGAAAG-AAGAAAGAA
1 A-AAAGAAAAAAAGAA
1904687 AA
1 AA
1904689 TGATCAAATA
Statistics
Matches: 168, Mismatches: 5, Indels: 24
0.85 0.03 0.12
Matches are distributed among these distances:
13 43 0.26
14 19 0.11
15 18 0.11
16 35 0.21
17 35 0.21
18 17 0.10
19 1 0.01
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.01
Consensus pattern (15 bp):
AAAAGAAAAAAAGAA
Found at i:1904524 original size:18 final size:17
Alignment explanation
Indices: 1904475--1904679 Score: 197
Period size: 17 Copynumber: 12.1 Consensus size: 17
1904465 AAGATATATA
*
1904475 AAAAAAAGACATAGAAAAG
1 AAAAAAAGAGA-A-AAAAG
*
1904494 AAAGAAAG-GAAAAAAG
1 AAAAAAAGAGAAAAAAG
*
1904510 AGAAAAAGAGAAAAAGAG
1 AAAAAAAGAGAAAAA-AG
1904528 AAAAAAAGAGAAAAAAG
1 AAAAAAAGAGAAAAAAG
*
1904545 AAAAAAA-AAAAAAAAG
1 AAAAAAAGAGAAAAAAG
*
1904561 AAAAAAA-A-AAAAAAA
1 AAAAAAAGAGAAAAAAG
* * *
1904576 AAAAAAAAAAAAAAAAA
1 AAAAAAAGAGAAAAAAG
* * *
1904593 AAAAAAAAAAAAAAAAA
1 AAAAAAAGAGAAAAAAG
*
1904610 AAAAAAAGA-AAAAAAA
1 AAAAAAAGAGAAAAAAG
*
1904626 AAAAAAAAAGAAAAATA-
1 AAAAAAAGAGAAAAA-AG
1904643 AAAAAAAGAGAAAAAGAG
1 AAAAAAAGAGAAAAA-AG
*
1904661 AAAAAAAGAGAAGAAAG
1 AAAAAAAGAGAAAAAAG
1904678 AA
1 AA
1904680 GAAAGAAAAT
Statistics
Matches: 167, Mismatches: 12, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
15 13 0.08
16 43 0.26
17 72 0.43
18 32 0.19
19 7 0.04
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.01
Consensus pattern (17 bp):
AAAAAAAGAGAAAAAAG
Found at i:1904567 original size:8 final size:8
Alignment explanation
Indices: 1904475--1904688 Score: 194
Period size: 8 Copynumber: 26.5 Consensus size: 8
1904465 AAGATATATA
1904475 AAAAAAAG
1 AAAAAAAG
1904483 ACATAGAAAAG
1 A-A-A-AAAAG
*
1904494 AAAGAAAGG
1 AAA-AAAAG
1904503 AAAAAAGAG
1 AAAAAA-AG
*
1904512 AAAAAGAG
1 AAAAAAAG
*
1904520 AAAAAGAG
1 AAAAAAAG
1904528 AAAAAAAG
1 AAAAAAAG
1904536 AGAAAAAAG
1 A-AAAAAAG
*
1904545 AAAAAAAA
1 AAAAAAAG
1904553 AAAAAAAG
1 AAAAAAAG
1904561 AAAAAAA-
1 AAAAAAAG
1904568 AAAAAAA-
1 AAAAAAAG
1904575 AAAAAAA-
1 AAAAAAAG
1904582 AAAAAAA-
1 AAAAAAAG
1904589 AAAAAAA-
1 AAAAAAAG
1904596 AAAAAAA-
1 AAAAAAAG
1904603 AAAAAAA-
1 AAAAAAAG
1904610 AAAAAAAG
1 AAAAAAAG
*
1904618 AAAAAAAAAA
1 --AAAAAAAG
1904628 AAAAAAAG
1 AAAAAAAG
1904636 AAAAATAA-
1 AAAAA-AAG
1904644 AAAAAAGAG
1 AAAAAA-AG
*
1904653 AAAAAGAG
1 AAAAAAAG
1904661 AAAAAAAG
1 AAAAAAAG
*
1904669 AGAAGAAAG
1 A-AAAAAAG
*
1904678 -AAGAAAG
1 AAAAAAAG
1904685 AAAA
1 AAAA
1904689 TGATCAAATA
Statistics
Matches: 181, Mismatches: 12, Indels: 26
0.83 0.05 0.12
Matches are distributed among these distances:
7 57 0.31
8 72 0.40
9 37 0.20
10 9 0.05
11 6 0.03
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1904667 original size:1 final size:1
Alignment explanation
Indices: 1904528--1904649 Score: 181
Period size: 1 Copynumber: 122.0 Consensus size: 1
1904518 AGAAAAAGAG
* * * *
1904528 AAAAAAAGAGAAAAAAGAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
1904593 AAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAGAAAAATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1904650 GAGAAAAAGA
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 107 1.00
ACGTcount: A:0.94, C:0.00, G:0.05, T:0.01
Consensus pattern (1 bp):
A
Found at i:1906879 original size:98 final size:98
Alignment explanation
Indices: 1906705--1906909 Score: 279
Period size: 98 Copynumber: 2.1 Consensus size: 98
1906695 TGAGTTTTTT
* * * * *
1906705 GAAATTAAGCCTAATTTTCAGGGGTTTCTTGATGATGTTTTTCAATGAGTTTTTAAAAGGAAGCT
1 GAAACTAAGCCTAATTTTCACGGGTTTATTGATGATGTTTTTCAATGAGTTTTTAAAAGGAAACC
*
1906770 AAACCTAATTTTTAGGGGTTTC-TTAATAACTAA
66 AAACCTAATTTTTAGGGG-TTCATTAACAACTAA
* *
1906803 GAAACTAAGCCTGATTTTTACGGGTTTATTGATGATGGTTTTT-AATGAGTTTTTAAAAGGAAAC
1 GAAACTAAGCCTAATTTTCACGGGTTTATTGATGAT-GTTTTTCAATGAGTTTTTAAAAGGAAAC
** *
1906867 CAAGTCTAATTTTTAGGGGTTCATTGACAACTAA
65 CAAACCTAATTTTTAGGGGTTCATTAACAACTAA
1906901 GAAACTAAG
1 GAAACTAAG
1906910 ATTCATTTTC
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
97 3 0.03
98 85 0.90
99 6 0.06
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (98 bp):
GAAACTAAGCCTAATTTTCACGGGTTTATTGATGATGTTTTTCAATGAGTTTTTAAAAGGAAACC
AAACCTAATTTTTAGGGGTTCATTAACAACTAA
Found at i:1907042 original size:41 final size:41
Alignment explanation
Indices: 1906930--1907042 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 41
1906920 AAGGTTTGTT
* * * *
1906930 GATGAGTAAGTCCTTTGGGCCAT-CAGTAAGTCTTTCGAGTAC
1 GATGA-TAAGTCCTTCGGGCCATCCA-TAAGTCTTTCAAGCAA
* * * * *
1906972 GATGCTTAAATTCTTCGGGTCATCTATAAGTCTTTCAAGCAA
1 GATG-ATAAGTCCTTCGGGCCATCCATAAGTCTTTCAAGCAA
1907014 GATGATAAGTCCTTCGGGCCATCCATAAG
1 GATGATAAGTCCTTCGGGCCATCCATAAG
1907043 ACCTTCGGGT
Statistics
Matches: 55, Mismatches: 14, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
41 20 0.36
42 34 0.62
43 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (41 bp):
GATGATAAGTCCTTCGGGCCATCCATAAGTCTTTCAAGCAA
Found at i:1907372 original size:39 final size:39
Alignment explanation
Indices: 1907329--1907536 Score: 169
Period size: 39 Copynumber: 5.5 Consensus size: 39
1907319 AGGGATCAAC
* *
1907329 ATCTCGCTTGAGATAGCTTCACTCAAAACAAAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTT
* * *
1907368 ATCTCGCTTGAGATAGTTTCACTTGAAACATAAGATTTC
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTT
* * *
1907407 ATCTCACTTGAGACAGTTTCACTGGAAAC-AAA-ATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTT
* * * ** * * * *
1907444 ATCTCCCTTGAAATTGTTTTTCT-TAAA-ACAA-ACTTC
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTT
* *
1907480 ATCTCGCTTGAGACAGTTTTCACTAGAAAC-AAA-ATTTT
1 ATCTCGCTTGAGATAG-TTTCACTCGAAACAAAAGATTTT
* *
1907518 ATCTCACTTGAGATTGTTT
1 ATCTCGCTTGAGATAGTTT
1907537 TTCTTAAAAT
Statistics
Matches: 132, Mismatches: 33, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
36 20 0.15
37 29 0.22
38 23 0.17
39 60 0.45
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTT
Found at i:1907499 original size:36 final size:36
Alignment explanation
Indices: 1907402--1907625 Score: 144
Period size: 36 Copynumber: 6.1 Consensus size: 36
1907392 GAAACATAAG
** **
1907402 ATTTCATCTCACTTGAGACAGTTTCACTGGAAACAAA
1 ATTTCATCTCACTTGAGACAGTTTTTCTTAAAAC-AA
* * * **
1907439 ATTTTATCTCCCTTGAAATTGTTTTTCTTAAAACAA
1 ATTTCATCTCACTTGAGACAGTTTTTCTTAAAACAA
* * *
1907475 ACTTCATCTCGCTTGAGACAG-TTTTCACTAGAAACAAA
1 ATTTCATCTCACTTGAGACAGTTTTTC-TTA-AAAC-AA
* ** *
1907513 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAATAA
1 ATTTCATCTCACTTGAGACAGTTTTTCTTAAAACAA
** * * ** **
1907549 ACCTCATCTTACTAGAGACAGTTTCCCTCGAAACAA
1 ATTTCATCTCACTTGAGACAGTTTTTCTTAAAACAA
* * * * *
1907585 ATTTTATCTCACCTGAGATAGTTTCTCTTCAAACAA
1 ATTTCATCTCACTTGAGACAGTTTTTCTTAAAACAA
1907621 ATTTC
1 ATTTC
1907626 TTTTGATTCA
Statistics
Matches: 137, Mismatches: 46, Indels: 9
0.71 0.24 0.05
Matches are distributed among these distances:
35 5 0.04
36 75 0.55
37 32 0.23
38 20 0.15
39 5 0.04
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (36 bp):
ATTTCATCTCACTTGAGACAGTTTTTCTTAAAACAA
Found at i:1907518 original size:74 final size:73
Alignment explanation
Indices: 1907328--1907621 Score: 297
Period size: 74 Copynumber: 4.0 Consensus size: 73
1907318 GAGGGATCAA
* * * * *
1907328 CATCTCGCTTGAGATAGCTTCACTCA-AAACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTT
1 CATCTCACTTGAGACAGTTTCACT-AGAAAC-AAA-ATTTTATCTCCCTTGAGATAGTTTCTCTT
* *
1907392 GAAACATAAGATTT
63 -AAA-ACAA-ACTT
* * * *
1907406 CATCTCACTTGAGACAGTTTCACTGGAAACAAAATTTTATCTCCCTTGAAATTGTTTTTCTTAAA
1 CATCTCACTTGAGACAGTTTCACTAGAAACAAAATTTTATCTCCCTTGAGATAGTTTCTCTTAAA
1907471 ACAAACTT
66 ACAAACTT
* * * *
1907479 CATCTCGCTTGAGACAGTTTTCACTAGAAACAAAATTTTATCTCACTTGAGATTGTTTTTCTTAA
