Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008194.1 Hibiscus syriacus cultivar Beakdansim tig00110813_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: 2426039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:1726410 original size:103 final size:103
Alignment explanation
Indices: 1726283--1726490 Score: 416
Period size: 103 Copynumber: 2.0 Consensus size: 103
1726273 GAATCTCAAG
1726283 TGAGATCAATTTTGTTTCAAAAAATTTCAAAATTTGCGAAAACCTGTCACAAGTGAGACGATTTT
1 TGAGATCAATTTTGTTTCAAAAAATTTCAAAATTTGCGAAAACCTGTCACAAGTGAGACGATTTT
1726348 TTTTTGAGAAAAACAATCTTAAAGGCTTATAGAATGTC
66 TTTTTGAGAAAAACAATCTTAAAGGCTTATAGAATGTC
1726386 TGAGATCAATTTTGTTTCAAAAAATTTCAAAATTTGCGAAAACCTGTCACAAGTGAGACGATTTT
1 TGAGATCAATTTTGTTTCAAAAAATTTCAAAATTTGCGAAAACCTGTCACAAGTGAGACGATTTT
1726451 TTTTTGAGAAAAACAATCTTAAAGGCTTATAGAATGTC
66 TTTTTGAGAAAAACAATCTTAAAGGCTTATAGAATGTC
1726489 TG
1 TG
1726491 CTTGTTCCTG
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (103 bp):
TGAGATCAATTTTGTTTCAAAAAATTTCAAAATTTGCGAAAACCTGTCACAAGTGAGACGATTTT
TTTTTGAGAAAAACAATCTTAAAGGCTTATAGAATGTC
Found at i:1729072 original size:29 final size:27
Alignment explanation
Indices: 1729032--1729105 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 27
1729022 TGTCTTTTTT
* *
1729032 TTTGTTCTTTTCTTTG-TTTTTTTTCTC
1 TTTGTTTTTTTCTTTGATTTTTCTT-TC
1729059 TTTGCTTATTTTTCTTTGCATTTTTCTTTC
1 TTTG-TT-TTTTTCTTTG-ATTTTTCTTTC
1729089 TTTGTTTTTTCTCTTTG
1 TTTGTTTTTT-TCTTTG
1729106 CTTTGAGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
27 4 0.10
28 6 0.15
29 17 0.43
30 6 0.15
31 7 0.17
ACGTcount: A:0.03, C:0.15, G:0.08, T:0.74
Consensus pattern (27 bp):
TTTGTTTTTTTCTTTGATTTTTCTTTC
Found at i:1729100 original size:15 final size:14
Alignment explanation
Indices: 1729039--1729098 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
1729029 TTTTTTGTTC
1729039 TTTTCTTTGTTTTT
1 TTTTCTTTGTTTTT
* *
1729053 TTTCTCTTTGCTTAT
1 TTT-TCTTTGTTTTT
1729068 TTTTCTTTGCATTTTT
1 TTTTCTTTG--TTTTT
*
1729084 CTTTCTTTGTTTTT
1 TTTTCTTTGTTTTT
1729098 T
1 T
1729099 CTCTTTGCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 14 0.38
15 12 0.32
16 11 0.30
ACGTcount: A:0.03, C:0.13, G:0.07, T:0.77
Consensus pattern (14 bp):
TTTTCTTTGTTTTT
Found at i:1732906 original size:15 final size:14
Alignment explanation
Indices: 1732886--1732959 Score: 76
Period size: 15 Copynumber: 4.9 Consensus size: 14
1732876 AAAAATATGT
*
1732886 AAATAAGTATTAATA
1 AAATAA-TAATAATA
1732901 AAATAATAATAATA
1 AAATAATAATAATA
1732915 ATAATAATAATAATA
1 A-AATAATAATAATA
1732930 CTTATAATAATAATAATA
1 ---A-AATAATAATAATA
*
1732948 AATTAATAATAA
1 AAATAATAATAA
1732960 ATGAGAACCT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
14 18 0.34
15 20 0.38
18 15 0.28
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (14 bp):
AAATAATAATAATA
Found at i:1732910 original size:3 final size:3
Alignment explanation
Indices: 1732896--1732959 Score: 87
Period size: 3 Copynumber: 22.0 Consensus size: 3
1732886 AAATAAGTAT
* *
1732896 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAC TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1732943 TAA TAA -AT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1732960 ATGAGAACCT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 3 0.06
3 50 0.94
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1739698 original size:10 final size:9
Alignment explanation
Indices: 1739668--1739748 Score: 53
Period size: 9 Copynumber: 9.2 Consensus size: 9
1739658 GGATACATTG
1739668 ATATAATAT
1 ATATAATAT
*
1739677 -TCATATTAT
1 AT-ATAATAT
1739686 ATATTAATAT
1 ATA-TAATAT
1739696 ATATAATAT
1 ATATAATAT
* *
1739705 -TTTTATAT
1 ATATAATAT
*
1739713 AAATAATAT
1 ATATAATAT
*
1739722 TTATAATAT
1 ATATAATAT
**
1739731 A-ATTGTAT
1 ATATAATAT
1739739 -TATAATAT
1 ATATAATAT
1739747 AT
1 AT
1739749 TTTTATAATT
Statistics
Matches: 52, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
8 17 0.33
9 26 0.50
10 9 0.17
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (9 bp):
ATATAATAT
Found at i:1739704 original size:17 final size:15
Alignment explanation
Indices: 1739668--1739733 Score: 66
Period size: 17 Copynumber: 4.5 Consensus size: 15
1739658 GGATACATTG
*
1739668 ATATAATATTCATAT
1 ATATAATATTTATAT
*
1739683 -TAT-ATATTAATAT
1 ATATAATATTTATAT
1739696 ATATAATATTTTTATAT
1 ATATAATA--TTTATAT
*
1739713 AAATAATATTTATA-
1 ATATAATATTTATAT
1739727 ATATAAT
1 ATATAAT
1739734 TGTATTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
13 9 0.21
14 12 0.28
15 9 0.21
17 13 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATAATATTTATAT
Found at i:1739719 original size:26 final size:27
Alignment explanation
Indices: 1739668--1739748 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 27
1739658 GGATACATTG
*
1739668 ATATAATATTCATATTATATATTAATAT
1 ATATAATATT-ATATTATATAATAATAT
1739696 ATATAATATT-T-TTATATAAATAATAT
1 ATATAATATTATATTATAT-AATAATAT
* * *
1739722 TTATAATA-TA-ATTGTATTATAATAT
1 ATATAATATTATATTATATAATAATAT
1739747 AT
1 AT
1739749 TTTTATAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
25 15 0.33
26 20 0.44
28 10 0.22
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
ATATAATATTATATTATATAATAATAT
Found at i:1743526 original size:61 final size:61
Alignment explanation
Indices: 1743455--1743573 Score: 229
Period size: 61 Copynumber: 2.0 Consensus size: 61
1743445 ATATCTGTAG
1743455 AAGAATCTAATATCTGTAAGGTTAAATAGCTAAGATATTAACATATGCTCACAATCTATAT
1 AAGAATCTAATATCTGTAAGGTTAAATAGCTAAGATATTAACATATGCTCACAATCTATAT
*
1743516 AAGAATCTAATATCTGTAAGGTTAAATAGTTAAGATATTAACATATGCTCACAATCTA
1 AAGAATCTAATATCTGTAAGGTTAAATAGCTAAGATATTAACATATGCTCACAATCTA
1743574 ATGACCACTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.33
Consensus pattern (61 bp):
AAGAATCTAATATCTGTAAGGTTAAATAGCTAAGATATTAACATATGCTCACAATCTATAT
Found at i:1743550 original size:31 final size:30
Alignment explanation
Indices: 1743455--1743550 Score: 70
Period size: 31 Copynumber: 3.1 Consensus size: 30
1743445 ATATCTGTAG
1743455 AAGAATCTAATATCTGTAAGGTTAAATAGCT
1 AAGAATCTAATATCTGTAAGGTTAAATAG-T
* * * *** **
1743486 AAGATAT-TAACATATGCTCACAATCTATA-T
1 AAGA-ATCTAATATCTG-TAAGGTTAAATAGT
1743516 AAGAATCTAATATCTGTAAGGTTAAATAGTT
1 AAGAATCTAATATCTGTAAGGTTAAATAG-T
1743547 AAGA
1 AAGA
1743551 TATTAACATA
Statistics
Matches: 44, Mismatches: 16, Indels: 10
0.63 0.23 0.14
Matches are distributed among these distances:
29 8 0.18
30 12 0.27
31 16 0.36
32 8 0.18
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (30 bp):
AAGAATCTAATATCTGTAAGGTTAAATAGT
Found at i:1743700 original size:25 final size:25
Alignment explanation
Indices: 1743664--1743769 Score: 187
Period size: 25 Copynumber: 4.2 Consensus size: 25
1743654 GAGTTAGAGA
1743664 AAAAG-AGCTTAGAGGAAAAGAAAAG
1 AAAAGTAG-TTAGAGGAAAAGAAAAG
1743689 AAAAGTAGTTAGAGGAAAAGAAAAG
1 AAAAGTAGTTAGAGGAAAAGAAAAG
1743714 AAAAGTAGTTAGAGGAAAAGAAAAG
1 AAAAGTAGTTAGAGGAAAAGAAAAG
*
1743739 AAAAGTAGTTAGAAGAAAAGAAAAG
1 AAAAGTAGTTAGAGGAAAAGAAAAG
1743764 AAAAGT
1 AAAAGT
1743770 TAGAGGAAAA
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
25 77 0.97
26 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.26, T:0.11
Consensus pattern (25 bp):
AAAAGTAGTTAGAGGAAAAGAAAAG
Found at i:1743708 original size:15 final size:14
Alignment explanation
Indices: 1743654--1743734 Score: 52
Period size: 15 Copynumber: 6.1 Consensus size: 14
1743644 TGTCAAAAGT
*
1743654 GAGTTAGAGAAAAA
1 GAGTTAGAGGAAAA
1743668 GAGCTTAGAGGAAAA
1 GAG-TTAGAGGAAAA
*
1743683 GA---A-AAGAAAA
1 GAGTTAGAGGAAAA
1743693 GTAGTTAGAGGAAAA
1 G-AGTTAGAGGAAAA
*
1743708 GA---A-AAGAAAA
1 GAGTTAGAGGAAAA
1743718 GTAGTTAGAGGAAAA
1 G-AGTTAGAGGAAAA
1743733 GA
1 GA
1743735 AAAGAAAAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 22
0.65 0.06 0.28
Matches are distributed among these distances:
10 14 0.27
11 4 0.08
14 7 0.14
15 26 0.51
ACGTcount: A:0.57, C:0.01, G:0.30, T:0.12
Consensus pattern (14 bp):
GAGTTAGAGGAAAA
Found at i:1745144 original size:15 final size:15
Alignment explanation
Indices: 1745124--1745154 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1745114 AATTATTATT
1745124 GACCTTCTGGGGCAC
1 GACCTTCTGGGGCAC
1745139 GACCTTCTGGGGCAC
1 GACCTTCTGGGGCAC
1745154 G
1 G
1745155 TTCGCAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.32, G:0.35, T:0.19
Consensus pattern (15 bp):
GACCTTCTGGGGCAC
Found at i:1760080 original size:23 final size:24
Alignment explanation
Indices: 1760053--1760110 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 24
1760043 ATTTAAAAGT
*
1760053 AATAAAATATAGTT-TTTTATTAA
1 AATAAAATATAGTTAATTTATTAA
*
1760076 AATAAAATAAAGTTAATTTATTAA
1 AATAAAATATAGTTAATTTATTAA
1760100 AATAAAA-ATAG
1 AATAAAATATAG
1760111 AAAAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (24 bp):
AATAAAATATAGTTAATTTATTAA
Found at i:1760100 original size:24 final size:23
Alignment explanation
Indices: 1760053--1760106 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
1760043 ATTTAAAAGT
* *
1760053 AATAAAATATAGTTTTTTATTAA
1 AATAAAATAAAGTTATTTATTAA
1760076 AATAAAATAAAGTTAATTTATTAA
1 AATAAAATAAAGTT-ATTTATTAA
1760100 AATAAAA
1 AATAAAA
1760107 ATAGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
AATAAAATAAAGTTATTTATTAA
Found at i:1760115 original size:14 final size:14
Alignment explanation
Indices: 1760098--1760142 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1760088 TTAATTTATT
1760098 AAAATAAAAATAGAA
1 AAAATAAAAATA-AA
1760113 AAAATAAAAA-ATAA
1 AAAATAAAAATA-AA
*
1760127 AAAATAAATATAAA
1 AAAATAAAAATAAA
1760141 AA
1 AA
1760143 TTGAAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (14 bp):
AAAATAAAAATAAA
Found at i:1760121 original size:7 final size:7
Alignment explanation
Indices: 1760098--1760134 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
1760088 TTAATTTATT
1760098 AAAATAA
1 AAAATAA
*
1760105 AAATAGAA