1 CATCTCACTTGAGACAG-TTTCACTAGAAACAAAATTTTATCTCCCTTGAGATAGTTTCTCTTAA
* *
1907544 AATAAACCT
65 AACAAACTT
* * * * *
1907553 CATCTTACTAGAGACAGTTTCCCTCGAAAC-AAATTTTATCTCACC-TGAGATAGTTTCTCTTCA
1 CATCTCACTTGAGACAGTTTCACTAGAAACAAAATTTTATCTC-CCTTGAGATAGTTTCTCTTAA
1907616 AACAAA
65 AACAAA
1907622 TTTCTTTTGA
Statistics
Matches: 186, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
72 32 0.17
73 31 0.17
74 68 0.37
75 3 0.02
76 24 0.13
77 3 0.02
78 25 0.13
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (73 bp):
CATCTCACTTGAGACAGTTTCACTAGAAACAAAATTTTATCTCCCTTGAGATAGTTTCTCTTAAA
ACAAACTT
Found at i:1908102 original size:122 final size:122
Alignment explanation
Indices: 1907958--1908348 Score: 377
Period size: 122 Copynumber: 3.1 Consensus size: 122
1907948 AGCTCGTAAT
* * *
1907958 GAGAAGAACTTATTCAACCTTAACTCGTTTCATCGCATATGGAGTTGAAACAACAATAACTCGCT
1 GAGAAGAACTTATTCAACCTTAACTCGATTCATCACATATGGAGTTGAAACAACAATAACTCACT
**
1908023 CAAGGGATCAACATATCCGGTGGAGAGTTCATAACGAGAAGAACTCATCCGATGAGG
66 CAAGGGATCAACATATCCAATGGAGAGTTCATAACGAGAAGAACTCATCCGATGAGG
* * * **
1908080 GAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGATTTGAATCAGTAATAACTCACT
1 GAGAAGAACTTATTCAACCTTAACTCGATTCATCACATATGGAGTTGAAACAACAATAACTCACT
* * * *
1908145 CGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGG
66 CAAGGGATCAACATATCCAATGGAGAGTTCATAACGAGAAGAACTCATCCGATGAGG
* ** *
1908202 GAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAACTCGATTAATCACATATGGAGTTGA
1 GAGAAGAA---C-T--T-------A--T-TCAA-CCTTAACTCGATTCATCACATATGGAGTTGA
* * * * * * * * * *
1908267 ATCAGCAACACCTCACTCGAGGGATCAACATTTCCAGTAGAGAGTTAATAATGAGAAGAACTCAT
49 AACAACAATAACTCACTCAAGGGATCAACATATCCAATGGAGAGTTCATAACGAGAAGAACTCAT
1908332 CCGATGAGG
114 CCGATGAGG
1908341 GAGAAGAA
1 GAGAAGAA
1908349 GTTCATAATG
Statistics
Matches: 224, Mismatches: 28, Indels: 17
0.83 0.10 0.06
Matches are distributed among these distances:
122 115 0.51
125 1 0.00
126 1 0.00
128 1 0.00
137 1 0.00
138 2 0.01
139 103 0.46
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (122 bp):
GAGAAGAACTTATTCAACCTTAACTCGATTCATCACATATGGAGTTGAAACAACAATAACTCACT
CAAGGGATCAACATATCCAATGGAGAGTTCATAACGAGAAGAACTCATCCGATGAGG
Found at i:1908330 original size:139 final size:139
Alignment explanation
Indices: 1908080--1908464 Score: 599
Period size: 139 Copynumber: 2.8 Consensus size: 139
1908070 TCCGATGAGG
* * * *
1908080 GAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGATTTGAATCAGTAATAACTCACT
1 GAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTTGAATCAGAAACACCTCACT
*
1908145 CGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAAAA
66 CGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAAAA
1908210 GTTCATAAT
131 GTTCATAAT
* *
1908219 GAGAAGAACTTGTTCAACCTTAACTCGATTAATCACATATGGAGTTGAATCAGCAACACCTCACT
1 GAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTTGAATCAGAAACACCTCACT
* * * *
1908284 CGAGGGATCAACATTTCCAGTAGAGAGTTAATAATGAGAAGAACTCATCCGATGAGGGAGAAGAA
66 CGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAAAA
1908349 GTTCATAAT
131 GTTCATAAT
* * * *
1908358 GAGAATAACTTGTTCAACCTTAACTCGATTCATCTCATATAGAGTCGAATCAGAAACACCTCACT
1 GAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTTGAATCAGAAACACCTCACT
* * * *
1908423 TGAGAGATCAACATTTCAAATGGAGAGTTCATAATAAGAAGA
66 CGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGA
1908465 TATTGTTCAA
Statistics
Matches: 223, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
139 223 1.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (139 bp):
GAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTTGAATCAGAAACACCTCACT
CGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAAAA
GTTCATAAT
Found at i:1944672 original size:77 final size:78
Alignment explanation
Indices: 1944545--1944699 Score: 206
Period size: 77 Copynumber: 2.0 Consensus size: 78
1944535 AATTTTGAGG
** *
1944545 GTGTTTTATGTTTTTTAGGGAGGATATATGTTAATGCTGATGCAGATTTGAGGCGTGAGATT-TT
1 GTGTTTTATGTTTTCGAGGAAGGATATATGTTAATGCTGATGCAGATTTGAGGCGTGAGATTCTT
**
1944609 TTTTAGATGCATA
66 TTCGAGATGCATA
* * * *
1944622 GTGTTTTATGTTTTCGAGGAAGGATATGTGTTACTGGC-GATGTAGATTTGAGGCGTGCGATTCT
1 GTGTTTTATGTTTTCGAGGAAGGATATATGTTAAT-GCTGATGCAGATTTGAGGCGTGAGATTCT
1944686 TTTCGAGATGCATA
65 TTTCGAGATGCATA
1944700 ATGGATCATT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
77 52 0.78
78 15 0.22
ACGTcount: A:0.22, C:0.08, G:0.29, T:0.41
Consensus pattern (78 bp):
GTGTTTTATGTTTTCGAGGAAGGATATATGTTAATGCTGATGCAGATTTGAGGCGTGAGATTCTT
TTCGAGATGCATA
Found at i:1946030 original size:32 final size:32
Alignment explanation
Indices: 1945989--1946055 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
1945979 TAGAATGTTA
1945989 GTTGATCACTAGGCTTATAGCTCACACTAATT
1 GTTGATCACTAGGCTTATAGCTCACACTAATT
*
1946021 GTTGATCACTAGGGTTATAGCTCACACTAATT
1 GTTGATCACTAGGCTTATAGCTCACACTAATT
1946053 GTT
1 GTT
1946056 TAACACTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (32 bp):
GTTGATCACTAGGCTTATAGCTCACACTAATT
Found at i:1948162 original size:34 final size:36
Alignment explanation
Indices: 1948076--1948164 Score: 98
Period size: 34 Copynumber: 2.6 Consensus size: 36
1948066 ATGTATATAG
* *
1948076 CATATGGTTTTCATATTAAAGGGACATATATTCTAA
1 CATATAGTTTTCATATTAAAAGGACATATATTCTAA
* *
1948112 TATATAGTTTTC--ATTAAATAGTACATATA-T-T-A
1 CATATAGTTTTCATATTAAA-AGGACATATATTCTAA
1948144 CATATAGTTTTCATATTAAAA
1 CATATAGTTTTCATATTAAAA
1948165 AGCATATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
32 12 0.27
33 2 0.04
34 13 0.29
35 8 0.18
36 10 0.22
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (36 bp):
CATATAGTTTTCATATTAAAAGGACATATATTCTAA
Found at i:1949910 original size:23 final size:23
Alignment explanation
Indices: 1949879--1949933 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
1949869 TTTATTATTT
*
1949879 TATTAAATGTGTTTAATTATTAA
1 TATTGAATGTGTTTAATTATTAA
1949902 TATTGAATGTGTTTAATTATTAA
1 TATTGAATGTGTTTAATTATTAA
1949925 TATTGAATG
1 TATTGAATG
1949934 ATAACCTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (23 bp):
TATTGAATGTGTTTAATTATTAA
Found at i:1950953 original size:20 final size:20
Alignment explanation
Indices: 1950924--1950961 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1950914 ATACATAACA
*
1950924 GGTTTAAATATGAGAAAATC
1 GGTTTAAATATGACAAAATC
*
1950944 GGTTTCAATATGACAAAA
1 GGTTTAAATATGACAAAA
1950962 CTAGTAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (20 bp):
GGTTTAAATATGACAAAATC
Found at i:1951201 original size:194 final size:192
Alignment explanation
Indices: 1950805--1951423 Score: 815
Period size: 194 Copynumber: 3.2 Consensus size: 192
1950795 GTTGAAATTT
* * * * * * *
1950805 ATATCGATACTTTTCTAAGTATATGCACCAAATTATCAATACTCTAGGAATTTAAAAGAATTACA
1 ATATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTGCA
* * * *
1950870 ATAATAGCACCTATAAAGTATCAAGACTTTAGAAA-AAAGTATCG---AT---ACATAACAGGTT
66 ATAATAGCGCCTATAAAGTATCAATACTTTAGAAACATA-TATCGTACATACAACATAACATGTT
* * * *
1950928 TAAATATGAGAAAA-TCGGTTTCAATATGACAAAACTAGTAAAGAACTACCCGATATGTTGAAA
130 AAAATATGACAAAACT-GGTTTCAATATGAAAAAACTAGTAAAGAACTACCAGATATGTTGAAA
*
1950991 ATATCGA-ATCTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAATAATTGC
1 ATATCGATA-CTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTGC
*
1951055 AATAATAGCGCCTATAAAGTATCAATACTTTAGAAACATATATCAGTACATAACAACATAACATA
65 AATAATAGCGCCTATAAAGTATCAATACTTTAGAAACATATATC-GTACAT-ACAACATAACATG
* * * *
1951120 TTAAAATATGACAAAACTGGTTTCAATATGATAAAACCAGTAAAGAGCTACCATATATGTTGAAA
128 TTAAAATATGACAAAACTGGTTTCAATATGAAAAAACTAGTAAAGAACTACCAGATATGTTGAAA
1951185 ATATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTGCA
1 ATATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTGCA
** * * * *
1951250 ATAATAATGCCTATAAAGTATCGATACTTTATAAACATATATTGATACATGACAAAATAACATGT
66 ATAATAGCGCCTATAAAGTATCAATACTTTAGAAACATATATCG-TACAT-ACAACATAACATGT
* * ** *
1951315 TAAAATATGACAAAACTGTTTTCAATATGAAAAAACTGGTAAAGCTCTACCAGATATGTTGAAG
129 TAAAATATGACAAAACTGGTTTCAATATGAAAAAACTAGTAAAGAACTACCAGATATGTTGAAA
*
1951379 ATATCAATACTTTTATAAGTATATGTATCATATTATCGATACTTT
1 ATATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTT
1951424 TAAAAGAAAA
Statistics
Matches: 382, Mismatches: 38, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
185 1 0.00
186 92 0.24
187 3 0.01
190 2 0.01
193 1 0.00
194 281 0.74
195 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (192 bp):
ATATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTGCA
ATAATAGCGCCTATAAAGTATCAATACTTTAGAAACATATATCGTACATACAACATAACATGTTA
AAATATGACAAAACTGGTTTCAATATGAAAAAACTAGTAAAGAACTACCAGATATGTTGAAA
Found at i:1957752 original size:448 final size:442
Alignment explanation
Indices: 1956750--1957775 Score: 1294
Period size: 448 Copynumber: 2.3 Consensus size: 442
1956740 CCTAAGAAAA
* * * * * *
1956750 ATGTATCAATACATGAT-AATATAACAGGTTGAAAACTGAAAAAATAGGTTCAATATGCCAATAC
1 ATGTATCGATACATG-TCAATATAACAGGTTGAAAA-TGATAAAATCGTTTCAATATGACAA-AA
** * * *
1956814 TAGTAAAGAGATATTGGTTTACAAAAAATGAAACATCTCAAAAGTATCT-ATACCTTACACAG--
63 TAGTAAAGAGATACCGGTTTACAAAAAATAAAACGTCTCGAAAGTAT-TGATACCTT-CACAGAA
* ** * *
1956876 AAGTATCGATACCTAAGAAAGGGTAATGGTATTGATTAAATATTAATAACTTAACATGTTCAAAA
126 AAGTATCGATACCTAAGAAAGGGTAATGGTATCGATTAAATACAAATAACATAACAGGTTCAAAA
* *
1956941 TTGAAAAACTGGTTTCCATAATTGCGCCTATAAAATATCGATACGCGTATAAGAAGTATCGATTC
191 TTGAAAAACTGGTTTCCATAATTGCGCCTATAAAATATCGATACACATATAAGAAGTATCGATTC
* *
1957006 TTAAAACTTCGAAACAAATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGATAAAAATAT
256 CTAAAACTTCGAAACAAATTACTTCAAAGTAATAGGTAAATTTACAATGTAAGCGATAAAAATAT
* * * * *
1957071 ATCGGTTTAATGACAAAATACATTAACATAAAGTATTGGTACTTTTTGTATATGTATCGATACTT
321 ACCGATTTAATGACAAAATACATTAACATAAAGTATCGATACTTGTTGTATATGTATCGATACTT
* * * *
1957136 TTTTCCACTATGCTTCCCAAACTAGATGCACGCAGAACGTATTGATACCTAATACAC
386 TTATCCACTATGCTTCCCAAACTAGATGCACGCAGAAAGTATCGATACATAATACAC
* * * *
1957193 ATGTATCGATACATGACAATATAACAAGAT-ACAAATTGATAAAATCGGTTTCAAAATGACAAAA
1 ATGTATCGATACATGTCAATATAACAGGTTGA-AAA-TGATAAAATC-GTTTCAATATGACAAAA
* * * * *
1957257 CATGTAAAGAGTTACCAGTTTACATAAAAACAAAATGTCTCGAAAGTATTGATACCTTCA-AGAA
63 TA-GTAAAGAGATACCGGTTTACA-AAAAATAAAACGTCTCGAAAGTATTGATACCTTCACAGAA
* * *
1957321 AAGTATCGATACTTCAGTAAGGGTAATGGTATCGATTAAATACAAATAACATAACAGGTTCAAAA
126 AAGTATCGATACCTAAGAAAGGGTAATGGTATCGATTAAATACAAATAACATAACAGGTTCAAAA
* * *
1957386 TTGACAAAA-TCGGTTTTCATAATTGCGCCTATAAAGTATCGATACACATATGAGAAGTATCGAT
191 TTGA-AAAACT-GGTTTCCATAATTGCGCCTATAAAATATCGATACACATATAAGAAGTATCGAT
* * * *
1957450 TCCTAAAACTTTGAAACATATTACTTCAAAGTAATAGGTAAATTTACAATGTAAGTGGTAAAAAA
254 TCCTAAAACTTCGAAACAAATTACTTCAAAGTAATAGGTAAATTTACAATGTAAGCGAT-AAAAA
**
1957515 TATACCGATTTAATGACAAAATATGTTAACATAAAGTATCGATACTTGTTGTATATGTATCGATA
318 TATACCGATTTAATGACAAAATACATTAACATAAAGTATCGATACTTGTTGTATATGTATCGATA
* * * *
1957580 CGTTTTATCCAGTATTCTTCCCAAACTTGATGCACGTAGAAAGTATCGATACATAATACAC
383 C-TTTTATCCACTATGCTTCCCAAACTAGATGCACGCAGAAAGTATCGATACATAATACAC
*
1957641 ATGTATCGATACATGTCAATATAACAGGTTGAAAATAGATAAAATCGATTTTAATATGACAAAAT
1 ATGTATCGATACATGTCAATATAACAGGTTGAAAAT-GATAAAATCG-TTTCAATATGACAAAAT
* * * * *
1957706 AGGTAAAAAGATACCGGTTTACACAAATATAAAACGTCTGGAAAGTATCGATACCTT-ACACAAA
64 A-GTAAAGAGATACCGGTTTACA-AAAAATAAAACGTCTCGAAAGTATTGATACCTTCACAGAAA
1957770 AGTATC
127 AGTATC
1957776 AATAATTTGG
Statistics
Matches: 495, Mismatches: 72, Indels: 27
0.83 0.12 0.05
Matches are distributed among these distances:
442 1 0.00
443 40 0.08
444 32 0.06
445 88 0.18
446 105 0.21
447 67 0.14
448 161 0.33
449 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (442 bp):
ATGTATCGATACATGTCAATATAACAGGTTGAAAATGATAAAATCGTTTCAATATGACAAAATAG
TAAAGAGATACCGGTTTACAAAAAATAAAACGTCTCGAAAGTATTGATACCTTCACAGAAAAGTA
TCGATACCTAAGAAAGGGTAATGGTATCGATTAAATACAAATAACATAACAGGTTCAAAATTGAA
AAACTGGTTTCCATAATTGCGCCTATAAAATATCGATACACATATAAGAAGTATCGATTCCTAAA
ACTTCGAAACAAATTACTTCAAAGTAATAGGTAAATTTACAATGTAAGCGATAAAAATATACCGA
TTTAATGACAAAATACATTAACATAAAGTATCGATACTTGTTGTATATGTATCGATACTTTTATC
CACTATGCTTCCCAAACTAGATGCACGCAGAAAGTATCGATACATAATACAC
Found at i:1960231 original size:23 final size:24
Alignment explanation
Indices: 1960186--1960231 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1960176 ATCAGCTTTA
* *
1960186 ATAATGCGCTACCTATTACGTTAC
1 ATAATGCGCTACCTAATAAGTTAC
1960210 ATAA-GCGCTACCTAATAAGTTA
1 ATAATGCGCTACCTAATAAGTTA
1960232 TTATGCTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (24 bp):
ATAATGCGCTACCTAATAAGTTAC
Found at i:1960368 original size:17 final size:17
Alignment explanation
Indices: 1960348--1960381 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1960338 TAATAATACT
1960348 AATAACAAATTAAGTAA
1 AATAACAAATTAAGTAA
1960365 AATAACAAATTAAGTAA
1 AATAACAAATTAAGTAA
1960382 TTAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AATAACAAATTAAGTAA
Found at i:1960551 original size:243 final size:236
Alignment explanation
Indices: 1960028--1960742 Score: 843
Period size: 243 Copynumber: 3.1 Consensus size: 236
1960018 TAACAAATCA
* *
1960028 AGTAATTAACCGGTTATGTTATCGTCGGATTCC-AAGACTCCATCAGCTTAAACTTTGTTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTCCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* *
1960092 TTTAGGCGTTACCTAATATGTTGAT-A-AC-----AC---TG--ATAACAAATTAAGTCATTAAC
66 TTTAGGCGTTACCTAATATATTAATAACACTAATAACAAATGAAATAACAAATTAAGT-ATTAA-
* * * * * *
1960145 A-TATTTTGTTATCGTCGAATTTCTAAGGCCCATCAGCTTTAATAATGCGCTACCTATTACGTTA
129 ATTATTTTGTTATCGTCGGATTTCAAAGCCCCATCAGCTTTAAAAAGGTGCTACCTATTACGTTA
* * *
1960209 CATAAGCGCTACCTAATAAGTTATTATGCTTGACAATGTTTCT
194 CATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
* * *
1960252 AGCAATTAACCGGGTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTCCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* * *
1960317 TTTATGCGTTACCTAATATGTTAATAATACTAATAACAAATTAAGTAAAATAACAAATTAAGTAA
66 TTTAGGCGTTACCTAATATATTAATAACACTAATAACAAA-T--G--AAATAACAAATTAAGT-A
* * * *
1960382 TTAAATTATTTTGTTATCGTCGGATTTCCAAAGCCCCATCAACTTTTAGAAGGTGGTACCTATTA
125 TTAAATTATTTTGTTATCGTCGGATTT-CAAAGCCCCATCAGCTTTAAAAAGGTGCTACCTATTA
*
1960447 CGTTACGTAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
189 CGTTACATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
* *
1960495 AGTGATTAACCGATTATGTTATCGTCGGATTCCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTCCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* * * *
1960560 TTTAGGTGTTACCTAATATATTGATAACACTAATAACAAATGAAGT--C--ATTAACCTATT---
66 TTTAGGCGTTACCTAATATATTAATAACACTAATAACAAATGAAATAACAAATTAA-GTATTAAA
* * *
1960618 TTA-----TTATCATTGGATTTCAAAGCCCCATCAGCTTTAAAAAGGTGCTACTTATTACGTTAC
130 TTATTTTGTTATCGTCGGATTTCAAAGCCCCATCAGCTTTAAAAAGGTGCTACCTATTACGTTAC
1960678 ATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
195 ATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
* *
1960720 AATAATTAACTGGTTATGTTATC
1 AGTAATTAACCGGTTATGTTATC
1960743 TTCTATATTT
Statistics
Matches: 425, Mismatches: 45, Indels: 41
0.83 0.09 0.08
Matches are distributed among these distances:
224 30 0.07
225 150 0.35
226 13 0.03
227 2 0.00
231 3 0.01
232 2 0.00
234 8 0.02
235 1 0.00
236 2 0.00
238 4 0.01
240 1 0.00
241 1 0.00
242 40 0.09
243 168 0.40
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (236 bp):
AGTAATTAACCGGTTATGTTATCGTCGGATTCCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
TTTAGGCGTTACCTAATATATTAATAACACTAATAACAAATGAAATAACAAATTAAGTATTAAAT
TATTTTGTTATCGTCGGATTTCAAAGCCCCATCAGCTTTAAAAAGGTGCTACCTATTACGTTACA
TAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
Found at i:1964925 original size:31 final size:32
Alignment explanation
Indices: 1964890--1964952 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
1964880 TCGCGAGCCT
* *
1964890 AAAATTTTCAAGCTCGACTCGAACTC-AAAAG
1 AAAATATTCAAACTCGACTCGAACTCGAAAAG
*
1964921 AAAATATTGAAACTCGACTCGAACTCGAAAAG
1 AAAATATTCAAACTCGACTCGAACTCGAAAAG
1964953 GCTCGAACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.21
Consensus pattern (32 bp):
AAAATATTCAAACTCGACTCGAACTCGAAAAG
Found at i:1964993 original size:11 final size:11
Alignment explanation
Indices: 1964977--1965103 Score: 56
Period size: 11 Copynumber: 10.6 Consensus size: 11
1964967 AAATTTTAAG
1964977 AGCTCGATTCA
1 AGCTCGATTCA
*
1964988 AGCTCGAGACTCA
1 AGCTC--GATTCA
*
1965001 AGCTCGATTAA
1 AGCTCGATTCA
*
1965012 AGCTCGATTAAAA
1 AGCTCGATT--CA
* *
1965025 AACTCGATGCA
1 AGCTCGATTCA
*
1965036 AGCTCGATTGAGA
1 AGCTCGATT--CA
*
1965049 AGCTCGATTAAAAA
1 AGCTCGATT---CA
* *
1965063 AACTCGATTTTA
1 AGCTCGA-TTCA
*
1965075 AGCTCGTTTCA
1 AGCTCGATTCA
*
1965086 AGCTCAATTCA
1 AGCTCGATTCA
*
1965097 ATCTCGA
1 AGCTCGA
1965104 AAACGGGTTA
Statistics
Matches: 88, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
11 43 0.49
12 6 0.07
13 29 0.33
14 8 0.09
15 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:1965030 original size:24 final size:24
Alignment explanation
Indices: 1965003--1965060 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1964993 GAGACTCAAG
1965003 CTCGATTAAAGCTCGATTAAAAAA
1 CTCGATTAAAGCTCGATTAAAAAA
** * * *
1965027 CTCGATGCAAGCTCGATTGAGAAG
1 CTCGATTAAAGCTCGATTAAAAAA
1965051 CTCGATTAAA
1 CTCGATTAAA
1965061 AAAACTCGAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (24 bp):
CTCGATTAAAGCTCGATTAAAAAA
Found at i:1965031 original size:37 final size:40
Alignment explanation
Indices: 1964990--1965069 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 40
1964980 TCGATTCAAG
1964990 CTCGAGACT-CAAGCTCGATT-A-AAGCTCGATT-AAAAAA
1 CTCGAGA-TGCAAGCTCGATTGAGAAGCTCGATTAAAAAAA
1965027 CTC--GATGCAAGCTCGATTGAGAAGCTCGATTAAAAAAA
1 CTCGAGATGCAAGCTCGATTGAGAAGCTCGATTAAAAAAA
1965065 CTCGA
1 CTCGA
1965070 TTTTAAGCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
34 1 0.03
35 13 0.35
36 1 0.03
37 13 0.35
38 9 0.24
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (40 bp):
CTCGAGATGCAAGCTCGATTGAGAAGCTCGATTAAAAAAA
Found at i:1965089 original size:37 final size:35
Alignment explanation
Indices: 1964999--1965090 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 35
1964989 GCTCGAGACT
*
1964999 CAAGCTCGATTAAAGCTCGATTAAAAAACTCGATG
1 CAAGCTCGTTTAAAGCTCGATTAAAAAACTCGATG
* *
1965034 CAAGCTCGATTGAGAAGCTCGATTAAAAAAACTCGATTT
1 CAAGCTCG-TTTA-AAGCTCGATT-AAAAAACTCGA-TG
* *
1965073 TAAGCTCGTTTCAAGCTC
1 CAAGCTCGTTTAAAGCTC
1965091 AATTCAATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
35 8 0.17
36 2 0.04
37 16 0.34
38 13 0.28
39 8 0.17
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (35 bp):
CAAGCTCGTTTAAAGCTCGATTAAAAAACTCGATG
Found at i:1969772 original size:31 final size:31
Alignment explanation
Indices: 1969736--1969794 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1969726 AACTTAAAAG
* *
1969736 AGTTTTGCAATATTGAAATTTAAATAATTTT
1 AGTTTTACAATAATGAAATTTAAATAATTTT
*
1969767 AGTTTTATAATAATGAAATTTAAATAAT
1 AGTTTTACAATAATGAAATTTAAATAAT
1969795 CCATATAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (31 bp):
AGTTTTACAATAATGAAATTTAAATAATTTT
Found at i:1969843 original size:22 final size:22
Alignment explanation
Indices: 1969818--1970116 Score: 355
Period size: 22 Copynumber: 13.6 Consensus size: 22
1969808 ATAATAAATT
1969818 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
1969840 TTTTAAAATAAATCAA-TCTATG
1 TTTTAAAATAAATCAATTC-ATA
*
1969862 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
1969884 TTTTAAAATAAA--ATTTTCCATA
1 TTTTAAAATAAATCA-ATT-CATA
*
1969906 TTTTAAAATAAAT-AAATCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
1969928 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
1969950 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
1969972 TTTTAAAATAAAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
1969994 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
1970016 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
1970038 TTTTAAAATAAAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
1970060 TTTTAAAATAAATCAATAT-ATA
1 TTTTAAAATAAATCAAT-TCATA
1970082 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
1970104 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1970117 TTTAAAATAG
Statistics
Matches: 241, Mismatches: 20, Indels: 32
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.01
21 7 0.03
22 224 0.93
23 7 0.03
24 1 0.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:1969868 original size:44 final size:44
Alignment explanation
Indices: 1969818--1970116 Score: 392
Period size: 44 Copynumber: 6.8 Consensus size: 44
1969808 ATAATAAATT
* *
1969818 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCTATG
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
* **
1969862 TTTTAAAATAAATCAATCCATATTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAAT-AAATCAATCCATA
*
1969906 TTTTAAAATAAAT-AAATCTATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTC-ATATTTTAAAATAAATCAATCCATA
* ***
1969950 TTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
1969994 TTTTAAAATAAATCAA-TCTATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTC-ATATTTTAAAATAAATCAATCCATA
** **
1970038 TTTTAAAATAAAT-TTTTCCATATTTTAAAATAAATCAATATATA
1 TTTTAAAATAAATCAATT-CATATTTTAAAATAAATCAATCCATA
1970082 TTTTAAAATAAATCAA-TCTATATTTTAAAATAAAT
1 TTTTAAAATAAATCAATTC-ATATTTTAAAATAAAT
1970117 TTTAAAATAG
Statistics
Matches: 222, Mismatches: 24, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
43 9 0.04
44 205 0.92
45 8 0.04
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.41
Consensus pattern (44 bp):
TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
Found at i:1970118 original size:66 final size:66
Alignment explanation
Indices: 1969818--1970119 Score: 444
Period size: 66 Copynumber: 4.6 Consensus size: 66
1969808 ATAATAAATT
* *** * *
1969818 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCTATGTTTTAAAATAAATCAATCCAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCAT
1969883 A
66 A
** *** *
1969884 TTTTAAAATAAAAT-TTTCCATATTTTAAAATAAATAAATCTATATTTTAAAATAAATCAATCCA
1 TTTTAAAAT-AAATCAATCCATATTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCA
1969948 TA
65 TA
*
1969950 TTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCTAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCAT
1970015 A
66 A
**
1970016 TTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATATAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCAT
1970081 A
66 A
*
1970082 TTTTAAAATAAATCAATCTATATTTTAAAATAAATTTT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATTTT
1970120 AAAATAGATT
Statistics
Matches: 220, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
65 4 0.02
66 212 0.96
67 4 0.02
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (66 bp):
TTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCCAT
A
Found at i:1970133 original size:11 final size:12
Alignment explanation
Indices: 1970103--1970142 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1970093 ATCAATCTAT
1970103 ATTTTAAAATAA
1 ATTTTAAAATAA
*
1970115 ATTTTAAAATAG
1 ATTTTAAAATAA
1970127 A-TTT-AAAT-A