1 AAA-ATAA
1760113 AAAATAA
1 AAAATAA
1760120 AAAATAA
1 AAAATAA
1760127 AAAATAA
1 AAAATAA
1760134 A
1 A
1760135 TATAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:1762723 original size:2 final size:2
Alignment explanation
Indices: 1762716--1762745 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1762706 AGGAAAGGCT
1762716 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1762746 GTTGCTTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1763631 original size:21 final size:21
Alignment explanation
Indices: 1763588--1763631 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1763578 ATTTAATTTT
* * *
1763588 TTTAATGTTAATGTGACATTA
1 TTTAATGATAATATGACAGTA
*
1763609 TTTAATGATAATATGTCAGTA
1 TTTAATGATAATATGACAGTA
1763630 TT
1 TT
1763632 ATCATTAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.48
Consensus pattern (21 bp):
TTTAATGATAATATGACAGTA
Found at i:1765435 original size:39 final size:39
Alignment explanation
Indices: 1765381--1765458 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
1765371 CCACTGGTCC
1765381 CACTTCACATTCCAACCCTATCCTATGCCCCTATTGTTT
1 CACTTCACATTCCAACCCTATCCTATGCCCCTATTGTTT
1765420 CACTTCACATTCCAACCCTATCCTATGCCCCTATTGTTT
1 CACTTCACATTCCAACCCTATCCTATGCCCCTATTGTTT
1765459 AACCAAGGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.38, G:0.05, T:0.36
Consensus pattern (39 bp):
CACTTCACATTCCAACCCTATCCTATGCCCCTATTGTTT
Found at i:1766173 original size:23 final size:23
Alignment explanation
Indices: 1766147--1766209 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1766137 ATATAAGCAC
1766147 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1766170 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1766193 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1766210 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1767098 original size:199 final size:199
Alignment explanation
Indices: 1766354--1767669 Score: 2442
Period size: 199 Copynumber: 6.6 Consensus size: 199
1766344 TCATTTGCAC
1766354 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
1766419 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCAT
66 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCA-CCTGTTTTCCAT
*
1766484 TCATTCTGGACCAAAAATATCGACACAAACTAAAAAAATGTCGACACATTATTTAGACATATTCT
130 TCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCT
1766549 CTCAT
195 CTCAT
*
1766554 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTATATATTACATTATACTTTTGGTTTTCG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
1766619 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTGTTTTCCATT
66 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTGTTTTCCATT
*
1766684 CATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGATATATTCTC
131 CATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTC
1766749 TCAT
196 TCAT
1766753 AAAACCGGTATACTTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGTTTTCG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
* *
1766817 ATGTTTTTGGGATCGACATTTTTTATATATGGATCGACACTTTATGGTTGCACATGTTTTCCATT
66 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTGTTTTCCATT
1766882 CATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTC
131 CATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTC
1766947 TCAT
196 TCAT
1766951 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
*
1767016 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTATTTTCCATT
66 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTGTTTTCCATT
*
1767081 CATTCTGGACCAAAAATATCGACACAAACTAAAAAATTGTCGACACATTATTTAGACATATTCTC
131 CATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTC
1767146 TCAT
196 TCAT
*
1767150 AAAACCGGTATACTTGTACTGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
1767215 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCAT
66 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCA-CCTGTTTTCCAT
*
1767280 TCATTATGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCT
130 TCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCT
1767345 CTCAT
195 CTCAT
* * *
1767350 AAAACCGGTGTACTTGTACCGGTTAAATTGAAAAATTACATATTACATTATACTTTTGGTTTTTG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
1767415 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTGTTTTCCATT
66 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTGTTTTCCATT
* * *
1767480 CATTCTGGACCAAACATATCGACACAAACTAAAAAAGTGTCAACACATTATTTAGATATATTCTC
131 CATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTC
1767545 TCAT
196 TCAT
1767549 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
1767614 ATGTTTTTGGGATCGACACTTTTTATATATGG-T--ACACTTTATGGTTGCACCATGTT
66 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACC-TGTT
1767670 GGCCATATTG
Statistics
Matches: 1087, Mismatches: 26, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
196 18 0.02
197 4 0.00
198 195 0.18
199 562 0.52
200 308 0.28
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (199 bp):
AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTGTTTTCCATT
CATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTC
TCAT
Found at i:1767463 original size:399 final size:399
Alignment explanation
Indices: 1766354--1767669 Score: 2462
Period size: 399 Copynumber: 3.3 Consensus size: 399
1766344 TCATTTGCAC
1766354 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
*
1766419 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCAT
66 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCAT
*
1766484 TCATTCTGGACCAAAAATATCGACACAAACTAAAAAAATGTCGACACATTATTTAGACATATTCT
131 TCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCT
*
1766549 CTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTATATATTACATTATACTTTTGGT
196 CTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGT
1766614 TTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTGTTTT
261 TTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTGTTTT
1766679 CCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGATATA
326 CCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGATATA
1766744 TTCTCTCAT
391 TTCTCTCAT
1766753 AAAACCGGTATACTTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGTTTTCG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
*
1766817 ATGTTTTTGGGATCGACATTTTTTATATATGGATCGACACTTTATGGTTGCA-CATGTTTTCCAT
66 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCAT
1766881 TCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCT
131 TCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCT
1766946 CTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGT
196 CTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGT
*
1767011 TTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTATTTT
261 TTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTGTTTT
* *
1767076 CCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAATTGTCGACACATTATTTAGACATA
326 CCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGATATA
1767141 TTCTCTCAT
391 TTCTCTCAT
*
1767150 AAAACCGGTATACTTGTACTGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
*
1767215 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCAT
66 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCAT
*
1767280 TCATTATGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCT
131 TCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCT
* *
1767345 CTCATAAAACCGGTGTACTTGTACCGGTTAAATTGAAAAATTACATATTACATTATACTTTTGGT
196 CTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGT
*
1767410 TTTTGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTGTTTT
261 TTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTGTTTT
* *
1767475 CCATTCATTCTGGACCAAACATATCGACACAAACTAAAAAAGTGTCAACACATTATTTAGATATA
326 CCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGATATA
1767540 TTCTCTCAT
391 TTCTCTCAT
1767549 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
1767614 ATGTTTTTGGGATCGACACTTTTTATATATGG-T--ACACTTTATGGTTGCACCATGTT
66 ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTT
1767670 GGCCATATTG
Statistics
Matches: 894, Mismatches: 21, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
396 22 0.02
397 304 0.34
398 171 0.19
399 397 0.44
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (399 bp):
AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCG
ATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCAT
TCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCT
CTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGT
TTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTGTTTT
CCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGATATA
TTCTCTCAT
Found at i:1767799 original size:18 final size:18
Alignment explanation
Indices: 1767776--1767836 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1767766 TCTCATTCAT
*
1767776 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
1767794 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
1767813 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
1767832 AATTA
1 AATTA
1767837 ACCATACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:1767812 original size:19 final size:19
Alignment explanation
Indices: 1767788--1767836 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1767778 TTATATTCAC
1767788 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1767807 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1767826 ATACAAAATTA
1 ATACAAAATTA
1767837 ACCATACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1769664 original size:33 final size:33
Alignment explanation
Indices: 1769627--1769692 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1769617 CATCTTAATA
*
1769627 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* * *
1769660 TCACCCCTCAACATCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1769693 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1769751 original size:21 final size:21
Alignment explanation
Indices: 1769726--1769790 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1769716 CCCCTTATGC
* * *
1769726 CTCTCAAGTGTATCTTCAACT
1 CTCTCAAGTTTCTCTTCGACT
1769747 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1769768 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1769789 CT
1 CT
1769791 TGATTGTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.18, C:0.31, G:0.09, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1772032 original size:17 final size:18
Alignment explanation
Indices: 1772010--1772052 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1772000 ATATATCCGG
1772010 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1772027 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1772047 TATCAT
1 TATCAT
1772053 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1772070 original size:20 final size:19
Alignment explanation
Indices: 1772015--1772061 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1772005 TCCGGTATCA
1772015 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1772034 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1772055 TTTTACC
1 TTTTACC
1772062 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1772222 original size:20 final size:20
Alignment explanation
Indices: 1772195--1772241 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1772185 TCCGGTAACG
1772195 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
1772214 TTCTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
1772235 TTTTACC
1 TTTTACC
1772242 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.19, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:1772425 original size:182 final size:180
Alignment explanation
Indices: 1771982--1772453 Score: 696
Period size: 180 Copynumber: 2.6 Consensus size: 180
1771972 CGTACTTACG
* * *
1771982 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCA-TTTCATACCGGTTT
* * *
1772047 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATA-TTTTTTTTAAAGTATCGACACATTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
1772111 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
130 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
*
1772162 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTCTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCA-TTTCATACCGGTTT
* *
1772227 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
1772292 AGGAC-TTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AGG-CGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * * *
1772344 AAAGTACCGAAACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACTGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTC-ATACCGGTTT
* * *
1772409 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1772454 AATTTGGATC
Statistics
Matches: 265, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
180 97 0.37
181 73 0.28
182 95 0.36
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.42
Consensus pattern (180 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTCATACCGGTTTT
ATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATA
GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:1775301 original size:21 final size:21
Alignment explanation
Indices: 1775250--1775302 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1775240 ATTATGACTA
1775250 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1775271 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1775292 TCGCAATGCGA
1 TCGCAATGCGA
1775303 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1775335 original size:21 final size:20
Alignment explanation
Indices: 1775292--1775339 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1775282 TTTTCCCAAT
*
1775292 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
1775312 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
1775333 TCGCAAT
1 TCGCAAT
1775340 ACGATACTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1775357 original size:20 final size:20
Alignment explanation
Indices: 1775341--1775466 Score: 128
Period size: 20 Copynumber: 6.2 Consensus size: 20
1775331 AATCGCAATA
*
1775341 CGATACTGACTATCGCAAGG
1 CGATACTGACTATCGCAACG
* *
1775361 CGATAAT-ACAAAATCGCAACG
1 CGATACTGAC--TATCGCAACG
*
1775382 CGATACTGACTTTCGCAACG
1 CGATACTGACTATCGCAACG
* *
1775402 CGATTCTGACTTTCGCAACG
1 CGATACTGACTATCGCAACG
* *
1775422 CGATTCTGACTTTCGCAACG
1 CGATACTGACTATCGCAACG
* *
1775442 AGATTCTGACTATCGCAACG
1 CGATACTGACTATCGCAACG
*
1775462 AGATA
1 CGATA
1775467 ATACATAATC
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 75 0.81
21 14 0.15
22 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
CGATACTGACTATCGCAACG
Found at i:1775405 original size:41 final size:42
Alignment explanation
Indices: 1775329--1775441 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 42
1775319 GCGAATTTGG
** * *
1775329 AAAATCGCAATACGATACTGACTATCGCAAGGCGATAAT-AC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
**
1775370 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
** *
1775412 --TTTCGCAACGCGATTCTGACTTTCGCAACG
1 AAAATCGCAACGCGATACTGACTTTCGCAACG
1775442 AGATTCTGAC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 27 0.44
41 33 0.53
42 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
Found at i:1775431 original size:40 final size:40
Alignment explanation
Indices: 1775373--1775466 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
1775363 ATAATACAAA
*
1775373 ATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACTTTCGCAACGAGATTCTGACT
* *
1775413 TTCGCAACGCGATTCTGACTTTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACTTTCGCAACGAGATTCTGACT
*
1775453 ATCGCAACGAGATA
1 ATCGCAACGCGATA
1775467 ATACATAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
ATCGCAACGCGATACTGACTTTCGCAACGAGATTCTGACT
Found at i:1776037 original size:20 final size:20
Alignment explanation
Indices: 1776012--1776067 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1776002 CAACGGGGAA
*
1776012 ATCGCAACGCGAAAATGACT
1 ATCGCAACGAGAAAATGACT
* *
1776032 ATCGCAAAGAGAAAATGGCT
1 ATCGCAACGAGAAAATGACT
1776052 ATCGCAACGAGAAAAT
1 ATCGCAACGAGAAAAT
1776068 CTTAATGCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAAAATGACT
Found at i:1776131 original size:19 final size:16
Alignment explanation
Indices: 1776086--1776137 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 16
1776076 GAAATGAAAA
1776086 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
*
1776102 TCG--TTGTGATTTTC
1 TCGCATTGCGATTTTC
1776116 ATTTCGCATTGCGATTTTC
1 ---TCGCATTGCGATTTTC
1776135 TCG
1 TCG
1776138 TTGCGATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 10 0.34
16 6 0.21
17 3 0.10
19 10 0.34
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.48
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:1777759 original size:39 final size:40
Alignment explanation
Indices: 1777716--1777805 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 40
1777706 CCTCTTCAAC
* *
1777716 GATGACAGTGGCCTCTTGAACG-GGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGTGGAGGGGACTCTTGAGG
*
1777755 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACG--TGGAGGGGACTCTTGAGG
1777797 GATGACAGG
1 GATGACAGG
1777806 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 20 0.45
42 24 0.55
ACGTcount: A:0.21, C:0.16, G:0.42, T:0.21
Consensus pattern (40 bp):
GATGACAGGGGCCTCTTGAACGTGGAGGGGACTCTTGAGG
Found at i:1777770 original size:21 final size:21
Alignment explanation
Indices: 1777741--1777801 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1777731 TTGAACGGGG
*
1777741 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
1777762 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
1777783 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
1777802 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:1778166 original size:20 final size:20
Alignment explanation
Indices: 1778141--1778179 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1778131 GAAGAATAGT
1778141 TTACTTTCGAAACACGAAAC
1 TTACTTTCGAAACACGAAAC
* *
1778161 TTACTTTCGCAACGCGAAA
1 TTACTTTCGAAACACGAAA
1778180 ATGACTATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGAAACACGAAAC
Found at i:1778190 original size:20 final size:20
Alignment explanation
Indices: 1778167--1778253 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
1778157 AAACTTACTT
1778167 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
1778187 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
1778207 TCAG-AACGCGGAAATGGCTA
1 TC-GCAACGCGAAAATGACTA
**
1778227 TCGCAACGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
1778246 TCGCAACG
1 TCGCAACG
1778254 ACAAAATCGC
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.25
20 44 0.73
21 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1778318 original size:14 final size:14
Alignment explanation
Indices: 1778299--1778357 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1778289 TTTCATTTCG
1778299 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1778313 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1778330 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1778346 CGTTGCGATTTT
1 CGTTGCGATTTT
1778358 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1778330 original size:33 final size:33
Alignment explanation
Indices: 1778283--1778373 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
1778273 CACAATCGCA
*
1778283 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1778315 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1778348 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1778374 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 6 0.11
33 51 0.89
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1778339 original size:19 final size:18
Alignment explanation
Indices: 1778278--1778373 Score: 91
Period size: 18 Copynumber: 5.7 Consensus size: 18