1 ATTTTAAAATAA
1970136 ATTTTAA
1 ATTTTAA
1970143 TTTATTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.29
11 4 0.17
12 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:1970869 original size:22 final size:22
Alignment explanation
Indices: 1970592--1970868 Score: 421
Period size: 22 Copynumber: 12.6 Consensus size: 22
1970582 ATAATAAATT
*
1970592 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*
1970614 TTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATA
**
1970636 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
1970658 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1970680 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1970702 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
*
1970724 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
1970746 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1970768 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*** *
1970790 TTTTAAAATAAATTTTTCTATA
1 TTTTAAAATAAATCAATCCATA
*
1970812 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
*
1970834 TTTTAAAATAAATTAATCCATA
1 TTTTAAAATAAATCAATCCATA
1970856 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1970869 TTTAAAATAT
Statistics
Matches: 233, Mismatches: 20, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
21 4 0.02
22 225 0.97
23 4 0.02
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1970870 original size:12 final size:12
Alignment explanation
Indices: 1970855--1970894 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1970845 ATTAATCCAT
1970855 ATTTTAAAATAA
1 ATTTTAAAATAA
*
1970867 ATTTTAAAATAT
1 ATTTTAAAATAA
1970879 A-TTT-AAAT-A
1 ATTTTAAAATAA
1970888 ATTTTAA
1 ATTTTAA
1970895 TTTCTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.29
11 4 0.17
12 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:1972668 original size:26 final size:26
Alignment explanation
Indices: 1972639--1972691 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
1972629 AAAATTTGTT
1972639 TTCATTCC-TAAAATTTTATAAGTTCG
1 TTCA-TCCTTAAAATTTTATAAGTTCG
1972665 TTCATCCTTTAAAATTTTATAAGTTCG
1 TTCATCC-TTAAAATTTTATAAGTTCG
1972692 CCCCTCTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 3 0.12
26 4 0.16
27 18 0.72
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (26 bp):
TTCATCCTTAAAATTTTATAAGTTCG
Found at i:1974326 original size:3 final size:3
Alignment explanation
Indices: 1974312--1974355 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
1974302 CCAAGAGTTC
1974312 TAA TAA -AA TAA TAA TAA -AA TAA TAA TAAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
1974355 T
1 T
1974356 CAAAATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.16
3 28 0.76
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1974328 original size:11 final size:11
Alignment explanation
Indices: 1974312--1974355 Score: 81
Period size: 11 Copynumber: 4.1 Consensus size: 11
1974302 CCAAGAGTTC
1974312 TAATAAAATAA
1 TAATAAAATAA
1974323 TAATAAAATAA
1 TAATAAAATAA
1974334 TAAT-AAATAA
1 TAATAAAATAA
1974344 TAATAAAATAA
1 TAATAAAATAA
1974355 T
1 T
1974356 CAAAATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.31
11 22 0.69
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:1974343 original size:21 final size:21
Alignment explanation
Indices: 1974312--1974363 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1974302 CCAAGAGTTC
1974312 TAATAAAATAATAATAAAATAA
1 TAAT-AAATAATAATAAAATAA
1974334 TAATAAATAATAATAAAATAA
1 TAATAAATAATAATAAAATAA
*
1974355 TCA-AAATAA
1 TAATAAATAA
1974364 AAATCTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 6 0.21
21 19 0.66
22 4 0.14
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
TAATAAATAATAATAAAATAA
Found at i:1977332 original size:11 final size:11
Alignment explanation
Indices: 1977316--1977343 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1977306 TGTGTTTTAA
1977316 GATGAATAAAG
1 GATGAATAAAG
1977327 GATGAATAAAG
1 GATGAATAAAG
1977338 GATGAA
1 GATGAA
1977344 CAAATGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.18
Consensus pattern (11 bp):
GATGAATAAAG
Found at i:1978193 original size:26 final size:27
Alignment explanation
Indices: 1978164--1978215 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
1978154 AAAGGCTTGG
1978164 CCTTCGTT-ATTTAAA-TCAAGGAATAT
1 CCTT-GTTCATTTAAATTCAAGGAATAT
*
1978190 CCTTGTTCTTTTAAATTCAAGGAATA
1 CCTTGTTCATTTAAATTCAAGGAATA
1978216 CTTTATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 3 0.13
26 10 0.43
27 10 0.43
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (27 bp):
CCTTGTTCATTTAAATTCAAGGAATAT
Found at i:1980544 original size:16 final size:16
Alignment explanation
Indices: 1980507--1980547 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1980497 AAAAAATGAG
*
1980507 AATAAA-AATAAGTAAA
1 AATAAATAA-AAGGAAA
1980523 AA-AAATAAAAGGAAA
1 AATAAATAAAAGGAAA
1980538 AATAAATAAA
1 AATAAATAAA
1980548 TAAATAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (16 bp):
AATAAATAAAAGGAAA
Found at i:1980573 original size:2 final size:2
Alignment explanation
Indices: 1980566--1980596 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1980556 TGAAATATTA
1980566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1980597 AATGAGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1980622 original size:3 final size:3
Alignment explanation
Indices: 1980614--1980670 Score: 50
Period size: 3 Copynumber: 20.3 Consensus size: 3
1980604 AAAATAGAAA
* * * *
1980614 AAT AAT AAT CAT AAC AAT AAT AAT AGT AAT -AT GA- AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1980660 -AT AAT -AT AAT A
1 AAT AAT AAT AAT A
1980671 TAAAAAAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
2 7 0.16
3 36 0.84
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1980653 original size:16 final size:15
Alignment explanation
Indices: 1980632--1980670 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1980622 TCATAACAAT
*
1980632 AATAATAGTAATATGA
1 AATAATAATAATAT-A
1980648 AATAATAATAATATA
1 AATAATAATAATATA
1980663 ATATAATA
1 A-ATAATA
1980671 TAAAAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (15 bp):
AATAATAATAATATA
Found at i:1980901 original size:21 final size:21
Alignment explanation
Indices: 1980877--1980958 Score: 60
Period size: 22 Copynumber: 3.8 Consensus size: 21
1980867 ATATATATAT
1980877 AAATAATAAATATAGTATTAA
1 AAATAATAAATATAGTATTAA
* * *
1980898 AAATAACCAAAT-TAATATAAA
1 AAATAA-TAAATATAGTATTAA
*
1980919 TAAATAAAAAATATATGTA-TAGA
1 -AAATAATAAATATA-GTATTA-A
*
1980942 TAATAATAATATATAGT
1 AAATAATAA-ATATAGT
1980959 GTAAAAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
21 17 0.36
22 22 0.47
23 8 0.17
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (21 bp):
AAATAATAAATATAGTATTAA
Found at i:1981478 original size:37 final size:37
Alignment explanation
Indices: 1981437--1981530 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
1981427 TCCTATCTTT
* *
1981437 AGGAGTTTAAATCATAGTAGAACTCTATCATATTTTA
1 AGGAGTTTGAATCCTAGTAGAACTCTATCATATTTTA
* * * * *
1981474 AGGAGTTTGAATCCTAGAAAAATTCTATCCTATTTTT
1 AGGAGTTTGAATCCTAGTAGAACTCTATCATATTTTA
1981511 AGGAGTTTGAATCCTAGTAG
1 AGGAGTTTGAATCCTAGTAG
1981531 GACGAAAAAG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (37 bp):
AGGAGTTTGAATCCTAGTAGAACTCTATCATATTTTA
Found at i:1982604 original size:106 final size:106
Alignment explanation
Indices: 1982261--1983954 Score: 2422
Period size: 106 Copynumber: 16.0 Consensus size: 106
1982251 AGCATTGTTC
* * ** * * *
1982261 TGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGAC
1 TGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGAC
** * * *
1982325 AACCAGCCATCCCTTAGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
1982367 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * * *
1982426 ATCAGCCGCCCCTTCGTCGTGAAGTGTTGAGCTTGTC-TTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAA--GTTGAACTTG-CGTTGTCT
* * *
1982469 TGGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
*
1982534 ACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
1982575 TGAGTCCAATATCCTACGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
*
1982640 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * ** *
1982681 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTTAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * *
1982746 ACCAGCGGTCCCTTCATCGTGAAGTTCAACTTGCATTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
1982787 GGAGTCCAATATCATTCGCTGTGAAGTTGCAATTGGCTTTGAAATTGGGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1982852 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* ** * *
1982893 TTAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* *
1982958 ACCAGCGGTCCCTTCGTTGTGATGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
1982999 TTAGT-CAA-ATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
*
1983062 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
1983103 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAGTTATTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
*
1983168 ACCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
1983209 TGAGTCCAATAT-CTACGCTGTGAAGTTGAAAGTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* *
1983273 ACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTTTC-
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
1983313 TGAAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTATTGAC
1 TG-AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGAC
*
1983378 AACCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
1983420 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1983485 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
1983526 TGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTAAAATTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* *
1983591 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTAT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * *
1983632 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAAGTGGCTCTGAAATTGAGAAGTCGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
*
1983697 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
1983738 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
*
1983803 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
1983844 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * * *
1983909 ACCATCGGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
1983950 TGAGT
1 TGAGT
1983955 GACACGATAT
Statistics
Matches: 1431, Mismatches: 141, Indels: 32
0.89 0.09 0.02
Matches are distributed among these distances:
100 27 0.02
101 1 0.00
102 53 0.04
103 2 0.00
104 94 0.07
105 104 0.07
106 1117 0.78
107 3 0.00
108 30 0.02
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:1984728 original size:22 final size:22
Alignment explanation
Indices: 1984702--1984778 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
1984692 TTATGTTTGG
1984702 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1984724 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1984746 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1984768 TCAATGGTTTG
1 TCAAAGGTTTG
1984779 ATGGGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.40
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1985474 original size:172 final size:171
Alignment explanation
Indices: 1985173--1985518 Score: 561
Period size: 172 Copynumber: 2.0 Consensus size: 171
1985163 TAAATAGGCC
* *
1985173 CAAACAAGTGTTTCATGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAATC---TCCTG
*
1985238 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCGGGAATG
63 CTCAAAATGTCTCTCTCTTAATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCGGGAATG
1985303 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
128 ATTGTGCTTGATCAATCTCATAG-TTGAAGCTTGATGTGCCATTT
* *
1985348 CAAACAAGTGTTTCAGGGTGTTGAACCAATGATCAATTCATTATGATGTCTTCAATC-CC-GCTC
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAATCTCCTGCTC
* *
1985411 AAAATGTTTCTCTCTCTTAATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTTGGGAATGA
66 AAAATG--TCTCTCTCTTAATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCGGGAATGA
1985476 TTGTGCTTGATCAATCTCATAGTTGAAGCTTGATGTGCCATTT
129 TTGTGCTTGATCAATCTCATAGTTGAAGCTTGATGTGCCATTT
1985519 TTTAGGAATC
Statistics
Matches: 162, Mismatches: 7, Indels: 8
0.92 0.04 0.05
Matches are distributed among these distances:
170 10 0.06
171 23 0.14
172 76 0.47
175 53 0.33
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (171 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAATCTCCTGCTC
AAAATGTCTCTCTCTTAATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCGGGAATGATT
GTGCTTGATCAATCTCATAGTTGAAGCTTGATGTGCCATTT
Found at i:1985585 original size:27 final size:26
Alignment explanation
Indices: 1985550--1985620 Score: 63
Period size: 27 Copynumber: 2.6 Consensus size: 26
1985540 TTTTGTCCCT
*
1985550 TTTTCTTTTGATTTTTG-TTCTTGTTTCTC
1 TTTT-TTTTG-TTTTTGCTTCTTG-CT-TC
* *
1985579 TTTTTTTTTTTTTTGCTTTTTTGCTTC
1 TTTTTTTTGTTTTTGC-TTCTTGCTTC
1985606 TTTTTTTTGTTTTTG
1 TTTTTTTTGTTTTTG
1985621 ATTGGATCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 22 0.61
28 5 0.14
29 9 0.25
ACGTcount: A:0.01, C:0.10, G:0.10, T:0.79
Consensus pattern (26 bp):
TTTTTTTTGTTTTTGCTTCTTGCTTC
Found at i:1985588 original size:24 final size:24
Alignment explanation
Indices: 1985561--1985616 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
1985551 TTTCTTTTGA
*
1985561 TTTTTGTT-CTTGTTTCT-CTTTTTT
1 TTTTTGTTGCTT-TTT-TGCTTCTTT
*
1985585 TTTTTTTTGCTTTTTTGCTTCTTT
1 TTTTTGTTGCTTTTTTGCTTCTTT
1985609 TTTTTGTT
1 TTTTTGTT
1985617 TTTGATTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 23 0.85
25 3 0.11
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.80
Consensus pattern (24 bp):
TTTTTGTTGCTTTTTTGCTTCTTT
Found at i:1989663 original size:2 final size:2
Alignment explanation
Indices: 1989656--1989682 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1989646 AATAAATGAA
1989656 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1989683 AATGAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1990514 original size:37 final size:36
Alignment explanation
Indices: 1990473--1990577 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 36
1990463 GTGCTTGTGG
*
1990473 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTAT-TTTAGGAGTTTAAATCCTAGTAGAACTCT
* * * *
1990510 ATCCTATTTTAAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTT-AGGAGTTTAAATCCTAGTAGAACTCT
*
1990547 ATCATATTTTTAGGAGTTTAAATCCTAGTAG
1 ATCCTA-TTTTAGGAGTTTAAATCCTAGTAG
1990578 GACGAAAAGG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
36 3 0.05
37 50 0.88
38 4 0.07
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:2002262 original size:139 final size:137
Alignment explanation
Indices: 2001942--2002273 Score: 355
Period size: 139 Copynumber: 2.4 Consensus size: 137
2001932 ATTAATCCAA
* *
2001942 ATCAATTTTAACCAATTATTGAATCGAATAATTAAAATGGAACCTCGAGCAAAAATGATGACCAA
1 ATCAATTTTAACCAATTATTGATTCGAATAATTAAAATGGAACCTCGAGCAAAAGTGATGACCAA
* * * * *
2002007 ATAAAAAATTCTCCTAAATTTAAGGATTAGTTATGAAATTAAACCTAAAATCAAGGTTCTAAATA
66 ATAAAAAATTCTACTAAATTAAAGGATAAATTATGAAATTAAACCTAAAATCAAGGGTCTAAATA
2002072 TTAACCT
131 TTAACCT
* * * * *
2002079 ATTAATTTTTATCAATTATGTGATTCAAATGATTAAAATGGAACCTCGAGCAAAAGTGA-GAACC