1778268 CGAAACACAA
1778278 TCGCATTGCGATTTCATT
1 TCGCATTGCGATTTCATT
* *
1778296 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
1778312 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
1778329 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
1778345 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
1778362 TCGCATTGCGAT
1 TCGCATTGCGAT
1778374 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 8 0.13
18 17 0.27
19 12 0.19
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:1778380 original size:19 final size:19
Alignment explanation
Indices: 1778358--1778401 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1778348 TTGCGATTTT
1778358 CATTTCGCA-TTGCGATAGC
1 CATTTC-CACTTGCGATAGC
*
1778377 CATTTCCACGTTGCGATAGT
1 CATTTCCAC-TTGCGATAGC
1778397 CATTT
1 CATTT
1778402 TCGTGTTGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (19 bp):
CATTTCCACTTGCGATAGC
Found at i:1778969 original size:18 final size:18
Alignment explanation
Indices: 1778946--1778993 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1778936 CGGGTCGATC
1778946 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
1778964 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1778982 AGGTGATGGCTC
1 AGGTGATGGCTC
1778994 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1780357 original size:20 final size:20
Alignment explanation
Indices: 1780309--1780365 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1780299 AATAGTTTCT
**
1780309 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACAC
*
1780329 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACAC
**
1780349 GAATTTGACTATCGCAA
1 GAAAATGACTATCGCAA
1780366 ATCGCGTTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:1780631 original size:22 final size:22
Alignment explanation
Indices: 1780604--1780647 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1780594 GATGGAGATA
1780604 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1780626 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1780648 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1780862 original size:20 final size:20
Alignment explanation
Indices: 1780834--1780906 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
1780824 GATTATGTAT
*
1780834 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1780854 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
1780874 TATCGCGTTACGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1780894 TATCGCGTTGCGA
1 TATCGCGTTGCGA
1780907 TTTTGTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1781010 original size:21 final size:22
Alignment explanation
Indices: 1780961--1781010 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1780951 TACTTATTCA
*
1780961 CATTGCG-AATTGGGAAAATCG
1 CATTGCGAAATTGAGAAAATCG
**
1780982 CAACGCGAAATT-AGAAAATCG
1 CATTGCGAAATTGAGAAAATCG
1781003 CATTGCGA
1 CATTGCGA
1781011 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (22 bp):
CATTGCGAAATTGAGAAAATCG
Found at i:1784148 original size:14 final size:15
Alignment explanation
Indices: 1784085--1784148 Score: 59
Period size: 14 Copynumber: 4.6 Consensus size: 15
1784075 TATCTATTTT
*
1784085 AATCTTAAATCT-TA
1 AATCTTAAAACTCTA
1784099 AATC--AAAACTCTA
1 AATCTTAAAACTCTA
*
1784112 AATCTTAAAA-TTTA
1 AATCTTAAAACTCTA
1784126 AAT-TCTAAAACTCT-
1 AATCT-TAAAACTCTA
1784140 AATCTTAAA
1 AATCTTAAA
1784149 TATATATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
12 5 0.12
13 7 0.17
14 22 0.54
15 7 0.17
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (15 bp):
AATCTTAAAACTCTA
Found at i:1785171 original size:20 final size:21
Alignment explanation
Indices: 1785124--1785171 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1785114 ATTTTCATTT
1785124 TATGAA-ATATAAAACAAATA
1 TATGAATATATAAAACAAATA
*
1785144 TATGAATATATAAAA-AATTA
1 TATGAATATATAAAACAAATA
*
1785164 TGTGAATA
1 TATGAATA
1785172 AGTTATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.31
Consensus pattern (21 bp):
TATGAATATATAAAACAAATA
Found at i:1786924 original size:21 final size:23
Alignment explanation
Indices: 1786895--1786943 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
1786885 GGAATTATTA
* *
1786895 TAATATTTTAAAATTAAT-A-AT
1 TAATTTTTTAAAATAAATGATAT
*
1786916 TAATTTTTTATAATAAATGATAT
1 TAATTTTTTAAAATAAATGATAT
1786939 TAATT
1 TAATT
1786944 ATTATATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 15 0.65
22 1 0.04
23 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TAATTTTTTAAAATAAATGATAT
Found at i:1788544 original size:30 final size:30
Alignment explanation
Indices: 1788503--1788693 Score: 341
Period size: 30 Copynumber: 6.4 Consensus size: 30
1788493 TCCGAAGGAC
1788503 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1788533 CTATACAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1788563 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1788593 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1788623 CTATCCAGAGGTCATAAAGATCCTC-GTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1788652 CTATCCAGAGGTCATAAAGAT-CTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1788681 CTATCCATAGGTC
1 CTATCCAGAGGTC
1788694 CCAAACAACC
Statistics
Matches: 155, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
28 3 0.02
29 41 0.26
30 111 0.72
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1788952 original size:4 final size:4
Alignment explanation
Indices: 1788943--1788967 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1788933 ATATAACCAT
1788943 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
1788968 GTCATCCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:1789131 original size:2 final size:2
Alignment explanation
Indices: 1789119--1789153 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1789109 TACACAACTC
*
1789119 AT AT A- AT AT AT AT AT AT AA 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
1789154 TGTAACATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1792971 original size:120 final size:115
Alignment explanation
Indices: 1792657--1793016 Score: 373
Period size: 112 Copynumber: 3.1 Consensus size: 115
1792647 ATTATGTTAC
* * * * * * * *
1792657 TCATGTCAGTACCCAAAGTTGTGAAAGGGCGTTCCTGGGGGGGCGCCTTCTATTATTTTATCAGA
1 TCATGTCAATACCAAAAGTGGTGAAAGCGTGTTCCCGGGGGGGCGCCTTCCATT-TTTTGTCAGA
*
1792722 TAATAT-TTATCATTGCCCTATTATGTCAC-CATGTC-CTTCGAGGGCACTAT
65 TAATATGTTATCATTGCCCTATTA-GTCACTCATGTCTC-TCGGGGGCACTAT
* *
1792772 TCATGT-AAGTACCCAAAGTGGTGAAAGCGTGTTCCCGGGGGCGCGCCTTCCA-TTTTTG-CAGA
1 TCATGTCAA-TACCAAAAGTGGTGAAAGCGTGTTCCCGGGGGGGCGCCTTCCATTTTTTGTCAGA
1792834 TAATATGTTATCATTGCCCTATTA-TCACTCATGTCTCTCGGGGGCACTAT
65 TAATATGTTATCATTGCCCTATTAGTCACTCATGTCTCTCGGGGGCACTAT
* * *
1792884 TTATGTCAATACCAAAAGT-GTGAAAGCACGT-TTCTCGGGGGGGGGGGGCGCCTTCGATTGTTT
1 TCATGTCAATACCAAAAGTGGTGAAAG--CGTGTTC-C----CGGGGGGGCGCCTTCCATT-TTT
* * *
1792947 TGTCAGAGAATATGTTATCATTG-CCTATTATGTCACTCATGTCTC-CTGGGGAACTAT
58 TGTCAGATAATATGTTATCATTGCCCTATTA-GTCACTCATGTCTCTCGGGGGCACTAT
1793004 TCATGTCAATACC
1 TCATGTCAATACC
1793017 TATTATTTAG
Statistics
Matches: 210, Mismatches: 18, Indels: 29
0.82 0.07 0.11
Matches are distributed among these distances:
111 11 0.05
112 45 0.21
113 28 0.13
114 2 0.01
115 43 0.20
117 14 0.07
118 1 0.00
119 12 0.06
120 41 0.20
121 13 0.06
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (115 bp):
TCATGTCAATACCAAAAGTGGTGAAAGCGTGTTCCCGGGGGGGCGCCTTCCATTTTTTGTCAGAT
AATATGTTATCATTGCCCTATTAGTCACTCATGTCTCTCGGGGGCACTAT
Found at i:1793286 original size:31 final size:31
Alignment explanation
Indices: 1793251--1793351 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 31
1793241 TATGTGAAGT
1793251 TTGAATAATTGGATAAAATGTTATGGATAAA
1 TTGAATAATTGGATAAAATGTTATGGATAAA
* * * * ***
1793282 TTGAATAAAT-G-TGAAGTGATCAGTTGG-TTGT
1 TTGAATAATTGGATAAAATG-TTA--TGGATAAA
*
1793313 TTGAATTATTGGATAAAATGTTATGGATAAA
1 TTGAATAATTGGATAAAATGTTATGGATAAA
1793344 TTGAATAA
1 TTGAATAA
1793352 ATGTGAAGTG
Statistics
Matches: 48, Mismatches: 16, Indels: 12
0.63 0.21 0.16
Matches are distributed among these distances:
29 5 0.10
30 6 0.12
31 26 0.54
32 6 0.12
33 5 0.10
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.38
Consensus pattern (31 bp):
TTGAATAATTGGATAAAATGTTATGGATAAA
Found at i:1793326 original size:62 final size:62
Alignment explanation
Indices: 1793249--1793505 Score: 275
Period size: 62 Copynumber: 4.0 Consensus size: 62
1793239 ATTATGTGAA
*
1793249 GTTTGAATAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTT
1 GTTTGAATAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
* *
1793311 GTTTGAATTATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTT
1 GTTTGAATAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
* * * * * *** *
1793373 GACATTG-A-AATTGTATGAAATGATCATCGACATGTTTTTACGAATAAATTTGAAGTGATAAGT
1 G--TTTGAATAATTGGATAAAATG-TTAT-G-GAT-AAATT--GAATAAATGTGAAGTGATAAGT
1793436 TGGTT
58 TGGTT
* * * *
1793441 GTTTAAATAAAATGGATAAAATATTATGGATAAATTGAATAAATGTGAAGTGAAAAGTTGGTT
1 GTTTGAAT-AATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
1793504 GT
1 GT
1793506 GACATTGAAA
Statistics
Matches: 159, Mismatches: 25, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
62 73 0.46
63 31 0.19
64 4 0.03
65 4 0.03
66 6 0.04
67 2 0.01
68 29 0.18
69 10 0.06
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.37
Consensus pattern (62 bp):
GTTTGAATAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
Found at i:1793470 original size:131 final size:131
Alignment explanation
Indices: 1793284--1793572 Score: 440
Period size: 133 Copynumber: 2.2 Consensus size: 131
1793274 TGGATAAATT
* * * *
1793284 GAATAAATGTGAAGTGATCAGTTGGTTGTTTGAATTATTGGATAAAATGTTATGGATAAATTGAA
1 GAATAAATGTGAAGTGAT-AGTTGGTTGTTTAAATAAATGGATAAAATATTATGGATAAATTGAA
** * *
1793349 TAAATGTGAAGTGATCAGTTGG-T-TGACATTGAAATTGTAT-GAAATGATCATCGACATGTTTT
65 TAAATGTGAAGTGAAAAGTTGGTTGTGACATTGAAATTGTATCG-AATGAGCATCGACATGTTCT
1793411 TAC
129 TAC
*
1793414 GAATAAATTTGAAGTGATAAGTTGGTTGTTTAAATAAAATGGATAAAATATTATGGATAAATTGA
1 GAATAAATGTGAAGTGAT-AGTTGGTTGTTTAAAT-AAATGGATAAAATATTATGGATAAATTGA
1793479 ATAAATGTGAAGTGAAAAGTTGGTTGTGACATTGAAATTGTATCGAATGAGCATCGACATGTTCT
64 ATAAATGTGAAGTGAAAAGTTGGTTGTGACATTGAAATTGTATCGAATGAGCATCGACATGTTCT
1793544 TAC
129 TAC
1793547 GAATAAATGTGAAGTGATAGTTGGTT
1 GAATAAATGTGAAGTGATAGTTGGTT
1793573 TAATGTATAC
Statistics
Matches: 144, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
130 32 0.22
131 47 0.33
132 9 0.06
133 55 0.38
134 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (131 bp):
GAATAAATGTGAAGTGATAGTTGGTTGTTTAAATAAATGGATAAAATATTATGGATAAATTGAAT
AAATGTGAAGTGAAAAGTTGGTTGTGACATTGAAATTGTATCGAATGAGCATCGACATGTTCTTA
C
Found at i:1794312 original size:21 final size:21
Alignment explanation
Indices: 1794261--1794312 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1794251 ATGGTCATAA
* *
1794261 AACCCTACGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
1794282 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
1794303 AACCCTGCGG
1 AACCCTGCGG
1794313 AGATGGCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 21 0.78
22 3 0.11
ACGTcount: A:0.23, C:0.27, G:0.33, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1794321 original size:42 final size:42
Alignment explanation
Indices: 1794275--1794378 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
1794265 CTACGGGCTA
* * * *
1794275 GGCATGTAACCTGGCGGGCTAGGAATGTAACCC-TGCGGAGAT
1 GGCATATAAACTGGCGGGCTAGGAATAT-ACCCATGAGGAGAT
* * *
1794317 GGCATATAAACTGGTGGGCTTGGCATATACCCATGAGGAGAT
1 GGCATATAAACTGGCGGGCTAGGAATATACCCATGAGGAGAT
* *
1794359 GGCATATGAACTGGAGGGCT
1 GGCATATAAACTGGCGGGCT
1794379 GGGCATCATC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 4 0.08
42 48 0.92
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (42 bp):
GGCATATAAACTGGCGGGCTAGGAATATACCCATGAGGAGAT
Found at i:1795760 original size:26 final size:27
Alignment explanation
Indices: 1795720--1795779 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
1795710 ACCAGTTTCC
*
1795720 TAAA-TAATATGAATT-A-TAAAAATT
1 TAAATTAATATAAATTCATTAAAAATT
*
1795744 TATAATTAATATAAATTCATTATAAATT
1 TA-AATTAATATAAATTCATTAAAAATT
1795772 TAAATTAA
1 TAAATTAA
1795780 AAATAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.07
25 2 0.07
26 10 0.33
27 7 0.23
28 9 0.30
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
TAAATTAATATAAATTCATTAAAAATT
Found at i:1795909 original size:20 final size:20
Alignment explanation
Indices: 1795884--1795940 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
1795874 CACTTTCCAT
1795884 TATAATTGTAG-ACAAAAAAA
1 TATAATT-TAGCACAAAAAAA
1795904 TATAA-TTAGCACAAAAAAA
1 TATAATTTAGCACAAAAAAA
1795923 TATAA-TTAGCACAAAAAA
1 TATAATTTAGCACAAAAAA
1795941 TTAATTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 3 0.08
19 28 0.78
20 5 0.14
ACGTcount: A:0.61, C:0.09, G:0.07, T:0.23
Consensus pattern (20 bp):
TATAATTTAGCACAAAAAAA
Found at i:1795919 original size:19 final size:19
Alignment explanation
Indices: 1795895--1795940 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1795885 ATAATTGTAG
1795895 ACAAAAAAATATAATTAGC
1 ACAAAAAAATATAATTAGC
1795914 ACAAAAAAATATAATTAGC
1 ACAAAAAAATATAATTAGC
1795933 ACAAAAAA
1 ACAAAAAA
1795941 TTAATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.67, C:0.11, G:0.04, T:0.17
Consensus pattern (19 bp):
ACAAAAAAATATAATTAGC
Found at i:1795938 original size:17 final size:18
Alignment explanation
Indices: 1795898--1795947 Score: 84
Period size: 19 Copynumber: 2.8 Consensus size: 18
1795888 ATTGTAGACA
1795898 AAAAAATATAATTAGCAC
1 AAAAAATATAATTAGCAC
1795916 AAAAAAATATAATTAGCAC
1 -AAAAAATATAATTAGCAC
1795935 AAAAAAT-TAATTA
1 AAAAAATATAATTA
1795948 ATAAATTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.19
18 7 0.23
19 18 0.58
ACGTcount: A:0.64, C:0.08, G:0.04, T:0.24
Consensus pattern (18 bp):
AAAAAATATAATTAGCAC
Found at i:1796333 original size:60 final size:61
Alignment explanation
Indices: 1796240--1796382 Score: 191
Period size: 60 Copynumber: 2.4 Consensus size: 61
1796230 TAATGCAAGG
* * * *
1796240 CGCGTCCCCAGGGATGCGCCTTACCCCCGTGGCATCCGACTCAGCAGAACCCCATG-AAAA
1 CGCGTCCCCAGGGATGCGCCTTACACACGTGGCATCCGACTCAGCAGAAACCCAAGTAAAA
* * * *
1796300 CGCGTCCCC-GAGGATGCGCCTTACACACGTGGCATCCTAGTCAGCATAAACCCAAGTAAAG
1 CGCGTCCCCAG-GGATGCGCCTTACACACGTGGCATCCGACTCAGCAGAAACCCAAGTAAAA
1796361 CGCGTCCCCAGGGATGCGCCTT
1 CGCGTCCCCAGGGATGCGCCTT
1796383 TGTGCCACTT
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
59 1 0.01
60 47 0.65
61 23 0.32
62 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.24, T:0.15
Consensus pattern (61 bp):
CGCGTCCCCAGGGATGCGCCTTACACACGTGGCATCCGACTCAGCAGAAACCCAAGTAAAA
Found at i:1799064 original size:2 final size:2
Alignment explanation
Indices: 1799057--1799125 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1799047 TACCCATTCA
1799057 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1799099 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
1799126 CAAATTAAGA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1799905 original size:20 final size:21
Alignment explanation
Indices: 1799866--1799905 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1799856 AATTTTAATT
* *
1799866 TTAAAATTAATTCTATTTATC
1 TTAAAATTAATACGATTTATC
1799887 TTAAAATTAA-ACGATTTAT
1 TTAAAATTAATACGATTTAT
1799906 TCATTTACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (21 bp):
TTAAAATTAATACGATTTATC
Found at i:1804607 original size:14 final size:14
Alignment explanation
Indices: 1804585--1804619 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1804575 TTAAAAGTTG
1804585 TAAAAATTAAAAAA
1 TAAAAATTAAAAAA
* *
1804599 TAAATATTAGAAAA
1 TAAAAATTAAAAAA
1804613 TAAAAAT
1 TAAAAAT
1804620 ATAAGCAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
TAAAAATTAAAAAA
Found at i:1805731 original size:37 final size:36
Alignment explanation
Indices: 1805678--1805749 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
1805668 TGTTCATGTT
** *
1805678 TGTTCATTTATTTTTTAAGATGCTTGTGTTTG-GTTCG
1 TGTTCATTTAAGTTTTAA-AT-ATTGTGTTTGTGTTCG
1805715 TGTTCATTTAAGTTTTAAATATTGTGTTTGTGTTC
1 TGTTCATTTAAGTTTTAAATATTGTGTTTGTGTTC
1805750 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 9 0.29
36 6 0.19
37 16 0.52
ACGTcount: A:0.17, C:0.07, G:0.19, T:0.57
Consensus pattern (36 bp):
TGTTCATTTAAGTTTTAAATATTGTGTTTGTGTTCG
Found at i:1805826 original size:23 final size:23
Alignment explanation
Indices: 1805796--1805875 Score: 151
Period size: 23 Copynumber: 3.5 Consensus size: 23
1805786 TTATTGTTCG
1805796 CGAACATGTTCATCTAGCTTTCA
1 CGAACATGTTCATCTAGCTTTCA
1805819 CGAACATGTTCATCTAGCTTTCA
1 CGAACATGTTCATCTAGCTTTCA
*
1805842 CGAACATGTTCATCTAGCGTTCA
1 CGAACATGTTCATCTAGCTTTCA
1805865 CGAACATGTTC
1 CGAACATGTTC
1805876 GTTTTGCGTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (23 bp):
CGAACATGTTCATCTAGCTTTCA
Found at i:1805913 original size:11 final size:11
Alignment explanation
Indices: 1805895--1805948 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
1805885 TCATTTAATG
1805895 TTCATTTAGCA
1 TTCATTTAGCA
* *
1805906 TTCGTTTAACA
1 TTCATTTAGCA
*
1805917 TTCATTTAGTA
1 TTCATTTAGCA
* *
1805928 TTCATTTTGCG
1 TTCATTTAGCA
1805939 TTCATTTAGC
1 TTCATTTAGC
1805949 GTTTGTTTAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (11 bp):
TTCATTTAGCA
Found at i:1805913 original size:22 final size:22
Alignment explanation
Indices: 1805870--1805948 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 22
1805860 GTTCACGAAC
* * *
1805870 ATGTTCGTTTTGCGTTCATTTA
1 ATGTTCATTTAGCATTCATTTA
*
1805892 ATGTTCATTTAGCATTCGTTTA
1 ATGTTCATTTAGCATTCATTTA
** * *
1805914 ACATTCATTTAGTATTCATTTT
1 ATGTTCATTTAGCATTCATTTA
**
1805936 GCGTTCATTTAGC
1 ATGTTCATTTAGC
1805949 GTTTGTTTAT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.20, C:0.15, G:0.14, T:0.51
Consensus pattern (22 bp):
ATGTTCATTTAGCATTCATTTA
Found at i:1805950 original size:11 final size:11
Alignment explanation
Indices: 1805881--1805951 Score: 61
Period size: 11 Copynumber: 6.5 Consensus size: 11
1805871 TGTTCGTTTT
1805881 GCGTTCATTTA
1 GCGTTCATTTA
**
1805892 ATGTTCATTTA
1 GCGTTCATTTA
* *
1805903 GCATTCGTTTA
1 GCGTTCATTTA
* *
1805914 ACATTCATTTA
1 GCGTTCATTTA
** *
1805925 GTATTCATTTT
1 GCGTTCATTTA
1805936 GCGTTCATTTA
1 GCGTTCATTTA
1805947 GCGTT
1 GCGTT
1805952 TGTTTATTGT
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 46 1.00
ACGTcount: A:0.21, C:0.15, G:0.14, T:0.49
Consensus pattern (11 bp):
GCGTTCATTTA
Found at i:1818913 original size:30 final size:30
Alignment explanation
Indices: 1818872--1818936 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
1818862 TTGCTACAGT
* ** *
1818872 GACCACCATAGGTCTTTAGGAGCACATGGC
1 GACCTCCATAGGTCTCCAGGAGCACACGGC
1818902 GACCTCCATAGGTCTCCAGGAGCACACGGC
1 GACCTCCATAGGTCTCCAGGAGCACACGGC
1818932 GACCT
1 GACCT
1818937 ATGTAGCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.17
Consensus pattern (30 bp):
GACCTCCATAGGTCTCCAGGAGCACACGGC
Found at i:1818968 original size:20 final size:20
Alignment explanation
Indices: 1818943--1818980 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1818933 ACCTATGTAG
1818943 CACTTGGCGACTTATGGACC
1 CACTTGGCGACTTATGGACC
1818963 CACTTGGCGACTTATGGA
1 CACTTGGCGACTTATGGA
1818981 GCTACAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (20 bp):
CACTTGGCGACTTATGGACC
Found at i:1825057 original size:21 final size:20
Alignment explanation
Indices: 1825029--1825067 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1825019 CATTGCAGAA
*
1825029 ATTTATGGCCTCGATAAAAG
1 ATTTATGGCCTCAATAAAAG
*
1825049 ATTTCATGGTCTCAATAAA
1 ATTT-ATGGCCTCAATAAA
1825068 GACCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
ATTTATGGCCTCAATAAAAG