1 ATCAATTTTAACCAATTAT-TGATTCGAATAATTAAAATGGAACCTCGAGCAAAAGTGATG-ACC
* * * * * * **
2002143 AAATTAAGAATTCTATTAAATTAAAAGGACTAAATT-TGAAATTAAGCTTAAATTGGAGGGTCTA
64 AAATAAAAAATTCTACTAAATT-AAAGGA-TAAATTATGAAATTAAACCTAAAATCAAGGGTCTA
*
2002207 ATTATTAACCT
127 AATATTAACCT
* * * * *
2002218 AGTCAGTTTTAACCAATTACTT-ATTCGAATAATTAAATTAGAACCTCAAGTAAAAG
1 A-TCAATTTTAACCAATTA-TTGATTCGAATAATTAAAATGGAACCTCGAGCAAAAG
2002274 CAAAGATCGA
Statistics
Matches: 158, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
137 17 0.11
138 56 0.35
139 66 0.42
140 18 0.11
141 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (137 bp):
ATCAATTTTAACCAATTATTGATTCGAATAATTAAAATGGAACCTCGAGCAAAAGTGATGACCAA
ATAAAAAATTCTACTAAATTAAAGGATAAATTATGAAATTAAACCTAAAATCAAGGGTCTAAATA
TTAACCT
Found at i:2004429 original size:2 final size:2
Alignment explanation
Indices: 2004424--2004502 Score: 135
Period size: 2 Copynumber: 40.0 Consensus size: 2
2004414 TTTTTAATCA
2004424 AT AT AT AT AT AT AT AT AT -T 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
2004465 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
2004503 TACTTAAACT
Statistics
Matches: 74, Mismatches: 0, Indels: 6
0.93 0.00 0.08
Matches are distributed among these distances:
1 2 0.03
2 70 0.95
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2014925 original size:18 final size:18
Alignment explanation
Indices: 2014902--2014963 Score: 106
Period size: 18 Copynumber: 3.4 Consensus size: 18
2014892 AATCAGGGTT
*
2014902 AGCGGGTTCTTCTGCTTC
1 AGCGGGCTCTTCTGCTTC
2014920 AGCGGGCTCTTCTGCTTC
1 AGCGGGCTCTTCTGCTTC
2014938 AGCGGGCTCTTCTGCTTC
1 AGCGGGCTCTTCTGCTTC
*
2014956 AGTGGGCT
1 AGCGGGCT
2014964 GAGGACTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.06, C:0.29, G:0.31, T:0.34
Consensus pattern (18 bp):
AGCGGGCTCTTCTGCTTC
Found at i:2025160 original size:16 final size:16
Alignment explanation
Indices: 2025141--2025174 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2025131 AATGTGAATG
2025141 AATGATATAATAAAGT
1 AATGATATAATAAAGT
*
2025157 AATGATGTAATAAAGT
1 AATGATATAATAAAGT
2025173 AA
1 AA
2025175 GAAAGACTCC
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:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (16 bp):
AATGATATAATAAAGT
Found at i:2034399 original size:17 final size:17
Alignment explanation
Indices: 2034377--2034448 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 17
2034367 AATTAAGAGT
2034377 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
2034394 TAGTTTTATGAATGGAC
1 TAGTTTAATAAATGAAC
* * * *
2034411 CAGTTTAATTAATAAAA
1 TAGTTTAATAAATGAAC
* *
2034428 TAACTTTATTAAATGAAC
1 T-AGTTTAATAAATGAAC
2034446 TAG
1 TAG
2034449 ATGCATGAAT
Statistics
Matches: 38, Mismatches: 16, Indels: 2
0.68 0.29 0.04
Matches are distributed among these distances:
17 26 0.68
18 12 0.32
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:2040727 original size:16 final size:17
Alignment explanation
Indices: 2040695--2040729 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2040685 AATGTGAATG
2040695 AATGATATAATTAAAGT
1 AATGATATAATTAAAGT
*
2040712 AATGATGTAA-TAAAGT
1 AATGATATAATTAAAGT
2040728 AA
1 AA
2040730 GAAAGAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (17 bp):
AATGATATAATTAAAGT
Found at i:2047747 original size:15 final size:15
Alignment explanation
Indices: 2047727--2047756 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2047717 AGGAGAGGTA
*
2047727 TTTCTTTTTCTTTTC
1 TTTCTTTTTCATTTC
2047742 TTTCTTTTTCATTTC
1 TTTCTTTTTCATTTC
2047757 ACGAAAGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTCTTTTTCATTTC
Found at i:2055028 original size:12 final size:12
Alignment explanation
Indices: 2055011--2055035 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2055001 GTATAAATAC
2055011 AGGATAGGAATT
1 AGGATAGGAATT
2055023 AGGATAGGAATT
1 AGGATAGGAATT
2055035 A
1 A
2055036 TATATGTTTT
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:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (12 bp):
AGGATAGGAATT
Found at i:2081421 original size:23 final size:23
Alignment explanation
Indices: 2081369--2081421 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
2081359 ATTATTTCTT
* *
2081369 ATATATATATATTTATAATAATA
1 ATATAAATATATTGATAATAATA
* *
2081392 TTTTAAATATATTGATAATAA-A
1 ATATAAATATATTGATAATAATA
2081414 CATATAAA
1 -ATATAAA
2081422 ATTAAAACCA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATAAATATATTGATAATAATA
Found at i:2082663 original size:3 final size:3
Alignment explanation
Indices: 2082657--2082705 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
2082647 TAATATTTAT
* * * *
2082657 TAA TAA TAA -AA CAA AAA TAA TAA TTA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2082704 TA
1 TA
2082706 TTCAAATGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2082683 original size:27 final size:27
Alignment explanation
Indices: 2082645--2082705 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
2082635 TTGGGCATGT
*
2082645 AATAATATTTATTAATAATAA-AACAAA
1 AATAATAATTA-TAATAATAATAACAAA
* * *
2082672 AATAATAATTATAATTATAATAATAAT
1 AATAATAATTATAATAATAATAACAAA
2082699 AATAATA
1 AATAATA
2082706 TTCAAATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
AATAATAATTATAATAATAATAACAAA
Found at i:2085001 original size:20 final size:20
Alignment explanation
Indices: 2084964--2085006 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2084954 ATTCCATCAC
*
2084964 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
2084984 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
2085004 ATG
1 ATG
2085007 TGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:2085578 original size:10 final size:10
Alignment explanation
Indices: 2085563--2085595 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
2085553 ATAATTTATA
2085563 TTTCTTTTTT
1 TTTCTTTTTT
2085573 TTTCTTTTTT
1 TTTCTTTTTT
2085583 TTTCCTTTTTT
1 TTT-CTTTTTT
2085594 TT
1 TT
2085596 ATGCGGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:2085583 original size:11 final size:11
Alignment explanation
Indices: 2085563--2085595 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2085553 ATAATTTATA
2085563 TTTC-TTTTTT
1 TTTCTTTTTTT
2085573 TTTCTTTTTTT
1 TTTCTTTTTTT
*
2085584 TTCCTTTTTTT
1 TTTCTTTTTTT
2085595 T
1 T
2085596 ATGCGGGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:2094002 original size:101 final size:101
Alignment explanation
Indices: 2093827--2094015 Score: 333
Period size: 101 Copynumber: 1.9 Consensus size: 101
2093817 ATCCACCGAG
* * *
2093827 TGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATGCTTCCTTCTTCAGA
*
2093892 TGAGTTCTTCTCGTTATGAACTCGACCTGGAAATGC
66 TGAGTTCTTCTCATTATGAACTCGACCTGGAAATGC
*
2093928 TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTGCTTCCTTCTTCAGA
1 TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATGCTTCCTTCTTCAGA
2093993 TGAGTTCTTCTCATTATGAACTC
66 TGAGTTCTTCTCATTATGAACTC
2094016 TTCTGGAAAT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 83 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.37
Consensus pattern (101 bp):
TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATGCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTCGACCTGGAAATGC
Found at i:2095205 original size:18 final size:19
Alignment explanation
Indices: 2095177--2095232 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
2095167 TTTACAAAAT
2095177 AAAAGAATAAATTGAATTTC
1 AAAA-AATAAATTGAATTTC
* *
2095197 -GAAAATAAATTGAATATC
1 AAAAAATAAATTGAATTTC
2095215 AAAAAATAAATTGAATTT
1 AAAAAATAAATTGAATTT
2095233 ATAGAAACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (19 bp):