Found at i:1834237 original size:15 final size:15
Alignment explanation
Indices: 1834217--1834247 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1834207 ACACTCTGAA
1834217 GCTCCTTAATCTCTC
1 GCTCCTTAATCTCTC
*
1834232 GCTCCTTCATCTCTC
1 GCTCCTTAATCTCTC
1834247 G
1 G
1834248 TATTATGTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.42, G:0.10, T:0.39
Consensus pattern (15 bp):
GCTCCTTAATCTCTC
Found at i:1837816 original size:6 final size:6
Alignment explanation
Indices: 1837805--1837861 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
1837795 TCAAAGACTT
1837805 GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG
1 GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG
1837853 GGAGTG GGA
1 GGAGTG GGA
1837862 CACAAGGTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.18, C:0.00, G:0.67, T:0.16
Consensus pattern (6 bp):
GGAGTG
Found at i:1839759 original size:12 final size:12
Alignment explanation
Indices: 1839742--1839775 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1839732 CCGGCCGGTA
1839742 ACTATTCATGTC
1 ACTATTCATGTC
1839754 ACTATTCCAT-TC
1 ACTATT-CATGTC
1839766 ACTATTCATG
1 ACTATTCATG
1839776 CCGATCACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.15
12 14 0.70
13 3 0.15
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.41
Consensus pattern (12 bp):
ACTATTCATGTC
Found at i:1840749 original size:137 final size:137
Alignment explanation
Indices: 1840502--1841280 Score: 1046
Period size: 137 Copynumber: 5.8 Consensus size: 137
1840492 TAACTAGTGT
* *
1840502 ATGACATTGTTCCTTCATGATGAGGACGTCTGGCCATCTTTGAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * * * * * * *
1840567 CCTTTGTGATGAGGATATATGGTTATATGAGGATGACTCG--GCTCCTACGTGATGAGGAGTTAT
66 CCTTCGTGATGAGGACATCTGGCTATCTAAGAATGA-T-GTTGCTCCTTCGTGATGAGGAGTTAT
1840630 GATCGGTGG
129 GATCGGTGG
1840639 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * * * *
1840704 CCTTCGTGATGAGAACATCTGGTTATCTAAAAATTATGTTTCTCCTTCGTGATGAGGAGTTATGA
66 CCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGTTATGA
1840769 TCGGTGG
131 TCGGTGG
* * **
1840776 ATGACATTGTTCCTTCATGATGAGGATGTCTGGCCATCTTTAAAGATATTTGAGATAACATTGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * *
1840841 TCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGATTTCTGA
66 CCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGTTATGA
1840906 TCGGTGG
131 TCGGTGG
* *
1840913 ATGACATTATTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACATGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
*
1840978 CCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGGTCCTTCGTGATGAGGAGTTATGA
66 CCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGTTATGA
*
1841043 TCGGTGA
131 TCGGTGG
*
1841050 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGATT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * * * * *
1841115 TCTTCGTGATGAGGACGTTTGGCTGTCTAAG---GA---TG----AT-GTGATGAGGAGTTCTGA
66 CCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGTTATGA
* *
1841169 TTGGTAG
131 TCGGTGG
* * *
1841176 ATGACATTGTTCCTTCGTGATGAGGCCATCTGGCCATCTTT-AAGATATTTGGGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * * * * *
1841240 CCTTCGTGATAATGACGTTTGGTTGTCTAAGAATGATGTTG
66 CCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTG
1841281 ATGGATACGA
Statistics
Matches: 580, Mismatches: 54, Indels: 22
0.88 0.08 0.03
Matches are distributed among these distances:
125 48 0.08
126 59 0.10
127 1 0.00
128 2 0.00
131 4 0.01
134 2 0.00
135 1 0.00
136 1 0.00
137 462 0.80
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (137 bp):
ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
CCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGTTATGA
TCGGTGG
Found at i:1840890 original size:43 final size:43
Alignment explanation
Indices: 1840836--1841035 Score: 138
Period size: 43 Copynumber: 4.5 Consensus size: 43
1840826 TGAGATAACA
*
1840836 TTGTTTCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATG
1 TTGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATG
* ** *** * **
1840879 TTGCTCCTTCGTGATGAGGATTTCT-G--ATCGGTGGATGACA
1 TTGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATG
* * *
1840919 TTATTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGA-G
1 TTGTTCCTTCGTGATGAGGACATCTGGCTATC--T-AAGA-A--TGATG
1840967 ATAACATGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATG
1 -T----T-GTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATG
*
1841016 TTGGTCCTTCGTGATGAGGA
1 TTGTTCCTTCGTGATGAGGA
1841036 GTTATGATCG
Statistics
Matches: 118, Mismatches: 23, Indels: 32
0.68 0.13 0.18
Matches are distributed among these distances:
40 29 0.25
41 1 0.01
42 1 0.01
43 41 0.35
44 1 0.01
46 1 0.01
47 1 0.01
48 4 0.03
49 5 0.04
50 1 0.01
51 4 0.03
52 1 0.01
53 1 0.01
54 27 0.23
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.35
Consensus pattern (43 bp):
TTGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATG
Found at i:1841283 original size:126 final size:126
Alignment explanation
Indices: 1841026--1841283 Score: 385
Period size: 126 Copynumber: 2.0 Consensus size: 126
1841016 TTGGTCCTTC
*
1841026 GTGATGAGGAGTTATGATCGGTGAATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTT
1 GTGATGAGGAGTTATGATCGGTGAATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTT
* * *
1841091 AAAGATATTTGAGATAACACGATTTCTTCGTGATGAGGACGTTTGGCTGTCTAAGGATGAT
66 AAAGATATTTGAGATAACACGATTCCTTCGTGATAAGGACGTTTGGCTGTCTAAGAATGAT
* * *
1841152 GTGATGAGGAGTTCTGATTGGT-AGATGACATTGTTCCTTCGTGATGAGGCCATCTGGCCATCTT
1 GTGATGAGGAGTTATGATCGGTGA-ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTT
* * * *
1841216 T-AAGATATTTGGGATAACACGGTTCCTTCGTGATAATGACGTTTGGTTGTCTAAGAATGAT
65 TAAAGATATTTGAGATAACACGATTCCTTCGTGATAAGGACGTTTGGCTGTCTAAGAATGAT
1841277 GTTGATG
1 G-TGATG
1841284 GATACGATAT
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
125 55 0.46
126 64 0.54
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (126 bp):
GTGATGAGGAGTTATGATCGGTGAATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTT
AAAGATATTTGAGATAACACGATTCCTTCGTGATAAGGACGTTTGGCTGTCTAAGAATGAT
Found at i:1841582 original size:58 final size:57
Alignment explanation
Indices: 1841479--1841602 Score: 176
Period size: 58 Copynumber: 2.2 Consensus size: 57
1841469 GTTGTGAAAT
* ** ** *
1841479 TGAAATTGACTCTGAATGATTTGAATTGTTGTTTGTTGAGTCCAATATCATCCGTTG
1 TGAAGTTGACTCTGAATGAACTGAAAAGTTGTTTGTTGAGTCCAATATCATCCGCTG
*
1841536 TGAAGTTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAGTCCAATATCATTCGCTG
1 TGAAGTTGACTCTGAATG-AACTGAAAAGTTGTTTGTTGAGTCCAATATCATCCGCTG
1841594 TGAAGTTGA
1 TGAAGTTGA
1841603 AATTAACTCT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
57 17 0.29
58 42 0.71
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (57 bp):
TGAAGTTGACTCTGAATGAACTGAAAAGTTGTTTGTTGAGTCCAATATCATCCGCTG
Found at i:1842782 original size:52 final size:50
Alignment explanation
Indices: 1842702--1842836 Score: 189
Period size: 51 Copynumber: 2.7 Consensus size: 50
1842692 ATATCCCAAC
* * * *
1842702 CTTTTTATGCCGGTGTGAGTCTTCAAGATGCCTCACATGGATCACTTCTGT
1 CTTTTTATGCTGGTGTGAGCCTTCAAGATGCC-CACATGGATAACTTATGT
* *
1842753 CTTTTTCATGCTGGTGTGAGCCTTTAAGATACCCACATGGATAACTTATGT
1 CTTTTT-ATGCTGGTGTGAGCCTTCAAGATGCCCACATGGATAACTTATGT
*
1842804 CTTTTTATGCTGATGTGAGCCTTCAAGATGCCC
1 CTTTTTATGCTGGTGTGAGCCTTCAAGATGCCC
1842837 CATATAGATA
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
50 24 0.32
51 28 0.38
52 22 0.30
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (50 bp):
CTTTTTATGCTGGTGTGAGCCTTCAAGATGCCCACATGGATAACTTATGT
Found at i:1844367 original size:9 final size:9
Alignment explanation
Indices: 1844347--1844405 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
1844337 CTTGATTCAA
1844347 TTTCTTTTT
1 TTTCTTTTT
1844356 TTT-TTCTTT
1 TTTCTT-TTT
*
1844365 TTTCTCTTT
1 TTTCTTTTT
1844374 TTTCTCTTTT
1 TTTCT-TTTT
*
1844384 TTTCTTCTT
1 TTTCTTTTT
1844393 TTTCTTCTTT
1 TTTCTT-TTT
1844403 TTT
1 TTT
1844406 TTGATGGATG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 2 0.05
9 26 0.62
10 14 0.33
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:1844374 original size:20 final size:19
Alignment explanation
Indices: 1844347--1844406 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 19
1844337 CTTGATTCAA
1844347 TTTCTTTTTTTTTTC-TTT
1 TTTCTTTTTTTTTTCTTTT
* *
1844365 TTTCTCTTTTTTCTCTTTT
1 TTTCTTTTTTTTTTCTTTT
*
1844384 TTTCTTCTTTTTCTTCTTTT
1 TTTCTT-TTTTTTTTCTTTT
1844404 TTT
1 TTT
1844407 TGATGGATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 13 0.37
19 8 0.23
20 14 0.40
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTCTTTTTTTTTTCTTTT
Found at i:1844391 original size:29 final size:29
Alignment explanation
Indices: 1844349--1844405 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1844339 TGATTCAATT
*
1844349 TCTTTTTTTTTTCTTTTT-TCTCTTTTTTC
1 TCTTTTTTTCTTCTTTTTCT-TCTTTTTTC
1844378 TCTTTTTTTCTTCTTTTTCTTCTTTTTT
1 TCTTTTTTTCTTCTTTTTCTTCTTTTTT
1844406 TTGATGGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (29 bp):
TCTTTTTTTCTTCTTTTTCTTCTTTTTTC
Found at i:1847804 original size:45 final size:45
Alignment explanation
Indices: 1847721--1847815 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 45
1847711 AAAAACATAA
* * * *
1847721 AAAGAAATAAATAATATACAACACACAAATATAATCTTTAAATCT
1 AAAGAAACAAATAATATACAAAAAACAAATATAATCTTTAAATAT
* * * * *
1847766 AAAGAAACAAATAATGTACAAAAAATAAATTTATTCTTTCAATAT
1 AAAGAAACAAATAATATACAAAAAACAAATATAATCTTTAAATAT
1847811 AAAGA
1 AAAGA
1847816 CATATAATTA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.27
Consensus pattern (45 bp):
AAAGAAACAAATAATATACAAAAAACAAATATAATCTTTAAATAT
Found at i:1850987 original size:83 final size:80
Alignment explanation
Indices: 1850851--1851006 Score: 249
Period size: 83 Copynumber: 1.9 Consensus size: 80
1850841 AACATATATT
*
1850851 AAATATTTAAATCGAGTTTTTGTTGTTATTATTATTATATTAAATATTGAATCTTAGACATTATA
1 AAATATTTAAATCGAGTTTTTGTTGTTATTATTATTATATTAAATATTGAATCTGAGACATTATA
*
1850916 TTCAAGGAAATTATA
66 TACAAGGAAATTATA
* *
1850931 AAATATTTAGATGGAGTTTTTGTTGTTATTATTATTATTATATTAAATATTGAATCTGAGACATT
1 AAATATTTAAATCGAGTTTTTGTTG---TTATTATTATTATATTAAATATTGAATCTGAGACATT
1850996 ATATACAAGGA
63 ATATACAAGGA
1851007 CATATACAAG
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
80 23 0.33
83 46 0.67
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (80 bp):
AAATATTTAAATCGAGTTTTTGTTGTTATTATTATTATATTAAATATTGAATCTGAGACATTATA
TACAAGGAAATTATA
Found at i:1857472 original size:34 final size:30
Alignment explanation
Indices: 1857434--1857502 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
1857424 TTGATATAAC
*
1857434 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTAGACTT-AATTG
1857468 AATTT-ACAAAATGTTTTTAGACTTAATTG
1 AATTTAACAAAATGTTTTTAGACTTAATTG
1857497 AATTTA
1 AATTTA
1857503 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTAGACTTAATTG
Found at i:1857513 original size:29 final size:30
Alignment explanation
Indices: 1857443--1857502 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1857433 CAATTTAAGG
*
1857443 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTAGACTTGAATTGAATTTA
1857474 CAAAATGTTTTTAGACTT-AATTGAATTTA
1 CAAAATGTTTTTAGACTTGAATTGAATTTA
1857503 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTAGACTTGAATTGAATTTA
Found at i:1857599 original size:21 final size:20
Alignment explanation
Indices: 1857573--1857616 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1857563 AAAATGCTAT
1857573 AGGGTACCGATACC-CCCTGCA
1 AGGGTACC-ATACCTCCCTG-A
*
1857594 AGGGTATCATACCTCCCTGA
1 AGGGTACCATACCTCCCTGA
1857614 AGG
1 AGG
1857617 CTCAAATTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (20 bp):
AGGGTACCATACCTCCCTGA
Found at i:1857662 original size:18 final size:18
Alignment explanation
Indices: 1857639--1857702 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 18
1857629 ATTTCTCAGA
1857639 GGGTATCTATACCCCCAG
1 GGGTATCTATACCCCCAG
*
1857657 GGGTATCCATA-CCCC--
1 GGGTATCTATACCCCCAG
*
1857672 GGGTATCGATACACCCCAG
1 GGGTATCTATAC-CCCCAG
*
1857691 GGGTGTCTATAC
1 GGGTATCTATAC
1857703 TCCCTGGCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 10 0.26
17 8 0.21
18 10 0.26
19 10 0.26
ACGTcount: A:0.22, C:0.31, G:0.25, T:0.22
Consensus pattern (18 bp):
GGGTATCTATACCCCCAG
Found at i:1857845 original size:20 final size:22
Alignment explanation
Indices: 1857807--1857846 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1857797 TTTGAGTAGA
1857807 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1857829 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1857847 ATATAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1867499 original size:24 final size:24
Alignment explanation
Indices: 1867471--1867547 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
1867461 GAATATTTTA
1867471 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATTTCTGATTTGAATTCTGT
** **
1867495 TCTGACATCTGATCTAAAATT-TGT
1 TCTGATTTCTGAT-TTGAATTCTGT
** *
1867519 TCTG-TTTCCTGACCTGGATTCTGT
1 TCTGATTT-CTGATTTGAATTCTGT
1867543 TCTGA
1 TCTGA
1867548 CATATTATCT
Statistics
Matches: 38, Mismatches: 11, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
23 4 0.11
24 29 0.76
25 5 0.13
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATTTCTGATTTGAATTCTGT
Found at i:1875596 original size:25 final size:25
Alignment explanation
Indices: 1875555--1875623 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
1875545 TATTAGGGGA
* *
1875555 TTAGGG-TTAAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
1875579 TTAGGGTTTGAAACCCTAATCTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
1875604 TTAGGGTTTGAAACCCTAAT
1 TTAGGGTTTGAAACCCTAAT
1875624 ATGATGGGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
24 6 0.14
25 36 0.86
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGTT
Found at i:1875749 original size:3 final size:3
Alignment explanation
Indices: 1875741--1875786 Score: 58
Period size: 3 Copynumber: 14.7 Consensus size: 3
1875731 ATTAATAAAC
1875741 ATA ATA ATA ATA ATA ATA ATA ATA A-A TATA TATAA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A ATA ATA ATA AT
1875787 TACAATTAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 1 0.03
3 32 0.80
4 6 0.15
5 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1876136 original size:43 final size:42
Alignment explanation
Indices: 1876001--1876445 Score: 230
Period size: 43 Copynumber: 10.4 Consensus size: 42
1875991 GTGACATTGT
* * * *
1876001 TCCTACGTGATGAGGAAATCTGG--TCGAGGGTTGACACTGC
1 TCCTACGTGATGAGGAGATCTGGTATCTATGGTTGACACGGC
* * * * * *
1876041 TCATACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACGG-
1 TCCTACGTGATGAGGAGATC-TGG-TATC-TATGGT--TGACACGGC
*
1876087 TCCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTGACACGGC
1 T-CCTACGTGATGAGGA-GATCTGG-TATCTATGGTTGACACGGC
* ** **
1876131 TCCTACGTGATGAGGAGATCTGGTCTGGA-GAATGACACGGC
1 TCCTACGTGATGAGGAGATCTGGTATCTATGGTTGACACGGC
* * * * * * * *
1876172 TCATACGTGATGAAGAGTTCTGGCCATTTAAAGGTGATAACACGGT
1 TCCTACGTGATGAGGAGATCTGG-TATCT-ATGGT--TGACACGGC
*
1876218 TCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAGGA-GATCTGG-TATCTATGGTTGACACGGC
* ** *
1876261 TCCTACGTGATGAAGAGATCTGG--TC-GGGGAATGACACGGC
1 TCCTACGTGATGAGGAGATCTGGTATCTATGG-TTGACACGGC
* * * * * * *
1876301 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGT
1 TCCTACGTGATGAGGAGATCTGG-TATCT-ATGGT--TGACACGGC
*
1876347 TCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAGGA-GATCTGG-TATCTATGGTTGACACGGC
* ** * *
1876390 TCCTACGTGATGAAGAGATCTGG--TCTGGGGATGACACGGT
1 TCCTACGTGATGAGGAGATCTGGTATCTATGGTTGACACGGC
*
1876430 TCCTACATGATGAGGA
1 TCCTACGTGATGAGGA
1876446 CGGCTGGCCA
Statistics
Matches: 308, Mismatches: 69, Indels: 56
0.71 0.16 0.13
Matches are distributed among these distances:
39 2 0.01
40 75 0.24
41 33 0.11
42 7 0.02
43 81 0.26
44 4 0.01
45 19 0.06
46 64 0.21
47 22 0.07
48 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (42 bp):
TCCTACGTGATGAGGAGATCTGGTATCTATGGTTGACACGGC
Found at i:1876355 original size:129 final size:129
Alignment explanation
Indices: 1876001--1876442 Score: 726
Period size: 129 Copynumber: 3.4 Consensus size: 129
1875991 GTGACATTGT
* * * *
1876001 TCCTACGTGATGAGGAAATCTGGTC-GAGGGTTGACACTGCTCATACGTGATGAAGAGTTCTTGG
1 TCCTACGTGATGAAGAGATCTGGTCTG-GGGATGACACGGCTCATACGTGATGAAGAGTTC-TGG
* *
1876065 CCATCTTAAGGTGATAACACGGTCCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGG
64 CCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGG
1876130 C
129 C
* *
1876131 TCCTACGTGATGAGGAGATCTGGTCTGGAGAATGACACGGCTCATACGTGATGAAGAGTTCTGGC
1 TCCTACGTGATGAAGAGATCTGGTCTGG-GGATGACACGGCTCATACGTGATGAAGAGTTCTGGC
*
1876196 CATTTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
65 CATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
1876261 TCCTACGTGATGAAGAGATCTGGTC-GGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGC
1 TCCTACGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGCTCATACGTGATGAAGAGTTCTGGC
1876325 CATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
65 CATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
* * *
1876390 TCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGA
1 TCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGA
1876443 GGACGGCTGG
Statistics
Matches: 295, Mismatches: 13, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
128 1 0.00
129 145 0.49
130 119 0.40
131 30 0.10
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (129 bp):
TCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
Found at i:1876646 original size:30 final size:30
Alignment explanation
Indices: 1876610--1876680 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
1876600 GGGAATTAAT
* *
1876610 CTCAAAGATCAGTGTTTCGAGAGAAACAAA
1 CTCAAAGATCAGTGTTTCAAGAAAAACAAA
***
1876640 CTCAAAGATGTTTTTGTTTCAAGAAAAACAAA
1 CTCAAAGA--TCAGTGTTTCAAGAAAAACAAA
1876672 CTCAAAGAT
1 CTCAAAGAT
1876681 TTTTCTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 9 0.26
32 25 0.74
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (30 bp):
CTCAAAGATCAGTGTTTCAAGAAAAACAAA
Found at i:1876669 original size:32 final size:31
Alignment explanation
Indices: 1876622--1876684 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
1876612 CAAAGATCAG
* *
1876622 TGTTTCGAGAGAAACAAACTCAAAGATGTTTT
1 TGTTTCAAGAAAAACAAACTCAAAGAT-TTTT
1876654 TGTTTCAAGAAAAACAAACTCAAAGATTTTT
1 TGTTTCAAGAAAAACAAACTCAAAGATTTTT
1876685 CTCAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 4 0.14
32 25 0.86
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (31 bp):
TGTTTCAAGAAAAACAAACTCAAAGATTTTT
Found at i:1877469 original size:67 final size:67
Alignment explanation
Indices: 1877383--1877624 Score: 414
Period size: 67 Copynumber: 3.6 Consensus size: 67
1877373 TCATTTTAAG
* *
1877383 AGAAACAGATTCAAAGATTTTTTTTTCAAAAGCAAA-TATCTTAAGAGAGACAAAATTTTGTTTC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAG-AAACTATCTTAAGAGAGACAAAATTTTGTTTC
1877447 CAA
65 CAA
*
1877450 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCC
1877515 AA
66 AA
* *
1877517 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACAATCTAAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCC
1877582 AA
66 AA
*
1877584 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACAATCT
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACTATCT
1877625 AAAAGATTTT
Statistics
Matches: 169, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
66 3 0.02
67 166 0.98
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (67 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:1877472 original size:30 final size:30
Alignment explanation
Indices: 1877438--1877644 Score: 136