AAAAAATAAATTGAATTTC
Found at i:2095622 original size:16 final size:18
Alignment explanation
Indices: 2095586--2095630 Score: 67
Period size: 16 Copynumber: 2.6 Consensus size: 18
2095576 TTGACCCTCC
*
2095586 TTTTTTATTTTCTTCTCT
1 TTTTTTCTTTTCTTCTCT
2095604 TTTTTTCTTTTC-TCT-T
1 TTTTTTCTTTTCTTCTCT
2095620 TTTTTTCTTTT
1 TTTTTTCTTTT
2095631 TTTTCATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
17 3 0.12
18 11 0.42
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTCTTTTCTTCTCT
Found at i:2095646 original size:25 final size:26
Alignment explanation
Indices: 2095593--2095651 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
2095583 TCCTTTTTTA
*
2095593 TTTTCTTCTCTTTTTTTCTTTTCTCT
1 TTTTCTTCTCTTTTTTTCATTTCTCT
*
2095619 TTTTTTTCT-TTTTTTTCATTTCAT-T
1 TTTTCTTCTCTTTTTTTCATTTC-TCT
2095644 TTTTCTTC
1 TTTTCTTC
2095652 AAGCATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 20 0.69
26 9 0.31
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTCTTCTCTTTTTTTCATTTCTCT
Found at i:2099192 original size:9 final size:9
Alignment explanation
Indices: 2099169--2099199 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2099159 GAAAAATAAT
2099169 GAATGTAAA
1 GAATGTAAA
2099178 -AATGTAAA
1 GAATGTAAA
2099186 GAATGTAAA
1 GAATGTAAA
2099195 GAATG
1 GAATG
2099200 ATTGCCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (9 bp):
GAATGTAAA
Found at i:2102889 original size:15 final size:15
Alignment explanation
Indices: 2102866--2102897 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2102856 TGCAATGAAT
2102866 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
2102881 AATGCATGTATGCAA
1 AATGAATGTATGCAA
2102896 AA
1 AA
2102898 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:2106997 original size:18 final size:20
Alignment explanation
Indices: 2106949--2106997 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
2106939 TAAAAGAAAA
2106949 ATAA-AATATATATTATTTC
1 ATAATAATATATATTATTTC
*
2106968 -TTATATATATATATATATTT-
1 ATAATA-ATATATAT-TATTTC
2106988 ATAATAATAT
1 ATAATAATAT
2106998 TTTAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
18 2 0.08
19 1 0.04
20 12 0.50
21 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAATAATATATATTATTTC
Found at i:2107026 original size:23 final size:23
Alignment explanation
Indices: 2106974--2107026 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
2106964 TTTCTTATAT
* *
2106974 ATATATATATATTTATAATAATA
1 ATATAAATATATTGATAATAATA
* *
2106997 TTTTAAATATATTGATAATAA-A
1 ATATAAATATATTGATAATAATA
2107019 CATATAAA
1 -ATATAAA
2107027 ATTAAAACAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATAAATATATTGATAATAATA
Found at i:2113000 original size:16 final size:16
Alignment explanation
Indices: 2112957--2113001 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2112947 CTGGTAAATA
2112957 ACTTG-TATT-ACCTG
1 ACTTGTTATTAACCTG
*
2112971 ACCTGTT-TTCAACCTG
1 ACTTGTTATT-AACCTG
2112987 ACTTGTTATTAACCT
1 ACTTGTTATTAACCT
2113002 AATCTGATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 6 0.24
15 1 0.04
16 16 0.64
17 2 0.08
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.42
Consensus pattern (16 bp):
ACTTGTTATTAACCTG
Found at i:2113154 original size:18 final size:19
Alignment explanation
Indices: 2113128--2113190 Score: 67
Period size: 18 Copynumber: 3.3 Consensus size: 19
2113118 GTTATAATAA
2113128 AATATTAATTATGATAATT
1 AATATTAATTATGATAATT
* *
2113147 AA-ATTAATAAAT-ATACTT
1 AATATTAAT-TATGATAATT
2113165 AATATATTAATTATGATAATT
1 -A-ATATTAATTATGATAATT
2113186 AATAT
1 AATAT
2113191 ACTTTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 11 0.31
19 9 0.26
20 4 0.11
21 11 0.31
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (19 bp):
AATATTAATTATGATAATT
Found at i:2113187 original size:21 final size:21
Alignment explanation
Indices: 2113121--2113191 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
2113111 TTTAAATGTT
*
2113121 ATAA-TAAAATATTAATTATG
1 ATAATTAATATATTAATTATG
*
2113141 ATAATT-A-A-ATTAATAAAT-
1 ATAATTAATATATTAAT-TATG
*
2113159 ATACTTAATATATTAATTATG
1 ATAATTAATATATTAATTATG
2113180 ATAATTAATATA
1 ATAATTAATATA
2113192 CTTTATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
18 11 0.27
19 4 0.10
20 8 0.20
21 18 0.44
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (21 bp):
ATAATTAATATATTAATTATG
Found at i:2113261 original size:24 final size:22
Alignment explanation
Indices: 2113195--2113267 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
2113185 TAATATACTT
*
2113195 TATA-TTTAATAC-TTATATTA
1 TATACTTTAATACTTTGTATTA
*
2113215 TATAGTTTAATACTTTGTATTA
1 TATACTTTAATACTTTGTATTA
* *
2113237 TATACTTTAGTACTTATGTGCTTA
1 TATACTTTAATACTT-TGT-ATTA
2113261 TATACTT
1 TATACTT
2113268 ATATTATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.09
21 8 0.18
22 20 0.44
23 3 0.07
24 10 0.22
ACGTcount: A:0.32, C:0.08, G:0.07, T:0.53
Consensus pattern (22 bp):
TATACTTTAATACTTTGTATTA
Found at i:2113410 original size:24 final size:24
Alignment explanation
Indices: 2113378--2113423 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2113368 TGATGAGGGA
2113378 TGAAATTGA-AGTAATTATAAAATG
1 TGAAATTGATAGTAA-TATAAAATG
* *
2113402 TGAAGTTGATATTAATATAAAA
1 TGAAATTGATAGTAATATAAAA
2113424 ATGGACTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (24 bp):
TGAAATTGATAGTAATATAAAATG
Found at i:2114822 original size:2 final size:2
Alignment explanation
Indices: 2114815--2114841 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2114805 TTTTTAAAAC
2114815 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2114842 CCCCCATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2115028 original size:24 final size:24
Alignment explanation
Indices: 2115001--2115052 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2114991 AACGGATATA
*
2115001 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
2115025 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
2115049 TCAA
1 TCAA
2115053 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:2115053 original size:24 final size:24
Alignment explanation
Indices: 2115021--2115135 Score: 135
Period size: 24 Copynumber: 4.8 Consensus size: 24
2115011 AAACATAAAT
2115021 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCATATCAG-AATC
* *
2115045 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
* *
2115069 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
*
2115093 CATGTC-AGATATCATATCAGAATC
1 CAGGTCAAG-TATCATATCAGAATC
* *
2115117 CATGTAAAGTATCATATCA
1 CAGGTCAAGTATCATATCA
2115136 AAATTCAAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 5 0.06
24 74 0.91
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAGAATC
Found at i:2118610 original size:33 final size:33
Alignment explanation
Indices: 2118573--2118643 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
2118563 ACTTATTTAA
*
2118573 ATATACATA-TATAAAAAATATAAGTATAAGTAT
1 ATATACAAAGTATAAAAAATA-AAGTATAAGTAT
* * **
2118606 ATATATAAAGTGTAAACTATAAAGTATAAGTAT
1 ATATACAAAGTATAAAAAATAAAGTATAAGTAT
2118639 ATATA
1 ATATA
2118644 TAATCTATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (33 bp):
ATATACAAAGTATAAAAAATAAAGTATAAGTAT
Found at i:2118687 original size:2 final size:2
Alignment explanation
Indices: 2118680--2118730 Score: 54
Period size: 2 Copynumber: 26.0 Consensus size: 2
2118670 ACTAAAACTT
*
2118680 TA TA TA TA T- TA TA TA CTT TA TA T- TA TA TA CT- 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
2118721 TA TA TA TA TA
1 TA TA TA TA TA
2118731 AAGTTTTAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
1 3 0.07
2 37 0.88
3 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.