Period size: 30 Copynumber: 6.4 Consensus size: 30
1877428 AGAGACAAAA
1877438 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
* **
1877468 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAA-A-
1 TTTTGTTTCCAAAG-AA--A-C-----AGACTCAAAGAT
1877505 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
* * *
1877535 TTTTGTTTCAAAAGAAACA-ATCTAAAGAGAGACAAAA
1 TTTTGTTTCCAAAGAAACAGA-CT-CA-A-AG----AT
1877572 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
* *
1877602 TTTTGTTTCAAAAGAAACA-ATCTAAAAGAT
1 TTTTGTTTCCAAAGAAACAGA-CTCAAAGAT
1877632 TTTT-TTTCACAAA
1 TTTTGTTTC-CAAA
1877645 ATTGTCTCAA
Statistics
Matches: 140, Mismatches: 15, Indels: 44
0.70 0.08 0.22
Matches are distributed among these distances:
28 7 0.05
29 7 0.05
30 67 0.48
31 3 0.02
32 1 0.01
33 4 0.03
34 4 0.03
35 1 0.01
36 3 0.02
37 34 0.24
38 2 0.01
39 7 0.05
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (30 bp):
TTTTGTTTCCAAAGAAACAGACTCAAAGAT
Found at i:1877768 original size:27 final size:28
Alignment explanation
Indices: 1877723--1877912 Score: 195
Period size: 29 Copynumber: 6.4 Consensus size: 28
1877713 CAAAACTTTG
* *
1877723 TTTCCAAAGAAACAGACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
1877751 TTTCAAAAGAAAC-AACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
1877778 TATTCAAAAGGAACAAACTCTAACAACTCAAAGATTTT
1 T-TTCAAAA-G---AAA--C--A-AACTCAAAGATTTT
*
1877816 TATTCAAAAGGAACAAACTCAAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
*
1877845 TATTCAAAAGGAACAAACTCAAAGA-TTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
* *
1877873 TTTCAAGAGGAACAAACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
*
1877901 TTTTAAAAGAAA
1 TTTCAAAAGAAA
1877913 TTGTCTTTAA
Statistics
Matches: 143, Mismatches: 7, Indels: 24
0.82 0.04 0.14
Matches are distributed among these distances:
27 36 0.25
28 35 0.24
29 40 0.28
30 1 0.01
32 4 0.03
34 3 0.02
37 1 0.01
38 23 0.16
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (28 bp):
TTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:1877809 original size:38 final size:38
Alignment explanation
Indices: 1877761--1877835 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
1877751 TTTCAAAAGA
1877761 AACAACTCAAAGATTTTTATTCAAAAGGAACAAACTCT
1 AACAACTCAAAGATTTTTATTCAAAAGGAACAAACTCT
1877799 AACAACTCAAAGATTTTTATTCAAAAGGAACAAACTC
1 AACAACTCAAAGATTTTTATTCAAAAGGAACAAACTC
1877836 AAAGATTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (38 bp):
AACAACTCAAAGATTTTTATTCAAAAGGAACAAACTCT
Found at i:1877844 original size:67 final size:66
Alignment explanation
Indices: 1877733--1877864 Score: 230
Period size: 67 Copynumber: 2.0 Consensus size: 66
1877723 TTTCCAAAGA
1877733 AACAGACTCAAAGATTTTTTTCAAAAGAAACAACTCAAAGATTTTTATTCAAAAGGAACAAACTC
1 AACAGACTCAAAGATTTTTTTCAAAAGAAACAACTCAAAGATTTTTATTCAAAAGGAACAAACTC
1877798 T
66 T
*
1877799 AACA-ACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTATTCAAAAGGAACAAAC
1 AACAGACTCAAAGATTTTT-TTCAAAAGAAAC-AACTCAAAGATTTTTATTCAAAAGGAACAAAC
1877863 TC
64 TC
1877865 AAAGATTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
65 14 0.22
66 15 0.24
67 34 0.54
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.27
Consensus pattern (66 bp):
AACAGACTCAAAGATTTTTTTCAAAAGAAACAACTCAAAGATTTTTATTCAAAAGGAACAAACTC
T
Found at i:1877889 original size:56 final size:57
Alignment explanation
Indices: 1877802--1877909 Score: 175
Period size: 56 Copynumber: 1.9 Consensus size: 57
1877792 AAACTCTAAC
1877802 AACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTATTCAAAAGGAACA
1 AACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTT-TTCAAAAGGAACA
* *
1877860 AACTCAAAGA-TTTT-TTCAAGAGGAACAAACTCAAAGATTTTTTTTAAAAG
1 AACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTTTCAAAAG
1877910 AAATTGTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
55 7 0.15
56 27 0.56
57 4 0.08
58 10 0.21
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (57 bp):
AACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTTTCAAAAGGAACA
Found at i:1878526 original size:66 final size:66
Alignment explanation
Indices: 1878455--1878652 Score: 396
Period size: 66 Copynumber: 3.0 Consensus size: 66
1878445 TTTGTTTTAA
1878455 AATTCTCAAAATTTGTGGAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTGTC
1 AATTCTCAAAATTTGTGGAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTGTC
1878520 T
66 T
1878521 AATTCTCAAAATTTGTGGAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTGTC
1 AATTCTCAAAATTTGTGGAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTGTC
1878586 T
66 T
1878587 AATTCTCAAAATTTGTGGAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTGTC
1 AATTCTCAAAATTTGTGGAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTGTC
1878652 T
66 T
1878653 CAAGCGAGAC
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 132 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (66 bp):
AATTCTCAAAATTTGTGGAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTGTC
T
Found at i:1878586 original size:38 final size:38
Alignment explanation
Indices: 1878544--1878679 Score: 123
Period size: 38 Copynumber: 3.8 Consensus size: 38
1878534 TGTGGAAAAA
*
1878544 TGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAAGAGAAAGT
* * **
1878582 TGTCT-AATTC---TCAAAATTTG---T---G-GAAAAA
1 TGTCTCAA-GCGAGACAAAATTTGTTTTAAAGAGAAAGT
*
1878610 TGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAAGAGAAAGT
*
1878648 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGA
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAAGA
1878680 AAACTGTCTC
Statistics
Matches: 74, Mismatches: 12, Indels: 24
0.67 0.11 0.22
Matches are distributed among these distances:
28 10 0.14
29 3 0.04
31 8 0.11
32 1 0.01
34 1 0.01
35 8 0.11
37 3 0.04
38 40 0.54
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (38 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTAAAGAGAAAGT
Found at i:1878671 original size:21 final size:21
Alignment explanation
Indices: 1878610--1878671 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
1878600 TGTGGAAAAA
*
1878610 TGTCTCAAGCGAGACATAATT
1 TGTCTCAAGCGAGACAAAATT
* * * *
1878631 TGTTTTAA---AGA-GAAAGT
1 TGTCTCAAGCGAGACAAAATT
1878648 TGTCTCAAGCGAGACAAAATT
1 TGTCTCAAGCGAGACAAAATT
1878669 TGT
1 TGT
1878672 TTTTAAGAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 8
0.62 0.20 0.18
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
20 3 0.11
21 13 0.46
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (21 bp):
TGTCTCAAGCGAGACAAAATT
Found at i:1878688 original size:36 final size:36
Alignment explanation
Indices: 1878604--1878712 Score: 119
Period size: 38 Copynumber: 2.9 Consensus size: 36
1878594 AAAATTTGTG
* *
1878604 GAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
*
1878640 GAGAAAGTTGTCTCAAGCGAGACAAAATTTGTTTTTAA
1 GA-AAA-ATGTCTCAAGCGAGACAAAATTTGTTTTTAA
* * * * *
1878678 GAAAACTGTCTCTAGTGAGACGACACTTTGTTTTT
1 GAAAAATGTCTCAAGCGAGAC-AAAATTTGTTTTT
1878713 TTAATAAGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
36 15 0.24
37 17 0.27
38 30 0.48
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (36 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
Found at i:1880277 original size:12 final size:11
Alignment explanation
Indices: 1880249--1880286 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1880239 CCTCTTTTTG
*
1880249 TTCTTTGCTTT
1 TTCTTTGATTT
1880260 TTCTTTGATTT
1 TTCTTTGATTT
1880271 TTGCTTTGATTT
1 TT-CTTTGATTT
1880283 TTCT
1 TTCT
1880287 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:1880290 original size:13 final size:12
Alignment explanation
Indices: 1880244--1880291 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
1880234 TTTGTCCTCT
1880244 TTTTGTTCTTTG-
1 TTTT-TTCTTTGA
*
1880256 CTTTTTCTTTGA
1 TTTTTTCTTTGA
*
1880268 TTTTTGCTTTGA
1 TTTTTTCTTTGA
1880280 TTTTTCTCTTTG
1 TTTTT-TCTTTG
1880292 CTCTTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 7 0.23
12 18 0.60
13 5 0.17
ACGTcount: A:0.04, C:0.12, G:0.12, T:0.71
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:1880303 original size:20 final size:20
Alignment explanation
Indices: 1880274--1880311 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1880264 TTGATTTTTG
1880274 CTTTGATTTTTCTCTTTGCT
1 CTTTGATTTTTCTCTTTGCT
* *
1880294 CTTTGTTTTTTTTCTTTG
1 CTTTGATTTTTCTCTTTG
1880312 GTTTGATCTT
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:0.03, C:0.16, G:0.11, T:0.71
Consensus pattern (20 bp):
CTTTGATTTTTCTCTTTGCT
Found at i:1883427 original size:31 final size:32
Alignment explanation
Indices: 1883371--1883432 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1883361 ATGAAAAATG
1883371 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1883403 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
1883433 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:1886880 original size:25 final size:25
Alignment explanation
Indices: 1886839--1886909 Score: 108
Period size: 25 Copynumber: 2.9 Consensus size: 25
1886829 TATTAGGGGA
* * *
1886839 TTAGGG-TTAAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTATT
1886863 TTAGGGTTTGAAACCCTAATCTATT
1 TTAGGGTTTGAAACCCTAATCTATT
1886888 TTAGGGTTTGAAACCCTAATCT
1 TTAGGGTTTGAAACCCTAATCT
1886910 GATGGGTTGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
24 6 0.14
25 37 0.86
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTATT
Found at i:1887033 original size:3 final size:3
Alignment explanation
Indices: 1887025--1887076 Score: 70
Period size: 3 Copynumber: 16.7 Consensus size: 3
1887015 ATTAATAAAC
1887025 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A TATA TATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A ATA ATA
1887072 ATA AT
1 ATA AT
1887077 TACAATTAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.02
3 38 0.83
4 6 0.13
5 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Done.